High-Resolution Melting Analysis for Rapid Detection of Sequence Type 131 Escherichia coli.

PubMed

Harrison, Lucas B; Hanson, Nancy D

2017-06-01

Escherichia coli isolates belonging to the sequence type 131 (ST131) clonal complex have been associated with the global distribution of fluoroquinolone and β-lactam resistance. Whole-genome sequencing and multilocus sequence typing identify sequence type but are expensive when evaluating large numbers of samples. This study was designed to develop a cost-effective screening tool using high-resolution melting (HRM) analysis to differentiate ST131 from non-ST131 E. coli in large sample populations in the absence of sequence analysis. The method was optimized using DNA from 12 E. coli isolates. Singleplex PCR was performed using 10 ng of DNA, Type-it HRM buffer, and multilocus sequence typing primers and was followed by multiplex PCR. The amplicon sizes ranged from 630 to 737 bp. Melt temperature peaks were determined by performing HRM analysis at 0.1°C resolution from 50 to 95°C on a Rotor-Gene Q 5-plex HRM system. Derivative melt curves were compared between sequence types and analyzed by principal component analysis. A blinded study of 191 E. coli isolates of ST131 and unknown sequence types validated this methodology. This methodology returned 99.2% specificity (124 true negatives and 1 false positive) and 100% sensitivity (66 true positives and 0 false negatives). This HRM methodology distinguishes ST131 from non-ST131 E. coli without sequence analysis. The analysis can be accomplished in about 3 h in any laboratory with an HRM-capable instrument and principal component analysis software. Therefore, this assay is a fast and cost-effective alternative to sequencing-based ST131 identification. Copyright © 2017 Harrison and Hanson.

Evaluation of PCR and high-resolution melt curve analysis for differentiation of Salmonella isolates.

PubMed

Saeidabadi, Mohammad Sadegh; Nili, Hassan; Dadras, Habibollah; Sharifiyazdi, Hassan; Connolly, Joanne; Valcanis, Mary; Raidal, Shane; Ghorashi, Seyed Ali

2017-06-01

Consumption of poultry products contaminated with Salmonella is one of the major causes of foodborne diseases worldwide and therefore detection and differentiation of Salmonella spp. in poultry is important. In this study, oligonucleotide primers were designed from hemD gene and a PCR followed by high-resolution melt (HRM) curve analysis was developed for rapid differentiation of Salmonella isolates. Amplicons of 228 bp were generated from 16 different Salmonella reference strains and from 65 clinical field isolates mainly from poultry farms. HRM curve analysis of the amplicons differentiated Salmonella isolates and analysis of the nucleotide sequence of the amplicons from selected isolates revealed that each melting curve profile was related to a unique DNA sequence. The relationship between reference strains and tested specimens was also evaluated using a mathematical model without visual interpretation of HRM curves. In addition, the potential of the PCR-HRM curve analysis was evaluated for genotyping of additional Salmonella isolates from different avian species. The findings indicate that PCR followed by HRM curve analysis provides a rapid and robust technique for genotyping of Salmonella isolates to determine the serovar/serotype.

High resolution melting analysis to genotype the most common variants in the HFE gene.

PubMed

Marotta, Roberta V; Turri, Olivia; Morandi, Antonella; Murano, Manuela; d'Eril, Gianlodovico Melzi; Biondi, Maria Luisa

2011-09-01

High resolution melting (HRM) analysis of PCR amplicons was recently introduced as a closed-tube, rapid, and inexpensive method of genotyping. This study evaluated this system as an option for detecting the three most common mutations in the HFE gene (C282Y, H63D, S65C), accounting for the main form of hereditary haemochromatosis. Ninety samples, previously screened by direct sequencing, and 27 controls were used. The analysis were performed on the Rotor Gene Q, using the commercial HRM mix containing the Eva Green dye (Qiagen). Specific primers allowed the amplification of the regions of interest in the HFE gene. Following amplification, a HRM analysis was conducted to detect DNA variants. The thermal denaturation profiles of the samples were compared with those of the controls. One hundred percent of heterozygous and homozygous samples were readily identified. Heterozygotes were easily identified because heteroduplexes altered the shape of the melting curves, but significant differences were also present in the melting curves of the homozygous carries compared with those of the wild-type subjects. HRM analysis is an appealing technology for HFE gene screening. It is a robust technique that can be widely adopted in diagnostic laboratories to facilitate gene mutation screening.

Evaluation of high-resolution melting curve analysis of ligation-mediated real-time PCR, a rapid method for epidemiological typing of ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter Species) pathogens.

PubMed

Woksepp, Hanna; Ryberg, Anna; Billström, Hanna; Hällgren, Anita; Nilsson, Lennart E; Marklund, Britt-Inger; Olsson-Liljequist, Barbro; Schön, Thomas

2014-12-01

A single-tube method, ligation-mediated real-time PCR high-resolution melt analysis (LMqPCR HRMA), was modified for the rapid typing of Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. (ESKAPE) pathogens. A 97% agreement (60/62 isolates) was achieved in comparison to pulsed-field gel electrophoresis (PFGE) results, which indicates that LMqPCR HRMA is a rapid and accurate screening tool for monitoring nosocomial outbreaks. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

High-resolution melting PCR analysis for rapid genotyping of Burkholderia mallei.

PubMed

Girault, G; Wattiau, P; Saqib, M; Martin, B; Vorimore, F; Singha, H; Engelsma, M; Roest, H J; Spicic, S; Grunow, R; Vicari, N; De Keersmaecker, S C J; Roosens, N H C; Fabbi, M; Tripathi, B N; Zientara, S; Madani, N; Laroucau, K

2018-05-08

Burkholderia (B.) mallei is the causative agent of glanders. A previous work conducted on single-nucleotide polymorphisms (SNP) extracted from the whole genome sequences of 45 B. mallei isolates identified 3 lineages for this species. In this study, we designed a high-resolution melting (HRM) method for the screening of 15 phylogenetically informative SNPs within the genome of B. mallei that subtype the species into 3 lineages and 12 branches/sub-branches/groups. The present results demonstrate that SNP-based genotyping represent an interesting approach for the molecular epidemiology analysis of B. mallei. Copyright © 2018 Elsevier B.V. All rights reserved.

High-Resolution Melting (HRM) of Hypervariable Mitochondrial DNA Regions for Forensic Science.

PubMed

Dos Santos Rocha, Alípio; de Amorim, Isis Salviano Soares; Simão, Tatiana de Almeida; da Fonseca, Adenilson de Souza; Garrido, Rodrigo Grazinoli; Mencalha, Andre Luiz

2018-03-01

Forensic strategies commonly are proceeding by analysis of short tandem repeats (STRs); however, new additional strategies have been proposed for forensic science. Thus, this article standardized the high-resolution melting (HRM) of DNA for forensic analyzes. For HRM, mitochondrial DNA (mtDNA) from eight individuals were extracted from mucosa swabs by DNAzol reagent, samples were amplified by PCR and submitted to HRM analysis to identify differences in hypervariable (HV) regions I and II. To confirm HRM, all PCR products were DNA sequencing. The data suggest that is possible discriminate DNA from different samples by HRM curves. Also, uncommon dual-dissociation was identified in a single PCR product, increasing HRM analyzes by evaluation of melting peaks. Thus, HRM is accurate and useful to screening small differences in HVI and HVII regions from mtDNA and increase the efficiency of laboratory routines based on forensic genetics. © 2017 American Academy of Forensic Sciences.

Rapid discrimination between Anopheles gambiae s.s. and Anopheles arabiensis by High-Resolution Melt (HRM) analysis.

PubMed

Zianni, Michael R; Nikbakhtzadeh, Mahmood R; Jackson, Bryan T; Panescu, Jenny; Foster, Woodbridge A

2013-04-01

There is a need for more cost-effective options to more accurately discriminate among members of the Anopheles gambiae complex, particularly An. gambiae and Anopheles arabiensis. These species are morphologically indistinguishable in the adult stage, have overlapping distributions, but are behaviorally and ecologically different, yet both are efficient vectors of malaria in equatorial Africa. The method described here, High-Resolution Melt (HRM) analysis, takes advantage of minute differences in DNA melting characteristics, depending on the number of incongruent single nucleotide polymorphisms in an intragenic spacer region of the X-chromosome-based ribosomal DNA. The two species in question differ by an average of 13 single-nucleotide polymorphisms giving widely divergent melting curves. A real-time PCR system, Bio-Rad CFX96, was used in combination with a dsDNA-specific dye, EvaGreen, to detect and measure the melting properties of the amplicon generated from leg-extracted DNA of selected mosquitoes. Results with seven individuals from pure colonies of known species, as well as 10 field-captured individuals unambiguously identified by DNA sequencing, demonstrated that the method provided a high level of accuracy. The method was used to identify 86 field mosquitoes through the assignment of each to the two common clusters with a high degree of certainty. Each cluster was defined by individuals from pure colonies. HRM analysis is simpler to use than most other methods and provides comparable or more accurate discrimination between the two sibling species but requires a specialized melt-analysis instrument and software.

Rapid Discrimination between Anopheles gambiae s.s. and Anopheles arabiensis by High-Resolution Melt (HRM) Analysis

PubMed Central

Zianni, Michael R.; Nikbakhtzadeh, Mahmood R.; Jackson, Bryan T.; Panescu, Jenny; Foster, Woodbridge A.

2013-01-01

There is a need for more cost-effective options to more accurately discriminate among members of the Anopheles gambiae complex, particularly An. gambiae and Anopheles arabiensis. These species are morphologically indistinguishable in the adult stage, have overlapping distributions, but are behaviorally and ecologically different, yet both are efficient vectors of malaria in equatorial Africa. The method described here, High-Resolution Melt (HRM) analysis, takes advantage of minute differences in DNA melting characteristics, depending on the number of incongruent single nucleotide polymorphisms in an intragenic spacer region of the X-chromosome-based ribosomal DNA. The two species in question differ by an average of 13 single-nucleotide polymorphisms giving widely divergent melting curves. A real-time PCR system, Bio-Rad CFX96, was used in combination with a dsDNA-specific dye, EvaGreen, to detect and measure the melting properties of the amplicon generated from leg-extracted DNA of selected mosquitoes. Results with seven individuals from pure colonies of known species, as well as 10 field-captured individuals unambiguously identified by DNA sequencing, demonstrated that the method provided a high level of accuracy. The method was used to identify 86 field mosquitoes through the assignment of each to the two common clusters with a high degree of certainty. Each cluster was defined by individuals from pure colonies. HRM analysis is simpler to use than most other methods and provides comparable or more accurate discrimination between the two sibling species but requires a specialized melt-analysis instrument and software. PMID:23543777

DNA melting analysis: application of the "open tube" format for detection of mutant KRAS.

PubMed

Botezatu, Irina V; Kondratova, Valentina N; Shelepov, Valery P; Lichtenstein, Anatoly V

2011-12-15

High-resolution melting (HRM) analysis is a very effective method for genotyping and mutation scanning that is usually performed just after PCR amplification (the "closed tube" format). Though simple and convenient, the closed tube format makes the HRM dependent on the PCR mix, not generally optimal for DNA melting analysis. Here, the "open tube" format, namely the post-PCR optimization procedure (amplicon shortening and solution chemistry modification), is proposed. As a result, mutation scanning of short amplicons becomes feasible on a standard real-time PCR instrument (not primarily designed for HRM) using SYBR Green I. This approach has allowed us to considerably enhance the sensitivity of detecting mutant KRAS using both low- and high-resolution systems (the Bio-Rad iQ5-SYBR Green I and Bio-Rad CFX96-EvaGreen, respectively). The open tube format, though more laborious than the closed tube one, can be used in situations when maximal sensitivity of the method is needed. It also permits standardization of DNA melting experiments and the introduction of instruments of a "lower level" into the range of those suitable for mutation scanning. Copyright © 2011 Elsevier Inc. All rights reserved.

Identification of Brucella spp. isolated from human brucellosis in Malaysia using high-resolution melt (HRM) analysis.

PubMed

Mohamed Zahidi, Jama'ayah; Bee Yong, Tay; Hashim, Rohaidah; Mohd Noor, Azura; Hamzah, Siti Hawa; Ahmad, Norazah

2015-04-01

Molecular approaches have been investigated to overcome difficulties in identification and differentiation of Brucella spp. using conventional phenotypic methods. In this study, high-resolution melt (HRM) analysis was used for rapid identification and differentiation of members of Brucella genus. A total of 41 Brucella spp. isolates from human brucellosis were subjected to HRM analysis using 4 sets of primers, which identified 40 isolates as Brucella melitensis and 1 as Brucella canis. The technique utilized low DNA concentration and was highly reproducible. The assay is shown to be a useful diagnostic tool, which can rapidly differentiate Brucella up to species level. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Recovering Paleo-Records from Antarctic Ice-Cores by Coupling a Continuous Melting Device and Fast Ion Chromatography.

PubMed

Severi, Mirko; Becagli, Silvia; Traversi, Rita; Udisti, Roberto

2015-11-17

Recently, the increasing interest in the understanding of global climatic changes and on natural processes related to climate yielded the development and improvement of new analytical methods for the analysis of environmental samples. The determination of trace chemical species is a useful tool in paleoclimatology, and the techniques for the analysis of ice cores have evolved during the past few years from laborious measurements on discrete samples to continuous techniques allowing higher temporal resolution, higher sensitivity and, above all, higher throughput. Two fast ion chromatographic (FIC) methods are presented. The first method was able to measure Cl(-), NO3(-) and SO4(2-) in a melter-based continuous flow system separating the three analytes in just 1 min. The second method (called Ultra-FIC) was able to perform a single chromatographic analysis in just 30 s and the resulting sampling resolution was 1.0 cm with a typical melting rate of 4.0 cm min(-1). Both methods combine the accuracy, precision, and low detection limits of ion chromatography with the enhanced speed and high depth resolution of continuous melting systems. Both methods have been tested and validated with the analysis of several hundred meters of different ice cores. In particular, the Ultra-FIC method was used to reconstruct the high-resolution SO4(2-) profile of the last 10,000 years for the EDML ice core, allowing the counting of the annual layers, which represents a key point in dating these kind of natural archives.

Assessment of genetic mutations in the XRCC2 coding region by high resolution melting curve analysis and the risk of differentiated thyroid carcinoma in Iran

PubMed Central

Fayaz, Shima; Fard-Esfahani, Pezhman; Fard-Esfahani, Armaghan; Mostafavi, Ehsan; Meshkani, Reza; Mirmiranpour, Hossein; Khaghani, Shahnaz

2012-01-01

Homologous recombination (HR) is the major pathway for repairing double strand breaks (DSBs) in eukaryotes and XRCC2 is an essential component of the HR repair machinery. To evaluate the potential role of mutations in gene repair by HR in individuals susceptible to differentiated thyroid carcinoma (DTC) we used high resolution melting (HRM) analysis, a recently introduced method for detecting mutations, to examine the entire XRCC2 coding region in an Iranian population. HRM analysis was used to screen for mutations in three XRCC2 coding regions in 50 patients and 50 controls. There was no variation in the HRM curves obtained from the analysis of exons 1 and 2 in the case and control groups. In exon 3, an Arg188His polymorphism (rs3218536) was detected as a new melting curve group (OR: 1.46; 95%CI: 0.432–4.969; p = 0.38) compared with the normal melting curve. We also found a new Ser150Arg polymorphism in exon 3 of the control group. These findings suggest that genetic variations in the XRCC2 coding region have no potential effects on susceptibility to DTC. However, further studies with larger populations are required to confirm this conclusion. PMID:22481871

High-resolution melting analysis for bird sexing: a successful approach to molecular sex identification using different biological samples.

PubMed

Morinha, Francisco; Travassos, Paulo; Seixas, Fernanda; Santos, Nuno; Sargo, Roberto; Sousa, Luís; Magalhães, Paula; Cabral, João A; Bastos, Estela

2013-05-01

High-resolution melting (HRM) analysis is a very attractive and flexible advanced post-PCR method with high sensitivity/specificity for simple, fast and cost-effective genotyping based on the detection of specific melting profiles of PCR products. Next generation real-time PCR systems, along with improved saturating DNA-binding dyes, enable the direct acquisition of HRM data after quantitative PCR. Melting behaviour is particularly influenced by the length, nucleotide sequence and GC content of the amplicons. This method is expanding rapidly in several research areas such as human genetics, reproductive biology, microbiology and ecology/conservation of wild populations. Here we have developed a successful HRM protocol for avian sex identification based on the amplification of sex-specific CHD1 fragments. The melting curve patterns allowed efficient sexual differentiation of 111 samples analysed (plucked feathers, muscle tissues, blood and oral cavity epithelial cells) of 14 bird species. In addition, we sequenced the amplified regions of the CHD1 gene and demonstrated the usefulness of this strategy for the genotype discrimination of various amplicons (CHD1Z and CHD1W), which have small size differences, ranging from 2 bp to 44 bp. The established methodology clearly revealed the advantages (e.g. closed-tube system, high sensitivity and rapidity) of a simple HRM assay for accurate sex differentiation of the species under study. The requirements, strengths and limitations of the method are addressed to provide a simple guide for its application in the field of molecular sexing of birds. The high sensitivity and resolution relative to previous real-time PCR methods makes HRM analysis an excellent approach for improving advanced molecular methods for bird sexing. © 2013 Blackwell Publishing Ltd.

Greenland Ice Sheet Surface Temperature, Melt, and Mass Loss: 2000-2006

NASA Technical Reports Server (NTRS)

Hall, Dorothy K.; Williams, Richard S., Jr.; Luthcke, Scott B.; DiGirolamo, Nocolo

2007-01-01

Extensive melt on the Greenland Ice Sheet has been documented by a variety of ground and satellite measurements in recent years. If the well-documented warming continues in the Arctic, melting of the Greenland Ice Sheet will likely accelerate, contributing to sea-level rise. Modeling studies indicate that an annual or summer temperature rise of 1 C on the ice sheet will increase melt by 20-50% therefore, surface temperature is one of the most important ice-sheet parameters to study for analysis of changes in the mass balance of the ice-sheet. The Greenland Ice Sheet contains enough water to produce a rise in eustatic sea level of up to 7.0 m if the ice were to melt completely. However, even small changes (centimeters) in sea level would cause important economic and societal consequences in the world's major coastal cities thus it is extremely important to monitor changes in the ice-sheet surface temperature and to ultimately quantify these changes in terms of amount of sea-level rise. We have compiled a high-resolution, daily time series of surface temperature of the Greenland Ice Sheet, using the I-km resolution, clear-sky land-surface temperature (LST) standard product from the Moderate-Resolution Imaging Spectroradiometer (MODIS), from 2000 - 2006. We also use Gravity Recovery and Climate Experiment (GRACE) data, averaged over 10-day periods, to measure change in mass of the ice sheet as it melt and snow accumulates. Surface temperature can be used to determine frequency of surface melt, timing of the start and the end of the melt season, and duration of melt. In conjunction with GRACE data, it can also be used to analyze timing of ice-sheet mass loss and gain.

High-resolution melting analysis (HRM) for differentiation of four major Taeniidae species in dogs Taenia hydatigena, Taenia multiceps, Taenia ovis, and Echinococcus granulosus sensu stricto.

PubMed

Dehghani, Mansoureh; Mohammadi, Mohammad Ali; Rostami, Sima; Shamsaddini, Saeedeh; Mirbadie, Seyed Reza; Harandi, Majid Fasihi

2016-07-01

Tapeworms of the genus Taenia include several species of important parasites with considerable medical and veterinary significance. Accurate identification of these species in dogs is the prerequisite of any prevention and control program. Here, we have applied an efficient method for differentiating four major Taeniid species in dogs, i.e., Taenia hydatigena, T. multiceps, T. ovis, and Echinococcus granulosus sensu stricto. High-resolution melting (HRM) analysis is simpler, less expensive, and faster technique than conventional DNA-based assays and enables us to detect PCR amplicons in a closed system. Metacestode samples were collected from local abattoirs from sheep. All the isolates had already been identified by PCR-sequencing, and their sequence data were deposited in the GenBank. Real-time PCR coupled with HRM analysis targeting mitochondrial cox1 and ITS1 genes was used to differentiate taeniid species. Distinct melting curves were obtained from ITS1 region enabling accurate differentiation of three Taenia species and E. granulosus in dogs. The HRM curves of Taenia species and E .granulosus were clearly separated at Tm of 85 to 87 °C. In addition, double-pick melting curves were produced in mixed infections. Cox1 melting curves were not decisive enough to distinguish four taeniids. In this work, the efficiency of HRM analysis to differentiate four major taeniid species in dogs has been demonstrated using ITS1 gene.

The WAIS Melt Monitor: An automated ice core melting system for meltwater sample handling and the collection of high resolution microparticle size distribution data

NASA Astrophysics Data System (ADS)

Breton, D. J.; Koffman, B. G.; Kreutz, K. J.; Hamilton, G. S.

2010-12-01

Paleoclimate data are often extracted from ice cores by careful geochemical analysis of meltwater samples. The analysis of the microparticles found in ice cores can also yield unique clues about atmospheric dust loading and transport, dust provenance and past environmental conditions. Determination of microparticle concentration, size distribution and chemical makeup as a function of depth is especially difficult because the particle size measurement either consumes or contaminates the meltwater, preventing further geochemical analysis. Here we describe a microcontroller-based ice core melting system which allows the collection of separate microparticle and chemistry samples from the same depth intervals in the ice core, while logging and accurately depth-tagging real-time electrical conductivity and particle size distribution data. This system was designed specifically to support microparticle analysis of the WAIS Divide WDC06A deep ice core, but many of the subsystems are applicable to more general ice core melting operations. Major system components include: a rotary encoder to measure ice core melt displacement with 0.1 millimeter accuracy, a meltwater tracking system to assign core depths to conductivity, particle and sample vial data, an optical debubbler level control system to protect the Abakus laser particle counter from damage due to air bubbles, a Rabbit 3700 microcontroller which communicates with a host PC, collects encoder and optical sensor data and autonomously operates Gilson peristaltic pumps and fraction collectors to provide automatic sample handling, melt monitor control software operating on a standard PC allowing the user to control and view the status of the system, data logging software operating on the same PC to collect data from the melting, electrical conductivity and microparticle measurement systems. Because microparticle samples can easily be contaminated, we use optical air bubble sensors and high resolution ice core density profiles to guide the melting process. The combination of these data allow us to analyze melt head performance, minimize outer-to-inner fraction contamination and avoid melt head flooding. The WAIS Melt Monitor system allows the collection of real-time, sub-annual microparticle and electrical conductivity data while producing and storing enough sample for traditional Coulter-Counter particle measurements as well long term acid leaching of bioactive metals (e.g., Fe, Co, Cd, Cu, Zn) prior to chemical analysis.

Competitive amplification of differentially melting amplicons (CADMA) enables sensitive and direct detection of all mutation types by high-resolution melting analysis.

PubMed

Kristensen, Lasse S; Andersen, Gitte B; Hager, Henrik; Hansen, Lise Lotte

2012-01-01

Sensitive and specific mutation detection is of particular importance in cancer diagnostics, prognostics, and individualized patient treatment. However, the majority of molecular methodologies that have been developed with the aim of increasing the sensitivity of mutation testing have drawbacks in terms of specificity, convenience, or costs. Here, we have established a new method, Competitive Amplification of Differentially Melting Amplicons (CADMA), which allows very sensitive and specific detection of all mutation types. The principle of the method is to amplify wild-type and mutated sequences simultaneously using a three-primer system. A mutation-specific primer is designed to introduce melting temperature decreasing mutations in the resulting mutated amplicon, while a second overlapping primer is designed to amplify both wild-type and mutated sequences. When combined with a third common primer very sensitive mutation detection becomes possible, when using high-resolution melting (HRM) as detection platform. The introduction of melting temperature decreasing mutations in the mutated amplicon also allows for further mutation enrichment by fast coamplification at lower denaturation temperature PCR (COLD-PCR). For proof-of-concept, we have designed CADMA assays for clinically relevant BRAF, EGFR, KRAS, and PIK3CA mutations, which are sensitive to, between 0.025% and 0.25%, mutated alleles in a wild-type background. In conclusion, CADMA enables highly sensitive and specific mutation detection by HRM analysis. © 2011 Wiley Periodicals, Inc.

Exploration of the fragmentation of laser shock-melted aluminum using x-ray backlighting

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Lin, E-mail: zhanglinbox@263.net, E-mail: zhanglinbox@caep.cn; Li, Ying-Hua; Li, Xue-Mei

The fragmentation of shock-melted metal material is an important scientific problem in shock physics and is suitable for experimentally investigating by the laser-driven x-ray backlighting technique. This letter reports on the exploration of laser shock-melted aluminum fragmentation by means of x-ray backlighting at the SGII high energy facility in China. High-quality and high-resolution radiographs with negligible motion blur were obtained and these images enabled analysis of the mass distribution of the fragmentation product.

Automated Microfluidic Platform for Serial Polymerase Chain Reaction and High-Resolution Melting Analysis.

PubMed

Cao, Weidong; Bean, Brian; Corey, Scott; Coursey, Johnathan S; Hasson, Kenton C; Inoue, Hiroshi; Isano, Taisuke; Kanderian, Sami; Lane, Ben; Liang, Hongye; Murphy, Brian; Owen, Greg; Shinoda, Nobuhiko; Zeng, Shulin; Knight, Ivor T

2016-06-01

We report the development of an automated genetic analyzer for human sample testing based on microfluidic rapid polymerase chain reaction (PCR) with high-resolution melting analysis (HRMA). The integrated DNA microfluidic cartridge was used on a platform designed with a robotic pipettor system that works by sequentially picking up different test solutions from a 384-well plate, mixing them in the tips, and delivering mixed fluids to the DNA cartridge. A novel image feedback flow control system based on a Canon 5D Mark II digital camera was developed for controlling fluid movement through a complex microfluidic branching network without the use of valves. The same camera was used for measuring the high-resolution melt curve of DNA amplicons that were generated in the microfluidic chip. Owing to fast heating and cooling as well as sensitive temperature measurement in the microfluidic channels, the time frame for PCR and HRMA was dramatically reduced from hours to minutes. Preliminary testing results demonstrated that rapid serial PCR and HRMA are possible while still achieving high data quality that is suitable for human sample testing. © 2015 Society for Laboratory Automation and Screening.

Authenticity analyses of Rhizoma Paridis using barcoding coupled with high resolution melting (Bar-HRM) analysis to control its quality for medicinal plant product.

PubMed

Duan, Bao-Zhong; Wang, Ya-Ping; Fang, Hai-Lan; Xiong, Chao; Li, Xi-Wen; Wang, Ping; Chen, Shi-Lin

2018-01-01

Rhizoma Paridis (Chonglou) is a commonly used and precious traditional Chinese medicine. Paris polyphylla Smith var. yunnanensis (Franch.) Hand. -Mazz. and Paris polyphylla Smith var . chinensis (Franch.) Hara are the two main sources of Chonglou under the monograph of Rhizoma Paridis in Chinese Pharmacopoeia. In the local marketplace, however, this medicine is prone to be accidentally contaminated, deliberately substituted or admixed with other species that are similar to Rhizoma Paridis in shape and color. Consequently, these adulterations might compromise quality control and result in considerable health concerns for consumers. This study aims to develop a rapid and sensitive method for accurate identification of Rhizoma Paridis and its common adulterants. DNA barcoding coupled with high resolution melting analysis was applied in this research to distinguish Rhizoma Paridis from its adulteration. The internal transcribed spacer 2 (ITS2) barcode was selected for HRM analysis to produce standard melting profile of the selected species. DNA of the tested herbal medicines was isolated and their melting profiles were generated and compared with the standard melting profile of P. polyphylla var. chinensis . The results indicate that the ITS2 molecular regions coupled with HRM analysis can effectively differentiate nine herbal species, including two authentic origins of Chonglou and their seven common adulterants. Ten herbal medicines labeled "Chonglou" obtained from a local market were collected and identified with our methods, and their sequence information was analyzed to validate the accuracy of HRM analysis. DNA barcoding coupled with HRM analysis is a accurate, reliable, rapid, cost-effective and robust tool, which could contribute to the quality control of Rhizoma Paridis in the supply chain of the natural health product industry (NHP).

Application of the High Resolution Melting analysis for genetic mapping of Sequence Tagged Site markers in narrow-leafed lupin (Lupinus angustifolius L.).

PubMed

Kamel, Katarzyna A; Kroc, Magdalena; Święcicki, Wojciech

2015-01-01

Sequence tagged site (STS) markers are valuable tools for genetic and physical mapping that can be successfully used in comparative analyses among related species. Current challenges for molecular markers genotyping in plants include the lack of fast, sensitive and inexpensive methods suitable for sequence variant detection. In contrast, high resolution melting (HRM) is a simple and high-throughput assay, which has been widely applied in sequence polymorphism identification as well as in the studies of genetic variability and genotyping. The present study is the first attempt to use the HRM analysis to genotype STS markers in narrow-leafed lupin (Lupinus angustifolius L.). The sensitivity and utility of this method was confirmed by the sequence polymorphism detection based on melting curve profiles in the parental genotypes and progeny of the narrow-leafed lupin mapping population. Application of different approaches, including amplicon size and a simulated heterozygote analysis, has allowed for successful genetic mapping of 16 new STS markers in the narrow-leafed lupin genome.

Thermodynamic limitations on the resolution obtainable with metal replicas.

PubMed

Woodward, J T; Zasadzinski, J A

1996-12-01

The major factor limiting resolution of metal-shadowed surfaces for electron and scanning tunnelling microscopy is the granularity of the metal film. This granularity had been believed to result from a recrystallization of the evaporated film, and hence could be limited by use of higher melting point materials for replication, or inhibited by adding carbon or other impurities to the film. However, evaporated and sputtered films of amorphous metal alloys that do not crystallize also show a granularity that decreases with increasing alloy melting point. A simple thermodynamic analysis shows that the granularity results from a dewetting of the typically low surface energy sample by the high surface energy metal film, similar to the beading up of drops of spilled mercury. The metal granularity and the resulting resolution of the metal-coated surface is proportional to the mobility of the metal on the surface after evaporation, which is related to the difference in temperature between the melting point of the metal and the sample surface temperature.

High resolution melting analysis: rapid and precise characterisation of recombinant influenza A genomes

PubMed Central

2013-01-01

Background High resolution melting analysis (HRM) is a rapid and cost-effective technique for the characterisation of PCR amplicons. Because the reverse genetics of segmented influenza A viruses allows the generation of numerous influenza A virus reassortants within a short time, methods for the rapid selection of the correct recombinants are very useful. Methods PCR primer pairs covering the single nucleotide polymorphism (SNP) positions of two different influenza A H5N1 strains were designed. Reassortants of the two different H5N1 isolates were used as a model to prove the suitability of HRM for the selection of the correct recombinants. Furthermore, two different cycler instruments were compared. Results Both cycler instruments generated comparable average melting peaks, which allowed the easy identification and selection of the correct cloned segments or reassorted viruses. Conclusions HRM is a highly suitable method for the rapid and precise characterisation of cloned influenza A genomes. PMID:24028349

Detection of plant oil DNA using high resolution melting (HRM) post PCR analysis: a tool for disclosure of olive oil adulteration.

PubMed

Vietina, Michelangelo; Agrimonti, Caterina; Marmiroli, Nelson

2013-12-15

Extra virgin olive oil is frequently subjected to adulterations with addition of oils obtained from plants other than olive. DNA analysis is a fast and economic tool to identify plant components in oils. Extraction and amplification of DNA by PCR was tested in olives, in milled seeds and in oils, to investigate its use in olive oil traceability. DNA was extracted from different oils made of hazelnut, maize, sunflower, peanut, sesame, soybean, rice and pumpkin. Comparing the DNA melting profiles in reference plant materials and in the oils, it was possible to identify any plant components in oils and mixtures of oils. Real-Time PCR (RT-PCR) platform has been added of the new methodology of high resolution melting (HRM), both were used to analyse olive oils mixed with different percentage of other oils. Results showed HRM a cost effective method for efficient detection of adulterations in olive oils. Copyright © 2013 Elsevier Ltd. All rights reserved.

Experimental Determination of Spinel/Melt, Olivine/Melt, and Pyroxene/Melt Partition Coefficients for Re, Ru, Pd, Au, and Pt

NASA Technical Reports Server (NTRS)

Righter, K.; Campbell, A. J.; Humayun, M.

2003-01-01

Experimental studies have identified spinels as important hosts phases for many of the highly siderophile elements (HSE). Yet experimental studies involving chromite or Cr-rich spinel have been lacking. Experimental studies of partitioning of HSEs between silicate, oxides and silicate melt are plagued by low solubilities and the presence of small metallic nuggets at oxygen fugacities relevant to magmas, which interfere with analysis of the phases of interest. We have circumvented these problems in two ways: 1) performing experiments at oxidized conditions, which are still relevant to natural systems but in which nuggets are not observed, and 2) analysis of run products with laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS), allowing a combination of high sensitivity and good spatial resolution.

High-Resolution Melt Analysis for Rapid Comparison of Bacterial Community Compositions

PubMed Central

Hjelmsø, Mathis Hjort; Hansen, Lars Hestbjerg; Bælum, Jacob; Feld, Louise; Holben, William E.

2014-01-01

In the study of bacterial community composition, 16S rRNA gene amplicon sequencing is today among the preferred methods of analysis. The cost of nucleotide sequence analysis, including requisite computational and bioinformatic steps, however, takes up a large part of many research budgets. High-resolution melt (HRM) analysis is the study of the melt behavior of specific PCR products. Here we describe a novel high-throughput approach in which we used HRM analysis targeting the 16S rRNA gene to rapidly screen multiple complex samples for differences in bacterial community composition. We hypothesized that HRM analysis of amplified 16S rRNA genes from a soil ecosystem could be used as a screening tool to identify changes in bacterial community structure. This hypothesis was tested using a soil microcosm setup exposed to a total of six treatments representing different combinations of pesticide and fertilization treatments. The HRM analysis identified a shift in the bacterial community composition in two of the treatments, both including the soil fumigant Basamid GR. These results were confirmed with both denaturing gradient gel electrophoresis (DGGE) analysis and 454-based 16S rRNA gene amplicon sequencing. HRM analysis was shown to be a fast, high-throughput technique that can serve as an effective alternative to gel-based screening methods to monitor microbial community composition. PMID:24610853

Identification case of evidence in timber tracing of Pinus radiate, using high-resolution melting (HRM) analysis.

PubMed

Solano, Jaime; Anabalón, Leonardo; Encina, Francisco

2016-03-01

Fast, accurate detection of plant species and their hybrids using molecular tools will facilitate assessment and monitoring of timber tracing evidence. In this study the origin of unknown pine samples is determined for a case of timber theft in the region of Araucania southern Chile. We evaluate the utility of the trnL marker region for species identification applied to pine wood based on High Resolution Melting. This efficient tracing methods can be incorporated into forestry applications such as certification of origin. The object of this work was genotype identification using high-resolution melting (HRM) and trnL approaches for Pinus radiata (Don) in timber tracing evidence. Our results indicate that trnL is a very sensitive marker for delimiting species and HRM analysis was used successfully for genotyping Pinus samples for timber tracing purposes. Genotyping samples by HRM analysis with the trnL1 approach allowed us to differentiate two wood samples from the Pinaceae family: Pinus radiata (Don) and Pseudotsuga menziesii (Mirb.) Franco. The same approach with Pinus trnL wood was not able to discriminate between samples of Pinus radiata, indicating that the samples were genetically indistinguishable, possibly because they have the same genotype at this locus. Timber tracing with HRM analysis is expected to contribute to future forest certification schemes, control of illegal trading, and molecular traceability of Pinus spp. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Rapid and efficient differentiation of Yersinia species using high-resolution melting analysis.

PubMed

Souza, Roberto A; Frazão, Miliane R; Almeida, Alzira M P; Falcão, Juliana P

2015-08-01

The primary goal of clinical microbiology is the accurate identification of the causative agent of the disease. Here, we describe a method for differentiation between Yersinia species using PCR-HRMA. The results revealed species-specific melting profiles. The herein developed assay can be used as an effective method to differentiate Yersinia species. Copyright © 2015 Elsevier B.V. All rights reserved.

Genotyping of Listeria monocytogenes isolates from poultry carcasses using high resolution melting (HRM) analysis.

PubMed

Sakaridis, Ioannis; Ganopoulos, Ioannis; Madesis, Panagiotis; Tsaftaris, Athanasios; Argiriou, Anagnostis

2014-01-02

An outbreak situation of human listeriosis requires a fast and accurate protocol for typing Listeria monocytogenes . Existing techniques are either characterized by low discriminatory power or are laborious and require several days to give a final result. Polymerase chain reaction (PCR) coupled with high resolution melting (HRM) analysis was investigated in this study as an alternative tool for a rapid and precise genotyping of L. monocytogenes isolates. Fifty-five isolates of L. monocytogenes isolated from poultry carcasses and the environment of four slaughterhouses were typed by HRM analysis using two specific markers, internalin B and ssrA genes. The analysis of genotype confidence percentage of L. monocytogenes isolates produced by HRM analysis generated dendrograms with two major groups and several subgroups. Furthermore, the analysis of the HRM curves revealed that all L. monocytogenes isolates could easily be distinguished. In conclusion, HRM was proven to be a fast and powerful tool for genotyping isolates of L. monocytogenes .

High-resolution melting analysis of gyrA codon 84 and grlA codon 80 mutations conferring resistance to fluoroquinolones in Staphylococcus pseudintermedius isolates from canine clinical samples.

PubMed

Loiacono, Monica; Martino, Piera A; Albonico, Francesca; Dell'Orco, Francesca; Ferretti, Manuela; Zanzani, Sergio; Mortarino, Michele

2017-09-01

Staphylococcus pseudintermedius is an opportunistic pathogen of dogs and cats. A high-resolution melting analysis (HRMA) protocol was designed and tested on 42 clinical isolates with known fluoroquinolone (FQ) susceptibility and gyrA codon 84 and grlA codon 80 mutation status. The HRMA approach was able to discriminate between FQ-sensitive and FQ-resistant strains and confirmed previous reports that the main mutation site associated with FQ resistance in S. pseudintermedius is located at position 251 (Ser84Leu) of gyrA. Routine, HRMA-based FQ susceptibility profiles may be a valuable tool to guide therapy. The FQ resistance-predictive power of the assay should be tested in a significantly larger number of isolates.

Identification and differentiation of Campylobacter species by high-resolution melting curve analysis.

PubMed

Hoseinpour, Fatemeh; Foroughi, Azadeh; Nomanpour, Bizhan; Nasab, Rezvan Sobhani

2017-07-01

Campylobacter jejuni and Campylobacter coli are the important food-born zoonotic pathogen, also are leading causes of human food borne illnesses worldwide. cadF gene is expressed in all C. jejuni and C. coli strains and mediates cell binding to the cell matrix protein, Fibronectin. High-resolution melting (HRM) analysis is emerging as an efficient and robust method for discriminating DNA sequence variants. The goal of this study was to apply HRM analysis to identification of C. jejuni and C. coli. A total of 100 samples were obtained from chicken in Kermanshah, Iran. HRM analysis based on cadF gene and Eva Green was developed to the identification of Campylobacter to the species level. Fifty-five of 100 samples were positive as campylobacter (7 C. jejuni, 29 C. coli, 16 mixes and 3 unknown). Minor variations were observed in melting point temperatures of C. coli or C. jejuni isolates and this variation can be used to the differentiation between C. coli or C. jejuni isolates. The results of this study indicated that HRM curve analysis can be a suitable technique and rapid technique for distinguishing between C. jejuni and C. coli isolates. Copyright © 2017 Elsevier Ltd. All rights reserved.

Real-time RT-PCR high-resolution melting curve analysis and multiplex RT-PCR to detect and differentiate grapevine leafroll-associated virus 3 variant groups I, II, III and VI.

PubMed

Bester, Rachelle; Jooste, Anna E C; Maree, Hans J; Burger, Johan T

2012-09-27

Grapevine leafroll-associated virus 3 (GLRaV-3) is the main contributing agent of leafroll disease worldwide. Four of the six GLRaV-3 variant groups known have been found in South Africa, but their individual contribution to leafroll disease is unknown. In order to study the pathogenesis of leafroll disease, a sensitive and accurate diagnostic assay is required that can detect different variant groups of GLRaV-3. In this study, a one-step real-time RT-PCR, followed by high-resolution melting (HRM) curve analysis for the simultaneous detection and identification of GLRaV-3 variants of groups I, II, III and VI, was developed. A melting point confidence interval for each variant group was calculated to include at least 90% of all melting points observed. A multiplex RT-PCR protocol was developed to these four variant groups in order to assess the efficacy of the real-time RT-PCR HRM assay. A universal primer set for GLRaV-3 targeting the heat shock protein 70 homologue (Hsp70h) gene of GLRaV-3 was designed that is able to detect GLRaV-3 variant groups I, II, III and VI and differentiate between them with high-resolution melting curve analysis. The real-time RT-PCR HRM and the multiplex RT-PCR were optimized using 121 GLRaV-3 positive samples. Due to a considerable variation in melting profile observed within each GLRaV-3 group, a confidence interval of above 90% was calculated for each variant group, based on the range and distribution of melting points. The intervals of groups I and II could not be distinguished and a 95% joint confidence interval was calculated for simultaneous detection of group I and II variants. An additional primer pair targeting GLRaV-3 ORF1a was developed that can be used in a subsequent real-time RT-PCR HRM to differentiate between variants of groups I and II. Additionally, the multiplex RT-PCR successfully validated 94.64% of the infections detected with the real-time RT-PCR HRM. The real-time RT-PCR HRM provides a sensitive, automated and rapid tool to detect and differentiate different variant groups in order to study the epidemiology of leafroll disease.

A novel typing method for Listeria monocytogenes using high-resolution melting analysis (HRMA) of tandem repeat regions.

PubMed

Ohshima, Chihiro; Takahashi, Hajime; Iwakawa, Ai; Kuda, Takashi; Kimura, Bon

2017-07-17

Listeria monocytogenes, which is responsible for causing food poisoning known as listeriosis, infects humans and animals. Widely distributed in the environment, this bacterium is known to contaminate food products after being transmitted to factories via raw materials. To minimize the contamination of products by food pathogens, it is critical to identify and eliminate factory entry routes and pathways for the causative bacteria. High resolution melting analysis (HRMA) is a method that takes advantage of differences in DNA sequences and PCR product lengths that are reflected by the disassociation temperature. Through our research, we have developed a multiple locus variable-number tandem repeat analysis (MLVA) using HRMA as a simple and rapid method to differentiate L. monocytogenes isolates. While evaluating our developed method, the ability of MLVA-HRMA, MLVA using capillary electrophoresis, and multilocus sequence typing (MLST) was compared for their ability to discriminate between strains. The MLVA-HRMA method displayed greater discriminatory ability than MLST and MLVA using capillary electrophoresis, suggesting that the variation in the number of repeat units, along with mutations within the DNA sequence, was accurately reflected by the melting curve of HRMA. Rather than relying on DNA sequence analysis or high-resolution electrophoresis, the MLVA-HRMA method employs the same process as PCR until the analysis step, suggesting a combination of speed and simplicity. The result of MLVA-HRMA method is able to be shared between different laboratories. There are high expectations that this method will be adopted for regular inspections at food processing facilities in the near future. Copyright © 2017. Published by Elsevier B.V.

Classification of Fowl Adenovirus Serotypes by Use of High-Resolution Melting-Curve Analysis of the Hexon Gene Region▿

PubMed Central

Steer, Penelope A.; Kirkpatrick, Naomi C.; O'Rourke, Denise; Noormohammadi, Amir H.

2009-01-01

Identification of fowl adenovirus (FAdV) serotypes is of importance in epidemiological studies of disease outbreaks and the adoption of vaccination strategies. In this study, real-time PCR and subsequent high-resolution melting (HRM)-curve analysis of three regions of the hexon gene were developed and assessed for their potential in differentiating 12 FAdV reference serotypes. The results were compared to previously described PCR and restriction enzyme analyses of the hexon gene. Both HRM-curve analysis of a 191-bp region of the hexon gene and restriction enzyme analysis failed to distinguish a number of serotypes used in this study. In addition, PCR of the region spanning nucleotides (nt) 144 to 1040 failed to amplify FAdV-5 in sufficient quantities for further analysis. However, HRM-curve analysis of the region spanning nt 301 to 890 proved a sensitive and specific method of differentiating all 12 serotypes. All melt curves were highly reproducible, and replicates of each serotype were correctly genotyped with a mean confidence value of more than 99% using normalized HRM curves. Sequencing analysis revealed that each profile was related to a unique sequence, with some sequences sharing greater than 94% identity. Melting-curve profiles were found to be related mainly to GC composition and distribution throughout the amplicons, regardless of sequence identity. The results presented in this study show that the closed-tube method of PCR and HRM-curve analysis provides an accurate, rapid, and robust genotyping technique for the identification of FAdV serotypes and can be used as a model for developing genotyping techniques for other pathogens. PMID:19036935

The spa typing of methicillin-resistant Staphylococcus aureus isolates by High Resolution Melting (HRM) analysis.

PubMed

Fasihi, Yasser; Fooladi, Saba; Mohammadi, Mohammad Ali; Emaneini, Mohammad; Kalantar-Neyestanaki, Davood

2017-09-06

Molecular typing is an important tool for control and prevention of infection. A suitable molecular typing method for epidemiological investigation must be easy to perform, highly reproducible, inexpensive, rapid and easy to interpret. In this study, two molecular typing methods including the conventional PCR-sequencing method and high resolution melting (HRM) analysis were used for staphylococcal protein A (spa) typing of 30 Methicillin-resistant Staphylococcus aureus (MRSA) isolates recovered from clinical samples. Based on PCR-sequencing method results, 16 different spa types were identified among the 30 MRSA isolates. Among the 16 different spa types, 14 spa types separated by HRM method. Two spa types including t4718 and t2894 were not separated from each other. According to our results, spa typing based on HRM analysis method is very rapid, easy to perform and cost-effective, but this method must be standardized for different regions, spa types, and real-time machinery.

Marine ice sheet model performance depends on basal sliding physics and sub-shelf melting

NASA Astrophysics Data System (ADS)

Gladstone, Rupert Michael; Warner, Roland Charles; Galton-Fenzi, Benjamin Keith; Gagliardini, Olivier; Zwinger, Thomas; Greve, Ralf

2017-01-01

Computer models are necessary for understanding and predicting marine ice sheet behaviour. However, there is uncertainty over implementation of physical processes at the ice base, both for grounded and floating glacial ice. Here we implement several sliding relations in a marine ice sheet flow-line model accounting for all stress components and demonstrate that model resolution requirements are strongly dependent on both the choice of basal sliding relation and the spatial distribution of ice shelf basal melting.Sliding relations that reduce the magnitude of the step change in basal drag from grounded ice to floating ice (where basal drag is set to zero) show reduced dependence on resolution compared to a commonly used relation, in which basal drag is purely a power law function of basal ice velocity. Sliding relations in which basal drag goes smoothly to zero as the grounding line is approached from inland (due to a physically motivated incorporation of effective pressure at the bed) provide further reduction in resolution dependence.A similar issue is found with the imposition of basal melt under the floating part of the ice shelf: melt parameterisations that reduce the abruptness of change in basal melting from grounded ice (where basal melt is set to zero) to floating ice provide improved convergence with resolution compared to parameterisations in which high melt occurs adjacent to the grounding line.Thus physical processes, such as sub-glacial outflow (which could cause high melt near the grounding line), impact on capability to simulate marine ice sheets. If there exists an abrupt change across the grounding line in either basal drag or basal melting, then high resolution will be required to solve the problem. However, the plausible combination of a physical dependency of basal drag on effective pressure, and the possibility of low ice shelf basal melt rates next to the grounding line, may mean that some marine ice sheet systems can be reliably simulated at a coarser resolution than currently thought necessary.

Rapid detection of Echinococcus species by a high-resolution melting (HRM) approach.

PubMed

Santos, Guilherme Brzoskowski; Espínola, Sergio Martín; Ferreira, Henrique Bunselmeyer; Margis, Rogerio; Zaha, Arnaldo

2013-11-14

High-resolution melting (HRM) provides a low-cost, fast and sensitive scanning method that allows the detection of DNA sequence variations in a single step, which makes it appropriate for application in parasite identification and genotyping. The aim of this work was to implement an HRM-PCR assay targeting part of the mitochondrial cox1 gene to achieve an accurate and fast method for Echinococcus spp. differentiation. For melting analysis, a total of 107 samples from seven species were used in this study. The species analyzed included Echinococcus granulosus (n = 41) and Echinococcus ortleppi (n = 50) from bovine, Echinococcus vogeli (n = 2) from paca, Echinococcus oligarthra (n = 3) from agouti, Echinococcus multilocularis (n = 6) from monkey and Echinococcus canadensis (n = 2) and Taenia hydatigena (n = 3) from pig. DNA extraction was performed, and a 444-bp fragment of the cox1 gene was amplified. Two approaches were used, one based on HRM analysis, and a second using SYBR Green Tm-based. In the HRM analysis, a specific profile for each species was observed. Although some species exhibited almost the same melting temperature (Tm) value, the HRM profiles could be clearly discriminated. The SYBR Green Tm-based analysis showed differences between E. granulosus and E. ortleppi and between E. vogeli and E. oligarthra. In this work, we report the implementation of HRM analysis to differentiate species of the genus Echinococcus using part of the mitochondrial gene cox1. This method may be also potentially applied to identify other species belonging to the Taeniidae family.

Rapid detection of Echinococcus species by a high-resolution melting (HRM) approach

PubMed Central

2013-01-01

Background High-resolution melting (HRM) provides a low-cost, fast and sensitive scanning method that allows the detection of DNA sequence variations in a single step, which makes it appropriate for application in parasite identification and genotyping. The aim of this work was to implement an HRM-PCR assay targeting part of the mitochondrial cox1 gene to achieve an accurate and fast method for Echinococcus spp. differentiation. Findings For melting analysis, a total of 107 samples from seven species were used in this study. The species analyzed included Echinococcus granulosus (n = 41) and Echinococcus ortleppi (n = 50) from bovine, Echinococcus vogeli (n = 2) from paca, Echinococcus oligarthra (n = 3) from agouti, Echinococcus multilocularis (n = 6) from monkey and Echinococcus canadensis (n = 2) and Taenia hydatigena (n = 3) from pig. DNA extraction was performed, and a 444-bp fragment of the cox1 gene was amplified. Two approaches were used, one based on HRM analysis, and a second using SYBR Green Tm-based. In the HRM analysis, a specific profile for each species was observed. Although some species exhibited almost the same melting temperature (Tm) value, the HRM profiles could be clearly discriminated. The SYBR Green Tm-based analysis showed differences between E. granulosus and E. ortleppi and between E. vogeli and E. oligarthra. Conclusions In this work, we report the implementation of HRM analysis to differentiate species of the genus Echinococcus using part of the mitochondrial gene cox1. This method may be also potentially applied to identify other species belonging to the Taeniidae family. PMID:24517106

High-resolution DNA melting analysis in plant research

USDA-ARS?s Scientific Manuscript database

Genetic and genomic studies provide valuable insight into the inheritance, structure, organization, and function of genes. The knowledge gained from the analysis of plant genes is beneficial to all aspects of plant research, including crop improvement. New methods and tools are continually developed...

High-resolution melting-curve (HRM) analysis for C. meleagridis identification in stool samples.

PubMed

Chelbi, Hanen; Essid, Rym; Jelassi, Refka; Bouzekri, Nesrine; Zidi, Ines; Ben Salah, Hamza; Mrad, Ilhem; Ben Sghaier, Ines; Abdelmalek, Rym; Aissa, Sameh; Bouratbine, Aida; Aoun, Karim

2018-02-01

Cryptosporidiosis represents a major public health problem. This infection, caused by a protozoan parasite of the genus Cryptosporidium, has been reported worldwide as a frequent cause of diarrhoea. In the immunocompetent host, the typical watery diarrhea can be self-limiting. However, it is severe and chronic, in the immunocompromised host and may cause death. Cryptosporidium spp. are coccidians, which complete their life cycle in both humans and animals. The two species C. hominis and C. parvum are the major cause of human infection. Compared to studies on C. hominis and C. parvum, only a few studies have developed methods to identify C. meleagridis. To develop a new real time PCR-coupled High resolution melting assay allowing the detection for C. meleagridis, in addition of the other dominant species (C. hominis and C. parvum). The polymorphic sequence on the dihydrofolate reductase gene (DHFR) of three species was sequenced to design primers pair and establish a sensitive real-time PCR coupled to a high-resolution melting-curve (HRM) analysis method, allowing the detection of Cryptosporidium sp. and discrimination between three prevalent species in Tunisia. We analyzed a collection of 42 archived human isolates of the three studied species. Real-time PCR coupled to HRM assay allowed detection of Cryptosporidium, using the new designed primers, and basing on melting profile, we can distinguish C. meleagridis species in addition to C. parvum and C. hominis. We developed a qPCR-HRM assay that allows Cryptosporidium genotyping. This method is sensitive and able to distinguish three Cryptosporidium species. Copyright © 2017. Published by Elsevier Ltd.

Spaceborne estimated long-term trends (1980s - 2013) of albedo and melting season length over the Greenland ice sheet and linkages to climate drivers

NASA Astrophysics Data System (ADS)

Tedesco, M.; Stroeve, J. C.

2014-12-01

The length of the melting season and surface albedo modulate the amount of meltwater produced over the Greenland ice sheet. The two quantities are intimately connected through a suite of non-linear processes: for example, early melting can reduce the surface albedo (through constructive grain size metamorphism), hence affecting the surface energy balance and further increasing melting. Over the past years, several studies have highlighted increased melting concurring, with a decrease of mean surface albedo over Greenland. However, few studies have examined the duration of the melting season, its implication for surface processes and linkages to climate drivers. Moreover, the majority (if not all) of the studies assessing albedo trends from spaceborne data over Greenland have focused on the last decade or so (2000 - 2013) because they use data collected over the same period by the Moderate Resolution Imaging Spectroradiometer (MODIS). Here, we evaluate and synthesize long-term trends in the length of the melting season (1979 - 2013) derived from spaceborne microwave observations together with surface albedo trends for the period 1982 - 2013 using data from the Advanced Very High Resolution Radiometer (AVHRR). To our knowledge, this is the first time that trends in Greenland albedo and melt season length are discussed for the periods considered in this study. Our results point to a lengthening of the melting season as a consequence of earlier melt onset and later refreeze and to a decrease of mean albedo (1982 - 2013) over the Greenland ice sheet, with trends being spatially variable. To account for this spatial variability, the results of an analysis at regional scales over 12 different regions (defined by elevation and drainage systems) are also reported. The robustness of the results is evaluated by means of a comparative analysis of the results obtained from both AVHRR and MODIS when overlapping data are available (2000 - 2013). Lastly, because large-scale circulation patterns and climate drivers can impact the amount of meltwater produced over Greenland (hence impacting albedo), we discuss the observed trends in the context of North Atlantic Oscillation (NAO) and Greenland Blocking Index (GBI) using a combination of regional climate model outputs and re-analysis data.

High Resolution Continuous Flow Analysis System for Polar Ice Cores

NASA Astrophysics Data System (ADS)

Dallmayr, Remi; Azuma, Kumiko; Yamada, Hironobu; Kjær, Helle Astrid; Vallelonga, Paul; Azuma, Nobuhiko; Takata, Morimasa

2014-05-01

In the last decades, Continuous Flow Analysis (CFA) technology for ice core analyses has been developed to reconstruct the past changes of the climate system 1), 2). Compared with traditional analyses of discrete samples, a CFA system offers much faster and higher depth resolution analyses. It also generates a decontaminated sample stream without time-consuming sample processing procedure by using the inner area of an ice-core sample.. The CFA system that we have been developing is currently able to continuously measure stable water isotopes 3) and electrolytic conductivity, as well as to collect discrete samples for the both inner and outer areas with variable depth resolutions. Chemistry analyses4) and methane-gas analysis 5) are planned to be added using the continuous water stream system 5). In order to optimize the resolution of the current system with minimal sample volumes necessary for different analyses, our CFA system typically melts an ice core at 1.6 cm/min. Instead of using a wire position encoder with typical 1mm positioning resolution 6), we decided to use a high-accuracy CCD Laser displacement sensor (LKG-G505, Keyence). At the 1.6 cm/min melt rate, the positioning resolution was increased to 0.27mm. Also, the mixing volume that occurs in our open split debubbler is regulated using its weight. The overflow pumping rate is smoothly PID controlled to maintain the weight as low as possible, while keeping a safety buffer of water to avoid air bubbles downstream. To evaluate the system's depth-resolution, we will present the preliminary data of electrolytic conductivity obtained by melting 12 bags of the North Greenland Eemian Ice Drilling (NEEM) ice core. The samples correspond to different climate intervals (Greenland Stadial 21, 22, Greenland Stadial 5, Greenland Interstadial 5, Greenland Interstadial 7, Greenland Stadial 8). We will present results for the Greenland Stadial -8, whose depths and ages are between 1723.7 and 1724.8 meters, and 35.520 to 35.636 kyr b2k 7), respectively. The results show the conductivity measured upstream and downstream of the debubbler. We will calculate the depth resolution of our system and compare it with earlier studies. 1) Bigler at al, "Optimization of High-Resolution Continuous Flow Analysis For Transient Climate Signals in Ice Cores". Environ. Sci. Technol. 2011, 45, 4483-4489 2) Kaufmann et al, "An Improved Continuous Flow Analysis System for High Resolution Field Measurements on Ice Cores". Environmental Environ. Sci. Technol. 2008, 42, 8044-8050 3) Gkinis, V., T. J. Popp, S. J. Johnsen and T, Blunier, 2010: A continuous stream flash evaporator for the calibration of an IR cavity ring down spectrometer for the isotopic analysis of water. Isotopes in Environmental and Health Studies, 46(4), 463-475. 4) McConnell et al, "Continuous ice-core chemical analyses using inductively coupled plasma mass spectrometry. Environ. Sci. Technol. 2002, 36, 7-11 5) Rhodes et al, "Continuous methane measurements from a late Holocene Greenland ice core : Atmospheric and in-situ signals" Earth and Planetary Science Letters. 2013, 368, 9-19 6) Breton et al, "Quantifying Signal Dispersion in a Hybrid Ice Core Melting System". Environ. Sci. Technol. 2012, 46, 11922-11928 7) Rasmussen et al, " A first chronology for the NEEM ice core". Climate of the Past. 2013, 9, 2967--3013

A new method for simultaneous detection and discrimination of Bovine herpesvirus types 1 (BoHV-1) and 5 (BoHV-5) using real time PCR with high resolution melting (HRM) analysis.

PubMed

Marin, M S; Quintana, S; Leunda, M R; Recavarren, M; Pagnuco, I; Späth, E; Pérez, S; Odeón, A

2016-01-01

Bovine herpesvirus types 1 (BoHV-1) and 5 (BoHV-5) are antigenically and genetically similar. The aim of this study was to develop a simple and reliable one-step real time PCR assay with high resolution melting (HRM) analysis for the simultaneous detection and differentiation of BoHV-1 and BoHV-5. Optimization of assay conditions was performed with DNA from reference strains. Then, DNA from field isolates, clinical samples and tissue samples of experimentally infected animals were studied by real time PCR-HRM. An efficient amplification of real time PCR products was obtained, and a clear melting curve and appropriate melting peaks for both viruses were achieved in the HRM curve analysis for BoHV type identification. BoHV was identified in all of the isolates and clinical samples, and BoHV types were properly differentiated. Furthermore, viral DNA was detected in 12/18 and 7/18 samples from BoHV-1- and BoHV-5-infected calves, respectively. Real time PCR-HRM achieved a higher sensitivity compared with virus isolation or conventional PCR. In this study, HRM was used as a novel procedure. This method provides rapid, sensitive, specific and simultaneous detection of bovine alpha-herpesviruses DNA. Thus, this technique is an excellent tool for diagnosis, research and epidemiological studies of these viruses in cattle. Copyright © 2015 Elsevier B.V. All rights reserved.

The Potential of Using Landsat 7 Data for the Classification of Sea Ice Surface Conditions During Summer

NASA Technical Reports Server (NTRS)

Markus, Thorsten; Cavalieri, Donald J.; Ivanoff, Alvaro; Koblinsky, Chester J. (Technical Monitor)

2001-01-01

During spring and summer, the Surface of the Arctic sea ice cover undergoes rapid changes that greatly affect the surface albedo and significantly impact the further decay of the sea ice. These changes are primarily the development of a wet snow cover and the development of melt ponds. As melt pond diameters generally do not exceed a couple of meters, the spatial resolutions of sensors like AVHRR and MODIS are too coarse for their identification. Landsat 7, on the other hand, has a spatial resolution of 30 m (15 m for the pan-chromatic band). The different wavelengths (bands) from blue to near-infrared offer the potential to distinguish among different surface conditions. Landsat 7 data for the Baffin Bay region for June 2000 have been analyzed. The analysis shows that different surface conditions, such as wet snow and meltponded areas, have different signatures in the individual Landsat bands. Consistent with in-situ albedo measurements, melt ponds show up as blueish whereas dry and wet ice have a white to gray appearance in the Landsat true-color image. These spectral differences enable the distinction of melt ponds. The melt pond fraction for the scene studied in this paper was 37%.

High resolution melting analysis is a more sensitive and effective alternative to gel-based platforms in analysis of SSR--an example in citrus.

PubMed

Distefano, Gaetano; Caruso, Marco; La Malfa, Stefano; Gentile, Alessandra; Wu, Shu-Biao

2012-01-01

High resolution melting curve analysis (HRM) has been used as an efficient, accurate and cost-effective tool to detect single nucleotide polymorphisms (SNPs) or insertions or deletions (INDELs). However, its efficiency, accuracy and applicability to discriminate microsatellite polymorphism have not been extensively assessed. The traditional protocols used for SSR genotyping include PCR amplification of the DNA fragment and the separation of the fragments on electrophoresis-based platform. However, post-PCR handling processes are laborious and costly. Furthermore, SNPs present in the sequences flanking repeat motif cannot be detected by polyacrylamide-gel-electrophoresis based methods. In the present study, we compared the discriminating power of HRM with the traditional electrophoresis-based methods and provided a panel of primers for HRM genotyping in Citrus. The results showed that sixteen SSR markers produced distinct polymorphic melting curves among the Citrus spp investigated through HRM analysis. Among those, 10 showed more genotypes by HRM analysis than capillary electrophoresis owing to the presence of SNPs in the amplicons. For the SSR markers without SNPs present in the flanking region, HRM also gave distinct melting curves which detected same genotypes as were shown in capillary electrophoresis (CE) analysis. Moreover, HRM analysis allowed the discrimination of most of the 15 citrus genotypes and the resulting genetic distance analysis clustered them into three main branches. In conclusion, it has been approved that HRM is not only an efficient and cost-effective alternative of electrophoresis-based method for SSR markers, but also a method to uncover more polymorphisms contributed by SNPs present in SSRs. It was therefore suggested that the panel of SSR markers could be used in a variety of applications in the citrus biodiversity and breeding programs using HRM analysis. Furthermore, we speculate that the HRM analysis can be employed to analyse SSR markers in a wide range of applications in all other species.

The use of high resolution melting analysis to detect Fabry mutations in heterozygous females via dry bloodspots.

PubMed

Tai, Chang-Long; Liu, Mei-Ying; Yu, Hsiao-Chi; Chiang, Chiang-Chuan; Chiang, Hung; Suen, Jeng-Hung; Kao, Shu-Min; Huang, Yu-Hsiu; Wu, Tina Jui-Ting; Yang, Chia-Feng; Tsai, Fang-Chih; Lin, Ching-Yuang; Chang, Jan-Gowth; Chen, Hong-Duo; Niu, Dau-Ming

2012-02-18

As an X-linked genetic disorder, Fabry disease was first thought to affect males only, and females were generally considered to be asymptomatic carriers. However, recent research suggests that female carriers of Fabry disease may still develop vital organ damage causing severe morbidity and mortality. In the previous newborn screening, from 299,007 newborns, we identified a total of 20 different Fabry mutations and 121 newborns with Fabry mutations. However, we found that most female carriers are not detected by enzyme assays. A streamlined method for high resolution melting (HRM) analysis was designed to screen for GLA gene mutations using a same PCR and melting program. Primer sets were designed to cover the 7 exons and the Chinese common intronic mutation, IVS4+919G>A of GLA gene. The HRM analysis was successful in identifying heterozygous and hemizygous patients with the 20 surveyed mutations. We were also successful in using this method to test dry blood spots of newborns afflicted with Fabry mutations without having to determine DNA concentration before PCR amplification. The results of this study show that HRM could be a reliable and sensitive method for use in the rapid screening of females for GLA mutations. Copyright © 2011 Elsevier B.V. All rights reserved.

High Resolution Melting (HRM) for High-Throughput Genotyping-Limitations and Caveats in Practical Case Studies.

PubMed

Słomka, Marcin; Sobalska-Kwapis, Marta; Wachulec, Monika; Bartosz, Grzegorz; Strapagiel, Dominik

2017-11-03

High resolution melting (HRM) is a convenient method for gene scanning as well as genotyping of individual and multiple single nucleotide polymorphisms (SNPs). This rapid, simple, closed-tube, homogenous, and cost-efficient approach has the capacity for high specificity and sensitivity, while allowing easy transition to high-throughput scale. In this paper, we provide examples from our laboratory practice of some problematic issues which can affect the performance and data analysis of HRM results, especially with regard to reference curve-based targeted genotyping. We present those examples in order of the typical experimental workflow, and discuss the crucial significance of the respective experimental errors and limitations for the quality and analysis of results. The experimental details which have a decisive impact on correct execution of a HRM genotyping experiment include type and quality of DNA source material, reproducibility of isolation method and template DNA preparation, primer and amplicon design, automation-derived preparation and pipetting inconsistencies, as well as physical limitations in melting curve distinction for alternative variants and careful selection of samples for validation by sequencing. We provide a case-by-case analysis and discussion of actual problems we encountered and solutions that should be taken into account by researchers newly attempting HRM genotyping, especially in a high-throughput setup.

High Resolution Melting (HRM) for High-Throughput Genotyping—Limitations and Caveats in Practical Case Studies

PubMed Central

Słomka, Marcin; Sobalska-Kwapis, Marta; Wachulec, Monika; Bartosz, Grzegorz

2017-01-01

High resolution melting (HRM) is a convenient method for gene scanning as well as genotyping of individual and multiple single nucleotide polymorphisms (SNPs). This rapid, simple, closed-tube, homogenous, and cost-efficient approach has the capacity for high specificity and sensitivity, while allowing easy transition to high-throughput scale. In this paper, we provide examples from our laboratory practice of some problematic issues which can affect the performance and data analysis of HRM results, especially with regard to reference curve-based targeted genotyping. We present those examples in order of the typical experimental workflow, and discuss the crucial significance of the respective experimental errors and limitations for the quality and analysis of results. The experimental details which have a decisive impact on correct execution of a HRM genotyping experiment include type and quality of DNA source material, reproducibility of isolation method and template DNA preparation, primer and amplicon design, automation-derived preparation and pipetting inconsistencies, as well as physical limitations in melting curve distinction for alternative variants and careful selection of samples for validation by sequencing. We provide a case-by-case analysis and discussion of actual problems we encountered and solutions that should be taken into account by researchers newly attempting HRM genotyping, especially in a high-throughput setup. PMID:29099791

Deep sequencing reveals double mutations in cis of MPL exon 10 in myeloproliferative neoplasms.

PubMed

Pietra, Daniela; Brisci, Angela; Rumi, Elisa; Boggi, Sabrina; Elena, Chiara; Pietrelli, Alessandro; Bordoni, Roberta; Ferrari, Maurizio; Passamonti, Francesco; De Bellis, Gianluca; Cremonesi, Laura; Cazzola, Mario

2011-04-01

Somatic mutations of MPL exon 10, mainly involving a W515 substitution, have been described in JAK2 (V617F)-negative patients with essential thrombocythemia and primary myelofibrosis. We used direct sequencing and high-resolution melt analysis to identify mutations of MPL exon 10 in 570 patients with myeloproliferative neoplasms, and allele specific PCR and deep sequencing to further characterize a subset of mutated patients. Somatic mutations were detected in 33 of 221 patients (15%) with JAK2 (V617F)-negative essential thrombocythemia or primary myelofibrosis. Only one patient with essential thrombocythemia carried both JAK2 (V617F) and MPL (W515L). High-resolution melt analysis identified abnormal patterns in all the MPL mutated cases, while direct sequencing did not detect the mutant MPL in one fifth of them. In 3 cases carrying double MPL mutations, deep sequencing analysis showed identical load and location in cis of the paired lesions, indicating their simultaneous occurrence on the same chromosome.

[High resolution melting analysis for detecting of JAK2V617F mutation in patients with myeloproliferative neoplasms].

PubMed

Chen, Hai-Hua; Yang, Ji-Long; Lu, Hui-Fang; Zhou, Wei-Jun; Yao, Fei; Deng, Lan

2014-02-01

This study was purposed to investigate the feasibility of high resolution melting (HRM) in the detection of JAK2V617F mutation in patients with myeloproliferative neoplasm (MPN). The 29 marrow samples randomly selected from patients with clinically diagnosed MPN from January 2008 to January 2011 were detected by HRM method. The results of HRM analysis were compared with that detected by allele specific polymerase chain reaction (AS-PCR) and DNA direct sequencing. The results showed that the JAK2V617F mutations were detected in 11 (37.9%, 11/29) cases by HRM, and its comparability with the direct sequencing result was 100%. While the consistency of AS-PCR with the direct sequencing was moderate (Kappa = 0.179, P = 0.316). It is concluded that the HRM analysis may be an optimal method for clinical screening of JAK2V617F mutation due to its simplicity and promptness with a high specificity.

Evaluation of Two Multiplex PCR-High-Resolution Melt Curve Analysis Methods for Differentiation of Campylobacter jejuni and Campylobacter coli Intraspecies.

PubMed

Banowary, Banya; Dang, Van Tuan; Sarker, Subir; Connolly, Joanne H; Chenu, Jeremy; Groves, Peter; Raidal, Shane; Ghorashi, Seyed Ali

2018-03-01

Campylobacter infection is a common cause of bacterial gastroenteritis in humans and remains a significant global public health issue. The capability of two multiplex PCR (mPCR)-high-resolution melt (HRM) curve analysis methods (i.e., mPCR1-HRM and mPCR2-HRM) to detect and differentiate 24 poultry isolates and three reference strains of Campylobacter jejuni and Campylobacter coli was investigated. Campylobacter jejuni and C. coli were successfully differentiated in both assays, but the differentiation power of mPCR2-HRM targeting the cadF gene was found superior to that of mPCR1-HRM targeting the gpsA gene or a hypothetical protein gene. However, higher intraspecies variation within C. coli and C. jejuni isolates was detected in mPCR1-HRM when compared with mPCR2-HRM. Both assays were rapid and required minimum interpretation skills for discrimination between and within Campylobacter species when using HRM curve analysis software.

Differentiation of Campylobacter jejuni and Campylobacter coli Using Multiplex-PCR and High Resolution Melt Curve Analysis

PubMed Central

Banowary, Banya; Dang, Van Tuan; Sarker, Subir; Connolly, Joanne H.; Chenu, Jeremy; Groves, Peter; Ayton, Michelle; Raidal, Shane; Devi, Aruna; Vanniasinkam, Thiru; Ghorashi, Seyed A.

2015-01-01

Campylobacter spp. are important causes of bacterial gastroenteritis in humans in developed countries. Among Campylobacter spp. Campylobacter jejuni (C. jejuni) and C. coli are the most common causes of human infection. In this study, a multiplex PCR (mPCR) and high resolution melt (HRM) curve analysis were optimized for simultaneous detection and differentiation of C. jejuni and C. coli isolates. A segment of the hippuricase gene (hipO) of C. jejuni and putative aspartokinase (asp) gene of C. coli were amplified from 26 Campylobacter isolates and amplicons were subjected to HRM curve analysis. The mPCR-HRM was able to differentiate between C. jejuni and C. coli species. All DNA amplicons generated by mPCR were sequenced. Analysis of the nucleotide sequences from each isolate revealed that the HRM curves were correlated with the nucleotide sequences of the amplicons. Minor variation in melting point temperatures of C. coli or C. jejuni isolates was also observed and enabled some intraspecies differentiation between C. coli and/or C. jejuni isolates. The potential of PCR-HRM curve analysis for the detection and speciation of Campylobacter in additional human clinical specimens and chicken swab samples was also confirmed. The sensitivity and specificity of the test were found to be 100% and 92%, respectively. The results indicated that mPCR followed by HRM curve analysis provides a rapid (8 hours) technique for differentiation between C. jejuni and C. coli isolates. PMID:26394042

Integrated microfluidic card with TaqMan probes and high-resolution melt analysis to detect tuberculosis drug resistance mutations across 10 genes.

PubMed

Pholwat, Suporn; Liu, Jie; Stroup, Suzanne; Gratz, Jean; Banu, Sayera; Rahman, S M Mazidur; Ferdous, Sara Sabrina; Foongladda, Suporn; Boonlert, Duangjai; Ogarkov, Oleg; Zhdanova, Svetlana; Kibiki, Gibson; Heysell, Scott; Houpt, Eric

2015-02-24

Genotypic methods for drug susceptibility testing of Mycobacterium tuberculosis are desirable to speed the diagnosis and proper therapy of tuberculosis (TB). However, the numbers of genes and polymorphisms implicated in resistance have proliferated, challenging diagnostic design. We developed a microfluidic TaqMan array card (TAC) that utilizes both sequence-specific probes and high-resolution melt analysis (HRM), providing two layers of detection of mutations. Twenty-seven primer pairs and 40 probes were designed to interrogate 3,200 base pairs of critical regions of the inhA, katG, rpoB, embB, rpsL, rrs, eis, gyrA, gyrB, and pncA genes. The method was evaluated on 230 clinical M. tuberculosis isolates from around the world, and it yielded 96.1% accuracy (2,431/2,530) in comparison to that of Sanger sequencing and 87% accuracy in comparison to that of the slow culture-based susceptibility testing. This TAC-HRM method integrates assays for 10 genes to yield fast, comprehensive, and accurate drug susceptibility results for the 9 major antibiotics used to treat TB and could be deployed to improve treatment outcomes. Multidrug-resistant tuberculosis threatens global tuberculosis control efforts. Optimal therapy utilizes susceptibility test results to guide individualized treatment regimens; however, the susceptibility testing methods in use are technically difficult and slow. We developed an integrated TaqMan array card method with high-resolution melt analysis that interrogates 10 genes to yield a fast, comprehensive, and accurate drug susceptibility result for the 9 major antituberculosis antibiotics. Copyright © 2015 Pholwat et al.

Cloudy Windows: What GCM Ensembles, Reanalyses and Observations Tell Us About Uncertainty in Greenland's Future Climate and Surface Melting

NASA Astrophysics Data System (ADS)

Reusch, D. B.

2016-12-01

Any analysis that wants to use a GCM-based scenario of future climate benefits from knowing how much uncertainty the GCM's inherent variability adds to the development of climate change predictions. This is extra relevant in the polar regions due to the potential of global impacts (e.g., sea level rise) from local (ice sheet) climate changes such as more frequent/intense surface melting. High-resolution, regional-scale models using GCMs for boundary/initial conditions in future scenarios inherit a measure of GCM-derived externally-driven uncertainty. We investigate these uncertainties for the Greenland ice sheet using the 30-member CESM1.0-CAM5-BGC Large Ensemble (CESMLE) for recent (1981-2000) and future (2081-2100, RCP 8.5) decades. Recent simulations are skill-tested against the ERA-Interim reanalysis and AWS observations with results informing future scenarios. We focus on key variables influencing surface melting through decadal climatologies, nonlinear analysis of variability with self-organizing maps (SOMs), regional-scale modeling (Polar WRF), and simple melt models. Relative to the ensemble average, spatially averaged climatological July temperature anomalies over a Greenland ice-sheet/ocean domain are mostly between +/- 0.2 °C. The spatial average hides larger local anomalies of up to +/- 2 °C. The ensemble average itself is 2 °C cooler than ERA-Interim. SOMs extend our diagnostics by providing a concise, objective summary of model variability as a set of generalized patterns. For CESMLE, the SOM patterns summarize the variability of multiple realizations of climate. Changes in pattern frequency by ensemble member show the influence of initial conditions. For example, basic statistical analysis of pattern frequency yields interquartile ranges of 2-4% for individual patterns across the ensemble. In climate terms, this tells us about climate state variability through the range of the ensemble, a potentially significant source of melt-prediction uncertainty. SOMs can also capture the different trajectories of climate due to intramodel variability over time. Polar WRF provides higher resolution regional modeling with improved, polar-centric model physics. Simple melt models allow us to characterize impacts of the upstream uncertainties on estimates of surface melting.

STR melting curve analysis as a genetic screening tool for crime scene samples.

PubMed

Nguyen, Quang; McKinney, Jason; Johnson, Donald J; Roberts, Katherine A; Hardy, Winters R

2012-07-01

In this proof-of-concept study, high-resolution melt curve (HRMC) analysis was investigated as a postquantification screening tool to discriminate human CSF1PO and THO1 genotypes amplified with mini-STR primers in the presence of SYBR Green or LCGreen Plus dyes. A total of 12 CSF1PO and 11 HUMTHO1 genotypes were analyzed on the LightScanner HR96 and LS-32 systems and were correctly differentiated based upon their respective melt profiles. Short STR amplicon melt curves were affected by repeat number, and single-source and mixed DNA samples were additionally differentiated by the formation of heteroduplexes. Melting curves were shown to be unique and reproducible from DNA quantities ranging from 20 to 0.4 ng and distinguished identical from nonidentical genotypes from DNA derived from different biological fluids and compromised samples. Thus, a method is described which can assess both the quantity and the possible probative value of samples without full genotyping. 2012 American Academy of Forensic Sciences. Published 2012. This article is a U.S. Government work and is in the public domain in the U.S.A.

Identification and discrimination of Toxoplasma gondii, Sarcocystis spp., Neospora spp., and Cryptosporidium spp. by righ-resolution melting analysis

PubMed Central

2017-01-01

The objective of this study was to standardize the high-resolution melting method for identification and discrimination of Toxoplasma gondii, Sarcocystis spp., Neospora spp., and Cryptosporidium spp. by amplification of 18S ribosomal DNA (rDNA) using a single primer pair. The analyses were performed on individual reactions (containing DNA from a single species of a protozoan), on duplex reactions (containing DNA from two species of protozoa in each reaction), and on a multiplex reaction (containing DNA of four parasites in a single reaction). The proposed method allowed us to identify and discriminate the four species by analyzing the derivative, normalized, and difference melting curves, with high reproducibility among and within the experiments, as demonstrated by low coefficients of variation (less than 2.2% and 2.0%, respectively). This is the first study where this method is used for discrimination of these four species of protozoa in a single reaction. PMID:28346485

Species identification in meat products: A new screening method based on high resolution melting analysis of cyt b gene.

PubMed

Lopez-Oceja, A; Nuñez, C; Baeta, M; Gamarra, D; de Pancorbo, M M

2017-12-15

Meat adulteration by substitution with lower value products and/or mislabeling involves economic, health, quality and socio-religious issues. Therefore, identification and traceability of meat species has become an important subject to detect possible fraudulent practices. In the present study the development of a high resolution melt (HRM) screening method for the identification of eight common meat species is reported. Samples from Bos taurus, Ovis aries, Sus scrofa domestica, Equus caballus, Oryctolagus cuniculus, Gallus gallus domesticus, Meleagris gallopavo and Coturnix coturnix were analyzed through the amplification of a 148 bp fragment from the cyt b gene with a universal primer pair in HRM analyses. Melting profiles from each species, as well as from several DNA mixtures of these species and blind samples, allowed a successful species differentiation. The results demonstrated that the HRM method here proposed is a fast, reliable, and low-cost screening technique. Copyright © 2017 Elsevier Ltd. All rights reserved.

High resolution melting analysis (HRM) for the assessment of clonality in feline B-cell lymphomas.

PubMed

Henrich, Manfred; Scheffold, Svenja; Hecht, Werner; Reinacher, Manfred

2018-06-01

Analysis of clonality is gaining importance in diagnosing lymphomas in veterinary medicine. Usually, PCR for the analysis of antigen receptor rearrangement (PARR) is followed by electrophoretic separation of the PCR products. Aim of this study was to test the feasibility of HRM for the assessment of clonality in B-cell lymphomas of cats. High resolution melting analysis differentiates PCR products by their different melting point using the decrease in fluorescence of an intercalating dye during melting of the PCR product. Additionally, the method is easy to use with no post-PCR manipulation of the samples. Forty-seven feline B-cell lymphomas and 31 reactive lymphatic proliferations of cats were investigated by PARR followed either by capillary electrophoresis or an HRM assay. To objectify the interpretation of the HRM results a recently published mathematical approach was applied to the melting curve. To overcome discrepancies between the visual interpretation and the mathematical approach, the latter was modified to include testing of reproducibility and recognition of pseudoclonality. In 11 of 47 lymphoma cases clonal populations were detectable by HRM assay compared to 14 of 47 lymphomas in which clonal populations were detected by capillary electrophoresis assay. Neither of the methods showed a clonal pattern in any of the reactive samples. However, the HRM assay showed a unique pattern in cases of follicular lymphatic hyperplasia that had no corresponding pattern in capillary electrophoresis. The capillary electrophoresis assay could identify 3 lymphomas that were not detected by the HRM assay and is therefore regarded superior to the HRM assay. The comparison however, was hampered by the overall bad performance of the PARR, that might be the consequence of insufficient primer binding due to somatic hypermutation of the binding sites during antigen stimulated proliferation of the B lymphocytes. Copyright © 2018 Elsevier B.V. All rights reserved.

Testing Snow Melt Algorithms in High Relief Topography Using Calibrated Enhanced-Resolution Brightness Temperatures, Hunza River Basin, Pakistan

NASA Astrophysics Data System (ADS)

Ramage, J. M.; Brodzik, M. J.; Hardman, M.; Troy, T. J.

2017-12-01

Snow is a vital part of the terrestrial hydrological cycle, a crucial resource for people and ecosystems. In mountainous regions snow is extensive, variable, and challenging to document. Snow melt timing and duration are important factors affecting the transfer of snow mass to soil moisture and runoff. Passive microwave brightness temperature (Tb) changes at 36 and 18 GHz are a sensitive way to detect snow melt onset due to their sensitivity to the abrupt change in emissivity. They are widely used on large icefields and high latitude watersheds. The coarse resolution ( 25 km) of historically available data has precluded effective use in high relief, heterogeneous regions, and gaps between swaths also create temporal data gaps at lower latitudes. New enhanced resolution data products generated from a scatterometer image reconstruction for radiometer (rSIR) technique are available at the original frequencies. We use these Calibrated Enhanced-resolution Brightness (CETB) Temperatures Earth System Data Records (ESDR) to evaluate existing snow melt detection algorithms that have been used in other environments, including the cross polarized gradient ratio (XPGR) and the diurnal amplitude variations (DAV) approaches. We use the 36/37 GHz (3.125 km resolution) and 18/19 GHz (6.25 km resolution) vertically and horizontally polarized datasets from the Special Sensor Microwave Imager (SSM/I) and Advanced Microwave Radiometer for EOS (AMSR-E) and evaluate them for use in this high relief environment. The new data are used to assess glacier and snow melt records in the Hunza River Basin [area 13,000 sq. km, located at 36N, 74E], a tributary to the Upper Indus Basin, Pakistan. We compare the melt timing results visually and quantitatively to the corresponding EASE-Grid 2.0 25-km dataset, SRTM topography, and surface temperatures from station and reanalysis data. The new dataset is coarser than the topography, but is able to differentiate signals of melt/refreeze timing for different altitudes and land cover in this remote area with significant hazards from snow melt and glacier discharge. The improved spatial resolution, enhanced to 3-6 km, and retaining twice daily observations is a key improvement to fully analyze snowpack melt characteristics in remote mountainous regions.

Analysis of Picosecond Pulsed Laser Melted Graphite

DOE R&D Accomplishments Database

Steinbeck, J.; Braunstein, G.; Speck, J.; Dresselhaus, M. S.; Huang, C. Y.; Malvezzi, A. M.; Bloembergen, N.

1986-12-01

A Raman microprobe and high resolution TEM have been used to analyze the resolidified region of liquid carbon generated by picosecond pulse laser radiation. From the relative intensities of the zone center Raman-allowed mode for graphite at 1582 cm{sup -1} and the disorder-induced mode at 1360 cm{sup -1}, the average graphite crystallite size in the resolidified region is determined as a function of position. By comparison with Rutherford backscattering spectra and Raman spectra from nanosecond pulsed laser melting experiments, the disorder depth for picosecond pulsed laser melted graphite is determined as a function of irradiating energy density. Comparisons of TEM micrographs for nanosecond and picosecond pulsed laser melting experiments show that the structure of the laser disordered regions in graphite are similar and exhibit similar behavior with increasing laser pulse fluence.

Differentiation of five enterohepatic Helicobacter species by nested PCR with high-resolution melting curve analysis.

PubMed

Wu, Miaoli; Rao, Dan; Zhu, Yujun; Wang, Jing; Yuan, Wen; Zhang, Yu; Huang, Ren; Guo, Pengju

2017-04-01

Enterohepatic Helicobacter species (EHS) are widespread in rodent species around the world. Several studies have demonstrated that infection with EHS can interfere with the outcomes of animal experiments in cancer research and significantly influence the study results. Therefore, it is essential to establish a rapid detection and identification of EHS for biomedical research using laboratory rodents. Our study aimed to develop a rapid and sensitive method to detect and distinguish five enterohepatic Helicobacter species. Nested PCR followed by high-resolution melting curve analysis (HRM) was developed for identification of H. bilis, H. rodentium, H. muridarum, H. typhlonius, as well as H. hepaticus. To validate the accuracy of nested PCR-HRM analysis, quantitative real-time PCR methods for five different enterohepatic Helicobacter species were developed. A total of 50 cecal samples were tested using both nested PCR-HRM analysis and qPCR method. The nested PCR-HRM method could distinguish five enterohepatic Helicobacter species by different melting temperatures. The melting curve were characterized by peaks of 78.7 ± 0.12°C for H. rodentium, 80.51 ± 0.09°C for H. bilis, 81.6 ± 0.1°C for H. typhlonius, 82.11 ± 0.18°C for H. muridarum, and 82.95 ± 0.09°C for H. hepaticus. The nested PCR-HRM assay is a simple, rapid, and cost-effective assay. This assay could be a useful tool for molecular epidemiology study of enterohepatic Helicobacter infection and an attractive alternative for genotyping of enterohepatic Helicobacter species. © 2016 John Wiley & Sons Ltd.

Identification and Differentiation of Monilinia Species Causing Brown Rot of Pome and Stone Fruit using High-Resolution Melting (HRM) Analysis.

PubMed

Papavasileiou, Antonios; Madesis, Panagiotis B; Karaoglanidis, George S

2016-09-01

Brown rot is a devastating disease of stone fruit caused by Monilinia spp. Among these species, Monilinia fructicola is a quarantine pathogen in Europe but has recently been detected in several European countries. Identification of brown rot agents relies on morphological differences or use of molecular methods requiring fungal isolation. The current study was initiated to develop and validate a high-resolution melting (HRM) method for the identification of the Monilinia spp. and for the detection of M. fructicola among other brown rot pathogens. Based on the sequence of the cytb intron from M. laxa, M. fructicola, M. fructigena, M. mumecola, M. linhartiana, and M. yunnanensis isolates originating from several countries, a pair of universal primers for species identification and a pair of primers specific to M. fructicola were designed. The specificity of the primers was verified to ensure against cross-reaction with other fungal species. The melting curve analysis using the universal primers generated six different HRM curve profiles, each one specific for each species. Τhe HRM analysis primers specific to M. fructicola amplified a 120-bp region with a distinct melt profile corresponding to the presence of M. fructicola, regardless of the presence of other species. HRM analysis can be a useful tool for rapid identification and differentiation of the six Monilinia spp. using a single primer pair. This novel assay has the potential for simultaneous identification and differentiation of the closely related Monilinia spp. as well as for the differentiation of M. fructicola from other common pathogens or saprophytes that may occur on the diseased fruit.

Application of high-resolution melting analysis for authenticity testing of valuable Dendrobium commercial products.

PubMed

Dong, Xiaoman; Jiang, Chao; Yuan, Yuan; Peng, Daiyin; Luo, Yuqin; Zhao, Yuyang; Huang, Luqi

2018-01-01

The accurate identification of botanical origin in commercial products is important to ensure food authenticity and safety for consumers. The Dendrobium species have long been commercialised as functional food supplements and herbal medicines in Asia. Three valuable Dendrobium species, namely Dendrobium officinale, D. huoshanense and D. moniliforme, are often mutually adulterated in trade products in pursuit of higher profit. In this paper, a rapid and reliable semi-quantitative method for identifying the botanical origin of Dendrobium products in terminal markets was developed using high-resolution melting (HRM) analysis with specific primer pairs to target the trnL-F region. The HRM analysis method detected amounts of D. moniliforme adulterants as low as 1% in D. huoshanense or D. officinale products. The results have demonstrated that HRM analysis is a fast and effective tool for the differentiation of these Dendrobium species both for their authenticity as well as for the semi-quantitative determination of the purity of their processed products. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Snow Coverage Analysis Using ASTER over the Sierra Nevada Mountain Range

NASA Astrophysics Data System (ADS)

Ross, B.

2017-12-01

Snow has strong impacts on human behavior, state and local activities, and the economy. The Sierra Nevada snowpack is California's most important natural reservoir of water. Such snow is melting sooner and faster. A recent California drought study showed that there was a deficit of 1.5 million acre-feet of water in 2014 due to the fast melting rates. Scientists have been using the Moderate Resolution Imaging Spectrometer (MODIS) which is available at the spatial resolution of 500-meter, to analyze the changes in snow coverage. While such analysis provides us with the valuable information, it would be more beneficial to employ the imageries at a higher spatial resolution for snow studies. Advanced Spaceborne Thermal Emission and Reflectance Radiometer (ASTER), which acquires the high-resolution imageries ranging from 15-meter to 90-meter, has recently become freely available to the public. Our study utilized two scenes obtained from ASTER to investigate the changes in snow extent over the Sierra Nevada's mountain area for an 8-year period. These two scenes were collected on April 11, 2007 and April 16, 2015 covering the same geographic region. Normalized Difference Snow Index (NDSI) was adopted to delineate the snow coverage in each scene. Our study shows a substantial decrease of snow coverage in the studied geographic region by pixel count.

Analysis of Summer 2002 Melt Extent on the Greenland Ice Sheet using MODIS and SSM/I Data

NASA Technical Reports Server (NTRS)

Hall, Dorothy K.; Williams, Richard S., Jr.; Steffen, Konrad; Chien, Y. L.; Foster, James L.; Robinson, David A.; Riggs, George A.

2004-01-01

Previous work has shown that the summer of 2002 had the greatest area of snow melt extent on the Greenland ice sheet ever recorded using passive-microwave data. In this paper, we compare the 0 degree isotherm derived from the Moderate-Resolution Imaging Spectroradiometer (MODIS) instrument, with Special Sensor Microwave/Imager (SSM/I)-derived melt, at the time of the maximum melt extent in 2002. To validate the MODIS-derived land-surface temperatures (LSTs), we compared the MODIS LSTs with air temperatures from nine stations (using 11 different data points) and found that they agreed to within 2.3 plus or minus 2.09 C, with station temperatures consistently lower than the MODIS LSTs. According to the MODIS LST, the maximum surface melt extended to approximately 2300 m in southern Greenland; while the SSM/I measurements showed that the maximum melt extended to nearly 2700 m in southeastern Greenland. The MODIS and SSM/I data are complementary in providing detailed information about the progression of surface and near-surface melt on the Greenland ice sheet.

Analysis of Summer 2002 Melt Extent on the Greenland Ice Sheet using MODIS and SSM/I Data

NASA Technical Reports Server (NTRS)

Hall, Dorothy K.; Williams, Richard S.; Steffen, Konrad; Chien, Janet Y. L.

2004-01-01

Previous work has shown that the summer of 2002 had the greatest area of snow melt extent on the Greenland ice sheet ever recorded using passive-microwave data. In this paper, we compare the 0 deg. isotherm derived from the Moderate-Resolution Imaging Spectroradiometer (MODIS) instrument, with Special Sensor Microwave/Imager (SSM/I)-derived melt, at the time of the maximum melt extent in 2002. To validate the MODIS derived land-surface temperatures (LSTs), we compared the MODIS LSTs with air temperatures from nine stations (using 11 different data points) and found that they agreed to within 2.3 +/- 2.09 C, with station temperatures consistently lower than the MODIS LSTs. According to the MODIS LST, the maximum surface melt extended to approx. 2300 m in southern Greenland; while the SSM/I measurements showed that the maximum melt extended to nearly 2700 m in southeastern Greenland. The MODIS and SSM/I data are complementary in providing detailed information about the progression of surface and near- surface melt on the Greenland ice sheet.

Analysis of summer 2002 melt extent on the Greenland ice sheet using MODIS and SSM/I data

USGS Publications Warehouse

Hall, D.K.; Williams, R.S.; Steffen, K.; Chien, Janet Y.L.

2004-01-01

Previous work has shown that the summer of 2002 had the greatest area of snow melt extent on the Greenland ice sheet ever recorded using passive-microwave data. In this paper, we compare the 0?? isotherm derived from the Moderate-Resolution Imaging Spectroradiometer (MODIS) instrument, with Special Sensor Microwave/Imager (SSM/I)-derived melt, at the time of the maximum melt extent in 2002. To validate the MODIS-derived land-surface temperatures (LSTs), we compared the MODIS LSTs with air temperatures from nine stations (using 11 different data points) and found that they agreed to within 2.3??2.09??C, with station temperatures consistently lower than the MODIS LSTs. According to the MODIS LST, the maximum surface melt extended to ???2300 m in southern Greenland; while the SSM/I measurements showed that the maximum melt extended to nearly 2700 m in southeastern Greenland. The MODIS and SSM/I data are complementary in providing detailed information about the progression of surface and near-surface melt on the Greenland ice sheet.

Analysis of summer 2002 melt extent on the Greenland ice sheet using MODIS and SSM/I data

USGS Publications Warehouse

Hall, D. K.; Williams, R.S.; Steffen, K.; Chien, Janet Y.L.

2004-01-01

Previous work has shown that the summer of 2002 had the greatest area of snow melt extent on the Greenland ice sheet ever recorded using passive-microwave data. In this paper, we compare the 0deg isotherm derived from the Moderate-Resolution Imaging Spectroradiometer (MODIS) instrument, with Special Sensor Microwave/Imager (SSM/I)-derived melt, at the time of the maximum melt extent in 2002. To validate the MODIS-derived land-surface temperatures (LSTs), we compared the MODIS LSTs with air temperatures from nine stations (using 11 different data points) and found that they agreed to within 2.3 plusmn 2.09 degC, with station temperatures consistently lower than the MODIS LSTs. According to the MODIS LST, the maximum surface melt extended to ~2300 m in southern Greenland; while the SSM/I measurements showed that the maximum melt extended to nearly 2700 m in southeastern Greenland. The MODIS and SSM/I data are complementary in providing detailed information about the progression of surface and near-surface melt on the Greenland ice sheet.

Optimizing high-resolution melting analysis for the detection of mutations of GPR30/GPER-1 in breast cancer.

PubMed

Aihara, Masamune; Yamamoto, Shigeru; Nishioka, Hiroko; Inoue, Yutaro; Hamano, Kimikazu; Oka, Masaaki; Mizukami, Yoichi

2012-06-15

G protein-coupled receptor 30/G protein estrogen receptor-1 (GPR30/GPER-1) is a novel membrane receptor for estrogen whose mRNA is expressed at high levels in estrogen-dependent cells such as breast cancer cell lines. However, mutations in GRP30 related to diseases remain unreported. To detect unknown mutations in the GPR30 open reading frame (ORF) quickly, the experimental conditions for high-resolution melting (HRM) analysis were examined for PCR primers, Taq polymerases, saturation DNA binding dyes, Mg(2+) concentration, and normalized temperatures. Nine known SNPs and 13 artificial point mutations within the GPR30 ORF, as well as single nucleotide variants in DNA extracted from subjects with breast cancers were tested under the optimal experimental conditions. The combination of Expand High Fidelity(PLUS) and SYTO9 in the presence of 2.0 mM MgCl(2) produced the best separation in melting curves of mutations in all regions of the GPR30 ORF. Under these experimental conditions, the mutations were clearly detected in both heterozygotes and homozygotes. HRM analysis of GPR30 using genomic DNA from subjects with breast cancers showed a novel single nucleotide variant, 111C>T in GPR30 and 4 known SNPs. The experimental conditions determined in this study for HRM analysis are useful for high throughput assays to detect unknown mutations within the GPR30 ORF. Copyright © 2012 Elsevier B.V. All rights reserved.

Retrieval of sea ice thickness during Arctic summer using melt pond color

NASA Astrophysics Data System (ADS)

Istomina, L.; Nicolaus, M.; Heygster, G.

2016-12-01

The thickness of sea ice is an important climatic variable. Together with the ice concentration, it defines the total sea ice volume, is linked within the climatic feedback mechanisms and affects the Arctic energy balance greatly. During Arctic summer, the sea ice cover changes rapidly, which includes the presence of melt ponds, as well as reduction of ice albedo and ice thickness. Currently available remote sensing retrievals of sea ice thickness utilize data from altimeter, microwave, thermal infrared sensors and their combinations. All of these methods are compromised in summer in the presence of melt. This only leaves in situ and airborne sea ice thickness data available in summer. At the same time, data of greater coverage is needed for assimilation in global circulation models and correct estimation of ice mass balance.This study presents a new approach to estimate sea ice thickness in summer in the presence of melt ponds. Analysis of field data obtained during the RV "Polarstern" cruise ARK27/3 (August - October 2012) has shown a clear connection of ice thickness under melt ponds to their measured spectral albedo and to melt pond color in the hue-saturation-luminance color space from field photographs. An empirical function is derived from the HSL values and applied to aerial imagery obtained during various airborne campaigns. Comparison to in situ ice thickness shows a good correspondence to the ice thickness value retrieved in the melt ponds. A similar retrieval is developed for satellite spectral bands using the connection of the measured pond spectral albedo to the ice thickness within the melt ponds. Correction of the retrieved ice thickness in ponds to derive total thickness of sea ice is discussed. Case studies and application to very high resolution optical data are presented, as well as a concept to transfer the method to satellite data of lower spatial resolution where melt ponds become subpixel features.

Gene Scanning of an Internalin B Gene Fragment Using High-Resolution Melting Curve Analysis as a Tool for Rapid Typing of Listeria monocytogenes

PubMed Central

Pietzka, Ariane T.; Stöger, Anna; Huhulescu, Steliana; Allerberger, Franz; Ruppitsch, Werner

2011-01-01

The ability to accurately track Listeria monocytogenes strains involved in outbreaks is essential for control and prevention of listeriosis. Because current typing techniques are time-consuming, cost-intensive, technically demanding, and difficult to standardize, we developed a rapid and cost-effective method for typing of L. monocytogenes. In all, 172 clinical L. monocytogenes isolates and 20 isolates from culture collections were typed by high-resolution melting (HRM) curve analysis of a specific locus of the internalin B gene (inlB). All obtained HRM curve profiles were verified by sequence analysis. The 192 tested L. monocytogenes isolates yielded 15 specific HRM curve profiles. Sequence analysis revealed that these 15 HRM curve profiles correspond to 18 distinct inlB sequence types. The HRM curve profiles obtained correlated with the five phylogenetic groups I.1, I.2, II.1, II.2, and III. Thus, HRM curve analysis constitutes an inexpensive assay and represents an improvement in typing relative to classical serotyping or multiplex PCR typing protocols. This method provides a rapid and powerful screening tool for simultaneous preliminary typing of up to 384 samples in approximately 2 hours. PMID:21227395

Simultaneous screening for JAK2 and calreticulin gene mutations in myeloproliferative neoplasms with high resolution melting.

PubMed

Matsumoto, Nariyoshi; Mori, Sayaka; Hasegawa, Hiroo; Sasaki, Daisuke; Mori, Hayato; Tsuruda, Kazuto; Imanishi, Daisuke; Imaizumi, Yoshitaka; Hata, Tomoko; Kaku, Norihito; Kosai, Kousuke; Uno, Naoki; Miyazaki, Yasushi; Yanagihara, Katsunori

2016-11-01

Recently, novel calreticulin (CALR) mutations were discovered in Janus kinase 2 (JAK2) non-mutated myelofibrosis (PMF) and essential thrombocythemia (ET) cases, with a frequency of 60-80%. We examined clinical correlations and CALR mutation frequency in our myeloproliferative neoplasms (MPN) cases, and introduce an effective test method for use in clinical practice. We examined 177 samples previously investigated for the JAK2 mutation for differential diagnosis of MPN. JAK2 and CALR mutations were analyzed using melting curve analysis and microchip electrophoresis, respectively. Next, we constructed a test for simultaneous screening of the JAK2 and CALR mutations utilizing high resolution melting (HRM). Among 99 MPN cases, 60 possessed the JAK2 mutation alone. Of the 39 MPN cases without the JAK2 mutation, 14 were positive for the CALR mutation, all of which were ET. Using our novel screening test for the JAK2 and CALR mutations by HRM, the concordance rate of conventional analysis with HRM was 96% for the JAK2 mutation and 95% for the CALR mutation. Our novel simultaneous screening test for the JAK2 and CALR gene mutations with HRM is useful for diagnosis of MPN. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

High-resolution melting analysis for detection of MYH9 mutations.

PubMed

Provaznikova, Dana; Kumstyrova, Tereza; Kotlin, Roman; Salaj, Peter; Matoska, Vaclav; Hrachovinova, Ingrid; Rittich, Simon

2008-09-01

May-Hegglin anomaly (MHA), Sebastian (SBS), Fechtner (FTNS) and Epstein (EPS) syndromes are rare autosomal dominant disorders with giant platelets and thrombocytopenia. Other manifestations of these disorders are combinations of the presence of granulocyte inclusions and deafness, cataracts and renal failure. Currently, MHA, SBS, FTNS and EPS are considered to be distinct clinical manifestation of a single illness caused by mutations of the MYH9 gene encoding the heavy chain of non-muscle myosin IIA (NMMHC-IIA). As the MYH9 gene has a high number of exons, it takes much time and material to use this method for the detection of MYH9 mutations. Recently, a new method has been introduced for scanning DNA mutations without the need for direct sequencing: high-resolution melting analysis (HRMA). Mutation detection with HRMA relies on the intercalation of the specific dye (LC Green plus) in double-strand DNA and fluorescence monitoring of PCR product melting profiles. In our study, we optimized the conditions and used HRMA for rapid screening of mutations in all MYH9 exons in seven affected individuals from four unrelated families with suspected MYH9 disorders. Samples identified by HRMA as positive for the mutation were analysed by direct sequencing. HRMA saved us over 85% of redundant sequencing.

Rapid and specific detection of Salmonella in water samples using real-time PCR and High Resolution Melt (HRM) curve analysis.

PubMed

van Blerk, G N; Leibach, L; Mabunda, A; Chapman, A; Louw, D

2011-01-01

A real-time PCR assay combined with a pre-enrichment step for the specific and rapid detection of Salmonella in water samples is described. Following amplification of the invA gene target, High Resolution Melt (HRM) curve analysis was used to discriminate between products formed and to positively identify invA amplification. The real-time PCR assay was evaluated for specificity and sensitivity. The assay displayed 100% specificity for Salmonella and combined with a 16-18 h non-selective pre-enrichment step, the assay proved to be highly sensitive with a detection limit of 1.0 CFU/ml for surface water samples. The detection assay also demonstrated a high intra-run and inter-run repeatability with very little variation in invA amplicon melting temperature. When applied to water samples received routinely by the laboratory, the assay showed the presence of Salmonella in particularly surface water and treated effluent samples. Using the HRM based assay, the time required for Salmonella detection was drastically shortened to less than 24 h compared to several days when using standard culturing methods. This assay provides a useful tool for routine water quality monitoring as well as for quick screening during disease outbreaks.

Century-scale simulations of the response of the West Antarctic Ice Sheet to a warming climate

DOE PAGES

Cornford, S. L.; Martin, D. F.; Payne, A. J.; ...

2015-03-23

We use the BISICLES adaptive mesh ice sheet model to carry out one, two, and three century simulations of the fast-flowing ice streams of the West Antarctic Ice Sheet. Each of the simulations begins with a geometry and velocity close to present day observations, and evolves according to variation in meteoric ice accumulation, ice shelf melting, and mesh resolution. Future changes in accumulation and melt rates range from no change, through anomalies computed by atmosphere and ocean models driven by the E1 and A1B emissions scenarios, to spatially uniform melt rates anomalies that remove most of the ice shelves overmore » a few centuries. We find that variation in the resulting ice dynamics is dominated by the choice of initial conditions, ice shelf melt rate and mesh resolution, although ice accumulation affects the net change in volume above flotation to a similar degree. Given sufficient melt rates, we compute grounding line retreat over hundreds of kilometers in every major ice stream, but the ocean models do not predict such melt rates outside of the Amundsen Sea Embayment until after 2100. Sensitivity to mesh resolution is spurious, and we find that sub-kilometer resolution is needed along most regions of the grounding line to avoid systematic under-estimates of the retreat rate, although resolution requirements are more stringent in some regions – for example the Amundsen Sea Embayment – than others – such as the Möller and Institute ice streams.« less

[Rapid detection of hot spot mutations of FGFR3 gene with PCR-high resolution melting assay].

PubMed

Li, Shan; Wang, Han; Su, Hua; Gao, Jinsong; Zhao, Xiuli

2017-08-10

To identify the causative mutations in five individuals affected with dyschondroplasia and develop an efficient procedure for detecting hot spot mutations of the FGFR3 gene. Genomic DNA was extracted from peripheral blood samples with a standard phenol/chloroform method. PCR-Sanger sequencing was used to analyze the causative mutations in the five probands. PCR-high resolution melting (HRM) was developed to detect the identified mutations. A c.1138G>A mutation in exon 8 was found in 4 probands, while a c.1620C>G mutation was found in exon 11 of proband 5 whom had a mild phenotype. All patients were successfully distinguished from healthy controls with the PCR-HRM method. The results of HRM analysis were highly consistent with that of Sanger sequencing. The Gly380Arg and Asn540Lys are hot spot mutations of the FGFR3 gene among patients with ACH/HCH. PCR-HRM analysis is more efficient for detecting hot spot mutations of the FGFR3 gene.

Rapid Molecular Analysis of the STAT3 Gene in Job Syndrome of Hyper-IgE and Recurrent Infectious Diseases

PubMed Central

Kumánovics, Attila; Wittwer, Carl T.; Pryor, Robert J.; Augustine, Nancy H.; Leppert, Mark F.; Carey, John C.; Ochs, Hans D.; Wedgwood, Ralph J.; Faville, Ralph J.; Quie, Paul G.; Hill, Harry R.

2010-01-01

With the recent discovery of mutations in the STAT3 gene in the majority of patients with classic Hyper-IgE syndrome, it is now possible to make a molecular diagnosis in most of these cases. We have developed a PCR-based high-resolution DNA-melting assay to scan selected exons of the STAT3 gene for mutations responsible for Hyper-IgE syndrome, which is then followed by targeted sequencing. We scanned for mutations in 10 unrelated pedigrees, which include 16 patients with classic Hyper-IgE syndrome. These pedigrees include both sporadic and familial cases and their relatives, and we have found STAT3 mutations in all affected individuals. High-resolution melting analysis allows a single day turn-around time for mutation scanning and targeted sequencing of the STAT3 gene, which will greatly facilitate the rapid diagnosis of the Hyper-IgE syndrome, allowing prompt and appropriate therapy, prophylaxis, improved clinical outcome, and accurate genetic counseling. PMID:20093388

High resolution melt curve analysis based on methylation status for human semen identification.

PubMed

Fachet, Caitlyn; Quarino, Lawrence; Karnas, K Joy

2017-03-01

A high resolution melt curve assay to differentiate semen from blood, saliva, urine, and vaginal fluid based on methylation status at the Dapper Isoform 1 (DACT1) gene was developed. Stains made from blood, saliva, urine, semen, and vaginal fluid were obtained from volunteers and DNA was isolated using either organic extraction (saliva, urine, and vaginal fluid) or Chelex ® 100 extraction (blood and semen). Extracts were then subjected to bisulfite modification in order to convert unmethylated cytosines to uracil, consequently creating sequences whose amplicons have melt curves that vary depending on their initial methylation status. When primers designed to amplify the promoter region of the DACT1 gene were used, DNA from semen samples was distinguishable from other fluids by a having a statistically significant lower melting temperature. The assay was found to be sperm-significant since semen from a vasectomized man produced a melting temperature similar to the non-semen body fluids. Blood and semen stains stored up to 5 months and tested at various intervals showed little variation in melt temperature indicating the methylation status was stable during the course of the study. The assay is a more viable method for forensic science practice than most molecular-based methods for body fluid stain identification since it is time efficient and utilizes instrumentation common to forensic biology laboratories. In addition, the assay is advantageous over traditional presumptive chemical methods for body fluid identification since results are confirmatory and the assay offers the possibility of multiplexing which may test for multiple body fluids simultaneously.

High-resolution melt PCR analysis for genotyping of Ureaplasma parvum isolates directly from clinical samples.

PubMed

Payne, Matthew S; Tabone, Tania; Kemp, Matthew W; Keelan, Jeffrey A; Spiller, O Brad; Newnham, John P

2014-02-01

Ureaplasma sp. infection in neonates and adults underlies a variety of disease pathologies. Of the two human Ureaplasma spp., Ureaplasma parvum is clinically the most common. We have developed a high-resolution melt (HRM) PCR assay for the differentiation of the four serovars of U. parvum in a single step. Currently U. parvum strains are separated into four serovars by sequencing the promoter and coding region of the multiple-banded antigen (MBA) gene. We designed primers to conserved sequences within this region for PCR amplification and HRM analysis to generate reproducible and distinct melt profiles that distinguish clonal representatives of serovars 1, 3, 6, and 14. Furthermore, our HRM PCR assay could classify DNA extracted from 74 known (MBA-sequenced) test strains with 100% accuracy. Importantly, HRM PCR was also able to identify U. parvum serovars directly from 16 clinical swabs. HRM PCR performed with DNA consisting of mixtures of combined known serovars yielded profiles that were easily distinguished from those for single-serovar controls. These profiles mirrored clinical samples that contained mixed serovars. Unfortunately, melt curve analysis software is not yet robust enough to identify the composition of mixed serovar samples, only that more than one serovar is present. HRM PCR provides a single-step, rapid, cost-effective means to differentiate the four serovars of U. parvum that did not amplify any of the known 10 serovars of Ureaplasma urealyticum tested in parallel. Choice of reaction reagents was found to be crucial to allow sufficient sensitivity to differentiate U. parvum serovars directly from clinical swabs rather than requiring cell enrichment using microbial culture techniques.

Competitive PCR-High Resolution Melting Analysis (C-PCR-HRMA) for large genomic rearrangements (LGRs) detection: A new approach to assess quantitative status of BRCA1 gene in a reference laboratory.

PubMed

Minucci, Angelo; De Paolis, Elisa; Concolino, Paola; De Bonis, Maria; Rizza, Roberta; Canu, Giulia; Scaglione, Giovanni Luca; Mignone, Flavio; Scambia, Giovanni; Zuppi, Cecilia; Capoluongo, Ettore

2017-07-01

Evaluation of copy number variation (CNV) in BRCA1/2 genes, due to large genomic rearrangements (LGRs), is a mandatory analysis in hereditary breast and ovarian cancers families, if no pathogenic variants are found by sequencing. LGRs cannot be detected by conventional methods and several alternative methods have been developed. Since these approaches are expensive and time consuming, identification of alternative screening methods for LGRs detection is needed in order to reduce and optimize the diagnostic procedure. The aim of this study was to investigate a Competitive PCR-High Resolution Melting Analysis (C-PCR-HRMA) as molecular tool to detect recurrent BRCA1 LGRs. C-PCR-HRMA was performed on exons 3, 14, 18, 19, 20 and 21 of the BRCA1 gene; exons 4, 6 and 7 of the ALB gene were used as reference fragments. This study showed that it is possible to identify recurrent BRCA1 LGRs, by melting peak height ratio between target (BRCA1) and reference (ALB) fragments. Furthermore, we underline that a peculiar amplicon-melting profile is associated to a specific BRCA1 LGR. All C-PCR-HRMA results were confirmed by Multiplex ligation-dependent probe amplification. C-PCR-HRMA has proved to be an innovative, efficient and fast method for BRCA1 LGRs detection. Given the sensitivity, specificity and ease of use, c-PCR-HRMA can be considered an attractive and powerful alternative to other methods for BRCA1 CNVs screening, improving molecular strategies for BRCA testing in the context of Massive Parallel Sequencing. Copyright © 2017 Elsevier B.V. All rights reserved.

Product differentiation during continuous-flow thermal gradient PCR.

PubMed

Crews, Niel; Wittwer, Carl; Palais, Robert; Gale, Bruce

2008-06-01

A continuous-flow PCR microfluidic device was developed in which the target DNA product can be detected and identified during its amplification. This in situ characterization potentially eliminates the requirement for further post-PCR analysis. Multiple small targets have been amplified from human genomic DNA, having sizes of 108, 122, and 134 bp. With a DNA dye in the PCR mixture, the amplification and unique melting behavior of each sample is observed from a single fluorescent image. The melting behavior of the amplifying DNA, which depends on its molecular composition, occurs spatially in the thermal gradient PCR device, and can be observed with an optical resolution of 0.1 degrees C pixel(-1). Since many PCR cycles are within the field of view of the CCD camera, melting analysis can be performed at any cycle that contains a significant quantity of amplicon, thereby eliminating the cycle-selection challenges typically associated with continuous-flow PCR microfluidics.

Continuous analysis of phosphate in a Greenland shallow ice core

NASA Astrophysics Data System (ADS)

Kjær, Helle Astrid; Svensson, Anders; Bigler, Matthias; Vallelonga, Paul; Kettner, Ernesto; Dahl-Jensen, Dorthe

2010-05-01

Phosphate is an important and sometimes limiting nutrient for primary production in the oceans. Because of deforestation and the use of phosphate as a fertilizer changes in the phosphate cycle have occurred over the last centuries. On longer time scales, sea level changes are thought to have also caused changes in the phosphate cycle. Analyzing phosphate concentrations in ice cores may help to gain important knowledge about those processes. In the present study, we attach a phosphate detection line to an existing continuous flow analysis (CFA) setup for ice core analysis at the University of Copenhagen. The CFA system is optimized for high-resolution measurements of insoluble dust particles, electrolytic melt water conductivity, and the concentrations of ammonium and sodium. For the phosphate analysis we apply a continuous and highly sensitive absorption method that has been successfully applied to determine phosphate concentrations of sea water (Zhang and Chi, 2002). A line of melt water from the CFA melt head (1.01 ml per minute) is combined with a molybdate blue reagent and an ascorbic acid buffer. An uncompleted reaction takes place in five meters of heated mixing coils before the absorption measurement at a wavelength of 710 nanometer takes place in a 2 m long liquid waveguide cell (LWCC) with an inner volume of 0.5 ml. The method has a detection limit of around 0.1 ppb and we are currently investigating a possible interference from molybdate reacting with silicates that are present in low amounts in the ice. Preliminary analysis of early Holocene samples from the NGRIP ice core show phosphate concentration values of a few ppb. In this study, we will attempt to determine past levels of phosphate in a shallow Northern Greenland firn core with an annual layer thickness of about 20 cm ice equivalent. With a melt speed of 2.5 cm ice per minute our method should allow the resolution of any seasonal variability in phosphate concentrations.

Compressible magma/mantle dynamics: 3-D, adaptive simulations in ASPECT

NASA Astrophysics Data System (ADS)

Dannberg, Juliane; Heister, Timo

2016-12-01

Melt generation and migration are an important link between surface processes and the thermal and chemical evolution of the Earth's interior. However, their vastly different timescales make it difficult to study mantle convection and melt migration in a unified framework, especially for 3-D global models. And although experiments suggest an increase in melt volume of up to 20 per cent from the depth of melt generation to the surface, previous computations have neglected the individual compressibilities of the solid and the fluid phase. Here, we describe our extension of the finite element mantle convection code ASPECT that adds melt generation and migration. We use the original compressible formulation of the McKenzie equations, augmented by an equation for the conservation of energy. Applying adaptive mesh refinement to this type of problems is particularly advantageous, as the resolution can be increased in areas where melt is present and viscosity gradients are high, whereas a lower resolution is sufficient in regions without melt. Together with a high-performance, massively parallel implementation, this allows for high-resolution, 3-D, compressible, global mantle convection simulations coupled with melt migration. We evaluate the functionality and potential of this method using a series of benchmarks and model setups, compare results of the compressible and incompressible formulation, and show the effectiveness of adaptive mesh refinement when applied to melt migration. Our model of magma dynamics provides a framework for modelling processes on different scales and investigating links between processes occurring in the deep mantle and melt generation and migration. This approach could prove particularly useful applied to modelling the generation of komatiites or other melts originating in greater depths. The implementation is available in the Open Source ASPECT repository.

High Resolution Melt analysis for mutation screening in PKD1 and PKD2

PubMed Central

2011-01-01

Background Autosomal dominant polycystic kidney disease (ADPKD) is the most common hereditary kidney disorder. It is characterized by focal development and progressive enlargement of renal cysts leading to end-stage renal disease. PKD1 and PKD2 have been implicated in ADPKD pathogenesis but genetic features and the size of PKD1 make genetic diagnosis tedious. Methods We aim to prove that high resolution melt analysis (HRM), a recent technique in molecular biology, can facilitate molecular diagnosis of ADPKD. We screened for mutations in PKD1 and PKD2 with HRM in 37 unrelated patients with ADPKD. Results We identified 440 sequence variants in the 37 patients. One hundred and thirty eight were different. We found 28 pathogenic mutations (25 in PKD1 and 3 in PKD2 ) within 28 different patients, which is a diagnosis rate of 75% consistent with literature mean direct sequencing diagnosis rate. We describe 52 new sequence variants in PKD1 and two in PKD2. Conclusion HRM analysis is a sensitive and specific method for molecular diagnosis of ADPKD. HRM analysis is also costless and time sparing. Thus, this method is efficient and might be used for mutation pre-screening in ADPKD genes. PMID:22008521

Measurement and Analysis of Porosity in Al-10Si-1Mg Components Additively Manufactured by Selective Laser Melting

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rao, Suraj; Cunningham, Ross; Ozturk, Tugce

Aluminum alloys are candidate materials for weight critical applications because of their excellent strength and stiffness to weight ratio. However, defects such as voids decrease the strength and fatigue life of these alloys, which can limit the application of Selective Laser Melting. In this study, the average volume fraction, average size, and size distribution of pores in Al10-Si-1Mg samples built using Selective Laser Melting have been characterized. Synchrotron high energy X-rays were used to perform computed tomography on volumes of order one cubic millimeter with a resolution of approximately 1.5 μm. Substantial variations in the pore size distributions were foundmore » as a function of process conditions. Even under conditions that ensured that all locations were melted at least once, a significant number density was found of pores above 5 μm in diameter.« less

High Resolution Melting Analysis is Very Useful to Identify BRCA1 c.4964_4982del19 (rs80359876) Founder Calabrian Pathogenic Variant on Peripheral Blood and Buccal Swab DNA.

PubMed

Minucci, Angelo; De Bonis, Maria; De Paolis, Elisa; Gentile, Leonarda; Santonocito, Concetta; Concolino, Paola; Mignone, Flavio; Capoluongo, Ettore

2017-04-01

Detection of pathogenic variants in hereditary breast and ovarian cancer-related breast cancer type 1 and type 2 susceptibility proteins (BRCA1/2) genes is an effective strategy in cancer prevention and treatment. Some ethnic and geographical regions show different BRCA1/2 mutation spectrum and prevalence. In Italy, elucidation of founder effect in BRCA1/2 genes can have an impact on the management of hereditary cancer families on a healthcare system level, making genetic testing more affordable and cost effective in certain regions. The purpose of this paper is to develop a rapid, low-cost, high-throughput single-tube technology for genotyping the Italian founder mutation c.4964_4982del19 (rs80359876) in the BRCA1 gene, starting from peripheral blood and/or buccal swab DNA. Heterozygote samples for c.4964_4982del19 variant were easily and unambiguously identified by the altered shape of the melting curves and were clearly distinguished by a change in melting temperature that differed by approximately 5 °C. The same results were obtained both with DNA from peripheral blood than buccal swab. We provide evidence about application of high-resolution melting analysis (HRMA) in unambiguously genotyping of the founder BRCA1 c.4964_4982del19 variant (rs80359876) in individuals from the Calabria region of Italy. In fact, HRMA was confirmed to be particularly suitable for the identification of BRCA1 c.4964_4982del19 variant, making this approach useful in clinical molecular diagnostics.

Rapid discrimination of Isaria javanica and Isaria poprawskii from Isaria spp. using high resolution DNA melting assays

USDA-ARS?s Scientific Manuscript database

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...

Sensitivity of an Antarctic Ice Sheet Model to Sub-Ice-Shelf Melting

NASA Astrophysics Data System (ADS)

Lipscomb, W. H.; Leguy, G.; Urban, N. M.; Berdahl, M.

2017-12-01

Theory and observations suggest that marine-based sectors of the Antarctic ice sheet could retreat rapidly under ocean warming and increased melting beneath ice shelves. Numerical models of marine ice sheets vary widely in sensitivity, depending on grid resolution and the parameterization of key processes (e.g., calving and hydrofracture). Here we study the sensitivity of the Antarctic ice sheet to ocean warming and sub-shelf melting in standalone simulations of the Community Ice Sheet Model (CISM). Melt rates either are prescribed based on observations and high-resolution ocean model output, or are derived from a plume model forced by idealized ocean temperature profiles. In CISM, we vary the model resolution (between 1 and 8 km), Stokes approximation (shallow-shelf, depth-integrated higher-order, or 3D higher-order) and calving scheme to create an ensemble of plausible responses to sub-shelf melting. This work supports a broader goal of building statistical and reduced models that can translate large-scale Earth-system model projections to changes in Antarctic ocean temperatures and ice sheet discharge, thus better quantifying uncertainty in Antarctic-sourced sea-level rise.

SNP-based differentiation of Phytophthora infestans clonal lineages using locked nucleic acid probes and high resolution melt analysis

USDA-ARS?s Scientific Manuscript database

Phytophthora infestans, the cause of the devastating late blight disease of potato and tomato, exhibits a clonal reproductive lifestyle in North America. Phenotypes such as fungicide sensitivity and host preference are conserved among individuals within clonal lineages, while substantial phenotypic ...

Differentiation of citrus Hop stunt viroid variants by real-time RT-PCR and high resolution melting analysis

USDA-ARS?s Scientific Manuscript database

Viroids are small, infectious, single-stranded RNA molecules that cause several important citrus diseases. Viroids are transmitted primarily in budwood, however, spread can also occur mechanically on pruning equipment, budding knives, hedging and topping equipment. Exocortis and cachexia are two we...

High-Resolution Melting-Curve Analysis of Ligation-Mediated Real-Time PCR for Rapid Evaluation of an Epidemiological Outbreak of Extended-Spectrum-Beta-Lactamase-Producing Escherichia coli ▿

PubMed Central

Woksepp, Hanna; Jernberg, Cecilia; Tärnberg, Maria; Ryberg, Anna; Brolund, Alma; Nordvall, Michaela; Olsson-Liljequist, Barbro; Wisell, Karin Tegmark; Monstein, Hans-Jürg; Nilsson, Lennart E.; Schön, Thomas

2011-01-01

Methods for the confirmation of nosocomial outbreaks of bacterial pathogens are complex, expensive, and time-consuming. Recently, a method based on ligation-mediated PCR (LM/PCR) using a low denaturation temperature which produces specific melting-profile patterns of DNA products has been described. Our objective was to further develop this method for real-time PCR and high-resolution melting analysis (HRM) in a single-tube system optimized in order to achieve results within 1 day. Following the optimization of LM/PCR for real-time PCR and HRM (LM/HRM), the method was applied for a nosocomial outbreak of extended-spectrum-beta-lactamase (ESBL)-producing and ST131-associated Escherichia coli isolates (n = 15) and control isolates (n = 29), including four previous clusters. The results from LM/HRM were compared to results from pulsed-field gel electrophoresis (PFGE), which served as the gold standard. All isolates from the nosocomial outbreak clustered by LM/HRM, which was confirmed by gel electrophoresis of the LM/PCR products and PFGE. Control isolates that clustered by LM/PCR (n = 4) but not by PFGE were resolved by confirmatory gel electrophoresis. We conclude that LM/HRM is a rapid method for the detection of nosocomial outbreaks of bacterial infections caused by ESBL-producing E. coli strains. It allows the analysis of isolates in a single-tube system within a day, and the discriminatory power is comparable to that of PFGE. PMID:21956981

High-resolution melting-curve analysis of ligation-mediated real-time PCR for rapid evaluation of an epidemiological outbreak of extended-spectrum-beta-lactamase-producing Escherichia coli.

PubMed

Woksepp, Hanna; Jernberg, Cecilia; Tärnberg, Maria; Ryberg, Anna; Brolund, Alma; Nordvall, Michaela; Olsson-Liljequist, Barbro; Wisell, Karin Tegmark; Monstein, Hans-Jürg; Nilsson, Lennart E; Schön, Thomas

2011-12-01

Methods for the confirmation of nosocomial outbreaks of bacterial pathogens are complex, expensive, and time-consuming. Recently, a method based on ligation-mediated PCR (LM/PCR) using a low denaturation temperature which produces specific melting-profile patterns of DNA products has been described. Our objective was to further develop this method for real-time PCR and high-resolution melting analysis (HRM) in a single-tube system optimized in order to achieve results within 1 day. Following the optimization of LM/PCR for real-time PCR and HRM (LM/HRM), the method was applied for a nosocomial outbreak of extended-spectrum-beta-lactamase (ESBL)-producing and ST131-associated Escherichia coli isolates (n = 15) and control isolates (n = 29), including four previous clusters. The results from LM/HRM were compared to results from pulsed-field gel electrophoresis (PFGE), which served as the gold standard. All isolates from the nosocomial outbreak clustered by LM/HRM, which was confirmed by gel electrophoresis of the LM/PCR products and PFGE. Control isolates that clustered by LM/PCR (n = 4) but not by PFGE were resolved by confirmatory gel electrophoresis. We conclude that LM/HRM is a rapid method for the detection of nosocomial outbreaks of bacterial infections caused by ESBL-producing E. coli strains. It allows the analysis of isolates in a single-tube system within a day, and the discriminatory power is comparable to that of PFGE.

Precise Detection of IDH1/2 and BRAF Hotspot Mutations in Clinical Glioma Tissues by a Differential Calculus Analysis of High-Resolution Melting Data

PubMed Central

Hatae, Ryusuke; Yoshimoto, Koji; Kuga, Daisuke; Akagi, Yojiro; Murata, Hideki; Suzuki, Satoshi O.; Mizoguchi, Masahiro; Iihara, Koji

2016-01-01

High resolution melting (HRM) is a simple and rapid method for screening mutations. It offers various advantages for clinical diagnostic applications. Conventional HRM analysis often yields equivocal results, especially for surgically obtained tissues. We attempted to improve HRM analyses for more effective applications to clinical diagnostics. HRM analyses were performed for IDH1R132 and IDH2R172 mutations in 192 clinical glioma samples in duplicate and these results were compared with sequencing results. BRAFV600E mutations were analyzed in 52 additional brain tumor samples. The melting profiles were used for differential calculus analyses. Negative second derivative plots revealed additional peaks derived from heteroduplexes in PCR products that contained mutations; this enabled unequivocal visual discrimination of the mutations. We further developed a numerical expression, the HRM-mutation index (MI), to quantify the heteroduplex-derived peak of the mutational curves. Using this expression, all IDH1 mutation statuses matched those ascertained by sequencing, with the exception of three samples. These discordant results were all derived from the misinterpretation of sequencing data. The effectiveness of our approach was further validated by analyses of IDH2R172 and BRAFV600E mutations. The present analytical method enabled an unequivocal and objective HRM analysis and is suitable for reliable mutation scanning in surgically obtained glioma tissues. This approach could facilitate molecular diagnostics in clinical environments. PMID:27529619

Passive Microwave Remote Sensing of Colorado Watersheds Using Calibrated, Enhanced-Resolution Brightness Temperatures (CETB) from AMSR-E and SSM/I for Estimation of Snowmelt Timing

NASA Astrophysics Data System (ADS)

Johnson, M.; Ramage, J. M.; Troy, T. J.; Brodzik, M. J.

2017-12-01

Understanding the timing of snowmelt is critical for water resources management in snow-dominated watersheds. Passive microwave remote sensing has been used to estimate melt-refreeze events through brightness temperature satellite observations taken with sensors like the Special Sensor Microwave Imager (SSM/I) and the Advanced Microwave Scanning Radiometer - Earth Observing System (AMSR-E). Previous studies were limited to lower resolution ( 25 km) datasets, making it difficult to quantify the snowpack in heterogeneous, high-relief areas. This study investigates the use of newly available passive microwave calibrated, enhanced-resolution brightness temperatures (CETB) produced at the National Snow and Ice Data Center to estimate melt timing at much higher spatial resolution ( 3-6 km). CETB datasets generated from SSM/I and AMSR-E records will be used to examine three mountainous basins in Colorado. The CETB datasets retain twice-daily (day/night) observations of brightness temperatures. Therefore, we employ the diurnal amplitude variation (DAV) method to detect melt onset and melt occurrences to determine if algorithms developed for legacy data are valid with the improved CETB dataset. We compare melt variability with nearby stream discharge records to determine an optimum melt onset algorithm using the newly reprocessed data. This study investigates the effectiveness of the CETB product for several locations in Colorado (North Park, Rabbit Ears, Fraser) that were the sites of previous ground/airborne surveys during the NASA Cold Land Processes Field Experiment (CLPX 2002-2003). In summary, this work lays the foundation for the utilization of higher resolution reprocessed CETB data for snow evolution more broadly in a range of environments. Consequently, the new processing methods and improved spatial resolution will enable hydrologists to better analyze trends in snow-dominated mountainous watersheds for more effective water resources management.

Lactase persistence genotyping on whole blood by loop-mediated isothermal amplification and melting curve analysis.

PubMed

Abildgaard, Anders; Tovbjerg, Sara K; Giltay, Axel; Detemmerman, Liselot; Nissen, Peter H

2018-03-26

The lactase persistence phenotype is controlled by a regulatory enhancer region upstream of the Lactase (LCT) gene. In northern Europe, specifically the -13910C > T variant has been associated with lactase persistence whereas other persistence variants, e.g. -13907C > G and -13915 T > G, have been identified in Africa and the Middle East. The aim of the present study was to compare a previously developed high resolution melting assay (HRM) with a novel method based on loop-mediated isothermal amplification and melting curve analysis (LAMP-MC) with both whole blood and DNA as input material. To evaluate the LAMP-MC method, we used 100 whole blood samples and 93 DNA samples in a two tiered study. First, we studied the ability of the LAMP-MC method to produce specific melting curves for several variants of the LCT enhancer region. Next, we performed a blinded comparison between the LAMP-MC method and our existing HRM method with clinical samples of unknown genotype. The LAMP-MC method produced specific melting curves for the variants at position -13909, -13910, -13913 whereas the -13907C > G and -13915 T > G variants produced indistinguishable melting profiles. The LAMP-MC assay is a simple method for lactase persistence genotyping and compares well with our existing HRM method. Copyright © 2018. Published by Elsevier B.V.

Rapid differentiation of citrus Hop stunt viroid variants by real-time RT-PCR and high resolution melting analysis.

PubMed

Loconsole, Giuliana; Onelge, Nuket; Yokomi, Raymond K; Kubaa, Raied Abou; Savino, Vito; Saponari, Maria

2013-01-01

The RNA genome of pathogenic and non-pathogenic variants of citrus Hop stunt viroid (HSVd) differ by five to six nucleotides located within the variable (V) domain referred to as the "cachexia expression motif". Sensitive hosts such as mandarin and its hybrids are seriously affected by cachexia disease. Current methods to differentiate HSVd variants rely on lengthy greenhouse biological indexing on Parson's Special mandarin and/or direct nucleotide sequence analysis of amplicons from RT-PCR of HSVd-infected plants. Two independent high throughput assays to segregate HSVd variants by real-time RT-PCR and High-Resolution Melting Temperature (HRM) analysis were developed: one based on EVAGreen dye; the other based on TaqMan probes. Primers for both assays targeted three differentiating nucleotides in the V domain which separated HSVd variants into three clusters by distinct melting temperatures with a confidence level higher than 98%. The accuracy of the HRM assays were validated by nucleotide sequencing of representative samples within each HRM cluster and by testing 45 HSVd-infected field trees from California, Italy, Spain, Syria and Turkey. To our knowledge, this is the first report of a rapid and sensitive approach to detect and differentiate HSVd variants associated with different biological behaviors. Although, HSVd is found in several crops including citrus, cachexia variants are restricted to some citrus-growing areas, particularly the Mediterranean Region. Rapid diagnosis for cachexia and non-cachexia variants is, thus, important for the management of HSVd in citrus and reduces the need for bioindexing and sequencing analysis. Copyright © 2013 Elsevier Ltd. All rights reserved.

High-resolution melting analysis of the single nucleotide polymorphism hot-spot region in the rpoB gene as an indicator of reduced susceptibility to rifaximin in Clostridium difficile.

PubMed

Pecavar, Verena; Blaschitz, Marion; Hufnagl, Peter; Zeinzinger, Josef; Fiedler, Anita; Allerberger, Franz; Maass, Matthias; Indra, Alexander

2012-06-01

Clostridium difficile, a Gram-positive, spore-forming, anaerobic bacterium, is the main causative agent of hospital-acquired diarrhoea worldwide. In addition to metronidazole and vancomycin, rifaximin, a rifamycin derivative, is a promising antibiotic for the treatment of recurring C. difficile infections (CDI). However, exposure of C. difficile to this antibiotic has led to the development of rifaximin-resistance due to point mutations in the β-subunit of the RNA polymerase (rpoB) gene. In the present study, 348 C. difficile strains with known PCR-ribotypes were investigated for respective single nucleotide polymorphisms (SNPs) within the proposed rpoB hot-spot region by using high-resolution melting (HRM) analysis. This method allows the detection of SNPs by comparing the altered melting behaviour of dsDNA with that of wild-type DNA. Discrimination between wild-type and mutant strains was enhanced by creating heteroduplexes by mixing sample DNA with wild-type DNA, leading to characteristic melting curve shapes from samples containing SNPs in the respective rpoB section. In the present study, we were able to identify 16 different rpoB sequence-types (ST) by sequencing analysis of a 325 bp fragment. The 16 PCR STs displayed a total of 24 different SNPs. Fifteen of these 24 SNPs were located within the proposed 151 bp SNP hot-spot region, resulting in 11 different HRM curve profiles (CP). Eleven SNPs (seven of which were within the proposed hot-spot region) led to amino acid substitutions associated with reduced susceptibility to rifaximin and 13 SNPs (eight of which were within the hot-spot region) were synonymous. This investigation clearly demonstrates that HRM analysis of the proposed SNP hot-spot region in the rpoB gene of C. difficile is a fast and cost-effective method for the identification of C. difficile samples with reduced susceptibility to rifaximin and even allows simultaneous SNP subtyping of the respective C. difficile isolates.

High-resolution melting analysis for prenatal diagnosis of beta-thalassemia in northern Thailand.

PubMed

Charoenkwan, Pimlak; Sirichotiyakul, Supatra; Phusua, Arunee; Suanta, Sudjai; Fanhchaksai, Kanda; Sae-Tung, Rattika; Sanguansermsri, Torpong

2017-12-01

High-resolution melting (HRM) analysis is a rapid mutation analysis which assesses the pattern of reduction of fluorescence signal after subjecting the amplified PCR product with saturated fluorescence dye to an increasing temperature. We used HRM analysis for prenatal diagnosis of beta-thalassemia disease in northern Thailand. Five PCR-HRM protocols were used to detect point mutations in five different segments of the beta-globin gene, and one protocol to detect the 3.4 kb beta-globin deletion. We sought to characterize the mutations in carriers and to enable prenatal diagnosis in 126 couples at risk of having a fetus with beta-thalassemia disease. The protocols identified 18 common mutations causing beta-thalassemia, including the rare codon 132 (A-T) mutation. Each mutation showed a specific HRM pattern and all results were in concordance with those from direct DNA sequencing or gap-PCR methods. In cases of beta-thalassemia disease resulting from homozygosity for a mutation or compound heterozygosity for two mutations on the same amplified segment, the HRM patterns were different to those of a single mutation and were specific for each combination. HRM analysis is a simple and useful method for mutation identification in beta-thalassemia carriers and prenatal diagnosis of beta-thalassemia in northern Thailand.

High resolution melting analysis for epidermal growth factor receptor mutations in formalin-fixed paraffin-embedded tissue and plasma free DNA from non-small cell lung cancer patients.

PubMed

Jing, Chang-Wen; Wang, Zhuo; Cao, Hai-Xia; Ma, Rong; Wu, Jian-Zhong

2014-01-01

The aim of the research was to explore a cost effective, fast, easy to perform, and sensitive method for epidermal growth factor receptor (EGFR) mutation testing. High resolution melting analysis (HRM) was introduced to evaluate the efficacy of the analysis for dectecting EGFR mutations in exons 18 to 21 using formalin-fixed paraffin-embedded (FFPE) tissues and plasma free DNA from 120 patients. The total EGFR mutation rate was 37.5% (45/120) detected by direct sequencing. There were 48 mutations in 120 FFPE tissues assessed by HRM. For plasma free DNA, the EGFR mutation rate was 25.8% (31/120). The sensitivity of HRM assays in FFPE samples was 100% by HRM. There was a low false-positive mutation rate but a high false-negative rate in plasma free DNA detected by HRM. Our results show that HRM analysis has the advantage of small tumor sample need. HRM applied with plasma free DNA showed a high false-negative rate but a low false-positive rate. Further research into appropriate methods and analysis needs to be performed before HRM for plasma free DNA could be accepted as an option in diagnostic or screening settings.

High Resolution Melting Analysis for Rapid Mutation Screening in Gyrase and Topoisomerase IV Genes in Quinolone-Resistant Salmonella enterica

PubMed Central

Thong, Kwai Lin

2014-01-01

The increased Salmonella resistance to quinolones and fluoroquinolones is a public health concern in the Southeast Asian region. The objective of this study is to develop a high resolution melt curve (HRM) assay to rapidly screen for mutations in quinolone-resistant determining region (QRDR) of gyrase and topoisomerase IV genes. DNA sequencing was performed on 62 Salmonella strains to identify mutations in the QRDR of gyrA, gyrB, parC, and parE genes. Mutations were detected in QRDR of gyrA (n = 52; S83F, S83Y, S83I, D87G, D87Y, and D87N) and parE (n = 1; M438I). Salmonella strains with mutations within QRDR of gyrA are generally more resistant to nalidixic acid (MIC 16 > 256 μg/mL). Mutations were uncommon within the QRDR of gyrB, parC, and parE genes. In the HRM assay, mutants can be distinguished from the wild-type strains based on the transition of melt curves, which is more prominent when the profiles are displayed in difference plot. In conclusion, HRM analysis allows for rapid screening for mutations at the QRDRs of gyrase and topoisomerase IV genes in Salmonella. This assay markedly reduced the sequencing effort involved in mutational studies of quinolone-resistance genes. PMID:25371903

High resolution melting analysis for rapid mutation screening in gyrase and Topoisomerase IV genes in quinolone-resistant Salmonella enterica.

PubMed

Ngoi, Soo Tein; Thong, Kwai Lin

2014-01-01

The increased Salmonella resistance to quinolones and fluoroquinolones is a public health concern in the Southeast Asian region. The objective of this study is to develop a high resolution melt curve (HRM) assay to rapidly screen for mutations in quinolone-resistant determining region (QRDR) of gyrase and topoisomerase IV genes. DNA sequencing was performed on 62 Salmonella strains to identify mutations in the QRDR of gyrA, gyrB, parC, and parE genes. Mutations were detected in QRDR of gyrA (n = 52; S83F, S83Y, S83I, D87G, D87Y, and D87N) and parE (n = 1; M438I). Salmonella strains with mutations within QRDR of gyrA are generally more resistant to nalidixic acid (MIC 16 > 256 μg/mL). Mutations were uncommon within the QRDR of gyrB, parC, and parE genes. In the HRM assay, mutants can be distinguished from the wild-type strains based on the transition of melt curves, which is more prominent when the profiles are displayed in difference plot. In conclusion, HRM analysis allows for rapid screening for mutations at the QRDRs of gyrase and topoisomerase IV genes in Salmonella. This assay markedly reduced the sequencing effort involved in mutational studies of quinolone-resistance genes.

Detection of α-thalassemia-1 Southeast Asian and Thai Type Deletions and β-thalassemia 3.5-kb Deletion by Single-tube Multiplex Real-time PCR with SYBR Green1 and High-resolution Melting Analysis

PubMed Central

Wiengkum, Thanatcha; Srithep, Sarinee; Chainoi, Isarapong; Singboottra, Panthong; Wongwiwatthananukit, Sanchai

2011-01-01

Background Prevention and control of thalassemia requires simple, rapid, and accurate screening tests for carrier couples who are at risk of conceiving fetuses with severe thalassemia. Methods Single-tube multiplex real-time PCR with SYBR Green1 and high-resolution melting (HRM) analysis were used for the identification of α-thalassemia-1 Southeast Asian (SEA) and Thai type deletions and β-thalassemia 3.5-kb gene deletion. The results were compared with those obtained using conventional gap-PCR. DNA samples were derived from 28 normal individuals, 11 individuals with α-thalassemia-1 SEA type deletion, 2 with α-thalassemia-1 Thai type deletion, and 2 with heterozygous β-thalassemia 3.5-kb gene deletion. Results HRM analysis indicated that the amplified fragments from α-thalassemia-1 SEA type deletion, α-thalassemia-1 Thai type deletion, β-thalassemia 3.5-kb gene deletion, and the wild-type β-globin gene had specific peak heights at mean melting temperature (Tm) values of 86.89℃, 85.66℃, 77.24℃, and 74.92℃, respectively. The results obtained using single-tube multiplex real-time PCR with SYBR Green1 and HRM analysis showed 100% consistency with those obtained using conventional gap-PCR. Conclusions Single-tube multiplex real-time PCR with SYBR Green1 and HRM analysis is a potential alternative for routine clinical screening of the common types of α- and β-thalassemia large gene deletions, since it is simple, cost-effective, and highly accurate. PMID:21779184

Real time quantitative imaging for semiconductor crystal growth, control and characterization

NASA Technical Reports Server (NTRS)

Wargo, Michael J.

1991-01-01

A quantitative real time image processing system has been developed which can be software-reconfigured for semiconductor processing and characterization tasks. In thermal imager mode, 2D temperature distributions of semiconductor melt surfaces (900-1600 C) can be obtained with temperature and spatial resolutions better than 0.5 C and 0.5 mm, respectively, as demonstrated by analysis of melt surface thermal distributions. Temporal and spatial image processing techniques and multitasking computational capabilities convert such thermal imaging into a multimode sensor for crystal growth control. A second configuration of the image processing engine in conjunction with bright and dark field transmission optics is used to nonintrusively determine the microdistribution of free charge carriers and submicron sized crystalline defects in semiconductors. The IR absorption characteristics of wafers are determined with 10-micron spatial resolution and, after calibration, are converted into charge carrier density.

Object-Based Arctic Sea Ice Feature Extraction through High Spatial Resolution Aerial photos

NASA Astrophysics Data System (ADS)

Miao, X.; Xie, H.

2015-12-01

High resolution aerial photographs used to detect and classify sea ice features can provide accurate physical parameters to refine, validate, and improve climate models. However, manually delineating sea ice features, such as melt ponds, submerged ice, water, ice/snow, and pressure ridges, is time-consuming and labor-intensive. An object-based classification algorithm is developed to automatically extract sea ice features efficiently from aerial photographs taken during the Chinese National Arctic Research Expedition in summer 2010 (CHINARE 2010) in the MIZ near the Alaska coast. The algorithm includes four steps: (1) the image segmentation groups the neighboring pixels into objects based on the similarity of spectral and textural information; (2) the random forest classifier distinguishes four general classes: water, general submerged ice (GSI, including melt ponds and submerged ice), shadow, and ice/snow; (3) the polygon neighbor analysis separates melt ponds and submerged ice based on spatial relationship; and (4) pressure ridge features are extracted from shadow based on local illumination geometry. The producer's accuracy of 90.8% and user's accuracy of 91.8% are achieved for melt pond detection, and shadow shows a user's accuracy of 88.9% and producer's accuracies of 91.4%. Finally, pond density, pond fraction, ice floes, mean ice concentration, average ridge height, ridge profile, and ridge frequency are extracted from batch processing of aerial photos, and their uncertainties are estimated.

Duffy blood group phenotype-genotype correlations using high-resolution melting analysis PCR and microarray reveal complex cases including a new null FY*A allele: the role for sequencing in genotyping algorithms.

PubMed

Lopez, G H; Morrison, J; Condon, J A; Wilson, B; Martin, J R; Liew, Y-W; Flower, R L; Hyland, C A

2015-10-01

Duffy blood group phenotypes can be predicted by genotyping for single nucleotide polymorphisms (SNPs) responsible for the Fy(a) /Fy(b) polymorphism, for weak Fy(b) antigen, and for the red cell null Fy(a-b-) phenotype. This study correlates Duffy phenotype predictions with serotyping to assess the most reliable procedure for typing. Samples, n = 155 (135 donors and 20 patients), were genotyped by high-resolution melt PCR and by microarray. Samples were in three serology groups: 1) Duffy patterns expected n = 79, 2) weak and equivocal Fy(b) patterns n = 29 and 3) Fy(a-b-) n = 47 (one with anti-Fy3 antibody). Discrepancies were observed for five samples. For two, SNP genotyping predicted weak Fy(b) expression discrepant with Fy(b-) (Group 1 and 3). For three, SNP genotyping predicted Fy(a) , discrepant with Fy(a-b-) (Group 3). DNA sequencing identified silencing mutations in these FY*A alleles. One was a novel FY*A 719delG. One, the sample with the anti-Fy3, was homozygous for a 14-bp deletion (FY*01N.02); a true null. Both the high-resolution melting analysis and SNP microarray assays were concordant and showed genotyping, as well as phenotyping, is essential to ensure 100% accuracy for Duffy blood group assignments. Sequencing is important to resolve phenotype/genotype conflicts which here identified alleles, one novel, that carry silencing mutations. The risk of alloimmunisation may be dependent on this zygosity status. © 2015 International Society of Blood Transfusion.

High-resolution melt-curve analysis of random amplified polymorphic DNA (RAPD-HRM) for the characterisation of pathogenic leptospires: intra-serovar divergence, inter-serovar convergence, and evidence of attenuation in Leptospira reference collections.

PubMed

Tulsiani, S M; Craig, S B; Graham, G C; Cobbold, R C; Dohnt, M F; Burns, M-A; Jansen, C C; Leung, L K-P; Field, H E; Smythe, L D

2010-07-01

High-resolution melt-curve analysis of random amplified polymorphic DNA (RAPD-HRM) is a novel technology that has emerged as a possible method to characterise leptospires to serovar level. RAPD-HRM has recently been used to measure intra-serovar convergence between strains of the same serovar as well as inter-serovar divergence between strains of different serovars. The results indicate that intra-serovar heterogeneity and inter-serovar homogeneity may limit the application of RAPD-HRM in routine diagnostics. They also indicate that genetic attenuation of aged, high-passage-number isolates could undermine the use of RAPD-HRM or any other molecular technology. Such genetic attenuation may account for a general decrease seen in titres of rabbit hyperimmune antibodies over time. Before RAPD-HRM can be further advanced as a routine diagnostic tool, strains more representative of the wild-type serovars of a given region need to be identified. Further, RAPD-HRM analysis of reference strains indicates that the routine renewal of reference collections, with new isolates, may be needed to maintain the genetic integrity of the collections.

High resolution melting (HRM) analysis in sugar beet: identification of SNP markers associated to Fusarium resistance

USDA-ARS?s Scientific Manuscript database

Fusarium spp. cause severe damage in many agricultural crops including sugar beet. Sugar beet needs to be protected from these soil borne pathogens to guarantee an optimal sugar yield in the field. The genetic control is the key to overcoming this disease. Identification of single nucleotide polymor...

Use and Limitations of a Climate-Quality Data Record to Study Temperature Trends on the Greenland Ice Sheet

NASA Technical Reports Server (NTRS)

Hall, Dorothy K.; Comiso, Josefino C.; Shuman, Christopher A.; Koenig, Lora S.; DiGirolamo, Nicolo E.

2011-01-01

Enhanced melting of the Greenland Ice Sheet has been documented in recent literature along with surface-temperature increases measured using infrared satellite data since 1981. Using a recently-developed climate-quality data record, 11- and 12-year trends in the clear-sky ice-surface temperature (IST) of the Greenland Ice Sheet have been studied using the Moderate-Resolution Imaging Spectroradiometer (MODIS) IST product. Daily and monthly MODIS ISTs of the Greenland Ice Sheet beginning on 1 March 2000 and continuing through 31 December 2010 are now available at 6.25-km spatial resolution on a polar stereographic grid as described in Hall et al. (submitted). This record will be elevated in status to a climate-data record (CDR) when more years of data become available either from the MODIS on the Terra or Aqua satellites, or from the Visible Infrared Imager Radiometer Suite (VIIRS) to be launched in October 2011. Maps showing the maximum extent of melt for the entire ice sheet and for the six major drainage basins have been developed from the MODIS IST dataset. Twelve-year trends of the duration of the melt season on the ice sheet vary in different drainage basins with some basins melting progressively earlier over the course of the study period. Some (but not all) of the basins also show a progressively-longer duration of melt. IST 12-year trends are compared with in-situ data, and climate data from the Modern Era Retrospective-Analysis for Research and Applications (MERRA) Reanalysis.

Geomorphologic mapping of the lunar crater Tycho and its impact melt deposits

NASA Astrophysics Data System (ADS)

Krüger, T.; van der Bogert, C. H.; Hiesinger, H.

2016-07-01

Using SELENE/Kaguya Terrain Camera and Lunar Reconnaissance Orbiter Camera (LROC) data, we produced a new, high-resolution (10 m/pixel), geomorphological and impact melt distribution map for the lunar crater Tycho. The distal ejecta blanket and crater rays were investigated using LROC wide-angle camera (WAC) data (100 m/pixel), while the fine-scale morphologies of individual units were documented using high resolution (∼0.5 m/pixel) LROC narrow-angle camera (NAC) frames. In particular, Tycho shows a large coherent melt sheet on the crater floor, melt pools and flows along the terraced walls, and melt pools on the continuous ejecta blanket. The crater floor of Tycho exhibits three distinct units, distinguishable by their elevation and hummocky surface morphology. The distribution of impact melt pools and ejecta, as well as topographic asymmetries, support the formation of Tycho as an oblique impact from the W-SW. The asymmetric ejecta blanket, significantly reduced melt emplacement uprange, and the depressed uprange crater rim at Tycho suggest an impact angle of ∼25-45°.

Melting dynamics of ice in the mesoscopic regime

PubMed Central

Citroni, Margherita; Fanetti, Samuele; Falsini, Naomi; Foggi, Paolo; Bini, Roberto

2017-01-01

How does a crystal melt? How long does it take for melt nuclei to grow? The melting mechanisms have been addressed by several theoretical and experimental works, covering a subnanosecond time window with sample sizes of tens of nanometers and thus suitable to determine the onset of the process but unable to unveil the following dynamics. On the other hand, macroscopic observations of phase transitions, with millisecond or longer time resolution, account for processes occurring at surfaces and time limited by thermal contact with the environment. Here, we fill the gap between these two extremes, investigating the melting of ice in the entire mesoscopic regime. A bulk ice Ih or ice VI sample is homogeneously heated by a picosecond infrared pulse, which delivers all of the energy necessary for complete melting. The evolution of melt/ice interfaces thereafter is monitored by Mie scattering with nanosecond resolution, for all of the time needed for the sample to reequilibrate. The growth of the liquid domains, over distances of micrometers, takes hundreds of nanoseconds, a time orders of magnitude larger than expected from simple H-bond dynamics. PMID:28536197

Investigation of transient melting of tungsten by ELMs in ASDEX Upgrade

NASA Astrophysics Data System (ADS)

Krieger, K.; Sieglin, B.; Balden, M.; Coenen, J. W.; Göths, B.; Laggner, F.; de Marne, P.; Matthews, G. F.; Nille, D.; Rohde, V.; Dejarnac, R.; Faitsch, M.; Giannone, L.; Herrmann, A.; Horacek, J.; Komm, M.; Pitts, R. A.; Ratynskaia, S.; Thoren, E.; Tolias, P.; ASDEX-Upgrade Team; EUROfusion MST1 Team

2017-12-01

Repetitive melting of tungsten by power transients originating from edge localized modes (ELMs) has been studied in the tokamak experiment ASDEX Upgrade. Tungsten samples were exposed to H-mode discharges at the outer divertor target plate using the Divertor Manipulator II system. The exposed sample was designed with an elevated sloped surface inclined against the incident magnetic field to increase the projected parallel power flux to a level were transient melting by ELMs would occur. Sample exposure was controlled by moving the outer strike point to the sample location. As extension to previous melt studies in the new experiment both the current flow from the sample to vessel potential and the local surface temperature were measured with sufficient time resolution to resolve individual ELMs. The experiment provided for the first time a direct link of current flow and surface temperature during transient ELM events. This allows to further constrain the MEMOS melt motion code predictions and to improve the validation of its underlying model assumptions. Post exposure ex situ analysis of the retrieved samples confirms the decreased melt motion observed at shallower magnetic field line to surface angles compared to that at leading edges exposed to the parallel power flux.

Development of cleaved amplified polymorphic sequence (CAPS) and high-resolution melting (HRM) markers from the chloroplast genome of Glycyrrhiza species.

PubMed

Jo, Ick-Hyun; Sung, Jwakyung; Hong, Chi-Eun; Raveendar, Sebastin; Bang, Kyong-Hwan; Chung, Jong-Wook

2018-05-01

Licorice ( Glycyrrhiza glabra ) is an important medicinal crop often used as health foods or medicine worldwide. The molecular genetics of licorice is under scarce owing to lack of molecular markers. Here, we have developed cleaved amplified polymorphic sequence (CAPS) and high-resolution melting (HRM) markers based on single nucleotide polymorphisms (SNP) by comparing the chloroplast genomes of two Glycyrrhiza species ( G. glabra and G. lepidota ). The CAPS and HRM markers were tested for diversity analysis with 24 Glycyrrhiza accessions. The restriction profiles generated with CAPS markers classified the accessions (2-4 genotypes) and melting curves (2-3) were obtained from the HRM markers. The number of alleles and major allele frequency were 2-6 and 0.31-0.92, respectively. The genetic distance and polymorphism information content values were 0.16-0.76 and 0.15-0.72, respectively. The phylogenetic relationships among the 24 accessions were estimated using a dendrogram, which classified them into four clades. Except clade III, the remaining three clades included the same species, confirming interspecies genetic correlation. These 18 CAPS and HRM markers might be helpful for genetic diversity assessment and rapid identification of licorice species.

Applying high-resolution melting (HRM) technology to identify five commonly used Artemisia species.

PubMed

Song, Ming; Li, Jingjian; Xiong, Chao; Liu, Hexia; Liang, Junsong

2016-10-04

Many members of the genus Artemisia are important for medicinal purposes with multiple pharmacological properties. Often, these herbal plants sold on the markets are in processed forms so it is difficult to authenticate. Routine testing and identification of these herbal materials should be performed to ensure that the raw materials used in pharmaceutical products are suitable for their intended use. In this study, five commonly used Artemisia species included Artemisia argyi, Artemisia annua, Artemisia lavandulaefolia, Artemisia indica, and Artemisia atrovirens were analyzed using high resolution melting (HRM) analysis based on the internal transcribed spacer 2 (ITS2) sequences. The melting profiles of the ITS2 amplicons of the five closely related herbal species are clearly separated so that they can be differentiated by HRM method. The method was further applied to authenticate commercial products in powdered. HRM curves of all the commercial samples tested are similar to the botanical species as labeled. These congeneric medicinal products were also clearly separated using the neighbor-joining (NJ) tree. Therefore, HRM method could provide an efficient and reliable authentication system to distinguish these commonly used Artemisia herbal products on the markets and offer a technical reference for medicines quality control in the drug supply chain.

High resolution melting curve analysis as a new tool for rapid identification of canine parvovirus type 2 strains.

PubMed

Bingga, Gali; Liu, Zhicheng; Zhang, Jianfeng; Zhu, Yujun; Lin, Lifeng; Ding, Shuangyang; Guo, Pengju

2014-01-01

A high resolution melting (HRM) curve method was developed to identify canine parvovirus type 2 (CPV-2) strains by nested PCR. Two sets of primers, CPV-426F/426R and CPV-87R/87F, were designed that amplified a 52 bp and 53 bp product from the viral VP2 capsid gene. The region amplified by CPV-426F/426R included the A4062G and T4064A mutations in CPV-2a, CPV-2b and CPV-2c. The region amplified by CPV-87F/87R included the A3045T mutation in the vaccine strains of CPV-2 and CPV-2a, CPV-2b and CPV-2c. Faecal samples were obtained from 30 dogs that were CPV antigen-positive. The DNA was isolated from the faecal samples and PCR-amplified using the two sets of primers, and genotyped by HRM curve analysis. The PCR-HRM assay was able to distinguish single nucleotide polymorphisms between CPV-2a, CPV-2b and CPV-2c using CPV-426F/426R. CPV-2a was distinguished from CPV-2b and CPV-2c by differences in the melting temperature. CPV-2b and CPV-2c could be distinguished based on the shape of the melting curve after generating heteroduplexes using a CPV-2b reference sample. The vaccine strains of CPV-2 were identified using CPV-87F/87R. Conventional methods for genotyping CPV strains are labor intensive, expensive or time consuming; the present PCR-based HRM assay might be an attractive alternative. Copyright © 2014 Elsevier Ltd. All rights reserved.

Simultaneous mutation detection of three homoeologous genes in wheat by High Resolution Melting analysis and Mutation Surveyor.

PubMed

Dong, Chongmei; Vincent, Kate; Sharp, Peter

2009-12-04

TILLING (Targeting Induced Local Lesions IN Genomes) is a powerful tool for reverse genetics, combining traditional chemical mutagenesis with high-throughput PCR-based mutation detection to discover induced mutations that alter protein function. The most popular mutation detection method for TILLING is a mismatch cleavage assay using the endonuclease CelI. For this method, locus-specific PCR is essential. Most wheat genes are present as three similar sequences with high homology in exons and low homology in introns. Locus-specific primers can usually be designed in introns. However, it is sometimes difficult to design locus-specific PCR primers in a conserved region with high homology among the three homoeologous genes, or in a gene lacking introns, or if information on introns is not available. Here we describe a mutation detection method which combines High Resolution Melting (HRM) analysis of mixed PCR amplicons containing three homoeologous gene fragments and sequence analysis using Mutation Surveyor software, aimed at simultaneous detection of mutations in three homoeologous genes. We demonstrate that High Resolution Melting (HRM) analysis can be used in mutation scans in mixed PCR amplicons containing three homoeologous gene fragments. Combining HRM scanning with sequence analysis using Mutation Surveyor is sensitive enough to detect a single nucleotide mutation in the heterozygous state in a mixed PCR amplicon containing three homoeoloci. The method was tested and validated in an EMS (ethylmethane sulfonate)-treated wheat TILLING population, screening mutations in the carboxyl terminal domain of the Starch Synthase II (SSII) gene. Selected identified mutations of interest can be further analysed by cloning to confirm the mutation and determine the genomic origin of the mutation. Polyploidy is common in plants. Conserved regions of a gene often represent functional domains and have high sequence similarity between homoeologous loci. The method described here is a useful alternative to locus-specific based methods for screening mutations in conserved functional domains of homoeologous genes. This method can also be used for SNP (single nucleotide polymorphism) marker development and eco-TILLING in polyploid species.

A massively parallel adaptive scheme for melt migration in geodynamics computations

NASA Astrophysics Data System (ADS)

Dannberg, Juliane; Heister, Timo; Grove, Ryan

2016-04-01

Melt generation and migration are important processes for the evolution of the Earth's interior and impact the global convection of the mantle. While they have been the subject of numerous investigations, the typical time and length-scales of melt transport are vastly different from global mantle convection, which determines where melt is generated. This makes it difficult to study mantle convection and melt migration in a unified framework. In addition, modelling magma dynamics poses the challenge of highly non-linear and spatially variable material properties, in particular the viscosity. We describe our extension of the community mantle convection code ASPECT that adds equations describing the behaviour of silicate melt percolating through and interacting with a viscously deforming host rock. We use the original compressible formulation of the McKenzie equations, augmented by an equation for the conservation of energy. This approach includes both melt migration and melt generation with the accompanying latent heat effects, and it incorporates the individual compressibilities of the solid and the fluid phase. For this, we derive an accurate and stable Finite Element scheme that can be combined with adaptive mesh refinement. This is particularly advantageous for this type of problem, as the resolution can be increased in mesh cells where melt is present and viscosity gradients are high, whereas a lower resolution is sufficient in regions without melt. Together with a high-performance, massively parallel implementation, this allows for high resolution, 3d, compressible, global mantle convection simulations coupled with melt migration. Furthermore, scalable iterative linear solvers are required to solve the large linear systems arising from the discretized system. Finally, we present benchmarks and scaling tests of our solver up to tens of thousands of cores, show the effectiveness of adaptive mesh refinement when applied to melt migration and compare the compressible and incompressible formulation. We then apply our software to large-scale 3d simulations of melting and melt transport in mantle plumes interacting with the lithosphere. Our model of magma dynamics provides a framework for modelling processes on different scales and investigating links between processes occurring in the deep mantle and melt generation and migration. The presented implementation is available online under an Open Source license together with an extensive documentation.

High-Resolution Melting Curve Analysis of the 16S Ribosomal Gene to Detect and Identify Pathogenic and Saprophytic Leptospira species in Colombian Isolates

PubMed Central

Peláez Sánchez, Ronald G.; Quintero, Juan Álvaro López; Pereira, Martha María; Agudelo-Flórez, Piedad

2017-01-01

It is important to identify the circulating Leptospira agent to enhance the performance of serodiagnostic tests by incorporating specific antigens of native species, develop vaccines that take into account the species/serovars circulating in different regions, and optimize prevention and control strategies. The objectives of this study were to develop a polymerase chain reaction (PCR)–high-resolution melting (HRM) assay for differentiating between species of the genus Leptospira and to verify its usefulness in identifying unknown samples to species level. A set of primers from the initial region of the 16S ribosomal gene was designed to detect and differentiate the 22 species of Leptospira. Eleven reference strains were used as controls to establish the reference species and differential melting curves. Twenty-five Colombian Leptospira isolates were studied to evaluate the usefulness of the PCR–HRM assay in identifying unknown samples to species level. This identification was confirmed by sequencing and phylogenetic analysis of the 16S ribosomal gene. Eleven Leptospira species were successfully identified, except for Leptospira meyeri/Leptospira yanagawae because the sequences were 100% identical. The 25 isolates from humans, animals, and environmental water sources were identified as Leptospira santarosai (twelve), Leptospira interrogans (nine), and L. meyeri/L. yanagawae (four). The species verification was 100% concordant between PCR–HRM and phylogenetic analysis of the 16S ribosomal gene. The PCR–HRM assay designed in this study is a useful tool for identifying Leptospira species from isolates. PMID:28500802

Rapid detection of pathological mutations and deletions of the haemoglobin beta gene (HBB) by High Resolution Melting (HRM) analysis and Gene Ratio Analysis Copy Enumeration PCR (GRACE-PCR).

PubMed

Turner, Andrew; Sasse, Jurgen; Varadi, Aniko

2016-10-19

Inherited disorders of haemoglobin are the world's most common genetic diseases, resulting in significant morbidity and mortality. The large number of mutations associated with the haemoglobin beta gene (HBB) makes gene scanning by High Resolution Melting (HRM) PCR an attractive diagnostic approach. However, existing HRM-PCR assays are not able to detect all common point mutations and have only a very limited ability to detect larger gene rearrangements. The aim of the current study was to develop a HBB assay, which can be used as a screening test in highly heterogeneous populations, for detection of both point mutations and larger gene rearrangements. The assay is based on a combination of conventional HRM-PCR and a novel Gene Ratio Analysis Copy Enumeration (GRACE) PCR method. HRM-PCR was extensively optimised, which included the use of an unlabelled probe and incorporation of universal bases into primers to prevent interference from common non-pathological polymorphisms. GRACE-PCR was employed to determine HBB gene copy numbers relative to a reference gene using melt curve analysis to detect rearrangements in the HBB gene. The performance of the assay was evaluated by analysing 410 samples. A total of 44 distinct pathological genotypes were detected. In comparison with reference methods, the assay has a sensitivity of 100 % and a specificity of 98 %. We have developed an assay that detects both point mutations and larger rearrangements of the HBB gene. This assay is quick, sensitive, specific and cost effective making it suitable as an initial screening test that can be used for highly heterogeneous cohorts.

Differentiation of BHV-1 isolates from vaccine virus by high-resolution melting analysis.

PubMed

Ostertag-Hill, Claire; Fang, Liang; Izume, Satoko; Lee, Megan; Reed, Aimee; Jin, Ling

2015-02-16

An efficacious bovine herpesvirus type-1 (BHV-1) vaccine has been used for many years. However, in the past few years, abortion and respiratory diseases have occurred after administration of the modified live vaccine. To investigate whether BHV-1 isolates from disease outbreaks are identical to those of the vaccines used, selected regions of the BHV-1 genome were investigated by high-resolution melting (HRM) analysis and PCR-DNA sequencing. When a target region within the thymidine kinase (TK) gene was examined by HRM analysis, 6 out of the 11 isolates from abortion cases and 22 out of the 25 isolates from bovine respiratory disease (BRD) cases had different melting curves compared to the vaccine virus. Surprisingly, when a conserved region within the US6 gene that encodes glycoprotein D (gD) was examined by HRM analysis, 5 out of the 11 abortion isolates and 18 out of the 23 BRD isolates had different melting curves from the vaccine virus. To determine whether SNPs within the coding regions of glycoprotein E (gE) and TK genes can be used to differentiate the isolates from the vaccine virus, PCR-DNA sequencing was used to examine these SNPs in all the isolates. This revealed that only 1 out of 11 of the abortion isolates and 4 out of 24 of the BRD isolates are different in the target region of gE from the vaccine virus, while 5 out of 11 abortion isolates and 4 out of 22 BRD isolates are different in the target region of TK from the vaccine virus. No DNA sequence differences were observed in glycoprotein G (gG) region between disease and vaccine isolates. Our study demonstrated that many disease isolates had genetic differences from the vaccine virus in regions examined by HRM and PCR-DNA sequencing analysis. In addition, many isolates contained more than one type of mutation and were composed of mixed variants. Our study suggests that a mixture of variants were present in isolates collected post-vaccination. HRM is a rapid diagnostic method that can be used for rapid differentiation of clinical isolates from vaccine strains. Copyright © 2014 Elsevier B.V. All rights reserved.

Detection of somatic mutations by high-resolution DNA melting (HRM) analysis in multiple cancers.

PubMed

Gonzalez-Bosquet, Jesus; Calcei, Jacob; Wei, Jun S; Garcia-Closas, Montserrat; Sherman, Mark E; Hewitt, Stephen; Vockley, Joseph; Lissowska, Jolanta; Yang, Hannah P; Khan, Javed; Chanock, Stephen

2011-01-17

Identification of somatic mutations in cancer is a major goal for understanding and monitoring the events related to cancer initiation and progression. High resolution melting (HRM) curve analysis represents a fast, post-PCR high-throughput method for scanning somatic sequence alterations in target genes. The aim of this study was to assess the sensitivity and specificity of HRM analysis for tumor mutation screening in a range of tumor samples, which included 216 frozen pediatric small rounded blue-cell tumors as well as 180 paraffin-embedded tumors from breast, endometrial and ovarian cancers (60 of each). HRM analysis was performed in exons of the following candidate genes known to harbor established commonly observed mutations: PIK3CA, ERBB2, KRAS, TP53, EGFR, BRAF, GATA3, and FGFR3. Bi-directional sequencing analysis was used to determine the accuracy of the HRM analysis. For the 39 mutations observed in frozen samples, the sensitivity and specificity of HRM analysis were 97% and 87%, respectively. There were 67 mutation/variants in the paraffin-embedded samples, and the sensitivity and specificity for the HRM analysis were 88% and 80%, respectively. Paraffin-embedded samples require higher quantity of purified DNA for high performance. In summary, HRM analysis is a promising moderate-throughput screening test for mutations among known candidate genomic regions. Although the overall accuracy appears to be better in frozen specimens, somatic alterations were detected in DNA extracted from paraffin-embedded samples.

Detection of Somatic Mutations by High-Resolution DNA Melting (HRM) Analysis in Multiple Cancers

PubMed Central

Gonzalez-Bosquet, Jesus; Calcei, Jacob; Wei, Jun S.; Garcia-Closas, Montserrat; Sherman, Mark E.; Hewitt, Stephen; Vockley, Joseph; Lissowska, Jolanta; Yang, Hannah P.; Khan, Javed; Chanock, Stephen

2011-01-01

Identification of somatic mutations in cancer is a major goal for understanding and monitoring the events related to cancer initiation and progression. High resolution melting (HRM) curve analysis represents a fast, post-PCR high-throughput method for scanning somatic sequence alterations in target genes. The aim of this study was to assess the sensitivity and specificity of HRM analysis for tumor mutation screening in a range of tumor samples, which included 216 frozen pediatric small rounded blue-cell tumors as well as 180 paraffin-embedded tumors from breast, endometrial and ovarian cancers (60 of each). HRM analysis was performed in exons of the following candidate genes known to harbor established commonly observed mutations: PIK3CA, ERBB2, KRAS, TP53, EGFR, BRAF, GATA3, and FGFR3. Bi-directional sequencing analysis was used to determine the accuracy of the HRM analysis. For the 39 mutations observed in frozen samples, the sensitivity and specificity of HRM analysis were 97% and 87%, respectively. There were 67 mutation/variants in the paraffin-embedded samples, and the sensitivity and specificity for the HRM analysis were 88% and 80%, respectively. Paraffin-embedded samples require higher quantity of purified DNA for high performance. In summary, HRM analysis is a promising moderate-throughput screening test for mutations among known candidate genomic regions. Although the overall accuracy appears to be better in frozen specimens, somatic alterations were detected in DNA extracted from paraffin-embedded samples. PMID:21264207

Rapid differentiation of citrus Hop stunt viroid variants by use of real-time RT-PCR and high resolution melting analysis

USDA-ARS?s Scientific Manuscript database

The RNA genome of Hop stunt viroid (HSVd) contains five to six nucleotides in a variable (V) domain, called the cachexia expression motif, which is associated with pathogenic and non-pathogenic variants in citrus. Current methods to differentiate HSVd variants rely on lengthy greenhouse biological i...

Modified Bridgman-Stockbarger growth and characterization of LiInSe{sub 2} single crystal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vijayakumar, P., E-mail: ramasamyp@ssn.edu.in; Magesh, M., E-mail: ramasamyp@ssn.edu.in; Arunkumar, A., E-mail: ramasamyp@ssn.edu.in

2014-04-24

The LiInSe{sub 2} polycrystalline materials were successfully synthesized from melt and temperature oscillation method. 8 mm diameter and 32 mm length single crystal was grown from Bridgman-Stockbarger method with steady ampoule rotation. Crystalline phase was confirmed by powder XRD pattern. Thermo gravimetric and differential thermal analysis confirms that the melting point of the grown crystal is 897°C. Rutherford backscattering analysis (RBS) gives the crystal composition as Li{sub 0.8}In{sub 1.16}Se{sub 2.04}. The crystalline perfection of the grown crystal was analyzed by High resolution X-ray diffraction measurements (HRXRD). The electrical properties of the grown crystal were analyzed by Hall effect measurements andmore » it confirms the n-type semiconducting nature.« less

Molecular differentiation of Opisthorchis viverrini and Clonorchis sinensis eggs by multiplex real-time PCR with high resolution melting analysis.

PubMed

Kaewkong, Worasak; Intapan, Pewpan M; Sanpool, Oranuch; Janwan, Penchom; Thanchomnang, Tongjit; Laummaunwai, Porntip; Lulitanond, Viraphong; Doanh, Pham Ngoc; Maleewong, Wanchai

2013-12-01

Opisthorchis viverrini and Clonorchis sinensis are parasites known to be carcinogenic and causative agents of cholangiocarcinoma in Asia. The standard method for diagnosis for those parasite infections is stool examination to detect parasite eggs. However, the method has low sensitivity, and eggs of O. viverrini and C. sinensis are difficult to distinguish from each other and from those of some other trematodes. Here, we report a multiplex real-time PCR coupled with high resolution melting (HRM) analysis for the differentiation of O. viverrini and C. sinensis eggs in fecal samples. Using 2 pairs of species-specific primers, DNA sequences from a portion of the mitochondrial NADH dehydrogenase subunit 2 (nad 2) gene, were amplified to generate 209 and 165 bp products for O. viverrini and C. sinensis, respectively. The distinct characteristics of HRM patterns were analyzed, and the melting temperatures peaked at 82.4±0.09℃ and 85.9±0.08℃ for O. viverrini and C. sinensis, respectively. This technique was able to detect as few as 1 egg of O. viverrini and 2 eggs of C. sinensis in a 150 mg fecal sample, which is equivalent to 7 and 14 eggs per gram of feces, respectively. The method is species-specific, rapid, simple, and does not require fluorescent probes or post-PCR processing for discrimination of eggs of the 2 species. It offers a new tool for differentiation and detection of Asian liver fluke infections in stool specimens.

Rapid detection and identification of four major Schistosoma species by high-resolution melt (HRM) analysis.

PubMed

Li, Juan; Zhao, Guang-Hui; Lin, RuiQing; Blair, David; Sugiyama, Hiromu; Zhu, Xing-Quan

2015-11-01

Schistosomiasis, caused by blood flukes belonging to several species of the genus Schistosoma, is a serious and widespread parasitic disease. Accurate and rapid differentiation of these etiological agents of animal and human schistosomiasis to species level can be difficult. We report a real-time PCR assay coupled with a high-resolution melt (HRM) assay targeting a portion of the nuclear 18S rDNA to detect, identify, and distinguish between four major blood fluke species (Schistosoma japonicum, Schistosoma mansoni, Schistosoma haematobium, and Schistosoma mekongi). Using this system, the Schistosoma spp. was accurately identified and could also be distinguished from all other trematode species with which they were compared. As little as 10(-5) ng genomic DNA from a Schistosoma sp. could be detected. This process is inexpensive, easy, and can be completed within 3 h. Examination of 21 representative Schistosoma samples from 15 geographical localities in seven endemic countries validated the value of the HRM detection assay and proved its reliability. The melting curves were characterized by peaks of 83.65 °C for S. japonicum and S. mekongi, 85.65 °C for S. mansoni, and 85.85 °C for S. haematobium. The present study developed a real-time PCR coupled with HRM analysis assay for detection and differential identification of S. mansoni, S. haematobium, S. japonicum, and S. mekongi. This method is rapid, sensitive, and inexpensive. It has important implications for epidemiological studies of Schistosoma.

A comparison of PCR assays for beak and feather disease virus and high resolution melt (HRM) curve analysis of replicase associated protein and capsid genes.

PubMed

Das, Shubhagata; Sarker, Subir; Ghorashi, Seyed Ali; Forwood, Jade K; Raidal, Shane R

2016-11-01

Beak and feather disease virus (BFDV) threatens a wide range of endangered psittacine birds worldwide. In this study, we assessed a novel PCR assay and genetic screening method using high-resolution melt (HRM) curve analysis for BFDV targeting the capsid (Cap) gene (HRM-Cap) alongside conventional PCR detection as well as a PCR method that targets a much smaller fragment of the virus genome in the replicase initiator protein (Rep) gene (HRM-Rep). Limits of detection, sensitivity, specificity and discriminatory power for differentiating BFDV sequences were compared. HRM-Cap had a high positive predictive value and could readily differentiate between a reference genotype and 17 other diverse BFDV genomes with more discriminatory power (genotype confidence percentage) than HRM-Rep. Melt curve profiles generated by HRM-Cap correlated with unique DNA sequence profiles for each individual test genome. The limit of detection of HRM-Cap was lower (2×10 -5 ng/reaction or 48 viral copies) than that for both HRM-Rep and conventional BFDV PCR which had similar sensitivity (2×10 -6 ng or 13 viral copies/reaction). However, when used in a diagnostic setting with 348 clinical samples there was strong agreement between HRM-Cap and conventional PCR (kappa=0.87, P<0.01, 98% specificity) and HRM-Cap demonstrated higher specificity (99.9%) than HRM-Rep (80.3%). Copyright © 2016 Elsevier B.V. All rights reserved.

Quantitative analysis of the effects of vertical magnetic fields on microsegregation in Te-doped LEC GaAs

NASA Technical Reports Server (NTRS)

Carlson, D. J.; Witt, A. F.

1992-01-01

Using near-IR transmission microscopy with computational absorption analysis, the effects of axial magnetic fields on micro- and macrosegregation during LP-LEC growth of GaAs were quantitatively investigated with a spatial resolution approaching 2 microns. Segregation inhomogeneities exceeding one order of magnitude are found to be related to fluid dynamics of the melt. The applicability of the BPS theory as well as the nonapplicability of the Cochran analysis are established.

The use of real-time polymerase chain reaction with high resolution melting (real-time PCR-HRM) analysis for the detection and discrimination of nematodes Bursaphelenchus xylophilus and Bursaphelenchus mucronatus.

PubMed

Filipiak, Anna; Hasiów-Jaroszewska, Beata

2016-04-01

The real-time PCR-HRM analysis was developed for the detection and discrimination of the quarantine nematode Bursaphelenchus xylophilus and Bursaphelenchus mucronatus. A set of primers was designed to target the ITS region of rDNA. The results have demonstrated that this analysis is a valuable tool for differentiation of these both species. Copyright © 2016 Elsevier Ltd. All rights reserved.

High Resolution Melting Analysis for JAK2 Exon 14 and Exon 12 Mutations

PubMed Central

Rapado, Inmaculada; Grande, Silvia; Albizua, Enriqueta; Ayala, Rosa; Hernández, José-Angel; Gallardo, Miguel; Gilsanz, Florinda; Martinez-Lopez, Joaquin

2009-01-01

JAK2 mutations are important criteria for the diagnosis of Philadelphia chromosome-negative myeloproliferative neoplasms. We aimed to assess JAK2 exon 14 and exon 12 mutations by high-resolution melting (HRM) analysis, which allows variation screening. The exon 14 analysis included 163 patients with polycythemia vera, secondary erythrocytoses, essential thrombocythemia, or secondary thrombocytoses, and 126 healthy subjects. The study of exon 12 included 40 JAK2 V617F-negative patients (nine of which had polycythemia vera, and 31 with splanchnic vein thrombosis) and 30 healthy subjects. HRM analyses of JAK2 exons 14 and 12 gave analytical sensitivities near 1% and both intra- and interday coefficients of variation of less than 1%. For HRM analysis of JAK2 exon 14 in polycythemia vera and essential thrombocythemia, clinical sensitivities were 93.5% and 67.9%, clinical specificities were 98.8% and 97.0%, positive predictive values were 93.5% and 79.2%, and negative predictive values were 98.8% and 94.6, respectively. Correlations were observed between the results from HRM and three commonly used analytical methods. The JAK2 exon 12 HRM results agreed completely with those from sequencing analysis, and the three mutations in exon 12 were detected by both methods. Hence, HRM analysis of exons 14 and 12 in JAK2 shows better diagnostic values than three other routinely used methods against which it was compared. In addition, HRM analysis has the advantage of detecting unknown mutations. PMID:19225136

Molecular characterization of dissolved organic matter during the Arctic spring melt period

NASA Astrophysics Data System (ADS)

Gueguen, C.; Mangal, V.; Shi, Y. X.

2016-02-01

The application of high resolution electrospray ionization mass spectrometry has advanced our understanding of dissolved organic matter (DOM) at molecular level. The arctic spring melt period has been largely undersampled owing to logistical and safety issues, yet this period is extremely important to the overall flux of DOM and related contaminants including metals from high latitude rivers. In this study, we present high resolution molecular composition of 35 DOM samples collected in the Churchill River (Manitoba) during the 2015 spring melt period. As spring melt progresses, a significant change in the two most dominant carbon pools, protein and lignin, was observed. For example, the relative abundance of proteins detected in the river DOM samples increased from 19 to 44% during the spring flush, likely reflecting a change in DOM source. Similar patterns were found using fluorescence spectroscopy.

Greenland in Warm (1.5 °C) and Warmer (RCP 8.5) Worlds: The Influence of the Paris Agreement on Ice Sheet Surface Melting

NASA Astrophysics Data System (ADS)

Reusch, D. B.

2017-12-01

Melting on the surface of the Greenland ice sheet has been changing dramatically as global air temperatures have increased in recent decades, including melt extent often exceeding the 1981-2010 median through much of the melt season and the onset of intermittent melt moving to earlier in the year. To evaluate potential future change, we investigate surface melting characteristics under both "low" (limited to 1.5 °C) and "high" (RCP 8.5) warming scenarios including analysis of differences in scenario outcomes. Climatologies of melt-relevant variables are developed from two publicly available ensembles of CESM1-CAM5-BGC GCM runs: the 30-member Large Ensemble (CESM LE; Kay et al. 2015) for historical calibration and the RCP 8.5 scenario and the 11-member Low Warming ensemble (CESM LW; Sanderson et al. 2017) for the 1.5 °C scenario. For higher spatial resolution (15 km) and improved polar-centric model physics, we also apply the regional forecast model Polar WRF to decadal subsets (1996-2005; 2071-80) using GCM data archived at sub-daily resolution for boundary conditions. Models were skill-tested against ERA-Interim Reanalysis (ERAI) and AWS observations. For example, CESM LE tends to overpredict both maximum (above-freezing) and minimum daily average surface temperatures compared to observations from the GC-Net Swiss Camp AWS. Ensembles of members differing only by initial conditions allow us to also estimate intramodel uncertainty. Historical (1981-2000) CESM LE spatially averaged July temperatures are 2 +/- 0.2 °C cooler than ERAI while local anomalies in individual members reach up to +/- 2 °C. As expected, Greenland does not escape future (2081-2100) warming (and expectations of more widespread surface melting) even in the LW scenario, but positive changes versus ERAI are mostly coastal (2-3 °C) with the interior showing only minor change (+/- 1 °C). In contrast, under RCP 8.5, the entire ice sheet has warmed by 2-6 °C, or a median increase of 5 °C versus LW. Adjusting for the CESM cold bias versus ERAI pushes these values even closer to more frequent melting conditions. We combine these measures of model skill and intramodel variability to develop improved estimates of uncertainty for our estimates of future surface melting based on calibrations of models to passive microwave observations of melting.

Rapid Identification of Echinococcus granulosus and E. canadensis Using High-Resolution Melting (HRM) Analysis by Focusing on a Single Nucleotide Polymorphism.

PubMed

Safa, Ahmad Hosseini; Harandi, Majid Fasihi; Tajaddini, Mohammadhasan; Rostami-Nejad, Mohammad; Mohtashami-Pour, Mehdi; Pestehchian, Nader

2016-07-22

High-resolution melting (HRM) is a reliable and sensitive scanning method to detect variation in DNA sequences. We used this method to better understand the epidemiology and transmission of Echinococcus granulosus. We tested the use of HRM to discriminate the genotypes of E. granulosus and E. canadensis. One hundred forty-one hydatid cysts were collected from slaughtered animals in different parts of Isfahan-Iran in 2013. After DNA extraction, the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene was amplified using PCR coupled with the HRM curve. The result of HRM analysis using partial the sequences of cox1 gene revealed that 93, 35, and 2 isolates were identified as G1, G3, and G6 genotypes, respectively. A single nucleotide polymorphism (SNP) was found in locus 9867 of the cox1 gene. This is a critical locus for the differentiation between the G6 and G7 genotypes. In the phylogenic tree, the sample with a SNP was located between the G6 and G7 genotypes, which suggest that this isolate has a G6/G7 genotype. The HRM analysis developed in the present study provides a powerful technique for molecular and epidemiological studies on echinococcosis in humans and animals.

Lack of CHEK2 gene mutations in differentiated thyroid carcinoma patients using high resolution melting analysis.

PubMed

Fayaz, Shima; Fard-Esfahani, Pezhman; Torbati, Peyman Mohammadi

2014-01-01

Recently, mutations in the genes involved in cell cycle control, including CHEK2, are being considered as etiological factors in different kinds of cancers. The CHEK2 protein plays an important role in protecting damaged DNA from entering mitosis. In this study the potential effects of two common mutations IVS2+1G?A and Ile157Thr of CHEK2 gene in differentiated thyroid carcinoma (DTC) were evaluated. A total of 100 patients admitted to the Research Institute for Nuclear Medicine were diagnosed with DTC based on pathology reports of surgery samples. An additional 100 people were selected as a control group with no cancer history. PCR-HRM (high resolution melting) analysis was performed to deal with each of mutations in all case and control samples separately. During the analysis of IVS2+1G?A and Ile157Thr mutations of CHEK2 gene in the case and control groups, all the samples were identified as wild homozygote type. The finding suggests that IVS2+1G?A and Ile157Thr mutations of CHEK2 gene do not constitute a risk factor for DTC in the Iranian population. However, further studies with a larger population are required to confirm the outcome.

Climate Variability, Melt-Flow Acceleration, and Ice Quakes at the Western Slope of the Greenland Ice Sheet

NASA Astrophysics Data System (ADS)

Steffen, K.; Zwally, J. H.; Rial, J. A.; Behar, A.; Huff, R.

2006-12-01

The Greenland ice sheet experienced surface melt increase over the past 15 years with record melt years in 1987, 1991, 1998, 2002 and 2005. For the western part of the ice sheet the melt area increased by 30 percent (1979-2005). Monthly mean air temperatures increased in spring and fall by 0.23 deg. C per year since 1990, extending the length of melt and total ablation. Winter air temperatures increased by as much as 0.5 deg. C per year during the past 15 years. The equilibrium line altitude ranged between 400 and 1530 m above sea level at 70 deg. north along the western slope of the ice sheet for the past 15 years, equaling a horizontal distance of 100 km. The ELA has been below the Swiss Camp (1100 m elevation) in the nineties, and since 1997 moved above the Swiss Camp height. An increase in ELA leads to an increase in melt water run-off which has been verified by regional model studies (high-resolution re-analysis). Interannual variability of snow accumulation varies from 0.3 to 2.0 m, whereas snow and ice ablation ranges from 0 to 1.5 m water equivalent at Swiss Camp during 1990-2005. A GPS network (10 stations) monitors ice velocity, acceleration, and surface height change at high temporal resolution throughout the year. The network covers a range of 500 and 1500 m above sea level, close to the Ilulissat Icefjord World Heritage region. The ice sheet continued to accelerate during the height of the melt season with short-term velocity increases up to 100 percent, and vertical uplift rates of 0.5 m. There seems to be a good correlation between the change in ice velocity and total surface melt, suggesting that melt water penetrates to great depth through moulins and cracks, lubricating the bottom of the ice sheet. A new bore-hole video movie will be shown from a 110 m deep moulin close to Swiss Camp. A PASSCAL array of 10 portable, 3-component seismic stations deployed around Swiss Camp from May to August 2006 detected numerous microearthquakes within the ice sheet and possibly at its contact with the underlying bedrock some 60 km to the south of Swiss Camp. The seismic data collected will be discussed.

Use and Limitations of a Climate-Quality Data Record to Study Temperature Trends on the Greenland Ice Sheet

NASA Astrophysics Data System (ADS)

Hall, D. K.; Comiso, J. C.; Shuman, C. A.; Koenig, L.; DiGirolamo, N. E.

2011-12-01

Enhanced melting of the Greenland Ice Sheet has been documented in recent literature along with surface-temperature increases measured using infrared satellite data since 1981. Using a recently-developed climate-quality data record, 11- and 12-year trends in the clear-sky ice-surface temperature (IST) of the Greenland Ice Sheet have been studied using the Moderate-Resolution Imaging Spectroradiometer (MODIS) IST product. Daily and monthly MODIS ISTs of the Greenland Ice Sheet beginning on 1 March 2000 and continuing through 31 December 2010 are now available at 6.25-km spatial resolution on a polar stereographic grid as described in Hall et al. (submitted). This record will be elevated in status to a climate-data record (CDR) when more years of data become available either from the MODIS on the Terra or Aqua satellites, or from the Visible Infrared Imager Radiometer Suite (VIIRS) to be launched in October 2011. Maps showing the maximum extent of melt for the entire ice sheet and for the six major drainage basins have been developed from the MODIS IST dataset. Twelve-year trends in the extent of melt and duration of the melt season on the ice sheet vary in different drainage basins with some basins melting progressively earlier over the course of the study period. Some (but not all) of the basins also show a progressively-longer duration of melt. Twelve-year trends in IST are compared with in-situ data, and climate data from the Modern Era Retrospective-Analysis for Research and Applications (MERRA) Reanalysis. Hall, D.K., J.C. Comiso, N.E. DiGirolamo, C.A. Shuman, J. Key and L.S. Koenig, submitted for journal publication: A Satellite-Derived Climate-Quality Data Record of the Clear-Sky Surface Temperature of the Greenland Ice Sheet.

Validation of Minim typing for fast and accurate discrimination of extended-spectrum, beta-lactamase-producing Klebsiella pneumoniae isolates in tertiary care hospital.

PubMed

Brhelova, Eva; Kocmanova, Iva; Racil, Zdenek; Hanslianova, Marketa; Antonova, Mariya; Mayer, Jiri; Lengerova, Martina

2016-09-01

Minim typing is derived from the multi-locus sequence typing (MLST). It targets the same genes, but sequencing is replaced by high resolution melt analysis. Typing can be performed by analysing six loci (6MelT), four loci (4MelT) or using data from four loci plus sequencing the tonB gene (HybridMelT). The aim of this study was to evaluate Minim typing to discriminate extended-spectrum beta-lactamase producing Klebsiella pneumoniae (ESBL-KLPN) isolates at our hospital. In total, 380 isolates were analyzed. The obtained alleles were assigned according to both the 6MelT and 4MelT typing scheme. In 97 isolates, the tonB gene was sequenced to enable HybridMelT typing. We found that the presented method is suitable to quickly monitor isolates of ESBL-KLPN; results are obtained in less than 2 hours and at a lower cost than MLST. We identified a local ESBL-KLPN outbreak and a comparison of colonizing and invasive isolates revealed a long term colonization of patients with the same strain. Copyright © 2016 Elsevier Inc. All rights reserved.

High-resolution melting analysis for noninvasive prenatal diagnosis of IVS-II-I (G-A) fetal DNA in minor beta-thalassemia mothers.

PubMed

Zafari, Mandana; Gill, Pooria; Kowsaryan, Mehrnoush; Alipour, Abbass; Banihashemi, Ali

2016-10-01

The high-resolution melting (HRM) technique is fast, effective and successful method for mutation detection. The aim of this study was to determine the sensitivity and specificity of the HRM method for detection of a paternally inherited mutation in a fetus as a noninvasive prenatal diagnosis of β-thalassemia. Genomic DNAs were prepared from 50 β-thalassemia minor couples whose pregnancy was at risk for homozygous β-thalassemia. Ten milliliters of the maternal blood from each pregnant woman were collected and after separating plasma stored at -80 °C until analysis. The extracted DNAs were analyzed by HRM real-time PCR for detection of IVS-II-I (G-A) as a paternally inherited mutation. The gold standard was the result of a chorionic villus sampling by a standard reverse dot blotting test. The sensitivity and specificity of HRM real-time PCR were 92.6% and 82.6%, respectively. Also, the positive and negative predictive values were 86.2% and 90.47%, respectively. HRM real-time PCR was a sensitive and specific method for determining the paternally inherited mutation in the fetus at risk with thalassemia major.

Rapid detection and differentiation of Clonorchis sinensis and Opisthorchis viverrini using real-time PCR and high resolution melting analysis.

PubMed

Cai, Xian-Quan; Yu, Hai-Qiong; Li, Rong; Yue, Qiao-Yun; Liu, Guo-Hua; Bai, Jian-Shan; Deng, Yan; Qiu, De-Yi; Zhu, Xing-Quan

2014-01-01

Clonorchis sinensis and Opisthorchis viverrini are both important fish-borne pathogens, causing serious public health problem in Asia. The present study developed an assay integrating real-time PCR and high resolution melting (HRM) analysis for the specific detection and rapid identification of C. sinensis and O. viverrini. Primers targeting COX1 gene were highly specific for these liver flukes, as evidenced by the negative amplification of closely related trematodes. Assays using genomic DNA extracted from the two flukes yielded specific amplification and their identity was confirmed by sequencing, having the accuracy of 100% in reference to conventional methods. The assay was proved to be highly sensitive with a detection limit below 1 pg of purified genomic DNA, 5 EPG, or 1 metacercaria of C. sinensis. Moreover, C. sinensis and O. viverrini were able to be differentiated by their HRM profiles. The method can reduce labor of microscopic examination and the contamination of agarose electrophoresis. Moreover, it can differentiate these two flukes which are difficult to be distinguished using other methods. The established method provides an alternative tool for rapid, simple, and duplex detection of C. sinensis and O. viverrini.

High-resolution melt and morphological analyses of mealybugs (Hemiptera: Pseudococcidae) from cacao: tools for the control of Cacao swollen shoot virus spread.

PubMed

Wetten, Andy; Campbell, Colin; Allainguillaume, Joël

2016-03-01

Mealybugs (Hemiptera: Coccoidea: Pseudococcidae) are key vectors of badnaviruses, including Cacao swollen shoot virus (CSSV), the most damaging virus affecting cacao (Theobroma cacao L.). The effectiveness of mealybugs as virus vectors is species dependent, and it is therefore vital that CSSV resistance breeding programmes in cacao incorporate accurate mealybug identification. In this work, the efficacy of a CO1-based DNA barcoding approach to species identification was evaluated by screening a range of mealybugs collected from cacao in seven countries. Morphologically similar adult females were characterised by scanning electron microscopy, and then, following DNA extraction, were screened with CO1 barcoding markers. A high degree of CO1 sequence homology was observed for all 11 individual haplotypes, including those accessions from distinct geographical regions. This has allowed the design of a high-resolution melt (HRM) assay capable of rapid identification of the commonly encountered mealybug pests of cacao. HRM analysis readily differentiated between mealybug pests of cacao that cannot necessarily be identified by conventional morphological analysis. This new approach, therefore, has potential to facilitate breeding for resistance to CSSV and other mealybug-transmitted diseases. © 2015 Society of Chemical Industry.

Rapid Detection and Simultaneous Genotyping of Cronobacter spp. (formerly Enterobacter sakazakii) in Powdered Infant Formula Using Real-time PCR and High Resolution Melting (HRM) Analysis

PubMed Central

Cai, Xian-Quan; Yu, Hai-Qiong; Ruan, Zhou-Xi; Yang, Lei-Liang; Bai, Jian-Shan; Qiu, De-Yi; Jian, Zhi-Hua; Xiao, Yi-Qian; Yang, Jie-Yang; Le, Thanh Hoa; Zhu, Xing-Quan

2013-01-01

Cronobacter spp. is an emerging pathogen that causes meningitis, sepsis, bacteremia, and necrotizing enterocolitis in neonates and children. The present study developed an assay integrating real-time PCR and high resolution melting (HRM) analysis targeting the OmpA gene for the specific detection and rapid identification of Cronobacter spp. (formerly Enterobacter sakazakii) in powdered infant formula. Eleven Cronobacter field isolates and 25 reference strains were examined using one pair of primers, having the accuracy of 100% in reference to conventional methods. The assay was proved to be highly sensitive with a detection limit of 102 CFU/ml without pre-enrichment, and highly concordant (100%) when compared with ISO-IDF 22964 in 89 actual samples. The method performed for Cronobacter spp. detection was less than 24 h, drastically shortened, compared to several days using standard culturing method, it is probe-free and reduces a risk of PCR carryover. Moreover, all Cronobacter strains examined in this study were genotyped into two species according to their HRM profiles. The established method should provide a molecular tool for direct detection and simultaneous genotyping of Cronobacter spp. in powdered infant formula. PMID:23825624

Rapid detection and simultaneous genotyping of Cronobacter spp. (formerly Enterobacter sakazakii) in powdered infant formula using real-time PCR and high resolution melting (HRM) analysis.

PubMed

Cai, Xian-Quan; Yu, Hai-Qiong; Ruan, Zhou-Xi; Yang, Lei-Liang; Bai, Jian-Shan; Qiu, De-Yi; Jian, Zhi-Hua; Xiao, Yi-Qian; Yang, Jie-Yang; Le, Thanh Hoa; Zhu, Xing-Quan

2013-01-01

Cronobacter spp. is an emerging pathogen that causes meningitis, sepsis, bacteremia, and necrotizing enterocolitis in neonates and children. The present study developed an assay integrating real-time PCR and high resolution melting (HRM) analysis targeting the OmpA gene for the specific detection and rapid identification of Cronobacter spp. (formerly Enterobacter sakazakii) in powdered infant formula. Eleven Cronobacter field isolates and 25 reference strains were examined using one pair of primers, having the accuracy of 100% in reference to conventional methods. The assay was proved to be highly sensitive with a detection limit of 10(2) CFU/ml without pre-enrichment, and highly concordant (100%) when compared with ISO-IDF 22964 in 89 actual samples. The method performed for Cronobacter spp. detection was less than 24 h, drastically shortened, compared to several days using standard culturing method, it is probe-free and reduces a risk of PCR carryover. Moreover, all Cronobacter strains examined in this study were genotyped into two species according to their HRM profiles. The established method should provide a molecular tool for direct detection and simultaneous genotyping of Cronobacter spp. in powdered infant formula.

The high resolution melting analysis (HRM) as a molecular tool for monitoring parasites of the wildlife.

PubMed

Héritier, Laurent; Verneau, Olivier; Breuil, Gregory; Meistertzheim, Anne-Leila

2017-04-01

In an interconnected world, the international pet trade on wild animals is becoming increasingly important. As a consequence, non-native parasite species are introduced, which affect the health of wildlife and contribute to the loss of biodiversity. Because the investigation of parasite diversity within vulnerable host species implies the molecular identification of large samples of parasite eggs, the sequencing of DNA barcodes is time-consuming and costly. Thereby, the objectives of our study were to apply the high resolution melting (HRM) approach for species determination from pools of parasite eggs. Molecular assays were validated on flatworm parasites (polystomes) infecting the Mediterranean pond turtle Mauremys leprosa and the invasive red-eared slider Trachemys scripta elegans in French natural environments. HRM analysis results indicated that double or multiple parasitic infections could be detected from wild animal populations. They also showed that the cycle of parasite eggs production was not regular over time and may depend on several factors, among which the ecological niche and the target species. Thereby, monitoring parasites from wild endangered animals implies periodic parasitological surveys to avoid false negative diagnostics, based solely on eggs production.

Rapid detection of HLA-B*51 by real-time polymerase chain reaction and high-resolution melting analysis.

PubMed

Imperiali, C; Alía-Ramos, P; Padró-Miquel, A

2015-08-01

HLA-B*51, a class I human leukocyte antigen (HLA) molecule, is the strongest known genetic risk factor for Behçet disease. However, there are only few articles reporting methods to determine the presence or absence of HLA-B51. For this reason, we designed and developed an easy, fast, and inexpensive real-time high-resolution melting (HRM) assay to detect HLA-B*51. We genotyped 61 samples by our HRM assay and by conventional polymerase chain reaction, and no discrepancies were found between results. Besides, a subgroup of 25 samples was also genotyped in a different laboratory, and another subgroup of 16 samples was obtained from the International Histocompatibility Working Group DNA Bank, and a full concordance of results was observed with those obtained by HRM. Regarding the identifying system evaluated, we obtained 100% of specificity, sensibility, and repeatability, and 0% of false positive and false negative rates. Therefore, this HRM analysis is easily applicable to the rapid detection of HLA-B*51, exhibits a high speed, and requires a very low budget. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Rapid Detection and Identification of Human Hookworm Infections through High Resolution Melting (HRM) Analysis

PubMed Central

Ngui, Romano; Lim, Yvonne A. L.; Chua, Kek Heng

2012-01-01

Background Hookworm infections are still endemic in low and middle income tropical countries with greater impact on the socioeconomic and public health of the bottom billion of the world's poorest people. In this study, a real-time polymerase chain reaction (PCR) coupled with high resolution melting-curve (HRM) analysis was evaluated for an accurate, rapid and sensitive tool for species identification focusing on the five human hookworm species. Methods Real-time PCR coupled with HRM analysis targeting the second internal transcribed spacer (ITS-2) of nuclear ribosomal DNA as the genetic marker was used to identify and distinguish hookworm species in human samples. Unique and distinct characteristics of HRM patterns were produced for each of the five hookworm species. The melting curves were characterized by peaks of 79.24±0.05°C and 83.00±0.04°C for Necator americanus, 79.12±0.10°C for Ancylostoma duodenale, 79.40±0.10°C for Ancylostoma ceylanicum, 79.63±0.05°C for Ancylostoma caninum and 79.70±0.14°C for Ancylostoma braziliense. An evaluation of the method's sensitivity and specificity revealed that this assay was able to detect as low as 0.01 ng/µl hookworm DNA and amplification was only recorded for hookworm positive samples. Conclusion The HRM assay developed in this study is a rapid and straightforward method for the diagnosis, identification and discrimination of five human hookworms. This assay is simple compared to other probe-based genotyping methods as it does not require multiplexing, DNA sequencing or post-PCR processing. Therefore, this method offers a new alternative for rapid detection of human hookworm species. PMID:22844538

Identification of Uvaria sp by barcoding coupled with high-resolution melting analysis (Bar-HRM).

PubMed

Osathanunkul, M; Madesis, P; Ounjai, S; Pumiputavon, K; Somboonchai, R; Lithanatudom, P; Chaowasku, T; Wipasa, J; Suwannapoom, C

2016-01-13

DNA barcoding, which was developed about a decade ago, relies on short, standardized regions of the genome to identify plant and animal species. This method can be used to not only identify known species but also to discover novel ones. Numerous sequences are stored in online databases worldwide. One of the ways to save cost and time (by omitting the sequencing step) in species identification is to use available barcode data to design optimized primers for further analysis, such as high-resolution melting analysis (HRM). This study aimed to determine the effectiveness of the hybrid method Bar-HRM (DNA barcoding combined with HRM) to identify species that share similar external morphological features, rather than conduct traditional taxonomic identification that require major parts (leaf, flower, fruit) of the specimens. The specimens used for testing were those, which could not be identified at the species level and could either be Uvaria longipes or Uvaria wrayias, indicated by morphological identification. Primer pairs derived from chloroplast regions (matK, psbA-trnH, rbcL, and trnL) were used in the Bar-HRM. The results obtained from psbA-trnH primers were good enough to help in identifying the specimen while the rest were not. Bar-HRM analysis was proven to be a fast and cost-effective method for plant species identification.

Identification and quantification of virulence factors of enterotoxigenic Escherichia coli by high-resolution melting curve quantitative PCR.

PubMed

Wang, Weilan; Zijlstra, Ruurd T; Gänzle, Michael G

2017-05-15

Diagnosis of enterotoxigenic E. coli (ETEC) associated diarrhea is complicated by the diversity of E.coli virulence factors. This study developed a multiplex quantitative PCR assay based on high-resolution melting curves analysis (HRM-qPCR) to identify and quantify genes encoding five ETEC fimbriae related to diarrhea in swine, i.e. K99, F41, F18, F6 and K88. Five fimbriae expressed by ETEC were amplified in multiple HRM-qPCR reactions to allow simultaneous identification and quantification of five target genes. The assay was calibrated to allow quantification of the most abundant target gene, and validated by analysis of 30 samples obtained from piglets with diarrhea and healthy controls, and comparison to standard qPCR detection. The five amplicons with melting temperatures (Tm) ranging from 74.7 ± 0.06 to 80.5 ± 0.15 °C were well-separated by HRM-qPCR. The area of amplicons under the melting peak correlated linearly to the proportion of the template in the calibration mixture if the proportion exceeded 4.8% (K88) or <1% (all other amplicons). The suitability of the method was evaluated using 30 samples from weaned pigs aged 6-7 weeks; 14 of these animals suffered from diarrhea in consequence of poor sanitary conditions. Genes encoding fimbriae and enterotoxins were quantified by HRM-qPCR and/or qPCR. The multiplex HRM-qPCR allowed accurate analysis when the total gene copy number of targets was more than 1 × 10 5 / g wet feces and the HRM curves were able to simultaneously distinguish fimbriae genes in the fecal samples. The relative quantification of the most abundant F18 based on melting peak area was highly correlated (P < 0.001; r 2  = 0.956) with that of individual qPCR result but the correlation for less abundant fimbriae was much lower. The multiplex HRM assay identifies ETEC virulence factors specifically and efficiently. It correctly indicated the predominant fimbriae type and additionally provides information of presence/ absence of other fimbriae types and it could find broad applications for pathogen diagnosis.

Assessment for Melting Temperature Measurement of Nucleic Acid by HRM.

PubMed

Wang, Jing; Pan, Xiaoming; Liang, Xingguo

2016-01-01

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 ( T m ) 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 T m was higher than 40°C. Both insufficiency and excessiveness of EvaGreen were found to give rise to a little bit higher T m , showing that the proportion of dye should be considered for precise T m measurement of nucleic acids. Finally, HRM method was also successfully used to measure T m s of DNA triplex, hairpin, and RNA duplex. In conclusion, HRM can be applied in the evaluation of thermal stability of nucleic acid (DNA or RNA) or secondary structural elements (even when dNTPs are present).

High-resolution melting (HRM) analysis as a feasible method for detecting spinal muscular atrophy via dried blood spots.

PubMed

Er, Tze-Kiong; Kan, Tzu-Min; Su, Yu-Fa; Liu, Ta-Chih; Chang, Jan-Gowth; Hung, Shih-Ya; Jong, Yuh-Jyh

2012-11-12

Spinal muscular atrophy (SMA) is a neurodegenerative disease with the leading genetic cause of infant mortality. More than 95% of patients with SMA have a homozygous disruption in the survival motor neuron1 (SMN1) gene, caused by mutation, deletion, or rearrangement. Recently, treatment in humans in the immediate postnatal period, prior to the development of weakness or very early in the course of the disease, may be effective. Therefore, our objective was to establish a feasible method for SMA screening. High-resolution melting (HRM) analysis is rapidly becoming the most important mutation-scanning methodology that allows mutation scanning and genotyping without the need for costly labeled oligonucleotides. In the current study, we aim to develop a method for identifying the substitution of single nucleotide in SMN1 exon 7 (c.840C>T) by HRM analysis. Genomic DNA was extracted from peripheral blood samples and dried blood spots obtained from 30 patients with SMA and 30 normal individuals. All results were previously confirmed by denaturing high-performance liquid chromatography (DHPLC). In order to identify the substitution of single nucleotide in SMN1 exon 7 (c.840C>T) by HRM analysis, a primer set was used in HRM analysis. At first, we failed to identify the substitution of single nucleotide in SMN1 exon 7 (c.840C>T) by HRM analysis because the homozygous CC and homozygous TT cannot be distinguished by HRM analysis. Therefore, all samples were mixed with a known SMN1/SMN2 copy number (SMN1/SMN2=0:3), which we may call driver. This strategy is used to differentiate between homozygous CC and homozygous TT. After mixing with driver, the melting profile of homozygous CC becomes heteroduplex; however, the homozygous TT remains the same in the normalized and temperature-shifted difference plots. HRM analysis can be successfully applied to screen SMA via DNA obtained from whole blood and dried blood spots. We strongly believe that HRM analysis, a high-throughput method, could be used for identifying affected infants prior to the presentation of clinical symptoms in future. Copyright © 2012 Elsevier B.V. All rights reserved.

Real time thermal imaging for analysis and control of crystal growth by the Czochralski technique

NASA Technical Reports Server (NTRS)

Wargo, M. J.; Witt, A. F.

1992-01-01

A real time thermal imaging system with temperature resolution better than +/- 0.5 C and spatial resolution of better than 0.5 mm has been developed. It has been applied to the analysis of melt surface thermal field distributions in both Czochralski and liquid encapsulated Czochralski growth configurations. The sensor can provide single/multiple point thermal information; a multi-pixel averaging algorithm has been developed which permits localized, low noise sensing and display of optical intensity variations at any location in the hot zone as a function of time. Temperature distributions are measured by extraction of data along a user selectable linear pixel array and are simultaneously displayed, as a graphic overlay, on the thermal image.

Ice shelf basal melt rates around Antarctica from simulations and observations

NASA Astrophysics Data System (ADS)

Schodlok, M. P.; Menemenlis, D.; Rignot, E. J.

2016-02-01

We introduce an explicit representation of Antarctic ice shelf cavities in the Estimating the Circulation and Climate of the Ocean, Phase II (ECCO2) ocean retrospective analysis; and compare resulting basal melt rates and patterns to independent estimates from satellite observations. Two simulations are carried out: the first is based on the original ECCO2 vertical discretization; the second has higher vertical resolution particularly at the depth range of ice shelf cavities. The original ECCO2 vertical discretization produces higher than observed melt rates and leads to a misrepresentation of Southern Ocean water mass properties and transports. In general, thicker levels at the base of the ice shelves lead to increased melting because of their larger heat capacity. This strengthens horizontal gradients and circulation within and outside the cavities and, in turn, warm water transports from the shelf break to the ice shelves. The simulation with more vertical levels produces basal melt rates (1735 ± 164 Gt/a) and patterns that are in better agreement with observations. Thinner levels in the sub-ice-shelf cavities improve the representation of a fresh/cold layer at the ice shelf base and of warm/salty water near the bottom, leading to a sharper pycnocline and reduced vertical mixing underneath the ice shelf. Improved water column properties lead to more accurate melt rates and patterns, especially for melt/freeze patterns under large cold-water ice shelves. At the 18 km grid spacing of the ECCO2 model configuration, the smaller, warm-water ice shelves cannot be properly represented, with higher than observed melt rates in both simulations.

On the Composition and Temperature of the Terrestrial Planetary Core

NASA Astrophysics Data System (ADS)

Fei, Yingwei

2013-06-01

The existence of liquid cores of terrestrial planets such as the Earth, Mar, and Mercury has been supported by various observation. The liquid state of the core provides a unique opportunity for us to estimate the temperature of the core if we know the melting temperature of the core materials at core pressure. Dynamic compression by shock wave, laser-heating in diamond-anvil cell, and resistance-heating in the multi-anvil device can melt core materials over a wide pressure range. There have been significant advances in both dynamic and static experimental techniques and characterization tool. In this tal, I will review some of the recent advances and results relevant to the composition and thermal state of the terrestrial core. I will also present new development to analyze the quenched samples recovered from laser-heating diamond-anvil cell experiments using combination of focused ion beam milling, high-resolution SEM imaging, and quantitative chemical analysi. With precision milling of the laser-heating spo, the melting point and element partitioning between solid and liquid can be precisely determined. It is also possible to re-construct 3D image of the laser-heating spot at multi-megabar pressures to better constrain melting point and understanding melting process. The new techniques allow us to extend precise measurements of melting relations to core pressures, providing better constraint on the temperature of the cor. The research is supported by NASA and NSF grants.

Detection and Characterization of Leishmania (Leishmania) and Leishmania (Viannia) by SYBR Green-Based Real-Time PCR and High Resolution Melt Analysis Targeting Kinetoplast Minicircle DNA

PubMed Central

Ceccarelli, Marcello; Galluzzi, Luca; Migliazzo, Antonella; Magnani, Mauro

2014-01-01

Leishmaniasis is a neglected disease with a broad clinical spectrum which includes asymptomatic infection. A thorough diagnosis, able to distinguish and quantify Leishmania parasites in a clinical sample, constitutes a key step in choosing an appropriate therapy, making an accurate prognosis and performing epidemiological studies. Several molecular techniques have been shown to be effective in the diagnosis of leishmaniasis. In particular, a number of PCR methods have been developed on various target DNA sequences including kinetoplast minicircle constant regions. The first aim of this study was to develop a SYBR green-based qPCR assay for Leishmania (Leishmania) infantum detection and quantification, using kinetoplast minicircle constant region as target. To this end, two assays were compared: the first used previously published primer pairs (qPCR1), whereas the second used a nested primer pairs generating a shorter PCR product (qPCR2). The second aim of this study was to evaluate the possibility to discriminate among subgenera Leishmania (Leishmania) and Leishmania (Viannia) using the qPCR2 assay followed by melting or High Resolution Melt (HRM) analysis. Both assays used in this study showed good sensitivity and specificity, and a good correlation with standard IFAT methods in 62 canine clinical samples. However, the qPCR2 assay allowed to discriminate between Leishmania (Leishmania) and Leishmania (Viannia) subgenera through melting or HRM analysis. In addition to developing assays, we investigated the number and genetic variability of kinetoplast minicircles in the Leishmania (L.) infantum WHO international reference strain (MHOM/TN/80/IPT1), highlighting the presence of minicircle subclasses and sequence heterogeneity. Specifically, the kinetoplast minicircle number per cell was estimated to be 26,566±1,192, while the subclass of minicircles amplifiable by qPCR2 was estimated to be 1,263±115. This heterogeneity, also observed in canine clinical samples, must be taken into account in quantitative PCR-based applications; however, it might also be used to differentiate between Leishmania subgenera. PMID:24551178

A laboratory examination of the three-equation model of ice-ocean interactions

NASA Astrophysics Data System (ADS)

McConnochie, Craig; Kerr, Ross

2017-11-01

Numerical models of ice-ocean interactions are typically unable to resolve the transport of heat and salt to the ice face. As such, models rely upon parameterizations that have not been properly validated by data. Recent laboratory experiments of ice-saltwater interactions allow us to test the standard parameterization of heat and salt transport to ice faces - the `three equation model'. We find a significant disagreement in the dependence of the melt rate on the fluid velocity. The three-equation model predicts that the melt rate is proportional to the fluid velocity while the experimental results typically show that the melt rate is independent of the fluid velocity. By considering a theoretical analysis of the boundary layer next to a melting ice face we suggest a resolution to this disagreement. We show that the three-equation model assumes that the thickness of the diffusive sublayer is set by a shear instability. However, at low flow velocities, the sublayer is instead set by a convective instability. This distinction leads to a threshold velocity of approximately 4 cm/s at geophysically relevant conditions, above which the form of the parameterization should be valid. In contrast, at flow speeds below 4 cm/s, the three-equation model will underestimate the melt rate. ARC DP120102772.

High resolution DNA melting analysis: an application for prenatal control of alpha-thalassemia.

PubMed

Sirichotiyakul, Supatra; Wanapirak, Chanane; Saetung, Rattika; Sanguansermsri, Torpong

2010-04-01

To report the use of real-time gap-PCR using SYTO9 with high-resolution melting analysis (HRMA) in prenatal diagnosis of alpha-thalassemia 1. Real-time gap-PCR using SYTO9 with HRMA was performed in 33 DNA samples from chorionic villi sampling (8 normal, 16 heterozygous, and 9 homozygous) to determine the alpha-thalassemia 1 gene [normal and Southeast Asia (-SEA) allele]. The dissociation curve analysis in normal and - SEA allele gave a peak of T(m) at 91.80 +/- 0.14 degrees C and 88.67 +/- 0.08 degrees C, respectively. Normal genotype and homozygous alpha-thalassemia 1 showed a single peak of T(m) that corresponded to their alleles. The heterozygotes gave both peaks with higher normal peak and smaller - SEA peak. Thirty one samples showed consistent results with the conventional gap-PCR. Two samples with ambiguous results were confirmed to be maternal DNA contamination on real-time quantitative PCR and microsatellite assay. HRMA from both samples showed similar pattern to that of heterozygotes. However, they showed much smaller normal peak compared with the - SEA peak, which is in contrast to those of heterozygotes and can readily be distinguished. HRMA with SYTO9 is feasible for prenatal diagnosis of alpha-thalassemia. It had potential advantage of prompt detection maternal DNA contamination. Copyright (c) 2010 John Wiley & Sons, Ltd.

High-resolution melt analysis to identify and map sequence-tagged site anchor points onto linkage maps: a white lupin (Lupinus albus) map as an exemplar.

PubMed

Croxford, Adam E; Rogers, Tom; Caligari, Peter D S; Wilkinson, Michael J

2008-01-01

* The provision of sequence-tagged site (STS) anchor points allows meaningful comparisons between mapping studies but can be a time-consuming process for nonmodel species or orphan crops. * Here, the first use of high-resolution melt analysis (HRM) to generate STS markers for use in linkage mapping is described. This strategy is rapid and low-cost, and circumvents the need for labelled primers or amplicon fractionation. * Using white lupin (Lupinus albus, x = 25) as a case study, HRM analysis was applied to identify 91 polymorphic markers from expressed sequence tag (EST)-derived and genomic libraries. Of these, 77 generated STS anchor points in the first fully resolved linkage map of the species. The map also included 230 amplified fragment length polymorphisms (AFLP) loci, spanned 1916 cM (84.2% coverage) and divided into the expected 25 linkage groups. * Quantitative trait loci (QTL) analyses performed on the population revealed genomic regions associated with several traits, including the agronomically important time to flowering (tf), alkaloid synthesis and stem height (Ph). Use of HRM-STS markers also allowed us to make direct comparisons between our map and that of the related crop, Lupinus angustifolius, based on the conversion of RFLP, microsatellite and single nucleotide polymorphism (SNP) markers into HRM markers.

High-resolution melting (HRM) re-analysis of a polyposis patients cohort reveals previously undetected heterozygous and mosaic APC gene mutations.

PubMed

Out, Astrid A; van Minderhout, Ivonne J H M; van der Stoep, Nienke; van Bommel, Lysette S R; Kluijt, Irma; Aalfs, Cora; Voorendt, Marsha; Vossen, Rolf H A M; Nielsen, Maartje; Vasen, Hans F A; Morreau, Hans; Devilee, Peter; Tops, Carli M J; Hes, Frederik J

2015-06-01

Familial adenomatous polyposis is most frequently caused by pathogenic variants in either the APC gene or the MUTYH gene. The detection rate of pathogenic variants depends on the severity of the phenotype and sensitivity of the screening method, including sensitivity for mosaic variants. For 171 patients with multiple colorectal polyps without previously detectable pathogenic variant, APC was reanalyzed in leukocyte DNA by one uniform technique: high-resolution melting (HRM) analysis. Serial dilution of heterozygous DNA resulted in a lowest detectable allelic fraction of 6% for the majority of variants. HRM analysis and subsequent sequencing detected pathogenic fully heterozygous APC variants in 10 (6%) of the patients and pathogenic mosaic variants in 2 (1%). All these variants were previously missed by various conventional scanning methods. In parallel, HRM APC scanning was applied to DNA isolated from polyp tissue of two additional patients with apparently sporadic polyposis and without detectable pathogenic APC variant in leukocyte DNA. In both patients a pathogenic mosaic APC variant was present in multiple polyps. The detection of pathogenic APC variants in 7% of the patients, including mosaics, illustrates the usefulness of a complete APC gene reanalysis of previously tested patients, by a supplementary scanning method. HRM is a sensitive and fast pre-screening method for reliable detection of heterozygous and mosaic variants, which can be applied to leukocyte and polyp derived DNA.

High resolution melting analysis (HRM) as a new tool for the identification of species belonging to the Lactobacillus casei group and comparison with species-specific PCRs and multiplex PCR.

PubMed

Iacumin, Lucilla; Ginaldi, Federica; Manzano, Marisa; Anastasi, Veronica; Reale, Anna; Zotta, Teresa; Rossi, Franca; Coppola, Raffaele; Comi, Giuseppe

2015-04-01

The correct identification and characterisation of bacteria is essential for several reasons: the classification of lactic acid bacteria (LAB) has changed significantly over the years, and it is important to distinguish and define them correctly, according to the current nomenclature, avoiding problems in the interpretation of literature, as well as mislabelling when probiotic are used in food products. In this study, species-specific PCR and HRM (high-resolution melting) analysis were developed to identify strains belonging to the Lactobacillus casei group and to classify them into L. casei, Lactobacillus paracasei and Lactobacillus rhamnosus. HRM analysis confirmed to be a potent, simple, fast and economic tool for microbial identification. In particular, 201 strains, collected from International collections and attributed to the L. casei group, were examined using these techniques and the results were compared with consolidated molecular methods, already published. Seven of the tested strains don't belong to the L. casei group. Among the remaining 194 strains, 6 showed inconsistent results, leaving identification undetermined. All the applied techniques were congruent for the identification of the vast majority of the tested strains (188). Notably, for 46 of the strains, the identification differed from the previous attribution. Copyright © 2014 Elsevier Ltd. All rights reserved.

Non-invasive Prenatal Diagnosis of Feto-Maternal Platelet Incompatibility by Cold High Resolution Melting Analysis.

PubMed

Ferro, Marta; Macher, Hada C; Noguerol, Pilar; Jimenez-Arriscado, Pilar; Molinero, Patrocinio; Guerrero, Juan M; Rubio, Amalia

2016-01-01

Fetal and Neonatal alloimmune thrombocytopenia (FNAIT) is a condition which could occur when pregnant women develop an alloimmunization against paternally inherited antigens of the fetal platelets. Approximately 80 % of FNAIT cases are caused by anti-HPA-1a, about 15 % by anti-HPA-5b and 5 % by other HPA antibodies. Only 2 % of the total population is HPA-1a negative (HPA-1b1b). The HPA-1a allele differs by one single nucleotide from HPA-1b allele, yet it represents around 27 % of total severe thrombocytopenias. HPA-1 was studied in serum cDNA from 12 volunteer pregnant women to determine their HPA-1 genotype by HRM (high resolution melting) PCR. When an homozygous HPA-1 gene was detected in a mother, a COLD HRM was performed to determine whether or not the fetal genotype differs from the mother's.The differences in the melting curve shapes allow us to accurately distinguish the three pregnants genotypes. The fetal heterozygous genotype of homozygous pregnant women was correctly detected by COLD PCR HRM in maternal serum. HPA-1 genotyping by HRM may be a useful aproach for genotyping all pregnant women in inexpensively. Moreover, when HPA-1 homozygosis was detected in a pregnant woman, fetal heterozygosis may be diagnosed by COLD HRM to select pregnancies for preventive monitoring.

KIT mutations in Russian patients with mucosal melanoma.

PubMed

Abysheva, Svetlana N; Iyevleva, Aglaya G; Efimova, Nina V; Mokhina, Yulia B; Sabirova, Feruza A; Ivantsov, Alexandr O; Artemieva, Anna S; Togo, Alexandr V; Moiseyenko, Vladimir M; Matsko, Dmitry E; Imyanitov, Evgeny N

2011-12-01

A single institution series of 48 mucosal melanomas (MMs) has been analyzed for the presence of KIT mutations using high-resolution melting and sequencing of abnormally melted DNA fragments. The analysis of exons 9, 11, 13, and 17 has revealed eight of 48 (17%) nonsynonymous alterations, including zero of seven head and neck, six of 24 anorectal, one of 15 genitourinary, one of one gastric, and zero of one mediastinal MMs. Seven of these mutations were potentially associated with the tumor sensitivity to KIT tyrosine kinase inhibitors. One tumor harbored somatically acquired silent nucleotide substitution c.1383A>G (T461T). This study adds to the evidence that a substantial portion of MMs carry a therapeutically relevant mutation in the KIT oncogene.

Microgravity

NASA Image and Video Library

1994-07-10

TEMPUS, an electromagnetic levitation facility that allows containerless processing of metallic samples in microgravity, first flew on the IML-2 Spacelab mission. The principle of electromagnetic levitation is used commonly in ground-based experiments to melt and then cool metallic melts below their freezing points without solidification occurring. The TEMPUS operation is controlled by its own microprocessor system; although commands may be sent remotely from the ground and real time adjustments may be made by the crew. Two video cameras, a two-color pyrometer for measuring sample temperatures, and a fast infrared detector for monitoring solidification spikes, will be mounted to the process chamber to facilitate observation and analysis. In addition, a dedicated high-resolution video camera can be attached to the TEMPUS to measure the sample volume precisely.

Rapid detection and non-subjective characterisation of infectious bronchitis virus isolates using high-resolution melt curve analysis and a mathematical model.

PubMed

Hewson, Kylie; Noormohammadi, Amir H; Devlin, Joanne M; Mardani, Karim; Ignjatovic, Jagoda

2009-01-01

Infectious bronchitis virus (IBV) is a coronavirus that causes upper respiratory, renal and/or reproductive diseases with high morbidity in poultry. Classification of IBV is important for implementation of vaccination strategies to control the disease in commercial poultry. Currently, the lengthy process of sequence analysis of the IBV S1 gene is considered the gold standard for IBV strain identification, with a high nucleotide identity (e.g. > or =95%) indicating related strains. However, this gene has a high propensity to mutate and/or undergo recombination, and alone it may not be reliable for strain identification. A real-time polymerase chain reaction (RT-PCR) combined with high-resolution melt (HRM) curve analysis was developed based on the 3'UTR of IBV for rapid detection and classification of IBV from commercial poultry. HRM curves generated from 230 to 435-bp PCR products of several IBV strains were subjected to further analysis using a mathematical model also developed during this study. It was shown that a combination of HRM curve analysis and the mathematical model could reliably group 189 out of 190 comparisons of pairs of IBV strains in accordance with their 3'UTR and S1 gene identities. The newly developed RT-PCR/HRM curve analysis model could detect and rapidly identify novel and vaccine-related IBV strains, as confirmed by S1 gene and 3'UTR nucleotide sequences. This model is a rapid, reliable, accurate and non-subjective system for detection of IBVs in poultry flocks.

Comparison of DMSP SSM/I and Landsat 7 ETM+ Sea Ice Concentrations During Summer Melt

NASA Technical Reports Server (NTRS)

Cavalieri, Donald J.; Markus, Thorsten; Ivanoff, Alvaro; Koblinsky, Chester J. (Technical Monitor)

2001-01-01

As part of NASA's EOS Aqua sea ice validation program for the Advanced Microwave Scanning Radiometer (AMSR-E), Landsat 7 Enhanced Thematic Mapper (ETM+) images were acquired to develop a sea ice concentration data set with which to validate AMSR-E sea ice concentration retrievals. The standard AMSR-E Arctic sea ice concentration product will be obtained with the enhanced NASA Team (NT2) algorithm. The goal of this study is to assess the accuracy to which the NT2 algorithm, using DMSP Special Sensor Microwave Imager radiances, retrieves sea ice concentrations under summer melt conditions. Melt ponds are currently the largest source of error in the determination of Arctic sea ice concentrations with satellite passive microwave sensors. To accomplish this goal, Landsat 7 ETM+ images of Baffin Bay were acquired under clear sky conditions on the 26th and 27th of June 2000 and used to generate high-resolution sea ice concentration maps with which to compare the NT2 retrievals. Based on a linear regression analysis of 116 25-km samples, we find that overall the NT2 retrievals agree well with the Landsat concentrations. The regression analysis yields a correlation coefficient of 0.98. In areas of high melt ponding, the NT2 retrievals underestimate the sea ice concentrations by about 12% compared to the Landsat values.

Transient induced tungsten melting at the Joint European Torus (JET)

NASA Astrophysics Data System (ADS)

Coenen, J. W.; Matthews, G. F.; Krieger, K.; Iglesias, D.; Bunting, P.; Corre, Y.; Silburn, S.; Balboa, I.; Bazylev, B.; Conway, N.; Coffey, I.; Dejarnac, R.; Gauthier, E.; Gaspar, J.; Jachmich, S.; Jepu, I.; Makepeace, C.; Scannell, R.; Stamp, M.; Petersson, P.; Pitts, R. A.; Wiesen, S.; Widdowson, A.; Heinola, K.; Baron-Wiechec, A.; Contributors, JET

2017-12-01

Melting is one of the major risks associated with tungsten (W) plasma-facing components (PFCs) in tokamaks like JET or ITER. These components are designed such that leading edges and hence excessive plasma heat loads deposited at near normal incidence are avoided. Due to the high stored energies in ITER discharges, shallow surface melting can occur under insufficiently mitigated plasma disruption and so-called edge localised modes—power load transients. A dedicated program was carried out at the JET to study the physics and consequences of W transient melting. Following initial exposures in 2013 (ILW-1) of a W-lamella with leading edge, new experiments have been performed on a sloped surface (15{}\\circ slope) during the 2015/2016 (ILW-3) campaign. This new experiment allows significantly improved infrared thermography measurements and thus resolved important issue of power loading in the context of the previous leading edge exposures. The new lamella was monitored by local diagnostics: spectroscopy, thermography and high-resolution photography in between discharges. No impact on the main plasma was observed despite a strong increase of the local W source consistent with evaporation. In contrast to the earlier exposure, no droplet emission was observed from the sloped surface. Topological modifications resulting from the melting are clearly visible between discharges on the photographic images. Melt damage can be clearly linked to the infrared measurements: the emissivity drops in zones where melting occurs. In comparison with the previous leading edge experiment, no runaway melt motion is observed, consistent with the hypothesis that the escape of thermionic electrons emitted from the melt zone is largely suppressed in this geometry, where the magnetic field intersects the surface at lower angles than in the case of perpendicular impact on a leading edge. Utilising both exposures allows us to further test the model of the forces driving melt motion that successfully reproduced the findings from the original leading edge exposure. Since the ILW-1 experiments, the exposed misaligned lamella has now been retrieved from the JET machine and post mortem analysis has been performed. No obvious mass loss is observed. Profilometry of the ILW-1 lamella shows the structure of the melt damage which is in line with the modell predictions thus allowing further model validation. Nuclear reaction analysis shows a tenfold reduction in surface deuterium concentration in the molten surface in comparison to the non-molten part of the lamella.

Greenland ice sheet surface temperature, melt and mass loss: 2000-06

USGS Publications Warehouse

Hall, D.K.; Williams, R.S.; Luthcke, S.B.; DiGirolamo, N.E.

2008-01-01

A daily time series of 'clear-sky' surface temperature has been compiled of the Greenland ice sheet (GIS) using 1 km resolution moderate-resolution imaging spectroradiometer (MODIS) land-surface temperature (LST) maps from 2000 to 2006. We also used mass-concentration data from the Gravity Recovery and Climate Experiment (GRACE) to study mass change in relationship to surface melt from 2003 to 2006. The mean LST of the GIS increased during the study period by ???0.27??Ca-1. The increase was especially notable in the northern half of the ice sheet during the winter months. Melt-season length and timing were also studied in each of the six major drainage basins. Rapid (<15 days) and sustained mass loss below 2000 m elevation was triggered in 2004 and 2005 as recorded by GRACE when surface melt begins. Initiation of large-scale surface melt was followed rapidly by mass loss. This indicates that surface meltwater is flowing rapidly to the base of the ice sheet, causing acceleration of outlet glaciers, thus highlighting the metastability of parts of the GIS and the vulnerability of the ice sheet to air-temperature increases. If air temperatures continue to rise over Greenland, increased surface melt will play a large role in ice-sheet mass loss.

Investigation of FANCA gene in Fanconi anaemia patients in Iran

PubMed Central

Saffar Moghadam, Ali Akbar; Mahjoubi, Frouzandeh; Reisi, Nahid; Vosough, Parvaneh

2016-01-01

Background & objectives: Fanconi anaemia (FA) is a syndrome with a predisposition to bone marrow failure, congenital anomalies and malignancies. It is characterized by cellular hypersensitivity to cross-linking agents such as mitomycin C (MMC). In the present study, a new approach was selected to investigate FANCA (Fanconi anaemia complementation group A) gene in patients clinically diagnosed with cellular hypersensitivity to DNA cross-linking agent MMC. Methods: Chromosomal breakage analysis was performed to prove the diagnosis of Fanconi anaemia in 318 families. Of these, 70 families had a positive result. Forty families agreed to molecular genetic testing. In total, there were 27 patients with unknown complementary types. Genomic DNA was extracted and total RNA was isolated from fresh whole blood of the patients. The first-strand cDNA was synthesized and the cDNA of each patient was then tested with 21 pairs of overlapping primers. High resolution melting curve analysis was used to screen FANCA, and LinReg software version 1.7 was utilized for analysis of expression. Results: In total, six sequence alterations were identified, which included two stop codons, two frames-shift mutations, one large deletion and one amino acid exchange. FANCA expression was downregulated in patients who had sequence alterations. Interpretation & conclusions: The results of the present study show that high resolution melting (HRM) curve analysis may be useful in the detection of sequence alteration. It is simpler and more costeffective than the multiplex ligation-dependent probe amplification (MLPA) procedure. PMID:27121516

Investigation of FANCA gene in Fanconi anaemia patients in Iran.

PubMed

Moghadam, Ali Akbar Saffar; Mahjoubi, Frouzandeh; Reisi, Nahid; Vosough, Parvaneh

2016-02-01

Fanconi anaemia (FA) is a syndrome with a predisposition to bone marrow failure, congenital anomalies and malignancies. It is characterized by cellular hypersensitivity to cross-linking agents such as mitomycin C (MMC). In the present study, a new approach was selected to investigate FANCA (Fanconi anaemia complementation group A) gene in patients clinically diagnosed with cellular hypersensitivity to DNA cross-linking agent MMC. Chromosomal breakage analysis was performed to prove the diagnosis of Fanconi anaemia in 318 families. Of these, 70 families had a positive result. Forty families agreed to molecular genetic testing. In total, there were 27 patients with unknown complementary types. Genomic DNA was extracted and total RNA was isolated from fresh whole blood of the patients. The first-strand cDNA was synthesized and the cDNA of each patient was then tested with 21 pairs of overlapping primers. High resolution melting curve analysis was used to screen FANCA, and LinReg software version 1.7 was utilized for analysis of expression. In total, six sequence alterations were identified, which included two stop codons, two frames-shift mutations, one large deletion and one amino acid exchange. FANCA expression was downregulated in patients who had sequence alterations. The results of the present study show that high resolution melting (HRM) curve analysis may be useful in the detection of sequence alteration. It is simpler and more cost-effective than the multiplex ligation-dependent probe amplification (MLPA) procedure.

High-resolution melting analysis of sequence variations in the cytidine deaminase gene (CDA) in patients with cancer treated with gemcitabine.

PubMed

Raynal, Caroline; Ciccolini, Joseph; Mercier, Cédric; Boyer, Jean-Christophe; Polge, Anne; Lallemant, Benjamin; Mouzat, Kévin; Lumbroso, Serge; Brouillet, Jean-Paul; Evrard, Alexandre

2010-02-01

Gemcitabine (2',2'-difluorodeoxycytidine) is a major antimetabolite cytotoxic drug with a wide spectrum of activity against solid tumors. Hepatic elimination of gemcitabine depends on a catabolic pathway through a deamination step driven by the enzyme cytidine deaminase (CDA). Severe hematologic toxicity to gemcitabine was reported in patients harboring genetic polymorphisms in CDA gene. High-resolution melting (HRM) analysis of polymerase chain reaction amplicon emerges today as a powerful technique for both genotyping and gene scanning strategies. In this study, 46 DNA samples from gemcitabine-treated patients were subjected to HRM analysis on a LightCycler 480 platform. Residual serum CDA activity was assayed as a surrogate marker for the overall functionality of this enzyme. Genotyping of three well-described single nucleotide polymorphisms in coding region (c.79A>C, c.208G>A and c.435C>T) was successfully achieved by HRM analysis of small polymerase chain reaction fragments, whereas unknown single nucleotide polymorphisms were searched by a gene scanning strategy with longer amplicons (up to 622 bp). The gene scanning strategy allowed us to find a new intronic mutation c.246+37G>A in a female patient displaying marked CDA deficiency and who had an extreme toxic reaction with a fatal outcome to gemcitabine treatment. Our work demonstrates that HRM-based methods, owing to their simplicity, reliability, and speed, are useful tools for diagnosis of CDA deficiency and could be of interest for personalized medicine.

High resolution and high precision on line isotopic analysis of Holocene and glacial ice performed in the field

NASA Astrophysics Data System (ADS)

Gkinis, V.; Popp, T. J.; Johnsen, S. J.; Blunier, T.; Bigler, M.; Stowasser, C.; Schüpbach, S.; Leuenberger, D.

2010-12-01

Ice core records as obtained from polar ice caps provide a wealth of paleoclimatic information. One of the main features of ice cores is their potential for high temporal resolution. The isotopic signature of the ice, expressed through the relative abundances of the two heavy isotopologues H218O and HD16O, is a widely used proxy for the reconstruction of past temperature and accumulation. One step further the combined information obtained from these two isotopologues, commonly referred to as the deuterium excess, can be utilized to infer additional information about the source of the precipitated moisture. Until very recently isotopic analysis of polar ice was performed with isotope Ratio Mass Spectrometry (IRMS) in a discrete fashion resulting in a high workload related to the preparation of samples. Most important though the available temporal resolution of the ice core was in many cases not fully exploited. In order to overcome these limitations we have developed a system that interfaces a commercially available IR laser cavity ring-down spectrometer tailored for water isotope analysis to a stream of liquid water as extracted from a continuously melted ice rod. The system offers the possibility for simultaneous δ18O and δD analysis with a sample requirement of approximately 0.1 ml/min. The system has been deployed in the field during the NEEM ice core drilling project on 2009 and 2010. In this study we present actual on line measurements of Holocene and glacial ice. We also discuss how parameters as the melt rate, acquisition rate and integration time affect the obtained precision and resolution and we describe data analysis techniques that can improve these last two parameters. By applying spectral methods we are able to quantify the smoothing effects imposed by diffusion of the sample in the sample transfer lines and the optical cavity of the instrument. We demonstrate that with an acquisition rate of 0.2 Hz we are able to obtain a precision of 0.5‰ and 0.15‰ for δD and δ18O respectively. This is comparable to the performance of traditional IRMS systems for δD but slightly less precise for δ18O. With this acquisition rate the system’s 3db bandwidth is 0.006 Hz. With a melt rate equal to 3 cm/min, the latter translates to signals with wavelengths of 8.3 cm. We will comment on the quality of the acquired ice core data and their potential use for dating, paleotemperature reconstruction, isotopic firn diffusion and deuterium excess studies.

The potential of high resolution melting analysis (hrma) to streamline, facilitate and enrich routine diagnostics in medical microbiology.

PubMed

Ruskova, Lenka; Raclavsky, Vladislav

2011-09-01

Routine medical microbiology diagnostics relies on conventional cultivation followed by phenotypic techniques for identification of pathogenic bacteria and fungi. This is not only due to tradition and economy but also because it provides pure culture needed for antibiotic susceptibility testing. This review focuses on the potential of High Resolution Melting Analysis (HRMA) of double-stranded DNA for future routine medical microbiology. Search of MEDLINE database for publications showing the advantages of HRMA in routine medical microbiology for identification, strain typing and further characterization of pathogenic bacteria and fungi in particular. The results show increasing numbers of newly-developed and more tailor-made assays in this field. For microbiologists unfamiliar with technical aspects of HRMA, we also provide insight into the technique from the perspective of microbial characterization. We can anticipate that the routine availability of HRMA in medical microbiology laboratories will provide a strong stimulus to this field. This is already envisioned by the growing number of medical microbiology applications published recently. The speed, power, convenience and cost effectiveness of this technology virtually predestine that it will advance genetic characterization of microbes and streamline, facilitate and enrich diagnostics in routine medical microbiology without interfering with the proven advantages of conventional cultivation.

Conditions of High Resolution Melting Analysis on the Cobas z480 Instrument for the Genotyping of VKORC1 in the Clinical Routine Laboratory.

PubMed

Paar, Christian; Hammerl, Verena; Blessberger, Hermann; Stekel, Herbert; Steinwender, Clemens; Berg, Jörg

2016-12-01

High resolution melting (HRM) of amplicons is a simple method for genotyping of single nucleotide polymorphisms (SNPs). Albeit many applications reported, HRM seems to be rarely used in clinical laboratories. The suitability of HRM-PCR for the clinical laboratory was investigated for genotyping of SNPs of the vitamin K epoxide reductase complex unit 1 gene. About 100 DNA samples were analyzed by two different HRM-PCRs on the Cobas z480 instrument and compared with a PCR with fluorescently labeled probes (HybProbe-PCR) on the LightCycler 2.0 instrument as reference. Reliable genotyping with 100% matching results was obtained, when the amplicon size was small (63 bp) and DNA input was limited by e.g., sample dilution with salt-free water. DNA extracted by differing methods may be used for genotyping by HRM-PCR. Compared with HybProbe-PCR, HRM-PCR on the Cobas z480 instrument allows for higher through-put, however, at the cost of a higher degree of laboratory standardization and a slower turnaround.

High Resolution Melting (HRM) applied to wine authenticity.

PubMed

Pereira, Leonor; Gomes, Sónia; Castro, Cláudia; Eiras-Dias, José Eduardo; Brazão, João; Graça, António; Fernandes, José R; Martins-Lopes, Paula

2017-02-01

Wine authenticity methods are in increasing demand mainly in Denomination of Origin designations. The DNA-based methodologies are a reliable means of tracking food/wine varietal composition. The main aim of this work was the study of High Resolution Melting (HRM) application as a screening method for must and wine authenticity. Three sample types (leaf, must and wine) were used to validate the three developed HRM assays (Vv1-705bp; Vv2-375bp; and Vv3-119bp). The Vv1 HRM assay was only successful when applied to leaf and must samples. The Vv2 HRM assay successfully amplified all sample types, allowing genotype discrimination based on melting temperature values. The smallest amplicon, Vv3, produced a coincident melting curve shape in all sample types (leaf and wine) with corresponding genotypes. This study presents sensitive, rapid and efficient HRM assays applied for the first time to wine samples suitable for wine authenticity purposes. Copyright © 2016 Elsevier Ltd. All rights reserved.

Quality assessment of DNA derived from up to 30 years old formalin fixed paraffin embedded (FFPE) tissue for PCR-based methylation analysis using SMART-MSP and MS-HRM.

PubMed

Kristensen, Lasse S; Wojdacz, Tomasz K; Thestrup, Britta B; Wiuf, Carsten; Hager, Henrik; Hansen, Lise Lotte

2009-12-21

The High Resolution Melting (HRM) technology has recently been introduced as a rapid and robust analysis tool for the detection of DNA methylation. The methylation status of multiple tumor suppressor genes may serve as biomarkers for early cancer diagnostics, for prediction of prognosis and for prediction of response to treatment. Therefore, it is important that methodologies for detection of DNA methylation continue to evolve. Sensitive Melting Analysis after Real Time - Methylation Specific PCR (SMART-MSP) and Methylation Sensitive - High Resolution Melting (MS-HRM) are two methods for single locus DNA methylation detection based on HRM. Here, we have assessed the quality of DNA extracted from up to 30 years old Formalin Fixed Paraffin Embedded (FFPE) tissue for DNA methylation analysis using SMART-MSP and MS-HRM. The quality assessment was performed on DNA extracted from 54 Non-Small Cell Lung Cancer (NSCLC) samples derived from FFPE tissue, collected over 30 years and grouped into five years intervals. For each sample, the methylation levels of the CDKN2A (p16) and RARB promoters were estimated using SMART-MSP and MS-HRM assays designed to assess the methylation status of the same CpG positions. This allowed for a direct comparison of the methylation levels estimated by the two methods for each sample. CDKN2A promoter methylation levels were successfully determined by SMART-MSP and MS-HRM in all 54 samples. Identical methylation estimates were obtained by the two methods in 46 of the samples. The methylation levels of the RARB promoter were successfully determined by SMART-MSP in all samples. When using MS-HRM to assess RARB methylation five samples failed to amplify and 15 samples showed a melting profile characteristic for heterogeneous methylation. Twenty-seven of the remaining 34 samples, for which the methylation level could be estimated, gave the same result as observed when using SMART-MSP. MS-HRM and SMART-MSP can be successfully used for single locus methylation studies using DNA derived from up to 30 years old FFPE tissue. Furthermore, it can be expected that MS-HRM and SMART-MSP will provide similar methylation estimates when assays are designed to analyze the same CpG positions.

Contribution of high resolution remote sensing data to the modeling of the snow cover the in Atlas Mountains

NASA Astrophysics Data System (ADS)

Baba, Wassim; Gascoin, Simon; Hanich, Lahoucine; Kinnard, Christophe

2017-04-01

Snow melt from the Atlas Mountains watersheds represent an important water resource for the semi-arid, cultivated, lowlands. Due to the high incoming solar radiation and low precipitation, the spatial-temporal variability of the snowpack is expected to be strongly influenced by the topography. We explore this hypothesis using a distributed energy balance snow model (SnowModel) in the experimental watershed of the Rheraya River in Morocco (225 km2). The digital elevation model (DEM) in SnowModel is used for the computation of the gridded meteorological forcing from the automatic weather stations data. We acquired three Pléiades stereo pairs in to produce an accurate, high resolution DEM of the Rheraya watershed at 4 m posting. Then, the DEM was resampled to different spatial resolutions (8 m, 30 m, 90 m, 250 m and 500 m) to simulate the snowpack evolution over 2008-2009 snow season. As validation data we used a time series of 15 maps of the snow cover area (SCA) from Formosat-2 imagery over the same snow season in the upper Rheraya watershed. These maps have a resolution of 8 m, which enables to capture small-scale variability in the snow cover. We found that the simulations at 90 m, 30 m and 8 m yield similar results at the catchment scale, with significant differences in areas of very steep topography only. From February to April, an overall good agreement was observed between the simulated SCA and the Formosat-2 SCA at 8 m and 90 m. Before the melting season, true positive (TP) column of confusion matrix is close to 1, but it drops to 0.6 during the melting season. Heidke Skill Score is higher than 0.7 for the most of the validation dates and averages 0.8. On the contrary, 500 m simulation underestimates the SCA throughout the snow season and the TP score is always inferior to the one obtained at 8 m and 90 m. We further analyzed the effect of topography by comparing the distribution of meteorological and snowpack variables along north-south and east-west transects. This analysis indicates that the impact of the topography on the simulated SWE and snow melt is mainly driven by changes in the solar radiations and the precipitations.

Detection of sdhB Gene Mutations in SDHI-Resistant Isolates of Botrytis cinerea Using High Resolution Melting (HRM) Analysis.

PubMed

Samaras, Anastasios; Madesis, Panagiotis; Karaoglanidis, George S

2016-01-01

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. Based on the sequence of sdh B subunit of resistant and sensitive isolates, a universal primer pair was designed. The specificity of the HRM analysis primers was verified to ensure against the cross-reaction with other fungal species and its sensitivity was evaluated using concentrations of known amounts of mutant's DNA. The melting curve analysis generated nine distinct curve profiles, enabling the discrimination of all the four mutations located at codon 225, the N230I mutation, the three mutations located in codon 272, and the non-mutated isolates (isolates of wild-type sensitivity). Similar results were obtained when DNA was extracted directly from artificially inoculated strawberry fruit. The method was validated by monitoring the presence of sdh B mutations in samples of naturally infected strawberry fruits and stone fruit rootstock seedling plants showing damping-off symptoms. HRM analysis data were compared with a standard PIRA-PCR technique and an absolute agreement was observed suggesting that in both populations the H272R mutation was the predominant one, while H272Y, N230I, and P225H were detected in lower frequencies. The results of the study suggest that HRM analysis can be a useful tool for sensate, accurate, and rapid identification of several sdh B mutations in B. cinerea and it is expected to contribute in routine fungicide resistance monitoring or assessments of the effectiveness of anti-resistance strategies implemented in crops heavily treated with botryticides.

Detection of sdhB Gene Mutations in SDHI-Resistant Isolates of Botrytis cinerea Using High Resolution Melting (HRM) Analysis

PubMed Central

Samaras, Anastasios; Madesis, Panagiotis; Karaoglanidis, George S.

2016-01-01

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. Based on the sequence of sdhB subunit of resistant and sensitive isolates, a universal primer pair was designed. The specificity of the HRM analysis primers was verified to ensure against the cross-reaction with other fungal species and its sensitivity was evaluated using concentrations of known amounts of mutant’s DNA. The melting curve analysis generated nine distinct curve profiles, enabling the discrimination of all the four mutations located at codon 225, the N230I mutation, the three mutations located in codon 272, and the non-mutated isolates (isolates of wild-type sensitivity). Similar results were obtained when DNA was extracted directly from artificially inoculated strawberry fruit. The method was validated by monitoring the presence of sdhB mutations in samples of naturally infected strawberry fruits and stone fruit rootstock seedling plants showing damping-off symptoms. HRM analysis data were compared with a standard PIRA–PCR technique and an absolute agreement was observed suggesting that in both populations the H272R mutation was the predominant one, while H272Y, N230I, and P225H were detected in lower frequencies. The results of the study suggest that HRM analysis can be a useful tool for sensate, accurate, and rapid identification of several sdhB mutations in B. cinerea and it is expected to contribute in routine fungicide resistance monitoring or assessments of the effectiveness of anti-resistance strategies implemented in crops heavily treated with botryticides. PMID:27895633

A polymerase chain reaction-coupled high-resolution melting curve analytical approach for the monitoring of monospecificity of avian Eimeria species.

PubMed

Kirkpatrick, Naomi C; Blacker, Hayley P; Woods, Wayne G; Gasser, Robin B; Noormohammadi, Amir H

2009-02-01

Coccidiosis is a significant disease of poultry caused by different species of Eimeria. Differentiation of Eimeria species is important for the quality control of the live attenuated Eimeria vaccines derived from monospecific lines of Eimeria spp. In this study, high-resolution melting (HRM) curve analysis of the amplicons generated from the second internal transcribed spacer of nuclear ribosomal DNA (ITS-2) was used to distinguish between seven pathogenic Eimeria species of chickens, and the results were compared with those obtained from the previously described technique, capillary electrophoresis. Using a series of known monospecific lines of Eimeria species, HRM curve analysis was shown to distinguish between Eimeria acervulina, Eimeria brunetti, Eimeria maxima, Eimeria mitis, Eimeria necatrix, Eimeria praecox and Eimeria tenella. Computerized analysis of the HRM curves and capillary electrophoresis profiles could detect the dominant species in several specimens containing different ratios of E. necatrix and E. maxima and of E. tenella and E. acervulina. The HRM curve analysis identified all of the mixtures as "variation" to the reference species, and also identified the minor species in some mixtures. Computerized HRM curve analysis also detected impurities in 21 possible different combinations of the seven Eimeria species. The PCR-based HRM curve analysis of the ITS-2 provides a powerful tool for the detection and identification of pure Eimeria species. The HRM curve analysis could also be used as a rapid tool in the quality assurance of Eimeria vaccine production to confirm the purity of the monospecific cell lines. The HRM curve analysis is rapid and reliable and can be performed in a single test tube in less than 3 h.

Dynamic measurements of thermophysical properties of metals and alloys at high temperatures by subsecond pulse heating techniques

NASA Technical Reports Server (NTRS)

Cezairliyan, Ared

1993-01-01

Rapid (subsecond) heating techniques developed at the National Institute of Standards and Technology for the measurements of selected thermophysical and related properties of metals and alloys at high temperatures (above 1000 C) are described. The techniques are based on rapid resistive self-heating of the specimen from room temperature to the desired high temperature in short times and measuring the relevant experimental quantities, such as electrical current through the specimen, voltage across the specimen, specimen temperature, length, etc., with appropriate time resolution. The first technique, referred to as the millisecond-resolution technique, is for measurements on solid metals and alloys in the temperature range 1000 C to the melting temperature of the specimen. It utilizes a heavy battery bank for the energy source, and the total heating time of the specimen is typically in the range of 100-1000 ms. Data are recorded digitally every 0.5 ms with a full-scale resolution of about one part in 8000. The properties that can be measured with this system are as follows: specific heat, enthalpy, thermal expansion, electrical resistivity, normal spectral emissivity, hemispherical total emissivity, temperature and energy of solid-solid phase transformations, and melting temperature (solidus). The second technique, referred to as the microsecond-resolution technique, is for measurements on liquid metals and alloys in the temperature range 1200 to 6000 C. It utilizes a capacitor bank for the energy source, and the total heating time of the specimen is typically in the range 50-500 micro-s. Data are recorded digitally every 0.5 micro-s with a full-scale resolution of about one part in 4000. The properties that can be measured with this system are: melting temperature (solidus and liquidus), heat of fusion, specific heat, enthalpy, and electrical resistivity. The third technique is for measurements of the surface tension of liquid metals and alloys at their melting temperature. It utilizes a modified millisecond-resolution heating system designed for use in a microgravity environment.

Genotyping of beta thalassemia trait by high-resolution DNA melting analysis.

PubMed

Saetung, Rattika; Ongchai, Siriwan; Charoenkwan, Pimlak; Sanguansermsri, Torpong

2013-11-01

Beta thalassemia is a common hereditary hemalogogical disease in Thailand, with a prevalence of 5-8%. In this study, we evaluated the high resolution DNA melting (HRM) assay to identify beta thalassemia mutation in samples from 143 carriers of the beta thalassemia traits in at risk couples. The DNA was isolated from venous blood samples and tested for mutation under a series of 5 PCR-HRM (A, B, C, D and E primers) protocols. The A primers were for detection of beta thalassemia mutations in the HBB promoter region, the B primers for mutations in exon I, the C primers for exon II, the D primers for exon III and the E primers for the 3.4 kb deletion mutation. The mutations were diagnosed by comparing the complete melting curve profiles of a wild type control with those for each mutant sample. With the PCR-HRM technique, fourteen types of beta thalassemia mutations were detected. Each mutation had a unique and specific melting profile. The mutations included 36.4% (52 cases) codon 41/42-CTTT, 26.6% (38 cases) codon 17 A-T, 11.2% (16 cases) IVS1-1 G-T, 8.4% (12 cases) codon 71/72 +A, 8.4% (12 cases) of the 3.4 kb deletion and 3.5% (5 cases) -28 A-G. The remainder included one instance each of -87 C-A, -31 A-C, codon 27/28 +C, codon 30 G-A, IVS1-5 G-C, codon 35 C-A, codon 41-C and IVSII -654 C-T. Of the total cases, 85.8% of the mutations could be detected by primers B and C. The PCR-HRM method provides a rapid, simple and highly feasible strategy for mutation screening of beta thalassemia traits.

Terrestrial analogues for lunar impact melt flows

NASA Astrophysics Data System (ADS)

Neish, C. D.; Hamilton, C. W.; Hughes, S. S.; Nawotniak, S. Kobs; Garry, W. B.; Skok, J. R.; Elphic, R. C.; Schaefer, E.; Carter, L. M.; Bandfield, J. L.; Osinski, G. R.; Lim, D.; Heldmann, J. L.

2017-01-01

Lunar impact melt deposits have unique physical properties. They have among the highest observed radar returns at S-Band (12.6 cm wavelength), implying that they are rough at the decimeter scale. However, they are also observed in high-resolution optical imagery to be quite smooth at the meter scale. These characteristics distinguish them from well-studied terrestrial analogues, such as Hawaiian pāhoehoe and ´a´ā lava flows. The morphology of impact melt deposits can be related to their emplacement conditions, so understanding the origin of these unique surface properties will help to inform us as to the circumstances under which they were formed. In this work, we seek to find a terrestrial analogue for well-preserved lunar impact melt flows by examining fresh lava flows on Earth. We compare the radar return and high-resolution topographic variations of impact melt flows to terrestrial lava flows with a range of surface textures. The lava flows examined in this work range from smooth Hawaiian pāhoehoe to transitional basaltic flows at Craters of the Moon (COTM) National Monument and Preserve in Idaho to rubbly and spiny pāhoehoe-like flows at the recent eruption at Holuhraun in Iceland. The physical properties of lunar impact melt flows appear to differ from those of all the terrestrial lava flows studied in this work. This may be due to (a) differences in post-emplacement modification processes or (b) fundamental differences in the surface texture of the melt flows due to the melts' unique emplacement and/or cooling environment. Information about the surface properties of lunar impact melt deposits will be critical for future landed missions that wish to sample these materials.

DNA Barcoding Coupled with High Resolution Melting Analysis Enables Rapid and Accurate Distinction of Aspergillus species.

PubMed

Fidler, Gabor; Kocsube, Sandor; Leiter, Eva; Biro, Sandor; Paholcsek, Melinda

2017-08-01

We describe a high-resolution melting (HRM) analysis method that is rapid, reproducible, and able to identify reference strains and further 40 clinical isolates of Aspergillus fumigatus (14), A. lentulus (3), A. terreus (7), A. flavus (8), A. niger (2), A. welwitschiae (4), and A. tubingensis (2). Asp1 and Asp2 primer sets were designed to amplify partial sequences of the Aspergillus benA (beta-tubulin) genes in a closed-, single-tube system. Human placenta DNA, further Aspergillus (3), Candida (9), Fusarium (6), and Scedosporium (2) nucleic acids from type strains and clinical isolates were also included in this study to evaluate cross reactivity with other relevant pathogens causing invasive fungal infections. The barcoding capacity of this method proved to be 100% providing distinctive binomial scores; 14, 34, 36, 35, 25, 15, 26 when tested among species, while the within-species distinction capacity of the assay proved to be 0% based on the aligned thermodynamic profiles of the Asp1, Asp2 melting clusters allowing accurate species delimitation of all tested clinical isolates. The identification limit of this HRM assay was also estimated on Aspergillus reference gDNA panels where it proved to be 10-102 genomic equivalents (GE) except the A. fumigatus panel where it was 103 only. Furthermore, misidentification was not detected with human genomic DNA or with Candida, Fusarium, and Scedosporium strains. Our DNA barcoding assay introduced here provides results within a few hours, and it may possess further diagnostic utility when analyzing standard cultures supporting adequate therapeutic decisions. © The Author 2016. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Assessment for Melting Temperature Measurement of Nucleic Acid by HRM

PubMed Central

2016-01-01

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 (T m) 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 T m was higher than 40°C. Both insufficiency and excessiveness of EvaGreen were found to give rise to a little bit higher T m, showing that the proportion of dye should be considered for precise T m measurement of nucleic acids. Finally, HRM method was also successfully used to measure T ms of DNA triplex, hairpin, and RNA duplex. In conclusion, HRM can be applied in the evaluation of thermal stability of nucleic acid (DNA or RNA) or secondary structural elements (even when dNTPs are present). PMID:27833775

Quantifying the Evolution of Melt Ponds in the Marginal Ice Zone Using High Resolution Optical Imagery and Neural Networks

NASA Astrophysics Data System (ADS)

Ortiz, M.; Pinales, J. C.; Graber, H. C.; Wilkinson, J.; Lund, B.

2016-02-01

Melt ponds on sea ice play a significant and complex role on the thermodynamics in the Marginal Ice Zone (MIZ). Ponding reduces the sea ice's ability to reflect sunlight, and in consequence, exacerbates the albedo positive feedback cycle. In order to understand how melt ponds work and their effect on the heat uptake of sea ice, we must quantify ponds through their seasonal evolution first. A semi-supervised neural network three-class learning scheme using a gradient descent with momentum and adaptive learning rate backpropagation function is applied to classify melt ponds/melt areas in the Beaufort Sea region. The network uses high resolution panchromatic satellite images from the MEDEA program, which are collocated with autonomous platform arrays from the Marginal Ice Zone Program, including ice mass-balance buoys, arctic weather stations and wave buoys. The goal of the study is to capture the spatial variation of melt onset and freeze-up of the ponds within the MIZ, and gather ponding statistics such as size and concentration. The innovation of this work comes from training the neural network as the melt ponds evolve over time; making the machine learning algorithm time-dependent, which has not been previously done. We will achieve this by analyzing the image histograms through quantification of the minima and maxima intensity changes as well as linking textural variation information of the imagery. We will compare the evolution of the melt ponds against several different array sites on the sea ice to explore if there are spatial differences among the separated platforms in the MIZ.

Quantifying Melt Ponds in the Beaufort MIZ using Linear Support Vector Machines from High Resolution Panchromatic Images

NASA Astrophysics Data System (ADS)

Ortiz, M.; Graber, H. C.; Wilkinson, J.; Nyman, L. M.; Lund, B.

2017-12-01

Much work has been done on determining changes in summer ice albedo and morphological properties of melt ponds such as depth, shape and distribution using in-situ measurements and satellite-based sensors. Although these studies have dedicated much pioneering work in this area, there still lacks sufficient spatial and temporal scales. We present a prototype algorithm using Linear Support Vector Machines (LSVMs) designed to quantify the evolution of melt pond fraction from a recently government-declassified high-resolution panchromatic optical dataset. The study area of interest lies within the Beaufort marginal ice zone (MIZ), where several in-situ instruments were deployed by the British Antarctic Survey in joint with the MIZ Program, from April-September, 2014. The LSVM uses four dimensional feature data from the intensity image itself, and from various textures calculated from a modified first-order histogram technique using probability density of occurrences. We explore both the temporal evolution of melt ponds and spatial statistics such as pond fraction, pond area, and number pond density, to name a few. We also introduce a linear regression model that can potentially be used to estimate average pond area by ingesting several melt pond statistics and shape parameters.

Core formation in the early solar system through percolation: 4-D in-situ visualization of melt migration

NASA Astrophysics Data System (ADS)

Bromiley, G.; Berg, M.; Le Godec, Y.; Mezouar, N.; Atwood, R. C.; Phillipe, J.

2015-12-01

Although core formation was a key stage in the evolution of terrestrial planets, the physical processes which resulted in segregation of iron and silicate remain poorly understood. Formation of a silicate magma oceans provides an obvious mechanism for segregation of core-forming liquids, although recent work has strengthened arguments for a complex, multi-stage model of core formation. Extreme pressure1 and the effects of deformation2 have both been shown to promote percolation of Fe-rich melts in a solid silicate matrix, providing mechanisms for early, low temperature core-formation. However, the efficiency of these processes remains untested and we lack meaningful experimental data on resulting melt segregation velocities. Arguments regarding the efficiency of core formation through percolation of Fe-rich melts in solid silicate are based on simple, empirical models. Here, we review textural evidence from recent experiments which supports early core formation driven by deformation-aided percolation of Fe-rich melts. We then present results of novel in-situ synchrotron studies designed to provide time-resolved 3-D microimaging of percolating melt in model systems under extreme conditions. Under low strain rates characteristic of deformation-aided core formation, segregation of metallic (core-forming) melts by percolation is driven by stress gradients. This is expected to ultimately result in channelization and efficient segregation of melts noted in high-strain, low pressure experiments3. In-situ visualization also demonstrates that percolation of viscous metallic melts is surprisingly rapid. A combination of melt channelization and hydraulic fracture results in rapid, episodic melt migration, even over the limited time scale of experiments. The efficiency of this process depends strongly on the geometry of the melt network and is scaled to grain size in the matrix. We use both in-situ visualization and high-resolution ex-situ analysis to provide accurate constraints on melt migration velocities via this combined mechanism and will propose a model by which results can be scaled to core formation in the early solar system. References[1] Shi et al. Nature GeoSc. 6, 971 (2013).[2] Bruhn et al. Nature 403, 883 (2000).[3] Kohlstedt & Holtzman Ann. Rev. Earth. Planet. Sci. 37, 561 (2009).

The Potential Power of Bar-HRM Technology in Herbal Medicine Identification

PubMed Central

Sun, Wei; Li, Jing-jian; Xiong, Chao; Zhao, Bo; Chen, Shi-lin

2016-01-01

The substitution of low-cost or adulterated herbal products for high-priced herbs makes it important to be able to identify and trace herbal plant species and their processed products in the drug supply chain. PCR-based methods play an increasing role in monitoring the safety of herbal medicines by detecting adulteration. Recent studies have shown the potential of DNA barcoding combined with high resolution melting (Bar-HRM) analysis in herbal medicine identification. This method involves precisely monitoring the change in fluorescence caused by the release of an intercalating DNA dye from a DNA duplex as it is denatured by a gradual increase in temperature. Since the melting profile depends on the GC content, length, and strand complementarity of the amplification product, Bar-HRM analysis opens up the possibility of detecting single-base variants or species-specific differences in a short region of DNA. This review summarizes key factors affecting Bar-HRM analysis and describes how Bar-HRM is performed. We then discuss advances in Bar-HRM analysis of medicinal plant ingredients (herbal materia medica) as a contribution toward safe and effective herbal medicines. PMID:27066026

The Potential Power of Bar-HRM Technology in Herbal Medicine Identification.

PubMed

Sun, Wei; Li, Jing-Jian; Xiong, Chao; Zhao, Bo; Chen, Shi-Lin

2016-01-01

The substitution of low-cost or adulterated herbal products for high-priced herbs makes it important to be able to identify and trace herbal plant species and their processed products in the drug supply chain. PCR-based methods play an increasing role in monitoring the safety of herbal medicines by detecting adulteration. Recent studies have shown the potential of DNA barcoding combined with high resolution melting (Bar-HRM) analysis in herbal medicine identification. This method involves precisely monitoring the change in fluorescence caused by the release of an intercalating DNA dye from a DNA duplex as it is denatured by a gradual increase in temperature. Since the melting profile depends on the GC content, length, and strand complementarity of the amplification product, Bar-HRM analysis opens up the possibility of detecting single-base variants or species-specific differences in a short region of DNA. This review summarizes key factors affecting Bar-HRM analysis and describes how Bar-HRM is performed. We then discuss advances in Bar-HRM analysis of medicinal plant ingredients (herbal materia medica) as a contribution toward safe and effective herbal medicines.

Investigating methods to estimate melting event parameters over Arctic sea- ice using SSM/I, OKEAN, and RADARSAT Data

NASA Astrophysics Data System (ADS)

Belchansky, G.; Eremeev, V.; Mordvintsev, I.; Platonov, N.; Douglas, D.

The melting events (early melt, melt onset, melt ponding, freeze-up onset) over Arctic sea-ice area are critical for climate and global change studies. They are combined with accuracy of surface energy balances estimates (due to contrasts in the short wave albedo of snow and ice, open water or melt ponds) and drives a number of important processes (onset of snow melt, thawing of boreal forest, etc). M icrowave measurements identify seasonal transition zones due to large differences in emissivity during melt onset, melt ponding and freeze-up periods. This report presents near coincident observation of backscatter cross section (0 ) and brightness temperature (Tb) from Russian OKEAN 01 satellite series, backscatter cross section (0) from RADARSAT-1, brightness temperatures (Tbs) from SSM/I sensors, and near-surface temperature derived from the International Arctic Buoy Program data (IABP) (Belchansky and Douglas, 2000, 2002). To determine the melt duration (time of freeze-up onset minus time of melt onset) passive and active microwave methods were developed. These methods used differences between SSM /I 19.3GHz,H and SSM/I 37.0 GHz, H channels (SSM/I Tb), OKEAN 0 (9.52GHz, VV) and Tb (37.47 GHz, H) channels, RADARSAT-1 0 (5.3GHz, HH), and a threshold technique. An evolution of the SSM/I Tb, OKEAN-01 0 and Tb, RADARSAT ScanSAR 0, MEAN ( 0), SD(0) and SD(0 ) / MEAN(0 ) as function of time was investigated along FY and MY dominant type ice areas during January 1996 through December 1998. The SSM/I, OKEAN and RADARSAT melt onset and freeze up onset algorithms were constructed. The SSM/I algorithm was based- on analysis of the SSM/I Tb. The OKEAN and RADARSAT ScanSAR algorithms were based, respectively, on analysis of OKEAN 0 and Tb of MY and FY sea ice at each MY and FY ice region (200 km by 200 km) determined in OKEAN imagery prior to melting period and changes in RADARSAT SD(0 ) / MEAN(0) of sea-ice during different stages of melting processes at each ice site (75 km by 75 km) determined prior to spring period in ScanSAR imagery. The averaged 12-h near surface temperatures derived from the IABP wer e used to analyze changes in the SSM/I Tb, OKEAN 0 and OKEAN Tb, RADARSAT SD(0) / MEAN(0), and to estimate respective thresholds associated with the melt onset and freeze-up onset. To highlight the sources of differences among various sensors results were compared to understand how the average the melt onset, melt duration and freeze-up onset estimates varied between different instruments and algorithms. A discrepancy in estimates resulted due to the nature of active and passive microwave measurements, frequency and polarization, number of channels, temperature and emissivity effects, and algorithm types. Higher spatial resolution of OKEAN-01 and RADARSAT-1 SAR was an important characteristic for obtaining better estimates of melting parameters. The SSM/ data provide a spatial resolution with global coverageI suitable for circulation models. Therefore OKEAN-01 and RADARSAT measurements can complement SSM/I data. These studies contribute to the growing body of documentation about the levels of disparity obtained when Arctic seasonal transition parameters are calculated using various types of satellite sensors and algorithms. ACKNOWLEDGEMENTS This work was carried out with the support from the International Arctic Research Center and Cooperative Institute for Arctic Research (IARC/CIFAR), University of Alaska Fairbanks. We would like to acknowledge the Alaska SAR Facility (Fairbanks), the National Snow and Ice Data Center (University of Colorado), and the Global Hydrology Resource Center, respectively, for providing RADARSAT images, the DMSP SSM/I Daily Polar Gridded Tb and Sea Ice Concentrations, the single-pass SSM/I brightness temperature data. REFERENCES Belchansky, G. I. and Douglas, D. C. (2000). Classification methods for monitoring Arctic sea-ice using OKEAN passive / active two-channel microwave data. J. Remote Sensing of Environment, Elsevier Science, New York. 73 (3): 307 -322. Belchansky, G. I. and Douglas, D. C. (2002). Seasonal comparisons of sea ice concentration estimates derived from SSM /I, OKEAN, and RADARSAT data. J. Remote Sensing of Environment, Elsevier Science, New York, 81 (1): 67-81.

The initiation of segmented buoyancy-driven melting during continental breakup

PubMed Central

Gallacher, Ryan J.; Keir, Derek; Harmon, Nicholas; Stuart, Graham; Leroy, Sylvie; Hammond, James O. S.; Kendall, J-Michael; Ayele, Atalay; Goitom, Berhe; Ogubazghi, Ghebrebrhan; Ahmed, Abdulhakim

2016-01-01

Melting of the mantle during continental breakup leads to magmatic intrusion and volcanism, yet our understanding of the location and dominant mechanisms of melt generation in rifting environments is impeded by a paucity of direct observations of mantle melting. It is unclear when during the rifting process the segmented nature of magma supply typical of seafloor spreading initiates. Here, we use Rayleigh-wave tomography to construct a high-resolution absolute three-dimensional shear-wave velocity model of the upper 250 km beneath the Afar triple junction, imaging the mantle response during progressive continental breakup. Our model suggests melt production is highest and melting depths deepest early during continental breakup. Elevated melt production during continental rifting is likely due to localized thinning and melt focusing when the rift is narrow. In addition, we interpret segmented zones of melt supply beneath the rift, suggesting that buoyancy-driven active upwelling of the mantle initiates early during continental rifting. PMID:27752044

Rapid and inexpensive body fluid identification by RNA profiling-based multiplex High Resolution Melt (HRM) analysis

PubMed Central

Hanson, Erin K.; Ballantyne, Jack

2014-01-01

Positive identification of the nature of biological material present on evidentiary items can be crucial for understanding the circumstances surrounding a crime. However, traditional protein-based methods do not permit the identification of all body fluids and tissues, and thus molecular based strategies for the conclusive identification of all forensically relevant biological fluids and tissues need to be developed. Messenger RNA (mRNA) profiling is an example of such a molecular-based approach. Current mRNA body fluid identification assays involve capillary electrophoresis (CE) or quantitative RT-PCR (qRT-PCR) platforms, each with its own limitations. Both platforms require the use of expensive fluorescently labeled primers or probes. CE-based assays require separate amplification and detection steps thus increasing the analysis time. For qRT-PCR assays, only 3-4 markers can be included in a single reaction since each requires a different fluorescent dye. To simplify mRNA profiling assays, and reduce the time and cost of analysis, we have developed single- and multiplex body fluid High Resolution Melt (HRM) assays for the identification of common forensically relevant biological fluids and tissues. The incorporated biomarkers include IL19 (vaginal secretions), IL1F7 (skin), ALAS2 (blood), MMP10 (menstrual blood), HTN3 (saliva) and TGM4 (semen).  The HRM assays require only unlabeled PCR primers and a single saturating intercalating fluorescent dye (Eva Green). Each body-fluid-specific marker can easily be identified by the presence of a distinct melt peak. Usually, HRM assays are used to detect variants or isoforms for a single gene target. However, we have uniquely developed duplex and triplex HRM assays to permit the simultaneous detection of multiple targets per reaction. Here we describe the development and initial performance evaluation of the developed HRM assays. The results demonstrate the potential use of HRM assays for rapid, and relatively inexpensive, screening of biological evidence. PMID:24715968

Rapid and inexpensive body fluid identification by RNA profiling-based multiplex High Resolution Melt (HRM) analysis.

PubMed

Hanson, Erin K; Ballantyne, Jack

2013-01-01

Positive identification of the nature of biological material present on evidentiary items can be crucial for understanding the circumstances surrounding a crime. However, traditional protein-based methods do not permit the identification of all body fluids and tissues, and thus molecular based strategies for the conclusive identification of all forensically relevant biological fluids and tissues need to be developed. Messenger RNA (mRNA) profiling is an example of such a molecular-based approach. Current mRNA body fluid identification assays involve capillary electrophoresis (CE) or quantitative RT-PCR (qRT-PCR) platforms, each with its own limitations. Both platforms require the use of expensive fluorescently labeled primers or probes. CE-based assays require separate amplification and detection steps thus increasing the analysis time. For qRT-PCR assays, only 3-4 markers can be included in a single reaction since each requires a different fluorescent dye. To simplify mRNA profiling assays, and reduce the time and cost of analysis, we have developed single- and multiplex body fluid High Resolution Melt (HRM) assays for the identification of common forensically relevant biological fluids and tissues. The incorporated biomarkers include IL19 (vaginal secretions), IL1F7 (skin), ALAS2 (blood), MMP10 (menstrual blood), HTN3 (saliva) and TGM4 (semen).  The HRM assays require only unlabeled PCR primers and a single saturating intercalating fluorescent dye (Eva Green). Each body-fluid-specific marker can easily be identified by the presence of a distinct melt peak. Usually, HRM assays are used to detect variants or isoforms for a single gene target. However, we have uniquely developed duplex and triplex HRM assays to permit the simultaneous detection of multiple targets per reaction. Here we describe the development and initial performance evaluation of the developed HRM assays. The results demonstrate the potential use of HRM assays for rapid, and relatively inexpensive, screening of biological evidence.

Structural Fluctuation and Thermophysical Properties of Molten II-VI Compounds

NASA Technical Reports Server (NTRS)

2003-01-01

The objectives of the project is to conduct ground-based experimental and theoretical research on the structural fluctuations and thermophysical properties of molten II-VI compounds to enhance the basic understanding of the existing flight experiments in microgravity materials science programs and to study the fundamental heterophase fluctuations phenomena in these melts by: 1) Conducting neutron scattering analysis and measuring quantitatively the relevant thermophysical properties of the II-VI melts such as viscosity, electrical conductivity, thermal diffusivity and density as well as the relaxation characteristics of these properties to advance the understanding of the structural properties and the relaxation phenomena in these melts and 2) Performing theoretical analyses on the melt systems to interpret the experimental results. All the facilities required for the experimental measurements have been procured, installed and tested. A relaxation phenomenon, which shows a slow drift of the measured thermal conductivity toward the equilibrium value after cooling of the sample, was observed for the first time. An apparatus based on the transient torque induced by a rotating magnetic field has been developed to determine the viscosity and electrical conductivity of semiconducting liquids. Viscosity measurements on molten tellurium showed similar relaxation behavior as the measured diffusivity. Neutron scattering experiments were performed on the HgTe and HgZnTe melts and the results on pair distribution showed better resolution than previous reported.

Is High Resolution Melting Analysis (HRMA) Accurate for Detection of Human Disease-Associated Mutations? A Meta Analysis

PubMed Central

Ma, Feng-Li; Jiang, Bo; Song, Xiao-Xiao; Xu, An-Gao

2011-01-01

Background High Resolution Melting Analysis (HRMA) is becoming the preferred method for mutation detection. However, its accuracy in the individual clinical diagnostic setting is variable. To assess the diagnostic accuracy of HRMA for human mutations in comparison to DNA sequencing in different routine clinical settings, we have conducted a meta-analysis of published reports. Methodology/Principal Findings Out of 195 publications obtained from the initial search criteria, thirty-four studies assessing the accuracy of HRMA were included in the meta-analysis. We found that HRMA was a highly sensitive test for detecting disease-associated mutations in humans. Overall, the summary sensitivity was 97.5% (95% confidence interval (CI): 96.8–98.5; I2 = 27.0%). Subgroup analysis showed even higher sensitivity for non-HR-1 instruments (sensitivity 98.7% (95%CI: 97.7–99.3; I2 = 0.0%)) and an eligible sample size subgroup (sensitivity 99.3% (95%CI: 98.1–99.8; I2 = 0.0%)). HRMA specificity showed considerable heterogeneity between studies. Sensitivity of the techniques was influenced by sample size and instrument type but by not sample source or dye type. Conclusions/Significance These findings show that HRMA is a highly sensitive, simple and low-cost test to detect human disease-associated mutations, especially for samples with mutations of low incidence. The burden on DNA sequencing could be significantly reduced by the implementation of HRMA, but it should be recognized that its sensitivity varies according to the number of samples with/without mutations, and positive results require DNA sequencing for confirmation. PMID:22194806

Rapid identification of apolipoprotein E genotypes by high-resolution melting analysis in Chinese Han and African Fang populations.

PubMed

Zhan, Xiu-Hui; Zha, Guang-Cai; Jiao, Ji-Wei; Yang, Li-Ye; Zhan, Xiao-Fen; Chen, Jiang-Tao; Xie, Dong-DE; Eyi, Urbano Monsuy; Matesa, Rocio Apicante; Obono, Maximo Miko Ondo; Ehapo, Carlos Sala; Wei, Er-Jia; Zheng, Yu-Zhong; Yang, Hui; Lin, Min

2015-02-01

Apolipoprotein E (APOE) gene polymorphism can affect APOE gene transcription, serum lipid levels and repair of tissue damage, which could place individuals at serious risk of cardiovascular disease or certain infectious diseases. Recently, high-resolution melting (HRM) analysis was reported to be a simple, inexpensive, accurate and sensitive method for the genotyping or/and scanning of rare mutations. For this reason, an HRM analysis was used in the present study for APOE genotyping in the Southern Chinese Han and African Fang populations. A total of 100 healthy Southern Chinese Han and 175 healthy African Fang individuals attended the study. Polymerase chain reaction-DNA sequencing was used as a reference method for the genotyping of these samples. The six APOE genotypes could all be rapidly and efficiently identified by HRM analysis, and 100% concordance was found between the HRM analysis and the reference method. The allele frequencies of APOE in the Southern Chinese Han population were 7.0, 87.5 and 5.5% for ɛ2, ɛ3 and ɛ4, respectively. In the African Fang population, the allele frequencies of APOE were 24.3, 65.7 and 10.0% for ɛ2, ɛ3 and ɛ4, respectively. A statistically significant difference was found between the allele frequencies between the populations (P<0.05). In conclusion, the present study revealed the molecular characterization of APOE gene polymorphism in the Han population from the Chaozhou region of Southern China and the Fang population from Equatorial Guinea. The findings of the study indicated that HRM analysis could be used as an accurate and sensitive method for the rapid screening and identification of APOE genotypes in prospective clinical and population genetic analyses.

SYTO9 and SYBR GREEN1 with a high-resolution melting analysis for prenatal diagnosis of β⁰-thalassemia/hemoglobin-E.

PubMed

Pornprasert, Sakorn; Sukunthamala, Kanyakan

2010-11-01

The β⁰-thalassemia/Hb-E causes a wide range of severe conditions. A high medical cost is incurred in severe cases. Thus, the prevention of new cases of β⁰-thalassemia/Hb-E is required. The aim of this study is to use the SYTO9 and SYBR GREEN1 high-resolution melting (HRM) analysis for prenatal diagnosis of β⁰-thalassemia/Hb-E. DNA samples were extracted from amniotic fluid or cord blood of 11 pregnancies whose fetuses were at risk for β-thalassemia/Hb-E. PCR products from multiplex amplification refractory mutation system PCR for the detection of β⁰-thalassemia mutations at codons 17(A>T), 41/42(-TCTT), and 71/72(+A) and from amplification refractory mutation system PCR for the detection of Hb-E were characterized by SYTO9 HRM analysis. Moreover, β⁰-thalassemia 3.5- kb deletion was detected using real-time PCR with SYBR GREEN1 HRM analysis. Seven of 11 fetuses (64%) were diagnosed as β⁰-thalassemia/Hb-E (4 fetuses with mutation at codon 17, 2 with mutation at codon 41/42, and 1 with 3.5- kb deletion). Results from HRM analysis were completely consistent with those from fetal blood samplings analyzed at the time of delivery or pregnancy termination using HPLC. Therefore, the HRM analysis is easy to use. It is simple, flexible, non-destructive and has superb sensitivity and specificity. This approach might facilitate the laboratory diagnosis and genetic counseling for regions with a high prevalence of β⁰-thalassemia/Hb-E. © 2010 John Wiley & Sons A/S.

Pre-melting Behaviour in fcc Metals

NASA Astrophysics Data System (ADS)

Pamato, M. G.; Wood, I. G.; Dobson, D. P.; Hunt, S.; Vocadlo, L.

2016-12-01

Although the Earth's core is accepted to be made of an iron-nickel alloy with a few percent of light elements, its exact structure and composition are still unknown. Seismological and mineralogical models in the Earth's inner core do not agree, with mineralogical models derived from ab initiocalculations predicting shear-wave velocities up to 30% greater than seismically observed values. Recent computer simulations revealed that such difference may be explained by a dramatic, non-linear, softening of the elastic constants of Fe prior to melting. Up to date, computer calculations are the only result on pre-melting of direct applicability to the Earth's core and it is essential to systematically investigate such phenomena at inner core pressures and temperatures. Measuring the pressure dependence of pre-melting effects at such conditions and to the required precision is however extremely challenging. Also, pre-melting effects have been observed or suggested to occur in other materials, particularly noble metals, which exhibit large departures from linearity (modulus defects) at elevated temperatures. The aim of this study is to investigate to what extent pre-melting behaviour occurs in the physical properties of other metals at more experimentally tractable conditions. In particular, we report measurements of density and thermal expansion coefficients of both pure and alloyed gold (Au) up to their melting points. Au is an ideal test material since it crystallises in a simple monatomic face-centred structure and has a relatively low melting temperature. Precise measurements of unit cell lattice parameters were performed using a PANalytical X'Pert Pro powder diffractometer, equipped with an incident beam monochromator (giving very high resolution diffraction patterns) and with environmental stages covering the range from 40 K to 1373 K, with a readily achievable temperature resolution of 1K. We will discuss the circumstances under which pre-melting occurs, its mechanism(s), the effect of impurities and defects in the solid, and the consequences of pre-melting in the Earth's core.

First report of Tasmanian sheep strain (G2) genotype isolated from Iranian goat using the high resolution melting (HRM) analysis.

PubMed

Hosseini-Safa, Ahmad; Mohag Hegh, Mohammad Ali; Pestechian, Nader; Ganji, Maryam; Mohammadi, Rasoul; Mahmoudi Lamouki, Reza; Rostami-Nejad, Mohammad

2016-12-01

The present study was aimed to evaluate E. granulosus genotypes isolated from goats using HRM analysis in Isfahan province. Cystic echincoccosis, so-called hydatidosis, is widespread infection caused by the larval stage of Echinococcus granulosus . This is an important zoonotic disease worldwide, especially in the developing countries such as Iran. To date, molecular studies mainly based on the mitochondrial DNA sequences have identified distinct genotypes termed G1-G10 which can differ in some characteristics such as the growth and infectivity to different intermediate hosts or the survival rate in the definitive hosts that are important for the development of control strategies. From August to December 2014, 1341 goats were investigated and hydatid cysts were collected from the liver and lungs of 43 infected goats in Isfahan province abattoirs, Isfahan, Iran. Total genomic DNA was extracted from each sample, amplified for the presence of polymorphism of mitochondrial gene coding for cytochrome c oxidase subunit 1 (CO1), using high resolution melting curve (HRM) method. the results of HRM analysis using the sequence of CO1 gene for 43 Echinococcus granulosus isolates from goats showed 31, 2 and 10 isolates were identified as G1, G2, and G3 genotypes, respectively. G1 is the predominant genotype in the isolated goat samples in Isfahan province, and the presence of G2 strain was reported for the first time in goat in Iran.

A novel HRM assay for differentiating classical strains and highly pathogenic strains of type 2 porcine reproductive and respiratory syndrome virus.

PubMed

Sun, Junying; Bingga, Gali; Liu, Zhicheng; Zhang, Chunhong; Shen, Haiyan; Guo, Pengju; Zhang, Jianfeng

2018-06-01

Differentiation of classical strains and highly pathogenic strains of porcine reproductive and respiratory syndrome virus is crucial for effective vaccination programs and epidemiological studies. We used nested PCR and high resolution melting curve analysis with unlabeled probe to distinguish between the classical and the highly pathogenic strains of this virus. Two sets of primers and a 20 bp unlabeled probe were designed from the NSP3 gene. The unlabeled probe included two mutations specific for the classical and highly pathogenic strains of the virus. An additional primer set from the NSP2 gene of the highly pathogenic vaccine strain JXA1-R was used to detect its exclusive single nucleotide polymorphism. We tested 107 clinical samples, 21 clinical samples were positive for PRRSV (consistent with conventional PCR assay), among them four were positive for the classical strain with the remainder 17 for the highly pathogenic strain. Around 10 °C difference between probe melting temperatures showed the high discriminatory power of this method. Among highly pathogenic positive samples, three samples were determined as positive for JXA1-R vaccine-related strain with a 95% genotype confidence percentage. All these genotyping results using the high resolution melting curve assay were confirmed with DNA sequencing. This unlabeled probe method provides an alternative means to differentiate the classical strains from the highly pathogenic porcine reproductive and respiratory syndrome virus strains rapidly and accurately. Copyright © 2018. Published by Elsevier Ltd.

Quantifying ice cliff contribution to debris-covered glacier mass balance from multiple sensors

NASA Astrophysics Data System (ADS)

Brun, Fanny; Wagnon, Patrick; Berthier, Etienne; Kraaijenbrink, Philip; Immerzeel, Walter; Shea, Joseph; Vincent, Christian

2017-04-01

Ice cliffs on debris-covered glaciers have been recognized as a hot spot for glacier melt. Ice cliffs are steep (even sometimes overhanging) and fast evolving surface features, which make them challenging to monitor. We surveyed the topography of Changri Nup Glacier (Nepalese Himalayas, Everest region) in November 2015 and 2016 using multiple sensors: terrestrial photogrammetry, Unmanned Aerial Vehicle (UAV) photogrammetry, Pléiades stereo images and ASTER stereo images. We derived 3D point clouds and digital elevation models (DEMs) following a Structure-from-Motion (SfM) workflow for the first two sets of data to monitor surface elevation changes and calculate the associated volume loss. We derived only DEMs for the two last data sets. The derived DEMs had resolutions ranging from < 5 cm to 30 m. The derived point clouds and DEMs are used to quantify the ice melt of the cliffs at different scales. The very high resolution SfM point clouds, together with the surface velocity field, will be used to calculate the volume losses of 14 individual cliffs, depending on their size, aspect or the presence of supra glacial lake. Then we will extend this analysis to the whole glacier to quantify the contribution of ice cliff melt to the overall glacier mass balance, calculated with the UAV and Pléiades DEMs. This research will provide important tools to evaluate the role of ice cliffs in regional mass loss.

The genotyping of infectious bronchitis virus in Taiwan by a multiplex amplification refractory mutation system reverse transcription polymerase chain reaction.

PubMed

Huang, Shr-Wei; Ho, Chia-Fang; Chan, Kun-Wei; Cheng, Min-Chung; Shien, Jui-Hung; Liu, Hung-Jen; Wang, Chi-Young

2014-11-01

Infectious bronchitis virus (IBV; Avian coronavirus) causes acute respiratory and reproductive and urogenital diseases in chickens. Following sequence alignment of IBV strains, a combination of selective primer sets was designed to individually amplify the IBV wild-type and vaccine strains using a multiplex amplification refractory mutation system reverse transcription polymerase chain reaction (ARMS RT-PCR) approach. This system was shown to discriminate the IBV wild-type and vaccine strains. Moreover, an ARMS real-time RT-PCR (ARMS qRT-PCR) was combined with a high-resolution analysis (HRMA) to establish a melt curve analysis program. The specificity of the ARMS RT-PCR and the ARMS qRT-PCR was verified using unrelated avian viruses. Different melting temperatures and distinct normalized and shifted melting curve patterns for the IBV Mass, IBV H120, IBV TW-I, and IBV TW-II strains were detected. The new assays were used on samples of lung and trachea as well as virus from allantoic fluid and cell culture. In addition to being able to detect the presence of IBV vaccine and wild-type strains by ARMS RT-PCR, the IBV Mass, IBV H120, IBV TW-I, and IBV TW-II strains were distinguished using ARMS qRT-PCR by their melting temperatures and by HRMA. These approaches have acceptable sensitivities and specificities and therefore should be able to serve as options when carrying out differential diagnosis of IBV in Taiwan and China. © 2014 The Author(s).

Greenland Ice Sheet Melt from MODIS and Associated Atmospheric Variability

NASA Technical Reports Server (NTRS)

Hakkinen, Sirpa; Hall, Dorothy K.; Shuman, Christopher A.; Worthen, Denise L.; DiGirolamo, Nicolo E.

2014-01-01

Daily June-July melt fraction variations over the Greenland Ice Sheet (GIS) derived from the MODerate-resolution Imaging Spectroradiometer (MODIS) (2000-2013) are associated with atmospheric blocking forming an omega-shape ridge over the GIS at 500hPa height (from NCEPNCAR). Blocking activity with a range of time scales, from synoptic waves breaking poleward ( 5 days) to full-fledged blocks (5 days), brings warm subtropical air masses over the GIS controlling daily surface temperatures and melt. The temperature anomaly of these subtropical air mass intrusions is also important for melting. Based on the largest MODIS melt years (2002 and 2012), the area-average temperature anomaly of 2 standard deviations above the 14-year June-July mean, results in a melt fraction of 40 or more. Summer 2007 had the most blocking days, however atmospheric temperature anomalies were too small to instigate extreme melting.

High-resolution Melting Analysis for Gene Scanning of Adenomatous Polyposis Coli (APC) Gene With Oral Squamous Cell Carcinoma Samples.

PubMed

Chang, Ya-Sian; Lin, Chien-Yu; Yang, Shu-Fen; Ho, Cheng Mao; Chang, Jan-Gowth

2016-02-01

There have been many different mutations reported for the large adenomatous polyposis coli (APC) tumor suppressor gene. APC mutations result in inactivation of APC tumor suppressor action, allowing the progression of tumorigenesis. The present study utilized a highly efficient method to identify APC mutations and investigated the association between the APC genetic variants Y486Y, A545A, T1493T, and D1822V and susceptibility to oral squamous cell carcinoma (OSCC). High-resolution melting (HRM) analysis was used to characterize APC mutations. Genomic DNA was extracted from 83 patient specimens of OSCC and 50 blood samples from healthy control subjects. The 14 exons and mutation cluster region of exon 15 were screened by HRM analysis. All mutations were confirmed by direct DNA sequencing. Three mutations and 4 single nucleotide polymorphisms (SNPs) were found in this study. The mutations were c.573T>C (Y191Y) in exon 5, c.1005A>G (L335L) in exon 9, and c.1488A>T (T496T) in exon 11. Two SNPs, c.4479G>A (T1493T) and c.5465A>T (D1822V), were located in exon 15, whereas c.1458T>C (Y486Y) and c.1635G>A (A545A) were located in exon 11 and 13, respectively. There was no observed association between OSCC risk and genotype for any of the 4 APC SNPs. The mutation of APC is rare in Taiwanese patients with OSCC. HRM analysis is a reliable, accurate, and fast screening method for APC mutations.

Evaluation of the Capacity of PCR and High-Resolution Melt Curve Analysis for Identification of Mixed Infection with Mycoplasma gallisepticum Strains

PubMed Central

Ghorashi, Seyed A.; Kanci, Anna; Noormohammadi, Amir H.

2015-01-01

Pathogenicity and presentation of Mycoplasma gallisepticum (MG) infection may differ from one strain to another and this may have implications on control measures. Infection of individual birds with more than one MG strain has been reported. A PCR followed by high resolution melt (HRM) curve analysis has been developed in our laboratory and routinely used for detection and differentiation of MG strains. However the potential of this test for identification of MG strains in a mixed specimen has not been evaluated. In the present study, the capability of PCR-HRM curve analysis technique, targeting vlhA and pvpA genes was assessed for identification of individual MG strains in a mixed population. Different DNA ratios of two MG strains from 1 to 10-4 ng were tested with some generated conventional and normalized curves distinct from those of individual strains alone. Using genotype confidence percentages (GCP) generated from HRM curve analysis, it was found that vlhA PCR-HRM was more consistent than pvpA PCR-HRM for the detection of MG ts-11 vaccine strain mixed with any of the MG strains 6/85, F, S6 or a field isolate. The potential of vlhA PCR-HRM to detect mixed MG strains in a specimen was found to be primarily dependent on quantity and proportion of the target DNAs in the mixture. This is the first study examining the capacity of PCR-HRM technique for identification of individual MG strains in a mixed strain population. PMID:25970590

Comparison of a High-Resolution Melting Assay to Next-Generation Sequencing for Analysis of HIV Diversity

PubMed Central

Cousins, Matthew M.; Ou, San-San; Wawer, Maria J.; Munshaw, Supriya; Swan, David; Magaret, Craig A.; Mullis, Caroline E.; Serwadda, David; Porcella, Stephen F.; Gray, Ronald H.; Quinn, Thomas C.; Donnell, Deborah; Eshleman, Susan H.

2012-01-01

Next-generation sequencing (NGS) has recently been used for analysis of HIV diversity, but this method is labor-intensive, costly, and requires complex protocols for data analysis. We compared diversity measures obtained using NGS data to those obtained using a diversity assay based on high-resolution melting (HRM) of DNA duplexes. The HRM diversity assay provides a single numeric score that reflects the level of diversity in the region analyzed. HIV gag and env from individuals in Rakai, Uganda, were analyzed in a previous study using NGS (n = 220 samples from 110 individuals). Three sequence-based diversity measures were calculated from the NGS sequence data (percent diversity, percent complexity, and Shannon entropy). The amplicon pools used for NGS were analyzed with the HRM diversity assay. HRM scores were significantly associated with sequence-based measures of HIV diversity for both gag and env (P < 0.001 for all measures). The level of diversity measured by the HRM diversity assay and NGS increased over time in both regions analyzed (P < 0.001 for all measures except for percent complexity in gag), and similar amounts of diversification were observed with both methods (P < 0.001 for all measures except for percent complexity in gag). Diversity measures obtained using the HRM diversity assay were significantly associated with those from NGS, and similar increases in diversity over time were detected by both methods. The HRM diversity assay is faster and less expensive than NGS, facilitating rapid analysis of large studies of HIV diversity and evolution. PMID:22785188

Establishing high resolution melting analysis: method validation and evaluation for c-RET proto-oncogene mutation screening.

PubMed

Benej, Martin; Bendlova, Bela; Vaclavikova, Eliska; Poturnajova, Martina

2011-10-06

Reliable and effective primary screening of mutation carriers is the key condition for common diagnostic use. The objective of this study is to validate the method high resolution melting (HRM) analysis for routine primary mutation screening and accomplish its optimization, evaluation and validation. Due to their heterozygous nature, germline point mutations of c-RET proto-oncogene, associated to multiple endocrine neoplasia type 2 (MEN2), are suitable for HRM analysis. Early identification of mutation carriers has a major impact on patients' survival due to early onset of medullary thyroid carcinoma (MTC) and resistance to conventional therapy. The authors performed a series of validation assays according to International Conference on Harmonization of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH) guidelines for validation of analytical procedures, along with appropriate design and optimization experiments. After validated evaluation of HRM, the method was utilized for primary screening of 28 pathogenic c-RET mutations distributed among nine exons of c-RET gene. Validation experiments confirm the repeatability, robustness, accuracy and reproducibility of HRM. All c-RET gene pathogenic variants were detected with no occurrence of false-positive/false-negative results. The data provide basic information about design, establishment and validation of HRM for primary screening of genetic variants in order to distinguish heterozygous point mutation carriers among the wild-type sequence carriers. HRM analysis is a powerful and reliable tool for rapid and cost-effective primary screening, e.g., of c-RET gene germline and/or sporadic mutations and can be used as a first line potential diagnostic tool.

Greenland ice sheet melt from MODIS and associated atmospheric variability.

PubMed

Häkkinen, Sirpa; Hall, Dorothy K; Shuman, Christopher A; Worthen, Denise L; DiGirolamo, Nicolo E

2014-03-16

Daily June-July melt fraction variations over the Greenland ice sheet (GIS) derived from the Moderate Resolution Imaging Spectroradiometer (MODIS) (2000-2013) are associated with atmospheric blocking forming an omega-shape ridge over the GIS at 500 hPa height. Blocking activity with a range of time scales, from synoptic waves breaking poleward (<5 days) to full-fledged blocks (≥5 days), brings warm subtropical air masses over the GIS controlling daily surface temperatures and melt. The temperature anomaly of these subtropical air mass intrusions is also important for melting. Based on the years with the greatest melt (2002 and 2012) during the MODIS era, the area-average temperature anomaly of 2 standard deviations above the 14 year June-July mean results in a melt fraction of 40% or more. Though the summer of 2007 had the most blocking days, atmospheric temperature anomalies were too small to instigate extreme melting. Short-term atmospheric blocking over Greenland contributes to melt episodesAssociated temperature anomalies are equally important for the meltDuration and strength of blocking events contribute to surface melt intensity.

Generation of Well-Relaxed All-Atom Models of Large Molecular Weight Polymer Melts: A Hybrid Particle-Continuum Approach Based on Particle-Field Molecular Dynamics Simulations.

PubMed

De Nicola, Antonio; Kawakatsu, Toshihiro; Milano, Giuseppe

2014-12-09

A procedure based on Molecular Dynamics (MD) simulations employing soft potentials derived from self-consistent field (SCF) theory (named MD-SCF) able to generate well-relaxed all-atom structures of polymer melts is proposed. All-atom structures having structural correlations indistinguishable from ones obtained by long MD relaxations have been obtained for poly(methyl methacrylate) (PMMA) and poly(ethylene oxide) (PEO) melts. The proposed procedure leads to computational costs mainly related on system size rather than to the chain length. Several advantages of the proposed procedure over current coarse-graining/reverse mapping strategies are apparent. No parametrization is needed to generate relaxed structures of different polymers at different scales or resolutions. There is no need for special algorithms or back-mapping schemes to change the resolution of the models. This characteristic makes the procedure general and its extension to other polymer architectures straightforward. A similar procedure can be easily extended to the generation of all-atom structures of block copolymer melts and polymer nanocomposites.

The melt pond fraction and spectral sea ice albedo retrieval from MERIS data: validation and trends of sea ice albedo and melt pond fraction in the Arctic for years 2002-2011

NASA Astrophysics Data System (ADS)

Istomina, L.; Heygster, G.; Huntemann, M.; Schwarz, P.; Birnbaum, G.; Scharien, R.; Polashenski, C.; Perovich, D.; Zege, E.; Malinka, A.; Prikhach, A.; Katsev, I.

2014-10-01

The presence of melt ponds on the Arctic sea ice strongly affects the energy balance of the Arctic Ocean in summer. It affects albedo as well as transmittance through the sea ice, which has consequences on the heat balance and mass balance of sea ice. An algorithm to retrieve melt pond fraction and sea ice albedo (Zege et al., 2014) from the MEdium Resolution Imaging Spectrometer (MERIS) data is validated against aerial, ship borne and in situ campaign data. The result show the best correlation for landfast and multiyear ice of high ice concentrations (albedo: R = 0.92, RMS = 0.068, melt pond fraction: R = 0.6, RMS = 0.065). The correlation for lower ice concentrations, subpixel ice floes, blue ice and wet ice is lower due to complicated surface conditions and ice drift. Combining all aerial observations gives a mean albedo RMS equal to 0.089 and a mean melt pond fraction RMS equal to 0.22. The in situ melt pond fraction correlation is R = 0.72 with an RMS = 0.14. Ship cruise data might be affected by documentation of varying accuracy within the ASPeCT protocol, which is the reason for discrepancy between the satellite value and observed value: mean R = 0.21, mean RMS = 0.16. An additional dynamic spatial cloud filter for MERIS over snow and ice has been developed to assist with the validation on swath data. The case studies and trend analysis for the whole MERIS period (2002-2011) show pronounced and reasonable spatial features of melt pond fractions and sea ice albedo. The most prominent feature is the melt onset shifting towards spring (starting already in weeks 3 and 4 of June) within the multiyear ice area, north to the Queen Elizabeth Islands and North Greenland.

Candidate DNA Barcode Tags Combined With High Resolution Melting (Bar-HRM) Curve Analysis for Authentication of Senna alexandrina Mill. With Validation in Crude Drugs.

PubMed

Mishra, Priyanka; Shukla, Ashutosh K; Sundaresan, Velusamy

2018-01-01

Senna alexandrina (Fabaceae) is a globally recognized medicinal plant for its laxative properties as well as the only source of sennosides, and is highly exported bulk herb from India. Its major procurement is exclusively from limited cultivation, which leads to risks of deliberate or unintended adulteration. The market raw materials are in powdered or finished product form, which lead to difficulties in authentication. Here, DNA barcode tags based on chloroplast genes ( rbcL and matK ) and intergenic spacers ( psbA-trnH and ITS ) were developed for S. alexandrina along with the allied species. The ability and performance of the ITS1 region to discriminate among the Senna species resulted in the present proposal of the ITS1 tags as successful barcode. Further, these tags were coupled with high-resolution melting (HRM) curve analysis in a real-time PCR genotyping method to derive Bar-HRM (Barcoding-HRM) assays. Suitable HRM primer sets were designed through SNP detection and mutation scanning in genomic signatures of Senna species. The melting profiles of S. alexandrina and S . italica subsp. micrantha were almost identical and the remaining five species were clearly separated so that they can be differentiated by HRM method. The sensitivity of the method was utilized to authenticate market samples [Herbal Sample Assays (HSAs)]. HSA01 ( S. alexandrina crude drug sample from Bangalore) and HSA06 ( S. alexandrina crude drug sample from Tuticorin, Tamil Nadu, India) were found to be highly contaminated with S . italica subsp. micrantha . Species admixture samples mixed in varying percentage was identified sensitively with detection of contamination as low as 1%. The melting profiles of PCR amplicons are clearly distinct, which enables the authentic differentiation of species by the HRM method. This study reveals that DNA barcoding coupled with HRM is an efficient molecular tool to authenticate Senna herbal products in the market for quality control in the drug supply chain. CIMAP Communication Number: CIMAP/PUB/2017/31.

Candidate DNA Barcode Tags Combined With High Resolution Melting (Bar-HRM) Curve Analysis for Authentication of Senna alexandrina Mill. With Validation in Crude Drugs

PubMed Central

Mishra, Priyanka; Shukla, Ashutosh K.; Sundaresan, Velusamy

2018-01-01

Senna alexandrina (Fabaceae) is a globally recognized medicinal plant for its laxative properties as well as the only source of sennosides, and is highly exported bulk herb from India. Its major procurement is exclusively from limited cultivation, which leads to risks of deliberate or unintended adulteration. The market raw materials are in powdered or finished product form, which lead to difficulties in authentication. Here, DNA barcode tags based on chloroplast genes (rbcL and matK) and intergenic spacers (psbA-trnH and ITS) were developed for S. alexandrina along with the allied species. The ability and performance of the ITS1 region to discriminate among the Senna species resulted in the present proposal of the ITS1 tags as successful barcode. Further, these tags were coupled with high-resolution melting (HRM) curve analysis in a real-time PCR genotyping method to derive Bar-HRM (Barcoding-HRM) assays. Suitable HRM primer sets were designed through SNP detection and mutation scanning in genomic signatures of Senna species. The melting profiles of S. alexandrina and S. italica subsp. micrantha were almost identical and the remaining five species were clearly separated so that they can be differentiated by HRM method. The sensitivity of the method was utilized to authenticate market samples [Herbal Sample Assays (HSAs)]. HSA01 (S. alexandrina crude drug sample from Bangalore) and HSA06 (S. alexandrina crude drug sample from Tuticorin, Tamil Nadu, India) were found to be highly contaminated with S. italica subsp. micrantha. Species admixture samples mixed in varying percentage was identified sensitively with detection of contamination as low as 1%. The melting profiles of PCR amplicons are clearly distinct, which enables the authentic differentiation of species by the HRM method. This study reveals that DNA barcoding coupled with HRM is an efficient molecular tool to authenticate Senna herbal products in the market for quality control in the drug supply chain. CIMAP Communication Number: CIMAP/PUB/2017/31 PMID:29593755

Three-dimensional coherent x-ray diffraction imaging of molten iron in mantle olivine at nanoscale resolution.

PubMed

Jiang, Huaidong; Xu, Rui; Chen, Chien-Chun; Yang, Wenge; Fan, Jiadong; Tao, Xutang; Song, Changyong; Kohmura, Yoshiki; Xiao, Tiqiao; Wang, Yong; Fei, Yingwei; Ishikawa, Tetsuya; Mao, Wendy L; Miao, Jianwei

2013-05-17

We report quantitative 3D coherent x-ray diffraction imaging of a molten Fe-rich alloy and crystalline olivine sample, synthesized at 6 GPa and 1800 °C, with nanoscale resolution. The 3D mass density map is determined and the 3D distribution of the Fe-rich and Fe-S phases in the olivine-Fe-S sample is observed. Our results indicate that the Fe-rich melt exhibits varied 3D shapes and sizes in the olivine matrix. This work has potential for not only improving our understanding of the complex interactions between Fe-rich core-forming melts and mantle silicate phases but also paves the way for quantitative 3D imaging of materials at nanoscale resolution under extreme pressures and temperatures.

A screening method for the detection of the 35S promoter and the nopaline synthase terminator in genetically modified organisms in a real-time multiplex polymerase chain reaction using high-resolution melting-curve analysis.

PubMed

Akiyama, Hiroshi; Nakamura, Fumi; Yamada, Chihiro; Nakamura, Kosuke; Nakajima, Osamu; Kawakami, Hiroshi; Harikai, Naoki; Furui, Satoshi; Kitta, Kazumi; Teshima, Reiko

2009-11-01

To screen for unauthorized genetically modified organisms (GMO) in the various crops, we developed a multiplex real-time polymerase chain reaction high-resolution melting-curve analysis method for the simultaneous qualitative detection of 35S promoter sequence of cauliflower mosaic virus (35SP) and the nopaline synthase terminator (NOST) in several crops. We selected suitable primer sets for the simultaneous detection of 35SP and NOST and designed the primer set for the detection of spiked ColE1 plasmid to evaluate the validity of the polymerase chain reaction (PCR) analyses. In addition, we optimized the multiplex PCR conditions using the designed primer sets and EvaGreen as an intercalating dye. The contamination of unauthorized GMO with single copy similar to NK603 maize can be detected as low as 0.1% in a maize sample. Furthermore, we showed that the present method would be applicable in identifying GMO in various crops and foods like authorized GM soybean, authorized GM potato, the biscuit which is contaminated with GM soybeans and the rice which is contaminated with unauthorized GM rice. We consider this method to be a simple and reliable assay for screening for unauthorized GMO in crops and the processing food products.

High-resolution melting analysis (HRM) for mutational screening of Dnajc17 gene in patients affected by thyroid dysgenesis.

PubMed

Nettore, I C; Desiderio, S; De Nisco, E; Cacace, V; Albano, L; Improda, N; Ungaro, P; Salerno, M; Colao, A; Macchia, P E

2018-06-01

Congenital hypothyroidism is a frequent disease occurring with an incidence of about 1/1500 newborns/year. In about 75% of the cases, CH is caused by alterations in thyroid morphogenesis, defined "thyroid dysgenesis" (TD). TD is generally a sporadic disease but in about 5% of the cases a genetic origin has been demonstrated. Previous studies indicate that Dnajc17 as a candidate modifier gene for hypothyroidism, since it is expressed in the thyroid bud, interacts with NKX2.1 and PAX8 and it has been associated to the hypothyroid phenotype in mice carrying a single Nkx2.1 and Pax8 genes (double heterozygous knock-out). The work evaluates the possible involvement of DNAJC17 in the pathogenesis of TD. High-resolution DNA melting analysis (HRM) and direct sequencing have been used to screen for mutations in the DNAJC17 coding sequence in 89 patients with TD. Two mutations have been identified in the coding sequence of DNAJC17 gene, one in exon 5 (c.350A>C; rs79709714) and one in exon 9 (c.610G>C; rs117485355). The last one is a rare variant, while the rs79709714 is a polymorphism. Both are present in databases and the frequency of the alleles is not different between TD patients and controls. DNAJC17 mutations are not frequently present in patients with TD.

Validation of high-resolution DNA melting analysis for mutation scanning of the CDKL5 gene: identification of novel mutations.

PubMed

Raymond, Laure; Diebold, Bertrand; Leroux, Céline; Maurey, Hélène; Drouin-Garraud, Valérie; Delahaye, Andre; Dulac, Olivier; Metreau, Julia; Melikishvili, Gia; Toutain, Annick; Rivier, François; Bahi-Buisson, Nadia; Bienvenu, Thierry

2013-01-01

Mutations in the cyclin-dependent kinase-like 5 gene (CDKL5) have been predominantly described in epileptic encephalopathies of female, including infantile spasms with Rett-like features. Up to now, detection of mutations in this gene was made by laborious, expensive and/or time consuming methods. Here, we decided to validate high-resolution melting analysis (HRMA) for mutation scanning of the CDKL5 gene. Firstly, using a large DNA bank consisting to 34 samples carrying different mutations and polymorphisms, we validated our analytical conditions to analyse the different exons and flanking intronic sequences of the CDKL5 gene by HRMA. Secondly, we screened CDKL5 by both HRMA and denaturing high performance liquid chromatography (dHPLC) in a cohort of 135 patients with early-onset seizures. Our results showed that point mutations and small insertions and deletions can be reliably detected by HRMA. Compared to dHPLC, HRMA profiles are more discriminated, thereby decreasing unnecessary sequencing. In this study, we identified eleven novel sequence variations including four pathogenic mutations (2.96% prevalence). HRMA appears cost-effective, easy to set up, highly sensitive, non-toxic and rapid for mutation screening, ideally suited for large genes with heterogeneous mutations located along the whole coding sequence, such as the CDKL5 gene. Copyright © 2012 Elsevier B.V. All rights reserved.

Mutation scanning in a single and a stacked genetically modified (GM) event by real-time PCR and high resolution melting (HRM) analysis.

PubMed

Ben Ali, Sina-Elisabeth; Madi, Zita Erika; Hochegger, Rupert; Quist, David; Prewein, Bernhard; Haslberger, Alexander G; Brandes, Christian

2014-10-31

Genetic mutations must be avoided during the production and use of seeds. In the European Union (EU), Directive 2001/18/EC requires any DNA construct introduced via transformation to be stable. Establishing genetic stability is critical for the approval of genetically modified organisms (GMOs). In this study, genetic stability of two GMOs was examined using high resolution melting (HRM) analysis and real-time polymerase chain reaction (PCR) employing Scorpion primers for amplification. The genetic variability of the transgenic insert and that of the flanking regions in a single oilseed rape variety (GT73) and a stacked maize (MON88017×MON810) was studied. The GT73 and the 5' region of MON810 showed no instabilities in the examined regions. However; two out of 100 analyzed samples carried a heterozygous point mutation in the 3' region of MON810 in the stacked variety. These results were verified by direct sequencing of the amplified PCR products as well as by sequencing of cloned PCR fragments. The occurrence of the mutation suggests that the 5' region is more suitable than the 3' region for the quantification of MON810. The identification of the single nucleotide polymorphism (SNP) in a stacked event is in contrast to the results of earlier studies of the same MON810 region in a single event where no DNA polymorphism was found.

High Resolution Melting Analysis Targeting hsp70 as a Fast and Efficient Method for the Discrimination of Leishmania Species.

PubMed

Zampieri, Ricardo Andrade; Laranjeira-Silva, Maria Fernanda; Muxel, Sandra Marcia; Stocco de Lima, Ana Carolina; Shaw, Jeffrey Jon; Floeter-Winter, Lucile Maria

2016-02-01

Protozoan parasites of the genus Leishmania cause a large spectrum of clinical manifestations known as Leishmaniases. These diseases are increasingly important public health problems in many countries both within and outside endemic regions. Thus, an accurate differential diagnosis is extremely relevant for understanding epidemiological profiles and for the administration of the best therapeutic protocol. Exploring the High Resolution Melting (HRM) dissociation profiles of two amplicons using real time polymerase chain reaction (real-time PCR) targeting heat-shock protein 70 coding gene (hsp70) revealed differences that allowed the discrimination of genomic DNA samples of eight Leishmania species found in the Americas, including Leishmania (Leishmania) infantum chagasi, L. (L.) amazonensis, L. (L.) mexicana, L. (Viannia) lainsoni, L. (V.) braziliensis, L. (V.) guyanensis, L. (V.) naiffi and L. (V.) shawi, and three species found in Eurasia and Africa, including L. (L.) tropica, L. (L.) donovani and L. (L.) major. In addition, we tested DNA samples obtained from standard promastigote culture, naturally infected phlebotomines, experimentally infected mice and clinical human samples to validate the proposed protocol. HRM analysis of hsp70 amplicons is a fast and robust strategy that allowed for the detection and discrimination of all Leishmania species responsible for the Leishmaniases in Brazil and Eurasia/Africa with high sensitivity and accuracy. This method could detect less than one parasite per reaction, even in the presence of host DNA.

High-resolution melting (HRM) for genotyping bovine ephemeral fever virus (BEFV).

PubMed

Erster, Oran; Stram, Rotem; Menasherow, Shopia; Rubistein-Giuni, Marisol; Sharir, Binyamin; Kchinich, Evgeni; Stram, Yehuda

2017-02-02

In recent years there have been several major outbreaks of bovine ephemeral disease in the Middle East, including Israel. Such occurrences raise the need for quick identification of the viruses responsible for the outbreaks, in order to rapidly identify the entry of viruses that do not belong to the Middle-East BEFV lineage. This challenge was met by the development of a high-resolution melt (HRM) assay. The assay is based on the viral G gene sequence and generation of an algorithm that calculates and evaluates the GC content of various fragments. The algorithm was designed to scan 50- to 200-base-long segments in a sliding-window manner, compare and rank them using an Order of Technique of Preference by Similarity to Ideal Solution (TOPSIS) the technique for order preference by similarity to ideal solution technique, according to the differences in GC content of homologous fragments. Two fragments were selected, based on a match to the analysis criteria, in terms of size and GC content. These fragments were successfully used in the analysis to differentiate between different virus lineages, thus facilitating assignment of the viruses' geographical origins. Moreover, the assay could be used for differentiating infected from vaccinated animales (DIVA). The new algorithm may therefore be useful for development of improved genotyping studies for other viruses and possibly other microorganisms. Copyright © 2016. Published by Elsevier B.V.

Channelized Melting Drives Thinning Under a Rapidly Melting Antarctic Ice Shelf

NASA Astrophysics Data System (ADS)

Gourmelen, Noel; Goldberg, Dan N.; Snow, Kate; Henley, Sian F.; Bingham, Robert G.; Kimura, Satoshi; Hogg, Anna E.; Shepherd, Andrew; Mouginot, Jeremie; Lenaerts, Jan T. M.; Ligtenberg, Stefan R. M.; van de Berg, Willem Jan

2017-10-01

Ice shelves play a vital role in regulating loss of grounded ice and in supplying freshwater to coastal seas. However, melt variability within ice shelves is poorly constrained and may be instrumental in driving ice shelf imbalance and collapse. High-resolution altimetry measurements from 2010 to 2016 show that Dotson Ice Shelf (DIS), West Antarctica, thins in response to basal melting focused along a single 5 km-wide and 60 km-long channel extending from the ice shelf's grounding zone to its calving front. If focused thinning continues at present rates, the channel will melt through, and the ice shelf collapse, within 40-50 years, almost two centuries before collapse is projected from the average thinning rate. Our findings provide evidence of basal melt-driven sub-ice shelf channel formation and its potential for accelerating the weakening of ice shelves.

Process monitoring of additive manufacturing by using optical tomography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zenzinger, Guenter, E-mail: guenter.zenzinger@mtu.de, E-mail: alexander.ladewig@mtu.de; Bamberg, Joachim, E-mail: guenter.zenzinger@mtu.de, E-mail: alexander.ladewig@mtu.de; Ladewig, Alexander, E-mail: guenter.zenzinger@mtu.de, E-mail: alexander.ladewig@mtu.de

2015-03-31

Parts fabricated by means of additive manufacturing are usually of complex shape and owing to the fabrication procedure by using selective laser melting (SLM), potential defects and inaccuracies are often very small in lateral size. Therefore, an adequate quality inspection of such parts is rather challenging, while non-destructive-techniques (NDT) are difficult to realize, but considerable efforts are necessary in order to ensure the quality of SLM-parts especially used for aerospace components. Thus, MTU Aero Engines is currently focusing on the development of an Online Process Control system which monitors and documents the complete welding process during the SLM fabrication procedure.more » A high-resolution camera system is used to obtain images, from which tomographic data for a 3dim analysis of SLM-parts are processed. From the analysis, structural irregularities and structural disorder resulting from any possible erroneous melting process become visible and may be allocated anywhere within the 3dim structure. Results of our optical tomography (OT) method as obtained on real defects are presented.« less

Identification of squid species by melting temperature shifts on fluorescence melting curve analysis (FMCA) using single dual-labeled probe

NASA Astrophysics Data System (ADS)

Koh, Eunjung; Song, Ha Jeong; Kwon, Na Young; Kim, Gi Won; Lee, Kwang Ho; Jo, Soyeon; Park, Sujin; Park, Jihyun; Park, Eun Kyeong; Hwang, Seung Yong

2017-06-01

Real time PCR is a standard method for identification of species. One of limitations of the qPCR is that there would be false-positive result due to mismatched hybridization between target sequence and probe depending on the annealing temperature in the PCR condition. As an alternative, fluorescence melting curve analysis (FMCA) could be applied for species identification. FMCA is based on a dual-labeled probe. Even with subtle difference of target sequence, there are visible melting temperature (Tm) shift. One of FMCA applications is distinguishing organisms distributed and consumed globally as popular food ingredients. Their prices are set by species or country of origin. However, counterfeiting or distributing them without any verification procedure are becoming social problems and threatening food safety. Besides distinguishing them in naked eye is very difficult and almost impossible in any processed form. Therefore, it is necessary to identify species in molecular level. In this research three species of squids which have 1-2 base pair differences each are selected as samples since they have the same issue. We designed a probe which perfectly matches with one species and the others mismatches 2 and 1 base pair respectively and labeled with fluorophore and quencher. In an experiment with a single probe, we successfully distinguished them by Tm shift depending on the difference of base pair. By combining FMCA and qPCR chip, smaller-scale assay with higher sensitivity and resolution could be possible, andc furthermore, enabling results analysis with smart phone would realize point-of-care testing (POCT).

Enantiomeric Resolution of [Plus or Minus] Mandelic Acid by (1R,2S)-(--)-Ephedrine: An Organic Chemistry Laboratory Experiment Illustrating Stereoisomerism

ERIC Educational Resources Information Center

Baar, Marsha R.; Cerrone-Szakal, Andrea L.

2005-01-01

The experiment involving enantiomeric resolution, as an illustration of chiral technology, is an excellent early organic chemistry lab experiment. The success of this enantiomeric resolution can be judged by melting point, demonstrated by [plus or minus]-mandelic acid-(1R,2S)-(--)-ephedrine system.

Probing the atomic structure of basaltic melts generated by partial melting of upper mantle peridotite (KLB-1): Insights from high-resolution solid-state NMR study

NASA Astrophysics Data System (ADS)

Park, S. Y.; Lee, S. K.

2015-12-01

Probing the structural disorder in multi-component silicate glasses and melts with varying composition is essential to reveal the change of macroscopic properties in natural silicate melts. While a number of NMR studies for the structure of multi-component silicate glasses and melts including basaltic and andesitic glasses have been reported (e.g., Park and Lee, Geochim. Cosmochim. Acta, 2012, 80, 125; Park and Lee, Geochim. Cosmochim. Acta, 2014, 26, 42), many challenges still remain. The composition of multi-component basaltic melts vary with temperature, pressure, and melt fraction (Kushiro, Annu. Rev. Earth Planet. Sci., 2001, 71, 107). Especially, the eutectic point (the composition of first melt) of nepheline-forsterite-quartz (the simplest model of basaltic melts) moves with pressure from silica-saturated to highly undersaturated and alkaline melts. The composition of basaltic melts generated by partial melting of upper mantle peridotite (KLB-1, the xenolith from Kilbourne Hole) also vary with pressure. In this study we report experimental results for the effects of composition on the atomic structure of Na2O-MgO-Al2O3-SiO2 (NMAS) glasses in nepheline (NaAlSiO4)-forsterite (Mg2SiO4)-quartz (SiO2) eutectic composition and basaltic glasses generated by partial melting of upper mantle peridotite (KLB-1) using high-resolution multi-nuclear solid-state NMR. The Al-27 3QMAS (triple quantum magic angle spinning) NMR spectra of NMAS glasses in nepheline-forsterite-quartz eutectic composition show only [4]Al. The Al-27 3QMAS NMR spectra of KLB-1 basaltic glasses show mostly [4]Al and a non-negligible fraction of [5]Al. The fraction of [5]Al, the degree of configurational disorder, increases from 0 at XMgO [MgO/(MgO+Al2O3)]=0.55 to ~3% at XMgO=0.79 in KLB-1 basaltic glasses while only [4]Al are observed in nepheline-forsterite-quartz eutectic composition. The current experimental results provide that the fraction of [5]Al abruptly increases by the effect of composition as well as pressure in natural silicate melts. The changes of the fraction of highly coordinated Al in multi-component silicate glasses and melts with composition can provide insight into the changes of macroscopic properties (e.g., entropy, viscosity, and diffusivity) with varying composition of melt.

High resolution melting analytical platform for rapid prenatal and postnatal diagnosis of β-thalassemia common among Southeast Asian population.

PubMed

Prajantasen, Thanet; Fucharoen, Supan; Fucharoen, Goonnapa

2015-02-20

High resolution melting (HRM) analysis is a powerful technology for scanning sequence alteration. We have applied this HRM assay to screen common β-thalassemia mutations found among Southeast Asian population. Known DNA samples with 8 common mutations were used in initial development of the methods including -28 A-G, codon 17 A-T, IVSI-1G-T, IVSI-5G-C, codon 26G-A (Hb E), codons 41/42 -TTCT, codons 71/72+A and IVSII-654 C-T. Further validation was done on 60 postnatal and 6 prenatal diagnoses of β-thalassemia. Each mutation has specific HRM profile which could be used in rapid screening. Apart from those with DNA deletions, the results of HRM assay matched 100% with those of routine diagnosis made by routine allele specific PCR. In addition, the HRM assay could initially recognize three unknown mutations including a hitherto un-described one in Thai population. The established HRM assay should prove useful for rapid and high throughput platform for screening and prenatal diagnosis of β-thalassemia common in the region. Copyright © 2014 Elsevier B.V. All rights reserved.

Water isotopic ratios from a continuously melted ice core sample

NASA Astrophysics Data System (ADS)

Gkinis, V.; Popp, T. J.; Blunier, T.; Bigler, M.; Schüpbach, S.; Johnsen, S. J.

2011-06-01

A new technique for on-line high resolution isotopic analysis of liquid water, tailored for ice core studies is presented. We build an interface between an Infra Red Cavity Ring Down Spectrometer (IR-CRDS) and a Continuous Flow Analysis (CFA) system. The system offers the possibility to perform simultaneuous water isotopic analysis of δ18O and δD on a continuous stream of liquid water as generated from a continuously melted ice rod. Injection of sub μl amounts of liquid water is achieved by pumping sample through a fused silica capillary and instantaneously vaporizing it with 100 % efficiency in a home made oven at a temperature of 170 °C. A calibration procedure allows for proper reporting of the data on the VSMOW scale. We apply the necessary corrections based on the assessed performance of the system regarding instrumental drifts and dependance on humidity levels. The melt rates are monitored in order to assign a depth scale to the measured isotopic profiles. Application of spectral methods yields the combined uncertainty of the system at below 0.1 ‰ and 0.5 ‰ for δ18O and δD, respectively. This performance is comparable to that achieved with mass spectrometry. Dispersion of the sample in the transfer lines limits the resolution of the technique. In this work we investigate and assess these dispersion effects. By using an optimal filtering method we show how the measured profiles can be corrected for the smoothing effects resulting from the sample dispersion. Considering the significant advantages the technique offers, i.e. simultaneuous measurement of δ18O and δD, potentially in combination with chemical components that are traditionally measured on CFA systems, notable reduction on analysis time and power consumption, we consider it as an alternative to traditional isotope ratio mass spectrometry with the possibility to be deployed for field ice core studies. We present data acquired in the framework of the NEEM deep ice core drilling project in Greenland, during the 2010 field season.

Water isotopic ratios from a continuously melted ice core sample

NASA Astrophysics Data System (ADS)

Gkinis, V.; Popp, T. J.; Blunier, T.; Bigler, M.; Schüpbach, S.; Kettner, E.; Johnsen, S. J.

2011-11-01

A new technique for on-line high resolution isotopic analysis of liquid water, tailored for ice core studies is presented. We built an interface between a Wavelength Scanned Cavity Ring Down Spectrometer (WS-CRDS) purchased from Picarro Inc. and a Continuous Flow Analysis (CFA) system. The system offers the possibility to perform simultaneuous water isotopic analysis of δ18O and δD on a continuous stream of liquid water as generated from a continuously melted ice rod. Injection of sub μl amounts of liquid water is achieved by pumping sample through a fused silica capillary and instantaneously vaporizing it with 100% efficiency in a~home made oven at a temperature of 170 °C. A calibration procedure allows for proper reporting of the data on the VSMOW-SLAP scale. We apply the necessary corrections based on the assessed performance of the system regarding instrumental drifts and dependance on the water concentration in the optical cavity. The melt rates are monitored in order to assign a depth scale to the measured isotopic profiles. Application of spectral methods yields the combined uncertainty of the system at below 0.1‰ and 0.5‰ for δ18O and δD, respectively. This performance is comparable to that achieved with mass spectrometry. Dispersion of the sample in the transfer lines limits the temporal resolution of the technique. In this work we investigate and assess these dispersion effects. By using an optimal filtering method we show how the measured profiles can be corrected for the smoothing effects resulting from the sample dispersion. Considering the significant advantages the technique offers, i.e. simultaneuous measurement of δ18O and δD, potentially in combination with chemical components that are traditionally measured on CFA systems, notable reduction on analysis time and power consumption, we consider it as an alternative to traditional isotope ratio mass spectrometry with the possibility to be deployed for field ice core studies. We present data acquired in the field during the 2010 season as part of the NEEM deep ice core drilling project in North Greenland.

Comparison of snow melt properties across multiple spatial scales and landscape units in interior sub-Arctic boreal Alaskan watersheds

NASA Astrophysics Data System (ADS)

Bennett, K. E.; Cherry, J. E.; Hiemstra, C. A.; Bolton, W. R.

2013-12-01

Interior sub-Arctic Alaskan snow cover is rapidly changing and requires further study for correct parameterization in physically based models. This project undertook field studies during the 2013 snow melt season to capture snow depth, snow temperature profiles, and snow cover extent to compare with observations from the Moderate Resolution Imaging Spectroradiometer (MODIS) sensor at four different sites underlain by discontinuous permafrost. The 2013 melt season, which turned out to be the latest snow melt period on record, was monitored using manual field measurements (SWE, snow depth data collection), iButtons to record temperature of the snow pack, GoPro cameras to capture time lapse of the snow melt, and low level orthoimagery collected at ~1500 m using a Navion L17a plane mounted with a Nikon D3s camera. Sites were selected across a range of landscape conditions, including a north facing black spruce hill slope, a south facing birch forest, an open tundra site, and a high alpine meadow. Initial results from the adjacent north and south facing sites indicate a highly sensitive system where snow cover melts over just a few days, illustrating the importance of high resolution temporal data capture at these locations. Field observations, iButtons and GoPro cameras show that the MODIS data captures the melt conditions at the south and the north site with accuracy (2.5% and 6.5% snow cover fraction present on date of melt, respectively), but MODIS data for the north site is less variable around the melt period, owing to open conditions and sparse tree cover. However, due to the rapid melt rate trajectory, shifting the melt date estimate by a day results in a doubling of the snow cover fraction estimate observed by MODIS. This information can assist in approximating uncertainty associated with remote sensing data that is being used to populate hydrologic and snow models (the Sacramento Soil Moisture Accounting model, coupled with SNOW-17, and the Variable Infiltration Capacity hydrologic model) and provide greater understanding of error and resultant model sensitivities associated with regional observations of snow cover across the sub-Arctic boreal landscape.

Using Laboratory Experiments to Improve Ice-Ocean Parameterizations

NASA Astrophysics Data System (ADS)

McConnochie, C. D.; Kerr, R. C.

2017-12-01

Numerical models of ice-ocean interactions are typically unable to resolve the transport of heat and salt to the ice face. Instead, models rely upon parameterizations that have not been sufficiently validated by observations. Recent laboratory experiments of ice-saltwater interactions allow us to test the standard parameterization of heat and salt transport to ice faces - the three-equation model. The three-equation model predicts that the melt rate is proportional to the fluid velocity while the experimental results typically show that the melt rate is independent of the fluid velocity. By considering an analysis of the boundary layer that forms next to a melting ice face, we suggest a resolution to this disagreement. We show that the three-equation model makes the implicit assumption that the thickness of the diffusive sublayer next to the ice is set by a shear instability. However, at low flow velocities, the sublayer is instead set by a convective instability. This distinction leads to a threshold velocity of approximately 4 cm/s at geophysically relevant conditions, above which the form of the parameterization should be valid. In contrast, at flow speeds below 4 cm/s, the three-equation model will underestimate the melt rate. By incorporating such a minimum velocity into the three-equation model, predictions made by numerical simulations could be easily improved.

Molecular differentiation of three canine and feline hookworms in South China through HRM analysis.

PubMed

Wang, M W; Yan, X X; Hang, J X; Shi, X L; Fu, Y Q; Zhang, P; Yang, F; Pan, W D; Li, G Q

2018-02-05

To investigate the prevalence of canine and feline hookworms in South China, and to assess the risk of zoonotic hookworms to humans, one pair of primers (HRM-F/HRM-R) was designed to establish a high-resolution melting (HRM) method based on internal transcribed spacer 1 (ITS-1) rDNA for the detection of Ancylostoma ceylanicum, A. caninum and A. tubaeforme infection. The results showed that the HRM for the three hookworms produced different melting-curve profiles, where melting temperature (T m) values were 84.50°C for A. ceylanicum, 82.25°C for A. caninum and 81.73°C for A. tubaeforme, respectively. The reproducibility of intra- and inter-assay melting curves was almost perfect. The lowest concentration detected was about 5.69 ×10-4 g/μl. The HRM detection results from 18 canine and feline hookworm samples were in complete accordance with their sequencing results. The HRM method was more sensitive than the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique in the detection of 98 clinical samples. It is concluded that the HRM method can differentiate between A. ceylanicum, A. caninum, A. tubaeforme and their mixed infections, which may provide important technical support for the zoonotic risk assessment and molecular epidemiological survey of canine and feline hookworms.

Measuring the Surface Temperature of the Cryosphere using Remote Sensing

NASA Technical Reports Server (NTRS)

Hall, Dorothy K.

2012-01-01

A general description of the remote sensing of cryosphere surface temperatures from satellites will be provided. This will give historical information on surface-temperature measurements from space. There will also be a detailed description of measuring the surface temperature of the Greenland Ice Sheet using Moderate-Resolution Imaging Spectroradiometer (MODIS) data which will be the focus of the presentation. Enhanced melting of the Greenland Ice Sheet has been documented in recent literature along with surface-temperature increases measured using infrared satellite data since 1981. Using a recently-developed climate data record, trends in the clear-sky ice-surface temperature (IST) of the Greenland Ice Sheet have been studied using the MODIS IST product. Daily and monthly MODIS ISTs of the Greenland Ice Sheet beginning on 1 March 2000 and continuing through 31 December 2010 are now freely available to download at 6.25-km spatial resolution on a polar stereographic grid. Maps showing the maximum extent of melt for the entire ice sheet and for the six major drainage basins have been developed from the MODIS IST dataset. Twelve-year trends of the duration of the melt season on the ice sheet vary in different drainage basins with some basins melting progressively earlier over the course of the study period. Some (but not all) of the basins also show a progressively-longer duration of melt. The consistency of this IST record, with temperature and melt records from other sources will be discussed.

Multiscale radar mapping of surface melt over mountain glaciers in High Mountain Asia

NASA Astrophysics Data System (ADS)

Steiner, N.; McDonald, K. C.

2017-12-01

Glacier melt dominates input for many hydrologic systems in the Himalayan Hindukush region that feed rivers that are critical for downstream ecosystems and hydropower generation in this highly populated area. Deviation in seasonal surface melt timing and duration with a changing climate has the potential to affect up to a billion people on the Indian Subcontinent. Satellite-borne microwave remote sensing has unique capabilities that allow monitoring of numerous landscape processes associated with snowmelt and freeze/thaw state, without many of the limitations in optical-infrared sensors such as solar illumination or atmospheric conditions. The onset of regional freeze/thaw and surface melting transitions determine important surface hydrologic variables like river discharge. Theses regional events are abrupt therefore difficult to observe with low-frequency observation sensors. Recently launched synthetic aperture radar (SAR) onboard the Sentinel-1 A and B satellites from the European Space Agency (ESA) provide wide-swath and high spatial resolution (50-100 m) C-Band SAR observations with observations frequencies not previously available, on the order of 8 to 16 days. The Sentinel SARs provide unique opportunity to study freeze/thaw and mountain glacier melt dynamics at process level scales, spatial and temporal. The melt process of individual glaciers, being fully resolved by imaging radar, will inform on the radiometric scattering physics associated with surface hydrology during the transition from melted to thawed state and during refreeze. Backscatter observations, along with structural information about the surface will be compared with complimentary coarse spatial resolution C-Band radar scatterometers, Advanced Scatterometer (ASCAT Met Op A+B), to understand the sub-pixel contribution of surface melting and freeze/thaw signals. This information will inform on longer-scale records of backscatter from ASCAT, 2006-2017. We present a comparison of polarimetric C-Band melt signals contained in the multi-scale backscatter and present a coincident freeze/thaw and snowmelt records from ASCAT and Sentinel-1 for the Gandaki basin, Nepal.

CtGEM typing: Discrimination of Chlamydia trachomatis ocular and urogenital strains and major evolutionary lineages by high resolution melting analysis of two amplified DNA fragments.

PubMed

Giffard, Philip M; Andersson, Patiyan; Wilson, Judith; Buckley, Cameron; Lilliebridge, Rachael; Harris, Tegan M; Kleinecke, Mariana; O'Grady, Kerry-Ann F; Huston, Wilhelmina M; Lambert, Stephen B; Whiley, David M; Holt, Deborah C

2018-01-01

Chlamydia trachomatis infects the urogenital tract (UGT) and eyes. Anatomical tropism is correlated with variation in the major outer membrane protein encoded by ompA. Strains possessing the ocular ompA variants A, B, Ba and C are typically found within the phylogenetically coherent "classical ocular lineage". However, variants B, Ba and C have also been found within three distinct strains in Australia, all associated with ocular disease in children and outside the classical ocular lineage. CtGEM genotyping is a method for detecting and discriminating ocular strains and also the major phylogenetic lineages. The rationale was facilitation of surveillance to inform responses to C. trachomatis detection in UGT specimens from young children. CtGEM typing is based on high resolution melting analysis (HRMA) of two PCR amplified fragments with high combinatorial resolving power, as defined by computerised comparison of 65 whole genomes. One fragment is from the hypothetical gene defined by Jali-1891 in the C. trachomatis B_Jali20 genome, while the other is from ompA. Twenty combinatorial CtGEM types have been shown to exist, and these encompass unique genotypes for all known ocular strains, and also delineate the TI and T2 major phylogenetic lineages, identify LGV strains and provide additional resolution beyond this. CtGEM typing and Sanger sequencing were compared with 42 C. trachomatis positive clinical specimens, and there were no disjunctions. CtGEM typing is a highly efficient method designed and tested using large scale comparative genomics. It divides C. trachomatis into clinically and biologically meaningful groups, and may have broad application in surveillance.

Methylation-Sensitive High Resolution Melting (MS-HRM).

PubMed

Hussmann, Dianna; Hansen, Lise Lotte

2018-01-01

Methylation-Sensitive High Resolution Melting (MS-HRM) is an in-tube, PCR-based method to detect methylation levels at specific loci of interest. A unique primer design facilitates a high sensitivity of the assays enabling detection of down to 0.1-1% methylated alleles in an unmethylated background.Primers for MS-HRM assays are designed to be complementary to the methylated allele, and a specific annealing temperature enables these primers to anneal both to the methylated and the unmethylated alleles thereby increasing the sensitivity of the assays. Bisulfite treatment of the DNA prior to performing MS-HRM ensures a different base composition between methylated and unmethylated DNA, which is used to separate the resulting amplicons by high resolution melting.The high sensitivity of MS-HRM has proven useful for detecting cancer biomarkers in a noninvasive manner in urine from bladder cancer patients, in stool from colorectal cancer patients, and in buccal mucosa from breast cancer patients. MS-HRM is a fast method to diagnose imprinted diseases and to clinically validate results from whole-epigenome studies. The ability to detect few copies of methylated DNA makes MS-HRM a key player in the quest for establishing links between environmental exposure, epigenetic changes, and disease.

A Climate-Data Record (CDR) of the "Clear-Sky" Surface Temperature of the Greenland Ice Sheet

NASA Technical Reports Server (NTRS)

Hall, Dorothy K.; Comiso, Josefino C.; DiGirolamo, Nocolo E.; Shuman, Christopher A.

2011-01-01

We have developed a climate-data record (CDR) of "clear-sky" ice-surface temperature (IST) of the Greenland Ice Sheet using Moderate-Resolution Imaging Spectroradiometer (MODIS) data. The CDR provides daily and monthly-mean IST from March 2000 through December 2010 on a polar stereographic projection at a resolution of 6.25 km. The CDR is amenable to extension into the future using Visible/Infrared Imager Radiometer Suite (VIIRS) data. Regional "clear-sky" surface temperature increases since the early 1980s in the Arctic, measured using Advanced Very High Resolution Radiometer (AVHRR) infrared data, range from 0.57 +/- 0.02 to 0.72 +/- 0.1 c per decade. Arctic warming has important implications for ice-sheet mass balance because much of the periphery of the Greenland Ice Sheet is already near O C during the melt season, and is thus vulnerable to rapid melting if temperatures continue to increase. An increase in melting of the ice sheet would accelerate sea-level rise, an issue affecting potentially billions of people worldwide. The IST CDR will provide a convenient data set for modelers and for climatologists to track changes of the surface temperature of the ice sheet as a whole and of the individual drainage basins on the ice sheet. The daily and monthly maps will provide information on surface melt as well as "clear-sky" temperature. The CDR will be further validated by comparing results with automatic-weather station data and with satellite-derived surface-temperature products.

A multi-component evaporation model for beam melting processes

NASA Astrophysics Data System (ADS)

Klassen, Alexander; Forster, Vera E.; Körner, Carolin

2017-02-01

In additive manufacturing using laser or electron beam melting technologies, evaporation losses and changes in chemical composition are known issues when processing alloys with volatile elements. In this paper, a recently described numerical model based on a two-dimensional free surface lattice Boltzmann method is further developed to incorporate the effects of multi-component evaporation. The model takes into account the local melt pool composition during heating and fusion of metal powder. For validation, the titanium alloy Ti-6Al-4V is melted by selective electron beam melting and analysed using mass loss measurements and high-resolution microprobe imaging. Numerically determined evaporation losses and spatial distributions of aluminium compare well with experimental data. Predictions of the melt pool formation in bulk samples provide insight into the competition between the loss of volatile alloying elements from the irradiated surface and their advective redistribution within the molten region.

Submarine melt rates under Greenland's ice tongues

NASA Astrophysics Data System (ADS)

Wilson, Nat; Straneo, Fiametta; Heimbach, Patrick; Cenedese, Claudia

2017-04-01

The few remaining ice tongues (ice-shelf like extensions) of Greenland's glaciers are undergoing rapid changes with potential implications for the stability of the ice sheet. Submarine melting is recognized as a major contributor to mass loss, yet the magnitude and spatial distribution of melt are poorly known or understood. Here, we use high resolution satellite imagery to infer the magnitude and spatial variability of melt rates under Greenland's largest remaining ice tongues: Ryder Glacier, Petermann Glacier and Nioghalvfjerdsbræ (79 North Glacier). We find that submarine plus aerial melt approximately balance the ice flux from the grounded ice sheet for the first two while at Nioghalvfjerdsbræ the total melt flux exceeds the inflow of ice indicating thinning of the ice tongue. We also show that melt rates under the ice tongues vary considerably, exceeding 60 m yr-1 near the grounding zone and decaying rapidly downstream. Channels, likely originating from upstream subglacial channels, give rise to large melt variations across the ice tongues. Using derived melt rates, we test simplified melt parameterizations appropriate for ice sheet models and find the best agreement with those that incorporate ice tongue geometry in the form of depth and slope.

Greenland iceberg melt variability from high-resolution satellite observations

NASA Astrophysics Data System (ADS)

Enderlin, Ellyn M.; Carrigan, Caroline J.; Kochtitzky, William H.; Cuadros, Alexandra; Moon, Twila; Hamilton, Gordon S.

2018-02-01

Iceberg discharge from the Greenland Ice Sheet accounts for up to half of the freshwater flux to surrounding fjords and ocean basins, yet the spatial distribution of iceberg meltwater fluxes is poorly understood. One of the primary limitations for mapping iceberg meltwater fluxes, and changes over time, is the dearth of iceberg submarine melt rate estimates. Here we use a remote sensing approach to estimate submarine melt rates during 2011-2016 for 637 icebergs discharged from seven marine-terminating glaciers fringing the Greenland Ice Sheet. We find that spatial variations in iceberg melt rates generally follow expected patterns based on hydrographic observations, including a decrease in melt rate with latitude and an increase in melt rate with iceberg draft. However, we find no longitudinal variations in melt rates within individual fjords. We do not resolve coherent seasonal to interannual patterns in melt rates across all study sites, though we attribute a 4-fold melt rate increase from March to April 2011 near Jakobshavn Isbræ to fjord circulation changes induced by the seasonal onset of iceberg calving. Overall, our results suggest that remotely sensed iceberg melt rates can be used to characterize spatial and temporal variations in oceanic forcing near often inaccessible marine-terminating glaciers.

Sea-Ice Feature Mapping using JERS-1 Imagery

NASA Technical Reports Server (NTRS)

Maslanik, James; Heinrichs, John

1994-01-01

JERS-1 SAR and OPS imagery are examined in combination with other data sets to investigate the utility of the JERS-1 sensors for mapping fine-scale sea ice conditions. Combining ERS-1 C band and JERS-1 L band SAR aids in discriminating multiyear and first-year ice. Analysis of OPS imagery for a field site in the Canadian Archipelago highlights the advantages of OPS's high spatial and spectral resolution for mapping ice structure, melt pond distribution, and surface albedo.

Methods to Increase the Sensitivity of High Resolution Melting Single Nucleotide Polymorphism Genotyping in Malaria.

PubMed

Daniels, Rachel; Hamilton, Elizabeth J; Durfee, Katelyn; Ndiaye, Daouda; Wirth, Dyann F; Hartl, Daniel L; Volkman, Sarah K

2015-11-10

Despite decades of eradication efforts, malaria remains a global burden. Recent renewed interest in regional elimination and global eradication has been accompanied by increased genomic information about Plasmodium parasite species responsible for malaria, including characteristics of geographical populations as well as variations associated with reduced susceptibility to anti-malarial drugs. One common genetic variation, single-nucleotide polymorphisms (SNPs), offers attractive targets for parasite genotyping. These markers are useful not only for tracking drug resistance markers but also for tracking parasite populations using markers not under drug or other selective pressures. SNP genotyping methods offer the ability to track drug resistance as well as to fingerprint individual parasites for population surveillance, particularly in response to malaria control efforts in regions nearing elimination status. While informative SNPs have been identified that are agnostic to specific genotyping technologies, high-resolution melting (HRM) analysis is particularly suited to field-based studies. Compared to standard fluorescent-probe based methods that require individual SNPs in a single labeled probe and offer at best 10% sensitivity to detect SNPs in samples that contain multiple genomes (polygenomic), HRM offers 2-5% sensitivity. Modifications to HRM, such as blocked probes and asymmetric primer concentrations as well as optimization of amplification annealing temperatures to bias PCR towards amplification of the minor allele, further increase the sensitivity of HRM. While the sensitivity improvement depends on the specific assay, we have increased detection sensitivities to less than 1% of the minor allele. In regions approaching malaria eradication, early detection of emerging or imported drug resistance is essential for prompt response. Similarly, the ability to detect polygenomic infections and differentiate imported parasite types from cryptic local reservoirs can inform control programs. This manuscript describes modifications to high resolution melting technology that further increase its sensitivity to identify polygenomic infections in patient samples.

Channelized melting drives thinning under Dotson ice shelf, Western Antarctic Ice Sheet

NASA Astrophysics Data System (ADS)

Gourmelen, N.; Goldberg, D.; Snow, K.; Henley, S. F.; Bingham, R. G.; Kimura, S.; Hogg, A.; Shepherd, A.; Mouginot, J.; Lenaerts, J.; Ligtenberg, S.; Van De Berg, W. J.

2017-12-01

The majority of meteoric ice that forms in West Antarctica leaves the ice sheet through floating ice shelves, many of which have been thinning substantially over the last 25 years. A significant proportion of ice-shelf thinning has been driven by submarine melting facilitated by increased access of relatively warm (>0.6oC) modified Circumpolar Deep Water to sub-shelf cavities. Ice shelves play a significant role in stabilising the ice sheet from runaway retreat and regulating its contribution to sea level change. Ice-shelf melting has also been implicated in sustaining high primary productivity in Antarctica's coastal seas. However, these processes vary regionally and are not fully understood. Under some ice shelves, concentrated melting leads to the formation of inverted channels. These channels guide buoyant melt-laden outflow, which can lead to localised melting of the sea ice cover. The channels may also potentially lead to heightened crevassing, which in turn affects ice-shelf stability. Meanwhile, numerical studies suggest that buttressing loss is sensitive to the location of ice removal within an ice-shelf. Thus it is important that we observe spatial patterns, as well as magnitudes, of ice-shelf thinning, in order to improve understanding of the ocean drivers of thinning and of their impacts on ice-shelf stability. Here we show from high-resolution altimetry measurements acquired between 2010 to 2016 that Dotson Ice Shelf, West Antarctica, thins in response to basal melting focussed along a single 5 km-wide and 60 km-long channel extending from the ice shelf's grounding zone to its calving front. The coupled effect of geostrophic circulation and ice-shelf topography leads to the observed concentration of basal melting. Analysis of previous datasets suggests that this process has been ongoing for at least the last 25 years. If focused thinning continues at present rates, the channel would melt through within 40-50 years, almost two centuries before it is projected from the average thinning rate. Our findings provide evidence of basal melt-driven sub-ice shelf channel formation and its potential for accelerating the weakening of ice shelves.

A Melting Layer Model for Passive/Active Microwave Remote Sensing Applications. Part 2; Simulation of TRMM Observations

NASA Technical Reports Server (NTRS)

Olson, William S.; Bauer, Peter; Kummerow, Christian D.; Tao, Wei-Kuo

2000-01-01

The one-dimensional, steady-state melting layer model developed in Part I of this study is used to calculate both the microphysical and radiative properties of melting precipitation, based upon the computed concentrations of snow and graupel just above the freezing level at applicable horizontal gridpoints of 3-dimensional cloud resolving model simulations. The modified 3-dimensional distributions of precipitation properties serve as input to radiative transfer calculations of upwelling radiances and radar extinction/reflectivities at the TRMM Microwave Imager (TMI) and Precipitation Radar (PR) frequencies, respectively. At the resolution of the cloud resolving model grids (approx. 1 km), upwelling radiances generally increase if mixed-phase precipitation is included in the model atmosphere. The magnitude of the increase depends upon the optical thickness of the cloud and precipitation, as well as the scattering characteristics of ice-phase precipitation aloft. Over the set of cloud resolving model simulations utilized in this study, maximum radiance increases of 43, 28, 18, and 10 K are simulated at 10.65, 19.35 GHz, 37.0, and 85.5 GHz, respectively. The impact of melting on TMI-measured radiances is determined not only by the physics of the melting particles but also by the horizontal extent of the melting precipitation, since the lower-frequency channels have footprints that extend over 10''s of kilometers. At TMI resolution, the maximum radiance increases are 16, 15, 12, and 9 K at the same frequencies. Simulated PR extinction and reflectivities in the melting layer can increase dramatically if mixed-phase precipitation is included, a result consistent with previous studies. Maximum increases of 0.46 (-2 dB) in extinction optical depth and 5 dBZ in reflectivity are simulated based upon the set of cloud resolving model simulations.

Structural Fluctuations and Thermophysical Properties of Molten II-VI Compounds

NASA Technical Reports Server (NTRS)

Su, Ching-Hua; Zhu, S.; Li, C.; Scripa, R.; Lehoczky, S. L.; Kim, Y. M.; Baird, J. K.; Lin, B.; Ban, H.; Benmore, Chris;

Detection of monoclonal immunoglobulin heavy chain gene rearrangement (FR3) in Thai malignant lymphoma by High Resolution Melting curve analysis.

PubMed

Kummalue, Tanawan; Chuphrom, Anchalee; Sukpanichanant, Sanya; Pongpruttipan, Tawatchai; Sukpanichanant, Sathien

2010-05-19

Malignant lymphoma, especially non-Hodgkin lymphoma, is one of the most common hematologic malignancies in Thailand. The diagnosis of malignant lymphoma is often problematic, especially in early stages of the disease. Detection of antigen receptor gene rearrangement including T cell receptor (TCR) and immunoglobulin heavy chain (IgH) by polymerase chain reaction followed by heteroduplex has currently become standard whereas fluorescent fragment analysis (GeneScan) has been used for confirmation test. In this study, three techniques had been compared: thermocycler polymerase chain reaction (PCR) followed by heteroduplex and polyacrylamide gel electrophoresis, GeneScan analysis, and real time PCR with High Resolution Melting curve analysis (HRM). The comparison was carried out with DNA extracted from paraffin embedded tissues diagnosed as B- cell non-Hodgkin lymphoma. Specific PCR primers sequences for IgH gene variable region 3, including fluorescence labeled IgH primers were used and results were compared with HRM. In conclusion, the detection IgH gene rearrangement by HRM in the LightCycler System showed potential for distinguishing monoclonality from polyclonality in B-cell non-Hodgkin lymphoma. Malignant lymphoma, especially non-Hodgkin lymphoma, is one of the most common hematologic malignancies in Thailand. The incidence rate as reported by Ministry of Public Health is 3.1 per 100,000 population in female whereas the rate in male is 4.5 per 100,000 population 1. At Siriraj Hospital, the new cases diagnosed as malignant lymphoma were 214.6 cases/year 2. The diagnosis of malignant lymphoma is often problematic, especially in early stages of the disease. Therefore, detection of antigen receptor gene rearrangement including T cell receptor (TCR) and immunoglobulin heavy chain (IgH) by polymerase chain reaction (PCR) assay has recently become a standard laboratory test for discrimination of reactive from malignant clonal lymphoproliferation 34. Analyzing DNA extracted from formalin-fixed, paraffin-embedded tissues by multiplex PCR techniques is more rapid, accurate and highly sensitive. Measuring the size of the amplicon from PCR analysis could be used to diagnose malignant lymphoma with monoclonal pattern showing specific and distinct bands detected on acrylamide gel electrophoresis. However, this technique has some limitations and some patients might require a further confirmation test such as GeneScan or fragment analysis 56.GeneScan technique or fragment analysis reflects size and peak of DNA by using capillary gel electrophoresis. This technique is highly sensitive and can detect 0.5-1% of clonal lymphoid cells. It measures the amplicons by using various fluorescently labeled primers at forward or reverse sides and a specific size standard. Using a Genetic Analyzer machine and GeneMapper software (Applied Bioscience, USA), the monoclonal pattern revealed one single, sharp and high peak at the specific size corresponding to acrylamide gel pattern, whereas the polyclonal pattern showed multiple and small peak condensed at the same size standard. This technique is the most sensitive and accurate technique; however, it usually requires high technical experience and is also of high cost 7. Therefore, rapid and more cost effective technique are being sought.LightCycler PCR performs the diagnostic detection of amplicon via melting curve analysis within 2 hours with the use of a specific dye 89. This dye consists of two types: one known as SYBR-Green I which is non specific and the other named as High Resolution Melting analysis (HRM) which is highly sensitive, more accurate and stable. Several reports demonstrated that this new instrument combined with DNA intercalating dyes can be used to discriminate sequence changes in PCR amplicon without manual handling of PCR product 1011. Therefore, current investigations using melting curve analysis are being developed 1213.In this study, three different techniques were compared to evaluate the suitability of LightCycler PCR with HRM as the clonal diagnostic tool for IgH gene rearrangement in B-cell non-Hogdkin lymphoma, i.e. thermocycler PCR followed by heteroduplex analysis and PAGE, GeneScan analysis and LightCycler PCR with HRM.

NHM-SMAP: spatially and temporally high-resolution nonhydrostatic atmospheric model coupled with detailed snow process model for Greenland Ice Sheet

NASA Astrophysics Data System (ADS)

Niwano, Masashi; Aoki, Teruo; Hashimoto, Akihiro; Matoba, Sumito; Yamaguchi, Satoru; Tanikawa, Tomonori; Fujita, Koji; Tsushima, Akane; Iizuka, Yoshinori; Shimada, Rigen; Hori, Masahiro

2018-02-01

To improve surface mass balance (SMB) estimates for the Greenland Ice Sheet (GrIS), we developed a 5 km resolution regional climate model combining the Japan Meteorological Agency Non-Hydrostatic atmospheric Model and the Snow Metamorphism and Albedo Process model (NHM-SMAP) with an output interval of 1 h, forced by the Japanese 55-year reanalysis (JRA-55). We used in situ data to evaluate NHM-SMAP in the GrIS during the 2011-2014 mass balance years. We investigated two options for the lower boundary conditions of the atmosphere: an offline configuration using snow, firn, and ice albedo, surface temperature data from JRA-55, and an online configuration using values from SMAP. The online configuration improved model performance in simulating 2 m air temperature, suggesting that the surface analysis provided by JRA-55 is inadequate for the GrIS and that SMAP results can better simulate physical conditions of snow/firn/ice. It also reproduced the measured features of the GrIS climate, diurnal variations, and even a strong mesoscale wind event. In particular, it successfully reproduced the temporal evolution of the GrIS surface melt area extent as well as the record melt event around 12 July 2012, at which time the simulated melt area extent reached 92.4 %. Sensitivity tests showed that the choice of calculation schemes for vertical water movement in snow and firn has an effect as great as 200 Gt year-1 in the GrIS-wide accumulated SMB estimates; a scheme based on the Richards equation provided the best performance.

High-resolution modeling of coastal freshwater discharge and glacier mass balance in the Gulf of Alaska watershed

NASA Astrophysics Data System (ADS)

Beamer, J. P.; Hill, D. F.; Arendt, A.; Liston, G. E.

2016-05-01

A comprehensive study of the Gulf of Alaska (GOA) drainage basin was carried out to improve understanding of the coastal freshwater discharge (FWD) and glacier volume loss (GVL). Hydrologic processes during the period 1980-2014 were modeled using a suite of physically based, spatially distributed weather, energy-balance snow/ice melt, soil water balance, and runoff routing models at a high-resolution (1 km horizontal grid; daily time step). Meteorological forcing was provided by the North American Regional Reanalysis (NARR), Modern Era Retrospective Analysis for Research and Applications (MERRA), and Climate Forecast System Reanalysis (CFSR) data sets. Streamflow and glacier mass balance modeled using MERRA and CFSR compared well with observations in four watersheds used for calibration in the study domain. However, only CFSR produced regional seasonal and long-term trends in water balance that compared favorably with independent Gravity Recovery and Climate Experiment (GRACE) and airborne altimetry data. Mean annual runoff using CFSR was 760 km3 yr-1, 8% of which was derived from the long-term removal of stored water from glaciers (glacier volume loss). The annual runoff from CFSR was partitioned into 63% snowmelt, 17% glacier ice melt, and 20% rainfall. Glacier runoff, taken as the sum of rainfall, snow, and ice melt occurring each season on glacier surfaces, was 38% of the total seasonal runoff, with the remaining runoff sourced from nonglacier surfaces. Our simulations suggests that existing GRACE solutions, previously reported to represent glacier mass balance alone, are actually measuring the full water budget of land and ice surfaces.

Mutation Analysis of SLC26A4 for Pendred Syndrome and Nonsyndromic Hearing Loss by High-Resolution Melting

PubMed Central

Chen, Neng; Tranebjærg, Lisbeth; Rendtorff, Nanna Dahl; Schrijver, Iris

2011-01-01

Pendred syndrome and DFNB4 (autosomal recessive nonsyndromic congenital deafness, locus 4) are associated with autosomal recessive congenital sensorineural hearing loss and mutations in the SLC26A4 gene. Extensive allelic heterogeneity, however, necessitates analysis of all exons and splice sites to identify mutations for individual patients. Although Sanger sequencing is the gold standard for mutation detection, screening methods supplemented with targeted sequencing can provide a cost-effective alternative. One such method, denaturing high-performance liquid chromatography, was developed for clinical mutation detection in SLC26A4. However, this method inherently cannot distinguish homozygous changes from wild-type sequences. High-resolution melting (HRM), on the other hand, can detect heterozygous and homozygous changes cost-effectively, without any post-PCR modifications. We developed a closed-tube HRM mutation detection method specific for SLC26A4 that can be used in the clinical diagnostic setting. Twenty-eight primer pairs were designed to cover all 21 SLC26A4 exons and splice junction sequences. Using the resulting amplicons, initial HRM analysis detected all 45 variants previously identified by sequencing. Subsequently, a 384-well plate format was designed for up to three patient samples per run. Blinded HRM testing on these plates of patient samples collected over 1 year in a clinical diagnostic laboratory accurately detected all variants identified by sequencing. In conclusion, HRM with targeted sequencing is a reliable, simple, and cost-effective method for SLC26A4 mutation screening and detection. PMID:21704276

IGLOO: an Intermediate Complexity Framework to Simulate Greenland Ice-Ocean Interactions

NASA Astrophysics Data System (ADS)

Perrette, M.; Calov, R.; Beckmann, J.; Alexander, D.; Beyer, S.; Ganopolski, A.

2017-12-01

The Greenland ice-sheet is a major contributor to current and future sea level rise associated to climate warming. It is widely believed that over a century time scale, surface melting is the main driver of Greenland ice volume change, in contrast to melting by the ocean. It is due to relatively warmer air and less ice area exposed to melting by ocean water compared to Antarctica, its southern, larger twin. Yet most modeling studies do not have adequate grid resolution to represent fine-scale outlet glaciers and fjords at the margin of the ice sheet, where ice-ocean interaction occurs, and must use rather crude parameterizations to represent this process. Additionally, the ice-sheet area grounded below sea level has been reassessed upwards in the most recent estimates of bedrock elevation under the Greenland ice sheet, revealing a larger potential for marine-mediated melting than previously thought. In this work, we develop an original approach to estimate potential Greenland ice sheet contribution to sea level rise from ocean melting, in an intermediate complexity framework, IGLOO. We use a medium-resolution (5km) ice-sheet model coupled interactively to a number of 1-D flowline models for the individual outlet glaciers. We propose a semi-objective methodology to derive 1-D glacier geometries from 2-D Greenland datasets, as well as preliminary results of coupled ice-sheet-glaciers simulations with IGLOO.

Evaluation of Surface and Near-Surface Melt Characteristics on the Greenland Ice Sheet using MODIS and QuikSCAT Data

NASA Technical Reports Server (NTRS)

Hall, Dorothy K.; Nghiem, Son V.; Schaaf, Crystal B.; DiGirolamo, Nicolo E.

2009-01-01

The Greenland Ice Sheet has been the focus of much attention recently because of increasing melt in response to regional climate warming. To improve our ability to measure surface melt, we use remote-sensing data products to study surface and near-surface melt characteristics of the Greenland Ice Sheet for the 2007 melt season when record melt extent and runoff occurred. Moderate Resolution Imaging Spectroradiometer (MODIS) daily land-surface temperature (LST), MODIS daily snow albedo, and a special diurnal melt product derived from QuikSCAT (QS) scatterometer data, are all effective in measuring the evolution of melt on the ice sheet. These daily products, produced from different parts of the electromagnetic spectrum, are sensitive to different geophysical features, though QS- and MODIS-derived melt generally show excellent correspondence when surface melt is present on the ice sheet. Values derived from the daily MODIS snow albedo product drop in response to melt, and change with apparent grain-size changes. For the 2007 melt season, the QS and MODIS LST products detect 862,769 square kilometers and 766,184 square kilometers of melt, respectively. The QS product detects about 11% greater melt extent than is detected by the MODIS LST product probably because QS is more sensitive to surface melt, and can detect subsurface melt. The consistency of the response of the different products demonstrates unequivocally that physically-meaningful melt/freeze boundaries can be detected. We have demonstrated that these products, used together, can improve the precision in mapping surface and near-surface melt extent on the Greenland Ice Sheet.

Study of the role of tumor necrosis factor-α (-308 G/A) and interleukin-10 (-1082 G/A) polymorphisms as potential risk factors to acute kidney injury in patients with severe sepsis using high-resolution melting curve analysis.

PubMed

Hashad, Doaa I; Elsayed, Eman T; Helmy, Tamer A; Elawady, Samier M

2017-11-01

Septic acute kidney injury (AKI) is a prevalent complication in intensive care units with an increased incidence of complications. The aim of the present study was to assess the use of high-resolution melting curve (HRM) analysis in investigating whether the genetic polymorphisms; -308 G/A of tumor necrosis factor-α (TNF-α), and -1082 G /A of Interleukin-10 (IL-10) genes may predispose patients diagnosed with severe sepsis to the development of AKI. One hundred and fifty patients with severe sepsis participated in the present study; only sixty-six developed AKI. Both polymorphisms were studied using HRM analysis. The low producer genotype of both studied polymorphism of TNF-α and IL-10 genes was associated with AKI. Using logistic regression analysis, the low producer genotypes remained an independent risk factor for AKI. A statistically significant difference was detected between both studied groups as regards the low producer genotype in both TNF-α (-308 G/A) and interleukin-10 (IL-10) (-1082 G/A) polymorphisms being prevalent in patients developing AKI. Principle conclusions: The low producer genotypes of both TNF-α (-308 G/A) and IL-10 (-1082 G/A) polymorphisms could be considered a risk factor for the development of AKI in critically ill patients with severe sepsis, thus management technique implemented for this category should be modulated rescuing this sector of patients from the grave deterioration to acute kidney injury. Using HRM for genotyping proved to be a highly efficient, simple, cost-effective genotyping technique that is most appropriate for the routine study of large-scale samples.

Universal calibration of Raman spectroscopy for the analysis of volatiles in glasses of variable composition

NASA Astrophysics Data System (ADS)

Schiavi, Federica; Bolfan-Casanova, Nathalie

2017-04-01

The amount and distribution of volatiles (water, carbon dioxide …) in magmas represent key parameters for the understanding of magma processes and dynamics within volcanic plumbing systems. Micro-Raman spectroscopy is an excellent technique for accurate determination of volatile contents in magmas, as it combines several advantages. The technique is non-destructive and requires minimal sample preparation before the analysis. Its high lateral and in-depth spatial resolution is crucial for the study of small objects and samples that are chemically and texturally heterogeneous at the small scale (microns). Moreover, the high confocality allows analysis of sample regions not exposed to the surface and 3D mapping. We present a universal calibration of Raman spectroscopy for quantification of volatiles in silicate glasses. The proposed method is based on internal calibration, i.e., on the correlation between the glass water content and the ratio between the areas of the water and silicate Raman bands. Synthetic glasses with variable major element compositions (basaltic, andesitic, rhyolitic, dacitic ..) bearing different H2O (up to 7 wt%) and CO2 contents are used as standard glasses. Natural silicate glasses, mainly in the form of melt inclusions, are used to test the goodness of the proposed method. In addition to quantification of volatiles in glass, in bubble-bearing melt inclusions we perform micro-Raman spectroscopy investigation of gas-bearing bubbles for accurate determination of total volatile contents in melt inclusions.

Direct Detection of Rifampin and Isoniazid Resistance in Sputum Samples from Tuberculosis Patients by High-Resolution Melt Curve Analysis

PubMed Central

Anthwal, Divya; Gupta, Rakesh Kumar; Bhalla, Manpreet; Bhatnagar, Shinjini

2017-01-01

ABSTRACT Drug-resistant tuberculosis (TB) is a major threat to TB control worldwide. Globally, only 40% of the 340,000 notified TB patients estimated to have multidrug-resistant-TB (MDR-TB) were detected in 2015. This study was carried out to evaluate the utility of high-resolution melt curve analysis (HRM) for the rapid and direct detection of MDR-TB in Mycobacterium tuberculosis in sputum samples. A reference plasmid library was first generated of the most frequently observed mutations in the resistance-determining regions of rpoB, katG, and an inhA promoter and used as positive controls in HRM. The assay was first validated in 25 MDR M. tuberculosis clinical isolates. The assay was evaluated on DNA isolated from 99 M. tuberculosis culture-positive sputum samples that included 84 smear-negative sputum samples, using DNA sequencing as gold standard. Mutants were discriminated from the wild type by comparing melting-curve patterns with those of control plasmids using HRM software. Rifampin (RIF) and isoniazid (INH) monoresistance were detected in 11 and 21 specimens, respectively, by HRM. Six samples were classified as MDR-TB by sequencing, one of which was missed by HRM. The HRM-RIF, INH-katG, and INH-inhA assays had 89% (95% confidence interval [CI], 52, 100%), 85% (95% CI, 62, 97%), and 100% (95% CI, 74, 100%) sensitivity, respectively, in smear-negative samples, while all assays had 100% sensitivity in smear-positive samples. All assays had 100% specificity. Concordance of 97% to 100% (κ value, 0.9 to 1) was noted between sequencing and HRM. Heteroresistance was observed in 5 of 99 samples by sequencing. In conclusion, the HRM assay was a cost-effective (Indian rupee [INR]400/US$6), rapid, and closed-tube method for the direct detection of MDR-TB in sputum, especially for direct smear-negative cases. PMID:28330890

Polycrystalline magma behaviour in dykes: Insights from high-resolution numerical models

NASA Astrophysics Data System (ADS)

Yamato, Philippe; Duretz, Thibault; Tartèse, Romain; May, Dave

2013-04-01

The presence of a crystalline load in magmas modifies their effective rheology and thus their flow behaviour. In dykes, for instance, the presence of crystals denser than the melt reduces the ascent velocity and modifies the shape of the velocity profile from a Newtonian Poiseuille flow to a Bingham type flow. Nevertheless, several unresolved issues still remain poorly understood and need to be quantified: (1) What are the mechanisms controlling crystals segregation during magma ascent in dykes? (2) How does crystals transportation within a melt depend on their concentration, geometry, size and density? (3) Do crystals evolve in isolation to each other or as a cluster? (4) What is the influence of considering inertia of the melt within the system? In this study, we present numerical models following the setup previously used in Yamato et al. (2012). Our model setup simulates an effective pressure gradient between the base and the top of a channel (representing a dyke), by pushing a rigid piston into a magmatic mush that comprised crystals and melt and perforated by a hole. The initial resolution of the models (401x1551 nodes) has been doubled in order to ensure that the smallest crystalline fractions are sufficiently well resolved. Results show that the melt phase can be squeezed out from a crystal-rich magma when subjected to a given pressure gradient range and that clustering of crystals might be an important parameter controlling their behaviour. This demonstrates that crystal-melt segregation in dykes during magma ascent constitutes a viable mechanism for magmatic differentiation of residual melts. These results also explain how isolated crystal clusters and melt pockets, with different chemistry, can be formed. In addition, we discuss the impact of taking into account inertia in our models. Reference: Yamato, P., Tartèse, R., Duretz, T., May, D.A., 2012. Numerical modelling of magma transport in dykes. Tectonophysics 526-529, 97-109.

The extreme melt across the Greenland ice sheet in 2012

NASA Astrophysics Data System (ADS)

Nghiem, S. V.; Hall, D. K.; Mote, T. L.; Tedesco, M.; Albert, M. R.; Keegan, K.; Shuman, C. A.; DiGirolamo, N. E.; Neumann, G.

2012-10-01

The discovery of the 2012 extreme melt event across almost the entire surface of the Greenland ice sheet is presented. Data from three different satellite sensors - including the Oceansat-2 scatterometer, the Moderate-resolution Imaging Spectroradiometer, and the Special Sensor Microwave Imager/Sounder - are combined to obtain composite melt maps, representing the most complete melt conditions detectable across the ice sheet. Satellite observations reveal that melt occurred at or near the surface of the Greenland ice sheet across 98.6% of its entire extent on 12 July 2012, including the usually cold polar areas at high altitudes like Summit in the dry snow facies of the ice sheet. This melt event coincided with an anomalous ridge of warm air that became stagnant over Greenland. As seen in melt occurrences from multiple ice core records at Summit reported in the published literature, such a melt event is rare with the last significant one occurring in 1889 and the next previous one around seven centuries earlier in the Medieval Warm Period. Given its rarity, the 2012 extreme melt across Greenland provides an exceptional opportunity for new studies in broad interdisciplinary geophysical research.

ITS2 barcoding DNA region combined with high resolution melting (HRM) analysis of Hyoscyami Semen, the mature seed of Hyoscyamus niger.

PubMed

Xiong, Chao; Hu, Zhi-Gang; Tu, Yuan; Liu, He-Gang; Wang, Ping; Zhao, Ming-Ming; SHIi, Yu-Hua; Wu, Lan; Sun, Wei; Chen, Shi-Lin

2016-12-01

Hyoscyami Semen, the mature dried seed of Hyoscyamus niger L., has long been used as a traditional Chinese medicine to treat human diseases. Hyoscyami Semen is found in local markets in China. In markets, sellers and buyers commonly inadvertently mix the seeds of H. niger with the seeds of related species such as Hygrophila salicifolia (Vahl) Nees, Astragalus complanatus R. Br., Cuscuta australis R. Br., Cuscuta chinensis Lam., and Impatiens balsamina L. because of their similar morphologies or similar names. Thus, developing a reliable method for discriminating H. niger seeds from its adulterants is necessary to reduce confusion and ensure the safe use of Hyoscyami Semen. The present study was designed to evaluate the efficiency of high-resolution melting analysis combined with DNA barcoding (Bar-HRM) with internal transcribed spacer 2 to discriminate H. niger. Our results show that Bar-HRM successfully identified the adulterants and detected the proportion of H. niger DNA extract within an admixture. In particular, HRM detected H. niger DNA extract in A. complanatus DNA extract at concentrations as low as 1%. In conclusion, the Bar-HRM method developed in the present study for authenticating H. niger is rapid and cost-effective. It can be used in the future to guarantee the purity of Hyoscyami Semen for the clinical use. Copyright © 2016 China Pharmaceutical University. Published by Elsevier B.V. All rights reserved.

Mutation Scanning in a Single and a Stacked Genetically Modified (GM) Event by Real-Time PCR and High Resolution Melting (HRM) Analysis

PubMed Central

Ben Ali, Sina-Elisabeth; Madi, Zita Erika; Hochegger, Rupert; Quist, David; Prewein, Bernhard; Haslberger, Alexander G.; Brandes, Christian

2014-01-01

Genetic mutations must be avoided during the production and use of seeds. In the European Union (EU), Directive 2001/18/EC requires any DNA construct introduced via transformation to be stable. Establishing genetic stability is critical for the approval of genetically modified organisms (GMOs). In this study, genetic stability of two GMOs was examined using high resolution melting (HRM) analysis and real-time polymerase chain reaction (PCR) employing Scorpion primers for amplification. The genetic variability of the transgenic insert and that of the flanking regions in a single oilseed rape variety (GT73) and a stacked maize (MON88017 × MON810) was studied. The GT73 and the 5' region of MON810 showed no instabilities in the examined regions. However; two out of 100 analyzed samples carried a heterozygous point mutation in the 3' region of MON810 in the stacked variety. These results were verified by direct sequencing of the amplified PCR products as well as by sequencing of cloned PCR fragments. The occurrence of the mutation suggests that the 5' region is more suitable than the 3' region for the quantification of MON810. The identification of the single nucleotide polymorphism (SNP) in a stacked event is in contrast to the results of earlier studies of the same MON810 region in a single event where no DNA polymorphism was found. PMID:25365178

Optimization of the Divergent method for genotyping single nucleotide variations using SYBR Green-based single-tube real-time PCR.

PubMed

Gentilini, Fabio; Turba, Maria E

2014-01-01

A novel technique, called Divergent, for single-tube real-time PCR genotyping of point mutations without the use of fluorescently labeled probes has recently been reported. This novel PCR technique utilizes a set of four primers and a particular denaturation temperature for simultaneously amplifying two different amplicons which extend in opposite directions from the point mutation. The two amplicons can readily be detected using the melt curve analysis downstream to a closed-tube real-time PCR. In the present study, some critical aspects of the original method were specifically addressed to further implement the technique for genotyping the DNM1 c.G767T mutation responsible for exercise-induced collapse in Labrador retriever dogs. The improved Divergent assay was easily set up using a standard two-step real-time PCR protocol. The melting temperature difference between the mutated and the wild-type amplicons was approximately 5°C which could be promptly detected by all the thermal cyclers. The upgraded assay yielded accurate results with 157pg of genomic DNA per reaction. This optimized technique represents a flexible and inexpensive alternative to the minor grove binder fluorescently labeled method and to high resolution melt analysis for high-throughput, robust and cheap genotyping of single nucleotide variations. Copyright © 2014 Elsevier B.V. All rights reserved.

Microplate array diagonal gel electrophoresis (MADGE), CpG-PCR and temporal thermal ramp-MADGE (Melt-MADGE) for single nucleotide analyses in populations.

PubMed

Day, I N; O'Dell, S D; Spanakis, E; Weavind, G P

1999-02-01

Important requirements for molecular genetic epidemiological studies are economy, sample parallelism, convenience of setup and accessibility, goals inadequately met by existent approaches. We invented microplate array diagonal gel electrophoresis (MADGE) to gain simultaneously the advantages of simple setup, 96-well microplate compatibility, horizontal electrophoresis, and the resolution of polyacrylamide. At essentially no equipment cost (one simple plastic gel former), 10-100-fold savings on time for sample coding, liquid transfers, and data documentation, in addition to volume reductions and gel re-use, can be achieved. MADGE is compatible with ARMS, restriction analysis and other pattern analyses. CpG-PCR is a general PCR approach to CpG sites (10-20% of all human single base variation): both primers have 3' T, and are abutted to the CpG, forcing a TaqI restriction site if the CpG is intact. Typically, a 52 bp PCR product is then cut in half. CpG-PCR also illustrates that PAGE-MADGE readily permits analysis of 'ultrashort' PCRs. Melt-MADGE employs real-time-variable-temperature electrophoresis to examine duplex mobility during melting, achieving DGGE-like de novo, mutation scanning, but with the conveniences of arbitrary programmability, MADGE compatibility and short run time. This suite of methods enhances our capability to type or scan thousands of samples simultaneously, by 10-100-fold.

TEM Study of Intergranular Fluid Distributions in Rocks at a Nanometer Scale

NASA Astrophysics Data System (ADS)

Hiraga, T.; Anderson, I. M.; Kohlstedt, D. L.

2002-12-01

The distribution of intergranular fluids in rocks plays an essential role in fluid migration and rock rheology. Structural and chemical analyses with sub-nanometer resolution is possible with transmission and scanning-transmission electron microscopy; therefore, it is possible to perform the fine-scale structural analyses required to determine the presence or absence of very thin fluid films along grain boundaries. For aqueous fluids in crustal rocks, Hiraga et al. (2001) observed a fluid morphology controlled by the relative values of the solid-solid and solid-fluid interfacial energies, which resulted in well-defined dihedral angles. Their high-resolution transmission electron microscopy (TEM) observations demonstrate that grain boundaries are tight even at a nanometer scale, consistent with the absence of aqueous fluid films. For partially molten ultra-mafic rocks, two conflicting conclusions have been reached: nanometer-thick melt films wet grain boundaries (Drury and Fitz Gerald 1996; De Kloe et al. 2000) versus essentially all grain boundaries are melt-free (Vaughan et al. 1982; Kohlstedt 1990). To resolve this conflict, Hiraga et al. (2002) examined grain boundaries in quenched partially molten peridotites. Their observations demonstrate the following: (i) Although a small fraction of the grains are separated by relatively thick (~1 μm) layers of melt, lattice fringe images obtained with a high-resolution TEM reveal that most of the remaining boundaries do not contain a thin amorphous phase. (ii) In addition, the composition of olivine-olivine grain boundaries was analyzed with a nano-beam analytical scanning TEM with a probe size of <2 nm. Although the grain boundaries contained no melt film, the concentration of Ca, Al and Ti were enhanced near the boundaries. The segregation of these elements to the grain boundaries formed enriched regions <7 nm wide. A similar pattern of chemical segregation was detected in subsolidus systems. Creep experiments on the partially molten rocks that were analyzed in this study reveal little weakening even at melt contents approaching 4 vol%, consistent with our observations of melt-free grain boundaries.

3D Compressible Melt Transport with Adaptive Mesh Refinement

NASA Astrophysics Data System (ADS)

Dannberg, Juliane; Heister, Timo

2015-04-01

Melt generation and migration have been the subject of numerous investigations, but their typical time and length-scales are vastly different from mantle convection, which makes it difficult to study these processes in a unified framework. The equations that describe coupled Stokes-Darcy flow have been derived a long time ago and they have been successfully implemented and applied in numerical models (Keller et al., 2013). However, modelling magma dynamics poses the challenge of highly non-linear and spatially variable material properties, in particular the viscosity. Applying adaptive mesh refinement to this type of problems is particularly advantageous, as the resolution can be increased in mesh cells where melt is present and viscosity gradients are high, whereas a lower resolution is sufficient in regions without melt. In addition, previous models neglect the compressibility of both the solid and the fluid phase. However, experiments have shown that the melt density change from the depth of melt generation to the surface leads to a volume increase of up to 20%. Considering these volume changes in both phases also ensures self-consistency of models that strive to link melt generation to processes in the deeper mantle, where the compressibility of the solid phase becomes more important. We describe our extension of the finite-element mantle convection code ASPECT (Kronbichler et al., 2012) that allows for solving additional equations describing the behaviour of silicate melt percolating through and interacting with a viscously deforming host rock. We use the original compressible formulation of the McKenzie equations, augmented by an equation for the conservation of energy. This approach includes both melt migration and melt generation with the accompanying latent heat effects. We evaluate the functionality and potential of this method using a series of simple model setups and benchmarks, comparing results of the compressible and incompressible formulation and showing the potential of adaptive mesh refinement when applied to melt migration. Our model of magma dynamics provides a framework for modelling processes on different scales and investigating links between processes occurring in the deep mantle and melt generation and migration. This approach could prove particularly useful applied to modelling the generation of komatiites or other melts originating in greater depths. Keller, T., D. A. May, and B. J. P. Kaus (2013), Numerical modelling of magma dynamics coupled to tectonic deformation of lithosphere and crust, Geophysical Journal International, 195 (3), 1406-1442. Kronbichler, M., T. Heister, and W. Bangerth (2012), High accuracy mantle convection simulation through modern numerical methods, Geophysical Journal International, 191 (1), 12-29.

Signatures of present and past melt distribution along fast and intermediate spreading centers

NASA Astrophysics Data System (ADS)

Marjanovic, Milena

The work presented in this dissertation depicts past and present signatures of melt distribution at fast and intermediate spreading centers. The primary goal of the studies included in this thesis is to provide better understanding of melt distribution and variation in melt physical properties within and at the base of oceanic crust formed at these spreading centers. Furthermore, this work examines effects that melt presence might have on formation and structural characteristics of oceanic crust. To explore the above we use geophysical data collected during two expeditions conducted along the Juan de Fuca Ridge (intermediate) and the East Pacific Rise (fast). The major part of the thesis is based on the work conducted on high resolution reflection seismic data that investigate present day intracrustal melt distribution along the East Pacific Rise (EPR) axis extending between 8°20' and 10°10'N. Here, the character of the melt reservoir is examined from different aspects and by using different seismic data analysis methods. By systematic analysis of the seismic reflection data, we show that the axial melt lens (AML) is segmented at different segment scales. Locations of the mapped disruptions in the AML correspond to previously identified tectonic discontinuities well expressed in the seafloor bathymetry. The above result corroborates genetic relationship between tectonic and magmatic segmentation. To examine melt distribution along the EPR, here for the first time we use amplitude variation with angle of incidence (AVA) crossplotting technique that was developed by oil and gas industry experts to look for presence of hydrocarbons. Further data examination for the first time for the mid-ocean ridges show presence of deeper lenses (lenses that are present below the AML). Presence of gaps in these sub-events and their collocation with what is believed to be the location of origin of the last documented eruption occurred in 2005--06, may shed light on the mechanisms behind the mid-ocean ridges volcanic processes. To explore variation in crustal structure and melt distribution at present day along the Juan de Fuca Ridge and relicts of past melt presence near ridge propagators wakes, a combination of gravity and multi-channel seismic data was used. Gravity modeling, constrained by seismic data, showed that robust topography (shallow axial depth and wide axial high) and thicker crust observed for the southern portion of this ridge system originate from enhanced melt supply at the base of the crust. In addition, prominent crustal thickening on the younger crust side of the inner propagators wakes (now on the ridge flanks) is brought into relationship with collocated frozen magma lenses imaged at the base of the crust. Spatial relationship of the two argues for their causal relationship at the time of the crustal formation on the axis. Our study suggests that these frozen lenses represent the record of once molten reservoir that most probably actively participated in the formation of the thicker crust.

Nested Machine Learning Facilitates Increased Sequence Content for Large-Scale Automated High Resolution Melt Genotyping

PubMed Central

Fraley, Stephanie I.; Athamanolap, Pornpat; Masek, Billie J.; Hardick, Justin; Carroll, Karen C.; Hsieh, Yu-Hsiang; Rothman, Richard E.; Gaydos, Charlotte A.; Wang, Tza-Huei; Yang, Samuel

2016-01-01

High Resolution Melt (HRM) is a versatile and rapid post-PCR DNA analysis technique primarily used to differentiate sequence variants among only a few short amplicons. We recently developed a one-vs-one support vector machine algorithm (OVO SVM) that enables the use of HRM for identifying numerous short amplicon sequences automatically and reliably. Herein, we set out to maximize the discriminating power of HRM + SVM for a single genetic locus by testing longer amplicons harboring significantly more sequence information. Using universal primers that amplify the hypervariable bacterial 16 S rRNA gene as a model system, we found that long amplicons yield more complex HRM curve shapes. We developed a novel nested OVO SVM approach to take advantage of this feature and achieved 100% accuracy in the identification of 37 clinically relevant bacteria in Leave-One-Out-Cross-Validation. A subset of organisms were independently tested. Those from pure culture were identified with high accuracy, while those tested directly from clinical blood bottles displayed more technical variability and reduced accuracy. Our findings demonstrate that long sequences can be accurately and automatically profiled by HRM with a novel nested SVM approach and suggest that clinical sample testing is feasible with further optimization. PMID:26778280

Ultrasensitive Detection of Drug-Resistant Pandemic 2009 (H1N1) Influenza A Virus by Rare-Variant-Sensitive High-Resolution Melting-Curve Analysis▿‡

PubMed Central

Chen, Neng; Pinsky, Benjamin A.; Lee, Betty P.; Lin, Min; Schrijver, Iris

2011-01-01

Oseltamivir (Tamiflu), an oral neuraminidase inhibitor, has been widely used to treat pandemic 2009 (H1N1) influenza A. Although a majority of 2009 (H1N1) influenza A virus remains oseltamivir susceptible, the threat of resistance due to the His275Tyr mutation is highlighted by the limitations of alternative therapies and the potential for rapid, global fixation of this mutation in the circulating influenza A virus population. In order to better understand the emergence of resistance, we developed a rare-variant-sensitive high-resolution melting-curve analysis method (RVS-HRM) that is able to detect the His275Tyr oseltamivir resistance mutation to 0.5% in a background of susceptible virus. We applied RVS-HRM to clinical specimens from patients who developed oseltamivir resistance and demonstrated the ultrasensitive detection of influenza A virus N1 neuraminidase quasispecies. Interestingly, we were unable to detect the oseltamivir resistance mutation in pretreatment samples, suggesting that resistant virus does not reach even this very low detection threshold until exposed to selective drug pressure. Thus, patients naive to oseltamivir are most likely to be susceptible when this drug is used as a first-line treatment modality. PMID:21543559

Applying high-resolution melting (HRM) technology to olive oil and wine authenticity.

PubMed

Pereira, Leonor; Gomes, Sónia; Barrias, Sara; Fernandes, José Ramiro; Martins-Lopes, Paula

2018-01-01

Olive oil and wine production have a worldwide economic impact. Their market reliability is under great concern because of the increasing number of fraud and adulteration attempts. The need for a traceability system in all its extension is crucial particularly for the cases of olive oils and wines with certified labels, in which only a limited number of olives and grapevine varieties, respectively, are allowed in a restricted well-defined geographical area. Molecular markers have been vastly applied to the food sector, and in particular High-Resolution DNA Melting technology has been successfully applied for olive oil and wine authentication, as part of the traceability system. In this review, the applications of HRM and their usefulness for this sector considering, Safety, Security and Authenticity will be reviewed. A broad overview of the HRM technique will be presented, focusing on the aspects that are crucial for its success, in particular the new generation of fluorescent dsDNA dyes used for amplicon detection and quantification, and the data analysis. A brief outlook on the olive oil and wine authenticity procedures, based on new DNA technology advances, and in which way this may influence the future establishment of a traceability system will be discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Glacial Boundary Features Delineated Using Enhanced-resolution Passive-microwave Data to Determine Melt Season Variation of the Vatnajokull Ice Cap, Iceland

NASA Astrophysics Data System (ADS)

Marzillier, D. M.; Ramage, J. M.

2017-12-01

Temperate glaciers such as those seen in Iceland experience high annual mass flux, thereby responding to small scale changes in Earth's climate. Decadal changes in the glacial margins of Iceland's ice caps are observable in the Landsat record, however twice daily AMSR-E Calibrated Enhanced-Resolution Passive Microwave Daily EASE-Grid 2.0 Brightness Temperature (CETB) Earth System Data Record (ESDR) allow for observation on a daily temporal scale and a 3.125 km spatial scale, which can in turn be connected to patterns seen over longer periods of time. Passive microwave data allow for careful observation of melt onset and duration in Iceland's glacial regions by recording changes in emissivity of the ice surface, known as brightness temperature (TB), which is sensitive to fluctuations in the liquid water content of snow and ice seen during melting in glaciated regions. Enhanced resolution of this data set allows for a determination of a threshold that defines the melting season. The XPGR snowmelt algorithm originally presented by Abdalati and Steffen (1995) is used as a comparison with the diurnal amplitude variation (DAV) values on Iceland's Vatnajokull ice cap located at 64.4N, -16.8W. Ground-based air temperature data in this region, digital elevation models (DEMs), and river discharge dominated by glacial runoff are used to confirm the glacial response to changes in global climate. Results show that Iceland glaciers have a bimodal distribution of brightness temperature delineating when the snow/ice is melting and refreezing. Ground based temperatures have increased on a decadal trend. Clear glacial boundaries are visible on the passive microwave delineating strong features, and we are working to understand their variability and contribution to glacier evolution. The passive microwave data set allows connections to be made between observations seen on a daily scale and the long term glacier changes observed by the Landsat satellite record that integrates the overall glacier changes.

Growth Twinning and Generation of High-Frequency Surface Nanostructures in Ultrafast Laser-Induced Transient Melting and Resolidification.

PubMed

Sedao, Xxx; Shugaev, Maxim V; Wu, Chengping; Douillard, Thierry; Esnouf, Claude; Maurice, Claire; Reynaud, Stéphanie; Pigeon, Florent; Garrelie, Florence; Zhigilei, Leonid V; Colombier, Jean-Philippe

2016-07-26

The structural changes generated in surface regions of single crystal Ni targets by femtosecond laser irradiation are investigated experimentally and computationally for laser fluences that, in the multipulse irradiation regime, produce sub-100 nm high spatial frequency surface structures. Detailed experimental characterization of the irradiated targets combining electron back scattered diffraction analysis with high-resolution transmission electron microscopy reveals the presence of multiple nanoscale twinned domains in the irradiated surface regions of single crystal targets with (111) surface orientation. Atomistic- and continuum-level simulations performed for experimental irradiation conditions reproduce the generation of twinned domains and establish the conditions leading to the formation of growth twin boundaries in the course of the fast transient melting and epitaxial regrowth of the surface regions of the irradiated targets. The observation of growth twins in the irradiated Ni(111) targets provides strong evidence of the role of surface melting and resolidification in the formation of high spatial frequency surface structures. This also suggests that the formation of twinned domains can be used as a sensitive measure of the levels of liquid undercooling achieved in short pulse laser processing of metals.

In situ study on atomic mechanism of melting and freezing of single bismuth nanoparticles

PubMed Central

Li, Yingxuan; Zang, Ling; Jacobs, Daniel L.; Zhao, Jie; Yue, Xiu; Wang, Chuanyi

2017-01-01

Experimental study of the atomic mechanism in melting and freezing processes remains a formidable challenge. We report herein on a unique material system that allows for in situ growth of bismuth nanoparticles from the precursor compound SrBi2Ta2O9 under an electron beam within a high-resolution transmission electron microscope (HRTEM). Simultaneously, the melting and freezing processes within the nanoparticles are triggered and imaged in real time by the HRTEM. The images show atomic-scale evidence for point defect induced melting, and a freezing mechanism mediated by crystallization of an intermediate ordered liquid. During the melting and freezing, the formation of nucleation precursors, nucleation and growth, and the relaxation of the system, are directly observed. Based on these observations, an interaction–relaxation model is developed towards understanding the microscopic mechanism of the phase transitions, highlighting the importance of cooperative multiscale processes. PMID:28194017

In situ study on atomic mechanism of melting and freezing of single bismuth nanoparticles

NASA Astrophysics Data System (ADS)

Li, Yingxuan; Zang, Ling; Jacobs, Daniel L.; Zhao, Jie; Yue, Xiu; Wang, Chuanyi

2017-02-01

Experimental study of the atomic mechanism in melting and freezing processes remains a formidable challenge. We report herein on a unique material system that allows for in situ growth of bismuth nanoparticles from the precursor compound SrBi2Ta2O9 under an electron beam within a high-resolution transmission electron microscope (HRTEM). Simultaneously, the melting and freezing processes within the nanoparticles are triggered and imaged in real time by the HRTEM. The images show atomic-scale evidence for point defect induced melting, and a freezing mechanism mediated by crystallization of an intermediate ordered liquid. During the melting and freezing, the formation of nucleation precursors, nucleation and growth, and the relaxation of the system, are directly observed. Based on these observations, an interaction-relaxation model is developed towards understanding the microscopic mechanism of the phase transitions, highlighting the importance of cooperative multiscale processes.

In situ study on atomic mechanism of melting and freezing of single bismuth nanoparticles.

PubMed

Li, Yingxuan; Zang, Ling; Jacobs, Daniel L; Zhao, Jie; Yue, Xiu; Wang, Chuanyi

2017-02-13

Experimental study of the atomic mechanism in melting and freezing processes remains a formidable challenge. We report herein on a unique material system that allows for in situ growth of bismuth nanoparticles from the precursor compound SrBi 2 Ta 2 O 9 under an electron beam within a high-resolution transmission electron microscope (HRTEM). Simultaneously, the melting and freezing processes within the nanoparticles are triggered and imaged in real time by the HRTEM. The images show atomic-scale evidence for point defect induced melting, and a freezing mechanism mediated by crystallization of an intermediate ordered liquid. During the melting and freezing, the formation of nucleation precursors, nucleation and growth, and the relaxation of the system, are directly observed. Based on these observations, an interaction-relaxation model is developed towards understanding the microscopic mechanism of the phase transitions, highlighting the importance of cooperative multiscale processes.

Rapid screening of rpoB and katG mutations in Mycobacterium tuberculosis isolates by high-resolution melting curve analysis.

PubMed

Haeili, M; Fooladi, A I; Bostanabad, S Z; Sarokhalil, D D; Siavoshi, F; Feizabadi, M M

2014-01-01

Early detection of multidrug-resistant tuberculosis (MDR-TB) is essential to prevent its transmission in the community and initiate effective anti-TB treatment regimen. High-resolution melting curve (HRM) analysis was evaluated for rapid detection of resistance conferring mutations in rpoB and katG genes. We screened 95 Mycobacterium tuberculosis clinical isolates including 20 rifampin resistant (RIF-R), 21 isoniazid resistant (INH-R) and 54 fully susceptible (S) isolates determined by proportion method of drug susceptibility testing. Nineteen M. tuberculosis isolates with known drug susceptibility genotypes were used as references for the assay validation. The nucleotide sequences of the target regions rpoB and katG genes were determined to investigate the frequency and type of mutations and to confirm HRM results. HRM analysis of a 129-bp fragment of rpoB allowed correct identification of 19 of the 20 phenotypically RIF-R and all RIF-S isolates. All INH-S isolates generated wild-type HRM curves and 18 out of 21 INH-R isolates harboured any mutation in 109-bp fragment of katG exhibited mutant type HRM curves. However, 1 RIF-R and 3 INH-R isolates were falsely identified as susceptible which were confirmed for having no mutation in their target regions by sequencing. The main mutations involved in RIF and INH resistance were found at codons rpoB531 (60% of RIF-R isolates) and katG315 (85.7% of INH-R isolates), respectively. HRM was found to be a reliable, rapid and low cost method to characterise drug susceptibility of clinical TB isolates in resource-limited settings.

Methylation-sensitive high-resolution melting-curve analysis of the SNRPN gene as a diagnostic screen for Prader-Willi and Angelman syndromes.

PubMed

White, Helen E; Hall, Victoria J; Cross, Nicholas C P

2007-11-01

Angelman syndrome (AS) and Prader-Willi syndrome (PWS) are 2 distinct neurodevelopmental disorders caused primarily by deficiency of specific parental contributions at an imprinted domain within the chromosomal region 15q11.2-13. Lack of paternal contribution results in PWS either by paternal deletion (approximately 70%) or maternal uniparental disomy (UPD) (approximately 25%). Most cases of AS result from the lack of a maternal contribution from this same region, by maternal deletion (70%) or paternal UPD (approximately 5%). Analysis of allelic methylation differences at the small nuclear ribonucleoprotein polypeptide N (SNRPN) locus differentiates the maternally and paternally inherited chromosome 15 and can be used as a diagnostic test for AS and PWS. Methylation-sensitive high-resolution melting-curve analysis (MS-HRM) using the DNA binding dye EvaGreen was used to analyze methylation differences at the SNRPN locus in anonymized DNA samples from individuals with PWS (n = 39) or AS (n = 31) and from healthy control individuals (n = 95). Results from the MS-HRM assay were compared to those obtained by use of a methylation-specific PCR (MSP) protocol that is used commonly in diagnostic practice. With the MS-HRM assay 97.6% of samples were unambiguously assigned to the 3 diagnostic categories (AS, PWS, normal) by use of automated calling with an 80% confidence percentage threshold, and the failure rate was 0.6%. One PWS sample showed a discordant result for the MS-HRM assay compared to MSP data. MS-HRM is a simple, rapid, and robust method for screening methylation differences at the SNRPN locus and could be used as a diagnostic screen for PWS and AS.

Detecting differential allelic expression using high-resolution melting curve analysis: application to the breast cancer susceptibility gene CHEK2

PubMed Central

2011-01-01

Background The gene CHEK2 encodes a checkpoint kinase playing a key role in the DNA damage pathway. Though CHEK2 has been identified as an intermediate breast cancer susceptibility gene, only a small proportion of high-risk families have been explained by genetic variants located in its coding region. Alteration in gene expression regulation provides a potential mechanism for generating disease susceptibility. The detection of differential allelic expression (DAE) represents a sensitive assay to direct the search for a functional sequence variant within the transcriptional regulatory elements of a candidate gene. We aimed to assess whether CHEK2 was subject to DAE in lymphoblastoid cell lines (LCLs) from high-risk breast cancer patients for whom no mutation in BRCA1 or BRCA2 had been identified. Methods We implemented an assay based on high-resolution melting (HRM) curve analysis and developed an analysis tool for DAE assessment. Results We observed allelic expression imbalance in 4 of the 41 LCLs examined. All four were carriers of the truncating mutation 1100delC. We confirmed previous findings that this mutation induces non-sense mediated mRNA decay. In our series, we ruled out the possibility of a functional sequence variant located in the promoter region or in a regulatory element of CHEK2 that would lead to DAE in the transcriptional regulatory milieu of freely proliferating LCLs. Conclusions Our results support that HRM is a sensitive and accurate method for DAE assessment. This approach would be of great interest for high-throughput mutation screening projects aiming to identify genes carrying functional regulatory polymorphisms. PMID:21569354

The Contribution to High Asia Runoff from Ice and Snow (CHARIS): Understanding the source and trends of cryospheric contributions to the water balance

NASA Astrophysics Data System (ADS)

Rittger, K.; Armstrong, R. L.; Bair, N.; Racoviteanu, A.; Brodzik, M. J.; Hill, A. F.; Wilson, A. M.; Khan, A. L.; Ramage, J. M.; Khalsa, S. J. S.; Barrett, A. P.; Raup, B. H.; Painter, T. H.

2017-12-01

The Contribution to High Asia Runoff from Ice and Snow, or CHARIS, project is systematically assessing the role that glaciers and seasonal snow play in the freshwater resources of Central and South Asia. The study area encompasses roughly 3 million square kilometers of the Himalaya, Karakoram, Hindu Kush, Pamir and Tien Shan mountain ranges that drain to five major rivers: the Ganges, Brahmaputra, Indus, Amu Darya and Syr Darya. We estimate daily snow and glacier ice contributions to the water balance. Our automated partitioning method generates daily maps of 1) snow over ice (SOI), 2) exposed glacier ice (EGI), 3) debris covered glacier ice (DGI) and 4) snow over land (SOL) using fractional snow cover, snow grain size, and annual minimum ice and snow from the 500 m MODIS-derived MODSCAG and MODICE products. Maps of snow and ice cover are validated using high-resolution (30 m) maps of snow, ice, and debris cover from Landsat. The probability of detection is 0.91 and precision is 0.85 for MODICE. We examine trends in annual and monthly snow and ice maps and use daily maps as inputs to a calibrated temperature-index model and an uncalibrated energy balance model, ParBal. Melt model results and measurements of isotopes and specific ions used as an independent validation of melt modeling indicate a sharp geographic contrast in the role of snow and ice melt to downstream water supplies between the arid Tien Shan and Pamir ranges of Central Asia, where melt water dominates dry season flows, and the monsoon influenced central and eastern Himalaya where rain controls runoff. We also compare melt onset and duration from the melt models to the Calibrated, Enhanced Resolution Passive Microwave Brightness Temperature Earth Science Data Record. Trend analysis of annual and monthly area of permanent snow and ice (the union of SOI and EGI) for 2000 to 2016 shows statistically significant negative trends in the Ganges and Brahmaputra basins. There are no statistically significant trends in permanent snow and ice in the other basins and no statistically significant trends in SOL, the renewable and seasonal component of snow and ice cover, in any of the five basins. This work gives a better understanding of the current hydrologic regime to guide realistic estimates of the future availability and vulnerability of water resources in these regions.

Discrimination of three genetically close Aspergillus species by using high resolution melting analysis applied to indoor air as case study.

PubMed

Libert, Xavier; Packeu, Ann; Bureau, Fabrice; Roosens, Nancy H; De Keersmaecker, Sigrid C J

2017-04-04

Indoor air pollution caused by fungal contamination is suspected to have a public health impact. Monitoring of the composition of the indoor airborne fungal contaminants is therefore important. To avoid problems linked to culture-dependent protocols, molecular methods are increasingly being proposed as an alternative. Among these molecular methods, the polymerase chain reaction (PCR) and the real-time PCR are the most frequently used tools for indoor fungal detection. However, even if these tools have demonstrated their appropriate performance, some of them are not able to discriminate between species which are genetically close. A solution to this could be the use of a post-qPCR high resolution melting (HRM) analysis, which would allow the discrimination of these species based on the highly accurate determination of the difference in melting temperature of the obtained amplicon. In this study, we provide a proof-of-concept for this approach, using a dye adapted version of our previously developed qPCR SYBR®Green method to detect Aspergillus versicolor in indoor air, an important airborne fungus in terms of occurrence and cause of health problems. Despite the good performance observed for that qPCR method, no discrimination could previously be made between A. versicolor, Aspergillus creber and Aspergillus sydowii. In this study, we developed and evaluated an HRM assay for the discrimination between A. versicolor, Aspergillus creber and Aspergillus sydowii. Using HRM analysis, the discrimination of the 3 Aspergillus species could be made. No false positive, nor false negatives were observed during the performance assessment including 20 strains of Aspergillus. The limit of detection was determined for each species i.e., 0.5 pg of gDNA for A. creber and A. sydowii, and 0.1 pg of gDNA for A. versicolor. The HRM analysis was also successfully tested on environmental samples. We reported the development of HRM tools for the discrimination of A. versicolor, A. creber and A. sydowii. However, this study could be considered as a study case demonstrating that HRM based on existing qPCR assays, allows a more accurate identification of indoor air contaminants. This contributes to an improved insight in the diversity of indoor airborne fungi and hence, eventually in the causal link with health problems.

Relationship between passive microwave-derived snowmelt and surface-measured discharge, Wheaton River, Yukon Territory, Canada

NASA Astrophysics Data System (ADS)

Ramage, J. M.; McKenney, R. A.; Thorson, B.; Maltais, P.; Kopczynski, S. E.

2006-03-01

Snow volume and melt timing are major factors influencing the water cycle at northern high altitudes and latitudes, yet both are hard to quantify or monitor in remote mountainous regions. Twice-daily special sensor microwave imager (SSM/I) passive microwave observations of seasonal snow melt onset in the Wheaton River basin, Yukon Territory, Canada (60 ° 0805N, 134 ° 5345W), are used to test the idea that melt onset date and duration of snowpack melt-refreeze fluctuations control the timing of the early hydrograph peaks with predictable lags. This work uses the SSM/I satellite data from 1988 to 2002 to evaluate the chronology of melt and runoff patterns in the upper Yukon River basin. The Wheaton River is a small (875 km2) tributary to the Yukon, and is a subarctic, partly glacierized heterogeneous basin with near-continuous hydrographic records dating back to 1966. SSM/I pixels are sensitive to melt onset due to the strong increase in snow emissivity, and have a robust signal, in spite of coarse (>25 × 25 km2) pixel resolution and varied terrain. Results show that Wheaton River peak flows closely follow the end of large daily variations in brightness temperature of pixels covering the Wheaton River, but the magnitude of flow is highly variable, as might be expected from interannual snow mass variability. Spring rise in the hydrograph follows the end of high diurnal brightness temperature (Tb) amplitude variations (DAV) by 0 to 5 days approximately 90% of the time for this basin. Subsequent work will compare these findings for a larger (7250 km2), unglacierized tributary, the Ross River, which is farther northeast (61 ° 5940N, 132 ° 2240W) in the Yukon Territory. These techniques will also be used to try to determine the improvement in melt detection and runoff prediction from the higher resolution (15 × 15 km2) advanced microwave scanning radiometer for EOS (AMSR-E) sensor.

Estimating spring terminus submarine melt rates at a Greenlandic tidewater glacier using satellite imagery

NASA Astrophysics Data System (ADS)

Moyer, Alexis N.; Nienow, Peter W.; Gourmelen, Noel; Sole, Andrew J.; Slater, Donald A.

2017-12-01

Oceanic forcing of the Greenland Ice Sheet is believed to promote widespread thinning at tidewater glaciers, with submarine melting proposed as a potential trigger of increased glacier calving, retreat, and subsequent acceleration. The precise mechanism(s) driving glacier instability, however, remain poorly understood, and while increasing evidence points to the importance of submarine melting, estimates of melt rates are uncertain. Here we estimate submarine melt rate by examining freeboard changes in the seasonal ice tongue of Kangiata Nunaata Sermia at the head of Kangersuneq Fjord, southwest Greenland. We calculate melt rates for March and May 2013 by differencing along-fjord surface elevation, derived from high-resolution TanDEM-X digital elevation models, in combination with ice velocities derived from offset tracking applied to TerraSAR-X imagery. Estimated steady state melt rates reach up to 1.4 ± 0.5 m d^-1 near the glacier grounding line, with mean values of up to 0.8 ± 0.3 and 0.7 ± 0.3 m d^1 for the eastern and western parts of the ice tongue, respectively. Melt rates decrease with distance from the ice front and vary across the fjord. This methodology reveals spatio-temporal variations in submarine melt rates at tidewater glaciers which develop floating termini, and can be used to improve our understanding of ice-ocean interactions and submarine melting in glacial fjords.

Limited copy number - high resolution melting (LCN-HRM) enables the detection and identification by sequencing of low level mutations in cancer biopsies

PubMed Central

Do, Hongdo; Dobrovic, Alexander

2009-01-01

Background Mutation detection in clinical tumour samples is challenging when the proportion of tumour cells, and thus mutant alleles, is low. The limited sensitivity of conventional sequencing necessitates the adoption of more sensitive approaches. High resolution melting (HRM) is more sensitive than sequencing but identification of the mutation is desirable, particularly when it is important to discriminate false positives due to PCR errors or template degradation from true mutations. We thus developed limited copy number - high resolution melting (LCN-HRM) which applies limiting dilution to HRM. Multiple replicate reactions with a limited number of target sequences per reaction allow low level mutations to be detected. The dilutions used (based on Ct values) are chosen such that mutations, if present, can be detected by the direct sequencing of amplicons with aberrant melting patterns. Results Using cell lines heterozygous for mutations, we found that the mutations were not readily detected when they comprised 10% of total alleles (20% tumour cells) by sequencing, whereas they were readily detectable at 5% total alleles by standard HRM. LCN-HRM allowed these mutations to be identified by direct sequencing of those positive reactions. LCN-HRM was then used to review formalin-fixed paraffin-embedded (FFPE) clinical samples showing discordant findings between sequencing and HRM for KRAS exon 2 and EGFR exons 19 and 21. Both true mutations present at low levels and sequence changes due to artefacts were detected by LCN-HRM. The use of high fidelity polymerases showed that the majority of the artefacts were derived from the damaged template rather than replication errors during amplification. Conclusion LCN-HRM bridges the sensitivity gap between HRM and sequencing and is effective in distinguishing between artefacts and true mutations. PMID:19811662

Limited copy number-high resolution melting (LCN-HRM) enables the detection and identification by sequencing of low level mutations in cancer biopsies.

PubMed

Do, Hongdo; Dobrovic, Alexander

2009-10-08

Mutation detection in clinical tumour samples is challenging when the proportion of tumour cells, and thus mutant alleles, is low. The limited sensitivity of conventional sequencing necessitates the adoption of more sensitive approaches. High resolution melting (HRM) is more sensitive than sequencing but identification of the mutation is desirable, particularly when it is important to discriminate false positives due to PCR errors or template degradation from true mutations.We thus developed limited copy number - high resolution melting (LCN-HRM) which applies limiting dilution to HRM. Multiple replicate reactions with a limited number of target sequences per reaction allow low level mutations to be detected. The dilutions used (based on Ct values) are chosen such that mutations, if present, can be detected by the direct sequencing of amplicons with aberrant melting patterns. Using cell lines heterozygous for mutations, we found that the mutations were not readily detected when they comprised 10% of total alleles (20% tumour cells) by sequencing, whereas they were readily detectable at 5% total alleles by standard HRM. LCN-HRM allowed these mutations to be identified by direct sequencing of those positive reactions.LCN-HRM was then used to review formalin-fixed paraffin-embedded (FFPE) clinical samples showing discordant findings between sequencing and HRM for KRAS exon 2 and EGFR exons 19 and 21. Both true mutations present at low levels and sequence changes due to artefacts were detected by LCN-HRM. The use of high fidelity polymerases showed that the majority of the artefacts were derived from the damaged template rather than replication errors during amplification. LCN-HRM bridges the sensitivity gap between HRM and sequencing and is effective in distinguishing between artefacts and true mutations.

PBSM3D: A finite volume, scalar-transport blowing snow model for use with variable resolution meshes

NASA Astrophysics Data System (ADS)

Marsh, C.; Wayand, N. E.; Pomeroy, J. W.; Wheater, H. S.; Spiteri, R. J.

2017-12-01

Blowing snow redistribution results in heterogeneous snowcovers that are ubiquitous in cold, windswept environments. Capturing this spatial and temporal variability is important for melt and runoff simulations. Point scale blowing snow transport models are difficult to apply in fully distributed hydrological models due to landscape heterogeneity and complex wind fields. Many existing distributed snow transport models have empirical wind flow and/or simplified wind direction algorithms that perform poorly in calculating snow redistribution where there are divergent wind flows, sharp topography, and over large spatial extents. Herein, a steady-state scalar transport model is discretized using the finite volume method (FVM), using parameterizations from the Prairie Blowing Snow Model (PBSM). PBSM has been applied in hydrological response units and grids to prairie, arctic, glacier, and alpine terrain and shows a good capability to represent snow redistribution over complex terrain. The FVM discretization takes advantage of the variable resolution mesh in the Canadian Hydrological Model (CHM) to ensure efficient calculations over small and large spatial extents. Variable resolution unstructured meshes preserve surface heterogeneity but result in fewer computational elements versus high-resolution structured (raster) grids. Snowpack, soil moisture, and streamflow observations were used to evaluate CHM-modelled outputs in a sub-arctic and an alpine basin. Newly developed remotely sensed snowcover indices allowed for validation over large basins. CHM simulations of snow hydrology were improved by inclusion of the blowing snow model. The results demonstrate the key role of snow transport processes in creating pre-melt snowcover heterogeneity and therefore governing post-melt soil moisture and runoff generation dynamics.

Surface layering and melting in an ionic liquid studied by resonant soft X-ray reflectivity

PubMed Central

Mezger, Markus; Ocko, Benjamin M.; Reichert, Harald; Deutsch, Moshe

2013-01-01

The molecular-scale structure of the ionic liquid [C18mim]+[FAP]− near its free surface was studied by complementary methods. X-ray absorption spectroscopy and resonant soft X-ray reflectivity revealed a depth-decaying near-surface layering. Element-specific interfacial profiles were extracted with submolecular resolution from energy-dependent soft X-ray reflectivity data. Temperature-dependent hard X-ray reflectivity, small- and wide-angle X-ray scattering, and infrared spectroscopy uncovered an intriguing melting mechanism for the layered region, where alkyl chain melting drove a negative thermal expansion of the surface layer spacing. PMID:23431181

High Resolution Melt (HRM) analysis is an efficient tool to genotype EMS mutants in complex crop genomes.

PubMed

Lochlainn, Seosamh Ó; Amoah, Stephen; Graham, Neil S; Alamer, Khalid; Rios, Juan J; Kurup, Smita; Stoute, Andrew; Hammond, John P; Østergaard, Lars; King, Graham J; White, Phillip J; Broadley, Martin R

2011-12-08

Targeted Induced Loci Lesions IN Genomes (TILLING) is increasingly being used to generate and identify mutations in target genes of crop genomes. TILLING populations of several thousand lines have been generated in a number of crop species including Brassica rapa. Genetic analysis of mutants identified by TILLING requires an efficient, high-throughput and cost effective genotyping method to track the mutations through numerous generations. High resolution melt (HRM) analysis has been used in a number of systems to identify single nucleotide polymorphisms (SNPs) and insertion/deletions (IN/DELs) enabling the genotyping of different types of samples. HRM is ideally suited to high-throughput genotyping of multiple TILLING mutants in complex crop genomes. To date it has been used to identify mutants and genotype single mutations. The aim of this study was to determine if HRM can facilitate downstream analysis of multiple mutant lines identified by TILLING in order to characterise allelic series of EMS induced mutations in target genes across a number of generations in complex crop genomes. We demonstrate that HRM can be used to genotype allelic series of mutations in two genes, BraA.CAX1a and BraA.MET1.a in Brassica rapa. We analysed 12 mutations in BraA.CAX1.a and five in BraA.MET1.a over two generations including a back-cross to the wild-type. Using a commercially available HRM kit and the Lightscanner™ system we were able to detect mutations in heterozygous and homozygous states for both genes. Using HRM genotyping on TILLING derived mutants, it is possible to generate an allelic series of mutations within multiple target genes rapidly. Lines suitable for phenotypic analysis can be isolated approximately 8-9 months (3 generations) from receiving M3 seed of Brassica rapa from the RevGenUK TILLING service.

High Resolution Melt (HRM) analysis is an efficient tool to genotype EMS mutants in complex crop genomes

PubMed Central

2011-01-01

Background Targeted Induced Loci Lesions IN Genomes (TILLING) is increasingly being used to generate and identify mutations in target genes of crop genomes. TILLING populations of several thousand lines have been generated in a number of crop species including Brassica rapa. Genetic analysis of mutants identified by TILLING requires an efficient, high-throughput and cost effective genotyping method to track the mutations through numerous generations. High resolution melt (HRM) analysis has been used in a number of systems to identify single nucleotide polymorphisms (SNPs) and insertion/deletions (IN/DELs) enabling the genotyping of different types of samples. HRM is ideally suited to high-throughput genotyping of multiple TILLING mutants in complex crop genomes. To date it has been used to identify mutants and genotype single mutations. The aim of this study was to determine if HRM can facilitate downstream analysis of multiple mutant lines identified by TILLING in order to characterise allelic series of EMS induced mutations in target genes across a number of generations in complex crop genomes. Results We demonstrate that HRM can be used to genotype allelic series of mutations in two genes, BraA.CAX1a and BraA.MET1.a in Brassica rapa. We analysed 12 mutations in BraA.CAX1.a and five in BraA.MET1.a over two generations including a back-cross to the wild-type. Using a commercially available HRM kit and the Lightscanner™ system we were able to detect mutations in heterozygous and homozygous states for both genes. Conclusions Using HRM genotyping on TILLING derived mutants, it is possible to generate an allelic series of mutations within multiple target genes rapidly. Lines suitable for phenotypic analysis can be isolated approximately 8-9 months (3 generations) from receiving M3 seed of Brassica rapa from the RevGenUK TILLING service. PMID:22152063

High-Resolution Melting (HRM) of the Cytochrome B Gene: A Powerful Approach to Identify Blood-Meal Sources in Chagas Disease Vectors

PubMed Central

Peña, Victor H.; Fernández, Geysson J.; Gómez-Palacio, Andrés M.; Mejía-Jaramillo, Ana M.; Cantillo, Omar; Triana-Chávez, Omar

2012-01-01

Methods to determine blood-meal sources of hematophagous Triatominae bugs (Chagas disease vectors) are serological or based on PCR employing species-specific primers or heteroduplex analysis, but these are expensive, inaccurate, or problematic when the insect has fed on more than one species. To solve those problems, we developed a technique based on HRM analysis of the mitochondrial gene cytochrome B (Cyt b). This technique recognized 14 species involved in several ecoepidemiological cycles of the transmission of Trypanosoma cruzi and it was suitable with DNA extracted from intestinal content and feces 30 days after feeding, revealing a resolution power that can display mixed feedings. Field samples were analyzed showing blood meal sources corresponding to domestic, peridomiciliary and sylvatic cycles. The technique only requires a single pair of primers that amplify the Cyt b gene in vertebrates and no other standardization, making it quick, easy, relatively inexpensive, and highly accurate. PMID:22389739

In-situ GPS records of surface mass balance, firn compaction rates, and ice-shelf basal melt rates for Pine Island Glacier, Antarctica

NASA Astrophysics Data System (ADS)

Shean, D. E.; Christianson, K.; Larson, K. M.; Ligtenberg, S.; Joughin, I. R.; Smith, B.; Stevens, C.

2016-12-01

In recent decades, Pine Island Glacier (PIG) has experienced marked retreat, speedup and thinning due to ice-shelf basal melt, internal ice-stream instability and feedbacks between these processes. In an effort to constrain recent ice-stream dynamics and evaluate potential causes of retreat, we analyzed 2008-2010 and 2012-2014 GPS records for PIG. We computed time series of horizontal velocity, strain rate, multipath-based antenna height, surface elevation, and Lagrangian elevation change (Dh/Dt). These data provide validation for complementary high-resolution WorldView stereo digital elevation model (DEM) records, with sampled DEM vertical error of 0.7 m. The GPS antenna height time series document a relative surface elevation increase of 0.7-1.0 m/yr, which is consistent with estimated surface mass balance (SMB) of 0.7-0.9 m.w.e./yr from RACMO2.3 and firn compaction rates from the IMAU-FDM dynamic firn model. An abrupt 0.2-0.3 m surface elevation decrease due to surface melt and/or greater near-surface firn compaction is observed during a period of warm atmospheric temperatures from December 2012 to January 2013. Observed surface Dh/Dt for all PIG shelf sites is highly linear with trends of -1 to -4 m/yr and <0.4 m residuals. Similar Dh/Dt estimates with reduced variability are obtained after removing expected downward GPS pole base velocity from observed GPS antenna Dh/Dt. Estimated Dh/Dt basal melt rates are 10 to 40 m/yr for the outer PIG shelf and 4 m/yr for the South shelf. These melt rates are similar to those derived from ice-bottom acoustic ranging, phase-sensitive ice-penetrating radar, and high-resolution stereo DEM records. The GPS/DEM records document higher melt rates within and near transverse surface depressions and rifts associated with longitudinal extension. Basal melt rates for the 2012-2014 period show limited temporal variability, despite significant change in ocean heat content. This suggests that sub-shelf melt rates are less sensitive to ocean heat content than previously reported, at least for these locations and time periods.

Double Bright Band Observations with High-Resolution Vertically Pointing Radar, Lidar, and Profiles

NASA Technical Reports Server (NTRS)

Emory, Amber E.; Demoz, Belay; Vermeesch, Kevin; Hicks, Michael

2014-01-01

On 11 May 2010, an elevated temperature inversion associated with an approaching warm front produced two melting layers simultaneously, which resulted in two distinct bright bands as viewed from the ER-2 Doppler radar system, a vertically pointing, coherent X band radar located in Greenbelt, MD. Due to the high temporal resolution of this radar system, an increase in altitude of the melting layer of approximately 1.2 km in the time span of 4 min was captured. The double bright band feature remained evident for approximately 17 min, until the lower atmosphere warmed enough to dissipate the lower melting layer. This case shows the relatively rapid evolution of freezing levels in response to an advancing warm front over a 2 h time period and the descent of an elevated warm air mass with time. Although observations of double bright bands are somewhat rare, the ability to identify this phenomenon is important for rainfall estimation from spaceborne sensors because algorithms employing the restriction of a radar bright band to a constant height, especially when sampling across frontal systems, will limit the ability to accurately estimate rainfall.

Double bright band observations with high-resolution vertically pointing radar, lidar, and profilers

NASA Astrophysics Data System (ADS)

Emory, Amber E.; Demoz, Belay; Vermeesch, Kevin; Hicks, Micheal

2014-07-01

On 11 May 2010, an elevated temperature inversion associated with an approaching warm front produced two melting layers simultaneously, which resulted in two distinct bright bands as viewed from the ER-2 Doppler radar system, a vertically pointing, coherent X band radar located in Greenbelt, MD. Due to the high temporal resolution of this radar system, an increase in altitude of the melting layer of approximately 1.2 km in the time span of 4 min was captured. The double bright band feature remained evident for approximately 17 min, until the lower atmosphere warmed enough to dissipate the lower melting layer. This case shows the relatively rapid evolution of freezing levels in response to an advancing warm front over a 2 h time period and the descent of an elevated warm air mass with time. Although observations of double bright bands are somewhat rare, the ability to identify this phenomenon is important for rainfall estimation from spaceborne sensors because algorithms employing the restriction of a radar bright band to a constant height, especially when sampling across frontal systems, will limit the ability to accurately estimate rainfall.

Winter in Antarctica: dark, cold, windy, and .... wet?? Measurements and modeling of extensive wintertime surface melt

NASA Astrophysics Data System (ADS)

Kuipers Munneke, P.; Luckman, A. J.; Bevan, S. L.; Gilbert, E.; Smeets, P.; van den Broeke, M. R.; Wang, W.; Zender, C. S.; Ashmore, D. W.; Hubbard, B. P.; Orr, A.; King, J.

2017-12-01

We know that increased surface melt, driven by atmospheric warming, contributed to the collapse of ice shelves as observed in the Antarctic Peninsula. This has induced grounded-ice acceleration and increased ice discharge. You may associate this surface melt with the austral summer season, with plenty of solar radiation driving the melt. In contrast, winter in Antarctica evokes images of darkness, snow, and cold. However, we will make you rethink this picture by presenting observations of frequent snow surface melt in winter, from a weather station located in a previously unsurveyed area of the Larsen C Ice Shelf. Peak intensities of this wintertime melt even exceed summertime values, and thermal satellite images show that large ponds of meltwater are formed at the surface in the pitch-dark Antarctic winter. Obviously, we wanted to find out what could drive these strong melt events if it's not the sun. It turns out that these multi-day melt events occur when warm and dry föhn winds descend from the Antarctic Peninsula mountains. Simulations with a high-resolution weather model confirm that these winds generate turbulent fluxes of sensible heat, leading to melt fluxes in excess of 200 W m-2. In 2015 and 2016, about 23% of the annual melt was produced in winter. We use satellite radar to show that winter melt occurs on many more places in the Antarctic Peninsula. It happens every year, although in some years the melting is much more widespread than in others. We think that wintertime melt matters as its refreezing warms the snow and increases snow density. In this way, winter melt preconditions the ice shelf for more extensive surface drainage, potentially leading to meltwater-driven instability.

Joint small-angle X-ray and neutron scattering data analysis of asymmetric lipid vesicles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eicher, Barbara; Heberle, Frederick A.; Marquardt, Drew T.

2017-02-28

Low- and high-resolution models describing the internal transbilayer structure of asymmetric lipid vesicles have been developed. These models can be used for the joint analysis of small-angle neutron and X-ray scattering data. The models describe the underlying scattering length density/electron density profiles either in terms of slabs or through the so-called scattering density profile, previously applied to symmetric lipid vesicles. Both models yield structural details of asymmetric membranes, such as the individual area per lipid, and the hydrocarbon thickness of the inner and outer bilayer leaflets. The scattering density profile model, however, comes at a cost of increased computational effortmore » but results in greater structural resolution, showing a slightly lower packing of lipids in the outer bilayer leaflet of ~120 nm diameter palmitoyloleoyl phosphatidylcholine (POPC) vesicles, compared to the inner leaflet. Here, analysis of asymmetric dipalmitoyl phosphatidylcholine/POPC vesicles did not reveal evidence of transbilayer coupling between the inner and outer leaflets at 323 K, i.e.above the melting transition temperature of the two lipids.« less

High-resolution melting (HRM) assay for the detection of recurrent BRCA1/BRCA2 germline mutations in Tunisian breast/ovarian cancer families.

PubMed

Riahi, Aouatef; Kharrat, Maher; Lariani, Imen; Chaabouni-Bouhamed, Habiba

2014-12-01

Germline deleterious mutations in the BRCA1/BRCA2 genes are associated with an increased risk for the development of breast and ovarian cancer. Given the large size of these genes the detection of such mutations represents a considerable technical challenge. Therefore, the development of cost-effective and rapid methods to identify these mutations became a necessity. High resolution melting analysis (HRM) is a rapid and efficient technique extensively employed as high-throughput mutation scanning method. The purpose of our study was to assess the specificity and sensitivity of HRM for BRCA1 and BRCA2 genes scanning. As a first step we estimate the ability of HRM for detection mutations in a set of 21 heterozygous samples harboring 8 different known BRCA1/BRCA2 variations, all samples had been preliminarily investigated by direct sequencing, and then we performed a blinded analysis by HRM in a set of 68 further sporadic samples of unknown genotype. All tested heterozygous BRCA1/BRCA2 variants were easily identified. However the HRM assay revealed further alteration that we initially had not searched (one unclassified variant). Furthermore, sequencing confirmed all the HRM detected mutations in the set of unknown samples, including homozygous changes, indicating that in this cohort, with the optimized assays, the mutations detections sensitivity and specificity were 100 %. HRM is a simple, rapid and efficient scanning method for known and unknown BRCA1/BRCA2 germline mutations. Consequently the method will allow for the economical screening of recurrent mutations in Tunisian population.

Quantitative characterization of 3-dimensional melt distribution in partially molten olivine-basalt aggregates using X-ray synchrotron microtomography

NASA Astrophysics Data System (ADS)

Zhu, W.; Gaetani, G. A.; Fusseis, F.

2009-12-01

Quantitative knowledge of the distribution of small amounts of silicate melt in peridotite and of its influence on permeability are critical to our understanding of melt migration and segregation processes in the upper mantle. Estimates for the permeability of partially molten rock require 3D melt distribution at the grain-scale. Existing studies of melt distribution, carried out on 2D slices through experimental charges, have produced divergent models for melt distribution at small melt fractions. While some studies conclude that small amounts of melt are distributed primarily along triple junctions [e.g., Wark et al., 2003], others predict an important role for melt distribution along grain boundaries at low melt fractions [e.g., Faul 1997]. Using X-ray synchrotron microtomography, we have obtained the first high quality non-destructive imaging of 3D melt distribution in olivine-basalt aggregates. Textually equilibrated partially molten samples consisting of magnesian olivine plus 2, 5, 10, or 20% primitive basalt were synthesized at 1.5 GPa and 1350°C in experiments lasting 264-336 hours. Microtomographic images of melt distribution were obtained on cylindrical cores, 1 mm in diameter, at a spatial resolution of 1 micron. Textual information such as melt channel size, dihedral angle and channel connectivity was then quantified using AVIZO and MATLAB. Our results indicate that as melt fraction decreases, melt becomes increasingly distributed along 3 grain junctions, in agreement with theoretical predictions. We do not find significant amounts of melt along grain boundaries at low melt fractions. We found that the true dihedral angle ranges from 50 to 70°, in agreements with results using 2D microcopy. Comparison between the samples provides a quantitative characterization of how melt fraction affects melt distribution including connectivity. The geometrical data have been incorporated into our network model to obtain macroscale transport properties for partially molten dunite. Results from this tomographic study thus provide constraints on rates of melt migration and melt extraction within the partially molten regions beneath ocean ridges. Fig 1. Melt channels in an olivine-basalt sample with 10 vol% melt.

Variability of Surface Temperature and Melt on the Greenland Ice Sheet, 2000-2011

NASA Technical Reports Server (NTRS)

Hall, Dorothy K.; Comiso, Josefino, C.; Shuman, Christopher A.; Koenig, Lora S.; DiGirolamo, Nicolo E.

2012-01-01

Enhanced melting along with surface-temperature increases measured using infrared satellite data, have been documented for the Greenland Ice Sheet. Recently we developed a climate-quality data record of ice-surface temperature (IST) of the Greenland Ice Sheet using the Moderate-Resolution Imaging Spectroradiometer (MODIS) 1ST product -- http://modis-snow-ice.gsfc.nasa.gov. Using daily and mean monthly MODIS 1ST maps from the data record we show maximum extent of melt for the ice sheet and its six major drainage basins for a 12-year period extending from March of 2000 through December of 2011. The duration of the melt season on the ice sheet varies in different drainage basins with some basins melting progressively earlier over the study period. Some (but not all) of the basins also show a progressively-longer duration of melt. The short time of the study period (approximately 12 years) precludes an evaluation of statistically-significant trends. However the dataset provides valuable information on natural variability of IST, and on the ability of the MODIS instrument to capture changes in IST and melt conditions indifferent drainage basins of the ice sheet.

Examination of nanosecond laser melting thresholds in refractory metals by shear wave acoustics

NASA Astrophysics Data System (ADS)

Abdullaev, A.; Muminov, B.; Rakhymzhanov, A.; Mynbayev, N.; Utegulov, Z. N.

2017-07-01

Nanosecond laser pulse-induced melting thresholds in refractory (Nb, Mo, Ta and W) metals are measured using detected laser-generated acoustic shear waves. Obtained melting threshold values were found to be scaled with corresponding melting point temperatures of investigated materials displaying dissimilar shearing behavior. The experiments were conducted with motorized control of the incident laser pulse energies with small and uniform energy increments to reach high measurement accuracy and real-time monitoring of the epicentral acoustic waveforms from the opposite side of irradiated sample plates. Measured results were found to be in good agreement with numerical finite element model solving coupled elastodynamic and thermal conduction governing equations on structured quadrilateral mesh. Solid-melt phase transition was handled by means of apparent heat capacity method. The onset of melting was attributed to vanished shear modulus and rapid radial molten pool propagation within laser-heated metal leading to preferential generation of transverse acoustic waves from sources surrounding the molten mass resulting in the delay of shear wave transit times. Developed laser-based technique aims for applications involving remote examination of rapid melting processes of materials present in harsh environment (e.g. spent nuclear fuels) with high spatio-temporal resolution.

Mass Fluxes of Ice and Oxygen Across the Entire Lid of Lake Vostok from Observations of Englacial Radiowave Attenuation

NASA Astrophysics Data System (ADS)

Winebrenner, D. P.; Kintner, P. M. S.; MacGregor, J. A.

2017-12-01

Over deep Antarctic subglacial lakes, spatially varying ice thickness and the pressure-dependent melting point of ice result in areas of melting and accretion at the ice-water interface, i.e., the lake lid. These ice mass fluxes drive lake circulation and, because basal Antarctic ice contains air-clathrate, affect the input of oxygen to the lake, with implications for subglacial life. Inferences of melting and accretion from radar-layer tracking and geodesy are limited in spatial coverage and resolution. Here we develop a new method to estimate rates of accretion, melting, and the resulting oxygen input at a lake lid, using airborne radar data over Lake Vostok together with ice-temperature and chemistry data from the Vostok ice core. Because the lake lid is a coherent reflector of known reflectivity (at our radar frequency), we can infer depth-averaged radiowave attenuation in the ice, with spatial resolution 1 km along flight lines. Spatial variation in attenuation depends mostly on variation in ice temperature near the lid, which in turn varies strongly with ice mass flux at the lid. We model ice temperature versus depth with ice mass flux as a parameter, thus linking that flux to (observed) depth-averaged attenuation. The resulting map of melt- and accretion-rates independently reproduces features known from earlier studies, but now covers the entire lid. We find that accretion is dominant when integrated over the lid, with an ice imbalance of 0.05 to 0.07 km3 a-1, which is robust against uncertainties.

On the impact of ice-ocean interaction on Greenland glaciers versus calving speed.

NASA Astrophysics Data System (ADS)

Rignot, E. J.; Menemenlis, D.; Morlighem, M.; Wood, M.; Millan, R.; Mouginot, J.; An, L.

2016-12-01

Glacier retreat from frontal ablation is a delicate balance between subaqueous melt, calving processes and bed geometry. Here, we model subaqueous melt from a large number of Greenland tidewater glaciers using generalized 3D, high resolution simulations of ice melt from the MITgcm ocean model constrained by subglacial melt from RACMO2.3 and ISSM, ocean temperature from ECCO2-4km Arctic, and bed topography from OMG and MC for 1992-2015. The results are analyzed in combination with ice-front retreat and glacier speed from Landsat and imaging radar data since the 1990s. We find that subaqueous melt is 2-3 times greater in summer than in winter and doubled in magnitude since the 1990s because of enhanced ice sheet runoff and warmer ocean temperature. Glaciers that retreated rapidly are characterized by subaqueous melt rates comparable to their calving speed and favorable bed geometry. Glaciers dominated by calving processes are in contrast more resilient to thermal forcing from the ocean, especially in the presence of stabilizing geometry. The study highlights the fundamental importance of calving processes in controlling glacier retreat in Greenland.

The influence of the hydrologic cycle on the extent of sea ice with climatic implications

NASA Technical Reports Server (NTRS)

Dean, Kenneson G.; Stringer, William J.; Searcy, Craig

1993-01-01

Multi-temporal satellite images, field observations, and field measurements were used to investigate the mechanisms by which sea ice melts offshore from the Mackenzie River delta. Advanced Very High Resolution Radiometer (AVHRR) satellite data recorded in 1986 were analyzed. The satellite data were geometrically corrected and radiometrically calibrated so that albedo and temperature values could be extracted. The investigation revealed that sea ice melted approximately 2 weeks earlier offshore from the Mackenzie River delta than along coasts where river discharge is minimal or non-existent. There is significant intra-delta variability in the timing and patterns of ice melt. An estimation of energy flux indicates that 30 percent more of the visible wavelength energy and 25 percent more of the near-infrared wavelength energy is absorbed by water offshore of the delta compared to coastal areas with minimal river discharge. The analysis also revealed that the removal of sea ice involves the following: over-ice-flooding along the coast offshore from river delta channels; under-ice flow of 'warm' river water; melting and calving of the fast ice; and, the formation of a bight in the pack ice edge. Two stages in the melting of sea ice were identified: (1) an early stage where heat is supplied to overflows largely by solar radiation, and (2) a later stage where heat is supplied by river discharge in addition to solar radiation. A simple thermodynamic model of the thaw process in the fast ice zone was developed and parameterized based on events recorded by the satellite images. The model treats river discharge as the source of sensible heat at the base of the ice cover. The results of a series of sensitivity tests to assess the influence of river discharge on the near shore ice are presented.

Experimental determination of the thermal conductivity of liquid UO2 near the melting point

NASA Astrophysics Data System (ADS)

Sheindlin, M.; Staicu, D.; Ronchi, C.; Game-Arnaud, L.; Remy, B.; Degiovanni, A.

2007-05-01

The article gives an account of measurements of the thermal conductivity of liquid UO2. The sample was heated up to above the melting point by a laser pulse of a controlled shape, and the produced thermogram of temperature history was measured by a fast and accurate pyrometer with a time resolution of 10 μs. The experiment shows that the rate of temperature increase during the ascending part of the pulse changes moderately across the melting point. Due to the high power input, this effect cannot be explained in terms of the sole intake of latent heat of fusion. By solving the related heat transfer equation with a 2D-axisymmetric numerical model, it is demonstrated that this feature depends principally on heat conduction in the sample, and proves that the thermal conductivities of solid and liquid are not very different. A theoretical sensitivity study assessing the influence of the liquid thermal conductivity on the pulse temperature evolution showed that the conductivity of the liquid can be deduced from the fitting of the thermograms with a numerical precision of the order of 1%. The analysis reveals that the thermal conductivity is weakly correlated with the effective heat losses during the pulse and to the melting enthalpy, so that the uncertainty in its evaluation by fitting the experimental thermograms with model predictions is satisfactory. The value of the thermal conductivity of liquid UO2 near the melting point resulted to be 2.6±0.35 W m-1 K-1, where the magnitude of the uncertainty is much lower than the scatter of the previously published, discordant measurements.

Modeling of submarine melting in Petermann Fjord, Northwestern Greenland using an ocean general circulation model

NASA Astrophysics Data System (ADS)

Cai, C.; Rignot, E. J.; Xu, Y.; An, L.

2013-12-01

Basal melting of the floating tongue of Petermann Glacier, in northwestern Greenland is by far the largest process of mass ablation. Melting of the floating tongue is controlled by the buoyancy of the melt water plume, the pressure-dependence of the melting point of sea ice, and the mixing of warm subsurface water with fresh buoyant subglacial discharge. In prior simulations of this melting process, the role of subglacial discharge has been neglected because in similar configurations (floating ice shelves) in the Antarctic, surface runoff is negligible; this is however not true in Greenland. Here, we use the Mass Institute of Technology general circulation model (MITgcm) at a high spatial resolution (10 m x 10 m) to simulate the melting process of the ice shelf in 2-D. the model is constrained by ice shelf bathymetry and ice thickness from NASA Operation IceBridge, ocean temperature/salinity data from Johnson et al. (2011), and subglacial discharge estimated from output products of the Regional Atmospheric Climate Model (RACMO). We compare the results obtained in winter (no runoff) with summer, and the sensitivity of the results to thermal forcing from the ocean, and to the magnitude of subglacial runoff. We conclude on the impact of the ocean and surface melting on the melting regime of the floating ice tongue of Petermann. This work is performed under a contract with NASA Cryosphere Program.

Mapping Snow Grain Size over Greenland from MODIS

NASA Technical Reports Server (NTRS)

Lyapustin, Alexei; Tedesco, Marco; Wang, Yujie; Kokhanovsky, Alexander

2008-01-01

This paper presents a new automatic algorithm to derive optical snow grain size (SGS) at 1 km resolution using Moderate Resolution Imaging Spectroradiometer (MODIS) measurements. Differently from previous approaches, snow grains are not assumed to be spherical but a fractal approach is used to account for their irregular shape. The retrieval is conceptually based on an analytical asymptotic radiative transfer model which predicts spectral bidirectional snow reflectance as a function of the grain size and ice absorption. The analytical form of solution leads to an explicit and fast retrieval algorithm. The time series analysis of derived SGS shows a good sensitivity to snow metamorphism, including melting and snow precipitation events. Preprocessing is performed by a Multi-Angle Implementation of Atmospheric Correction (MAIAC) algorithm, which includes gridding MODIS data to 1 km resolution, water vapor retrieval, cloud masking and an atmospheric correction. MAIAC cloud mask (CM) is a new algorithm based on a time series of gridded MODIS measurements and an image-based rather than pixel-based processing. Extensive processing of MODIS TERRA data over Greenland shows a robust performance of CM algorithm in discrimination of clouds over bright snow and ice. As part of the validation analysis, SGS derived from MODIS over selected sites in 2004 was compared to the microwave brightness temperature measurements of SSM\\I radiometer, which is sensitive to the amount of liquid water in the snowpack. The comparison showed a good qualitative agreement, with both datasets detecting two main periods of snowmelt. Additionally, MODIS SGS was compared with predictions of the snow model CROCUS driven by measurements of the automatic whether stations of the Greenland Climate Network. We found that CROCUS grain size is on average a factor of two larger than MODIS-derived SGS. Overall, the agreement between CROCUS and MODIS results was satisfactory, in particular before and during the first melting period in mid-June. Following detailed time series analysis of SGS for four permanent sites, the paper presents SGS maps over the Greenland ice sheet for the March-September period of 2004.

Melt extraction during heating and cooling of felsic crystal mushes in shallow volcanic systems: An experimental study

NASA Astrophysics Data System (ADS)

Pistone, M.; Baumgartner, L. P.; Sisson, T. W.; Bloch, E. M.

2017-12-01

The dynamics and kinetics of melt extraction in near-solidus, rheologically stalled, felsic crystal mushes (> 50 vol.% crystals) are essential to feeding many volcanic eruptions. At shallow depths (< 15 km), most felsic crystal mushes would be volatile-saturated and may be thermally stable for long time periods (104-107 years). In absence of deformation, residual melt can segregate from the mush's crystalline framework stimulated by: 1) gas injecting from hot mafic magmas into felsic mushes (heating / partial melting scenario), and 2) gas exsolving from the crystallizing mush (cooling / crystallizing scenario). The conditions and efficiency of melt extraction from a mush in the two scenarios are not well understood. Thus, we conducted high-temperature (700 to 850 °C) and -pressure (1.1 kbar) cold seal experiments (8-day duration) on synthetic felsic mushes, composed of water-saturated (4.2 wt.%) rhyodacite melt bearing different proportions of added quartz crystals (60, 70, and 80 vol%; 68 mm average particle size). High-spatial resolution X-ray tomography of run products show: 1) in the heating scenario (> 750 °C) melt has not segregated due to coalescence of vesicles (≤ 23 vol%) and large melt connectivity (> 7 vol% glass) / low pressure gradient for melt movement up to 80 vol% crystals; 2) in the cooling scenario (≤ 750 °C) vesicle (< 11 vol%) coalescence is limited or absent and limited amount of melt (3 to 11 vol%) segregated from sample center to its outer periphery (30 to 100 mm melt-rich lenses), testifying to the efficiency of melt extraction dictated by increasing crystallinity. These results suggest that silicic melt hosted within a crystal-rich mush can accumulate rapidly due to the buildup of modest gas pressures during crystallization at temperatures near the solidus.

Identification of Trypanosoma cruzi discrete typing units (DTUs) through the implementation of a high-resolution melting (HRM) genotyping assay.

PubMed

Higuera, Sonia L; Guhl, Felipe; Ramírez, Juan David

2013-04-20

Chagas disease, caused by Trypanosoma cruzi, is a geographically widespread anthropozoonosis that is considered a major public health problem in Latin America. Because this parasite presents high genetic variability, a nomenclature has been adopted to classify the parasite into six discrete typing units (DTUs): TcI, TcII, TcIII, TcIV, TcV, and TcVI, which present different eco-epidemiological, clinical, and geographic associations. Currently, the available genotyping methods present a series of drawbacks that implies the need for developing new methods for characterizing T. cruzi DTU's. The aim of this work was to genotype reference populations from T. cruzi by means of a High-Resolution Melting (HRM) genotyping assay. Amplification of the mini-exon gene allowed the genotyping of three distinct groups: TcI, TcII- TcIV- TcV, and TcIII-TcVI, while amplification of the 24sα gene generated non-overlapping melting temperature ranges for each DTU that were used to identify the groups in the six existing DTUs of Trypanosoma cruzi. The proposed genotyping assay allowed discrimination of the six genetic groups by obtaining specific melting curves for each DTU. The application of this technique is proposed because of its specificity, sensitivity, high performance, and low cost compared with other previously described characterization methods.

Application of TlBr to nuclear medicine imaging

NASA Astrophysics Data System (ADS)

Cirignano, Leonard; Kim, Hadong; Kargar, Alireza; Churilov, Alexei V.; Ciampi, Guido; Higgins, William; Kim, Suyoung; Barber, Bradford; Haston, Kyle; Shah, Kanai

2012-10-01

Thallium bromide (TlBr) has been under development for room temperature gamma ray spectroscopy due to high density, high Z and wide bandgap of the material. Furthermore, its low melting point (460 °C), cubic crystal structure and congruent melting with no solid-solid phase transitions between the melting point and room temperature, TlBr can be grown by relatively simple melt based methods. As a result of improvements in material processing and detector fabrication over the last several years, TlBr with electron mobility-lifetime products (μeτe) in the mid 10-3 cm2/V range has been obtained. In this paper we are going to report on our unipolar charging TlBr results for the application as a small animal imaging. For SPECT application, about 5 mm thick pixellated detectors were fabricated and tested. About 1 % FWHM at 662 keV energy resolution was estimated at room temperature. By applying the depth correction technique, less than 1 % energy resolution was estimated. We are going to report the results from orthogonal strip TlBr detector for PET application. In this paper we also present our latest detector highlights and recent progress made in long term stability of TlBr detectors at or near room temperature. This work is being supported by the Domestic Nuclear Detection Office (DNDO) and the Department of Energy (DOE).

Universal digital high-resolution melt: a novel approach to broad-based profiling of heterogeneous biological samples.

PubMed

Fraley, Stephanie I; Hardick, Justin; Masek, Billie J; Jo Masek, Billie; Athamanolap, Pornpat; Rothman, Richard E; Gaydos, Charlotte A; Carroll, Karen C; Wakefield, Teresa; Wang, Tza-Huei; Yang, Samuel

2013-10-01

Comprehensive profiling of nucleic acids in genetically heterogeneous samples is important for clinical and basic research applications. Universal digital high-resolution melt (U-dHRM) is a new approach to broad-based PCR diagnostics and profiling technologies that can overcome issues of poor sensitivity due to contaminating nucleic acids and poor specificity due to primer or probe hybridization inaccuracies for single nucleotide variations. The U-dHRM approach uses broad-based primers or ligated adapter sequences to universally amplify all nucleic acid molecules in a heterogeneous sample, which have been partitioned, as in digital PCR. Extensive assay optimization enables direct sequence identification by algorithm-based matching of melt curve shape and Tm to a database of known sequence-specific melt curves. We show that single-molecule detection and single nucleotide sensitivity is possible. The feasibility and utility of U-dHRM is demonstrated through detection of bacteria associated with polymicrobial blood infection and microRNAs (miRNAs) associated with host response to infection. U-dHRM using broad-based 16S rRNA gene primers demonstrates universal single cell detection of bacterial pathogens, even in the presence of larger amounts of contaminating bacteria; U-dHRM using universally adapted Lethal-7 miRNAs in a heterogeneous mixture showcases the single copy sensitivity and single nucleotide specificity of this approach.

A characteristics-based method for solving the transport equation and its application to the process of mantle differentiation and continental root growth

NASA Astrophysics Data System (ADS)

de Smet, Jeroen H.; van den Berg, Arie P.; Vlaar, Nico J.; Yuen, David A.

2000-03-01

Purely advective transport of composition is of major importance in the Geosciences, and efficient and accurate solution methods are needed. A characteristics-based method is used to solve the transport equation. We employ a new hybrid interpolation scheme, which allows for the tuning of stability and accuracy through a threshold parameter ɛth. Stability is established by bilinear interpolations, and bicubic splines are used to maintain accuracy. With this scheme, numerical instabilities can be suppressed by allowing numerical diffusion to work in time and locally in space. The scheme can be applied efficiently for preliminary modelling purposes. This can be followed by detailed high-resolution experiments. First, the principal effects of this hybrid interpolation method are illustrated and some tests are presented for numerical solutions of the transport equation. Second, we illustrate that this approach works successfully for a previously developed continental evolution model for the convecting upper mantle. In this model the transport equation contains a source term, which describes the melt production in pressure-released partial melting. In this model, a characteristic phenomenon of small-scale melting diapirs is observed (De Smet et al.1998; De Smet et al. 1999). High-resolution experiments with grid cells down to 700m horizontally and 515m vertically result in highly detailed observations of the diapiric melting phenomenon.

Numerical modeling of polymorphic transformation of oleic acid via near-infrared spectroscopy and factor analysis.

PubMed

Liu, Ling; Cheng, Yuliang; Sun, Xiulan; Pi, Fuwei

2018-05-15

Near-infrared (NIR) spectroscopy as a tool for direct and quantitatively screening the minute polymorphic transitions of bioactive fatty acids was assessed basing on a thermal heating process of oleic acid. Temperature-dependent NIR spectral profiles indicate that dynamical variances of COOH group dominate its γ → α phase transition, while the transition from active α to β phase mainly relates to the conformational transfer of acyl chain. Through operating multivariate curve resolution-alternating least squares with factor analysis, instantaneous contribution of each active polymorph during the transition process was illustrated for displaying the progressive evolutions of functional groups. Calculated contributions reveal that the α phase of oleic acid initially is present at around -18 °C, but sharply grows up around -2.2 °C from the transformation of γ phase and finally disappears at the melting point. On the other hand, the β phase of oleic acid is sole self-generation after melt even it embryonically appears at -2.2 °C. Such mathematical approach based on NIR spectroscopy and factor analysis calculation provides a volatile strategy in quantitatively exploring the transition processes of bioactive fatty acids; meanwhile, it maintains promising possibility for instantaneous quantifying each active polymorph of lipid materials. Copyright © 2018 Elsevier B.V. All rights reserved.

Numerical modeling of polymorphic transformation of oleic acid via near-infrared spectroscopy and factor analysis

NASA Astrophysics Data System (ADS)

Liu, Ling; Cheng, Yuliang; Sun, Xiulan; Pi, Fuwei

2018-05-01

Near-infrared (NIR) spectroscopy as a tool for direct and quantitatively screening the minute polymorphic transitions of bioactive fatty acids was assessed basing on a thermal heating process of oleic acid. Temperature-dependent NIR spectral profiles indicate that dynamical variances of COOH group dominate its γ → α phase transition, while the transition from active α to β phase mainly relates to the conformational transfer of acyl chain. Through operating multivariate curve resolution-alternating least squares with factor analysis, instantaneous contribution of each active polymorph during the transition process was illustrated for displaying the progressive evolutions of functional groups. Calculated contributions reveal that the α phase of oleic acid initially is present at around -18 °C, but sharply grows up around -2.2 °C from the transformation of γ phase and finally disappears at the melting point. On the other hand, the β phase of oleic acid is sole self-generation after melt even it embryonically appears at -2.2 °C. Such mathematical approach based on NIR spectroscopy and factor analysis calculation provides a volatile strategy in quantitatively exploring the transition processes of bioactive fatty acids; meanwhile, it maintains promising possibility for instantaneous quantifying each active polymorph of lipid materials.

Identification of Molecular Markers Associated with Verticillium Wilt Resistance in Alfalfa (Medicago Sativa L.) Using High-Resolution Melting

PubMed Central

Zhang, Tiejun; Yu, Long-Xi; McCord, Per; Miller, David; Bhamidimarri, Suresh; Johnson, David; Monteros, Maria J.; Ho, Julie; Reisen, Peter; Samac, Deborah A.

2014-01-01

Verticillium wilt, caused by the soilborne fungus, Verticillium alfalfae, is one of the most serious diseases of alfalfa (Medicago sativa L.) worldwide. To identify loci associated with resistance to Verticillium wilt, a bulk segregant analysis was conducted in susceptible or resistant pools constructed from 13 synthetic alfalfa populations, followed by association mapping in two F1 populations consisted of 352 individuals. Simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers were used for genotyping. Phenotyping was done by manual inoculation of the pathogen to replicated cloned plants of each individual and disease severity was scored using a standard scale. Marker-trait association was analyzed by TASSEL. Seventeen SNP markers significantly associated with Verticillium wilt resistance were identified and they were located on chromosomes 1, 2, 4, 7 and 8. SNP markers identified on chromosomes 2, 4 and 7 co-locate with regions of Verticillium wilt resistance loci reported in M. truncatula. Additional markers identified on chromosomes 1 and 8 located the regions where no Verticillium resistance locus has been reported. This study highlights the value of SNP genotyping by high resolution melting to identify the disease resistance loci in tetraploid alfalfa. With further validation, the markers identified in this study could be used for improving resistance to Verticillium wilt in alfalfa breeding programs. PMID:25536106

Identification of molecular markers associated with Verticillium wilt resistance in alfalfa (Medicago sativa L.) using high-resolution melting.

PubMed

Zhang, Tiejun; Yu, Long-Xi; McCord, Per; Miller, David; Bhamidimarri, Suresh; Johnson, David; Monteros, Maria J; Ho, Julie; Reisen, Peter; Samac, Deborah A

2014-01-01

Verticillium wilt, caused by the soilborne fungus, Verticillium alfalfae, is one of the most serious diseases of alfalfa (Medicago sativa L.) worldwide. To identify loci associated with resistance to Verticillium wilt, a bulk segregant analysis was conducted in susceptible or resistant pools constructed from 13 synthetic alfalfa populations, followed by association mapping in two F1 populations consisted of 352 individuals. Simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers were used for genotyping. Phenotyping was done by manual inoculation of the pathogen to replicated cloned plants of each individual and disease severity was scored using a standard scale. Marker-trait association was analyzed by TASSEL. Seventeen SNP markers significantly associated with Verticillium wilt resistance were identified and they were located on chromosomes 1, 2, 4, 7 and 8. SNP markers identified on chromosomes 2, 4 and 7 co-locate with regions of Verticillium wilt resistance loci reported in M. truncatula. Additional markers identified on chromosomes 1 and 8 located the regions where no Verticillium resistance locus has been reported. This study highlights the value of SNP genotyping by high resolution melting to identify the disease resistance loci in tetraploid alfalfa. With further validation, the markers identified in this study could be used for improving resistance to Verticillium wilt in alfalfa breeding programs.

Validation of methylation-sensitive high-resolution melting (MS-HRM) for the detection of stool DNA methylation in colorectal neoplasms.

PubMed

Xiao, Zhujun; Li, Bingsheng; Wang, Guozhen; Zhu, Weisi; Wang, Zhongqiu; Lin, Jinfeng; Xu, Angao; Wang, Xinying

2014-04-20

Methylation-sensitive high-resolution melting (MS-HRM) is a new technique for assaying DNA methylation, but its feasibility for assaying stool in patients with colorectal cancer (CRC) is unknown. First, the MS-HRM and methylation-specific PCR (MSP) detection limits were tested. Second, the methylation statuses of SFRP2 and VIM were analyzed in stool samples by MS-HRM, and in matching tumor and normal colon tissues via bisulfite sequencing PCR (BSP). Third, a case-control study evaluated the diagnostic sensitivity and specificity of MS-HRM relative to results obtained with MSP and the fecal immunochemical test (FIT). Finally, the linearity and reproducibility of MS-HRM were assessed. The detection limits of MS-HRM and MSP were 1% and 5%, respectively. The diagnostic sensitivities of MS-HRM (87.3%, 55/63) in stool and BSP in matching tumor tissue (92.1%, 58/63) were highly consistent (κ=0.744). The MS-HRM assay detected 92.5% (37/40) methylation in CRCs, 94.4% (34/36) in advanced adenomas, and 8.8% (5/57) in normal controls. The results of MS-HRM analysis were stable and reliable and showed fairly good linearity for both SFRP2 (P<0.001, R(2)=0.957) and VIM (P<0.001, R(2)=0.954). MS-HRM shows potential for CRC screening. Copyright © 2014 Elsevier B.V. All rights reserved.

Spectroscopic studies on the interaction of sodium benzoate, a food preservative, with calf thymus DNA.

PubMed

Zhang, Guowen; Ma, Yadi

2013-11-01

The interaction between sodium benzoate (SB) and calf thymus DNA in simulated physiological buffer (pH 7.4) using acridine orange (AO) dye as a fluorescence probe, was investigated by UV-Vis absorption, fluorescence and circular dichroism (CD) spectroscopy along with DNA melting studies and viscosity measurements. An expanded UV-Vis spectral data matrix was resolved by multivariate curve resolution-alternating least squares (MCR-ALS) approach. The equilibrium concentration profiles and the pure spectra for SB, DNA and DNA-SB complex from the high overlapping composite response were simultaneously obtained. The results indicated that SB could bind to DNA, and hydrophobic interactions and hydrogen bonds played a vital role in the binding process. Moreover, SB was able to quench the fluorescence of DNA-AO complex through a static procedure. The quenching observed was indicative of an intercalative mode of interaction between SB and DNA, which was supported by melting studies, viscosity measurements and CD analysis. Copyright © 2013 Elsevier Ltd. All rights reserved.

Crystal Structure Variations of Sn Nanoparticles upon Heating

NASA Astrophysics Data System (ADS)

Mittal, Jagjiwan; Lin, Kwang-Lung

2018-04-01

Structural changes in Sn nanoparticles during heating below the melting point have been investigated using differential scanning calorimetry (DSC), x-ray diffraction (XRD) analysis, electron diffraction (ED), and high-resolution transmission electron microscopy (HRTEM). DSC revealed that the heat required to melt the nanoparticles (28.43 J/g) was about half compared with Sn metal (52.80 J/g), which was attributed to the large surface energy contribution for the nanoparticles. ED and XRD analyses of the Sn nanoparticles revealed increased intensity for crystal planes having large interplaner distances compared with regular crystal planes with increasing heat treatment temperature (HTT). HRTEM revealed an increase in interlayer spacing at the surface and near joints between nanoparticles with the HTT, leading to an amorphous structure of nanoparticles at the surface at 220°C. These results highlight the changes that occur in the morphology and crystal structure of Sn nanoparticles at the surface and in the interior with increase of the heat treatment temperature.

The Autumn of break-ups: When Jakobshavn Isbrae lost its floating tongue

NASA Astrophysics Data System (ADS)

Aschwanden, A.; Fahnestock, M. A.; Truffer, M.; Motyka, R. J.

2015-12-01

Capturing the temporal variability in outlet glacier flow remains one of the holy grails in ice sheet modeling. Here we demonstrate progress using the three-dimensional Parallel Ice Sheet Model. Using a first-order calving law and prescribed subshelf basal melt rates, we performed high-resolution (<1km) hindcasts of the Greenland Ice Sheet of the 1989-2012 period. These hindcasts allow us to study the processes governing ice-shelf thinning, break-up, and subsequent speed-ups and dynamic thinning. Focussing our analysis on the Jakobshavn basin we show that our simulations are able to capture the thinning of the floating tongue resulting from increased subshelf basal melt rates. Furthermore, our simulations capture both the magnitude and the timing of the dynamic thinning associated with the loss of the floating tongue, as well as the speed-up. We find little seasonal variations in surface speeds prior to 1995, and strong variations thereafter, in good agreement with observations of Echelmeyer and Harrison (1991) and Joughin et al (2012).

Continuous summer export of nitrogen-rich organic matter from the Greenland Ice Sheet inferred by ultrahigh resolution mass spectrometry.

PubMed

Lawson, Emily C; Bhatia, Maya P; Wadham, Jemma L; Kujawinski, Elizabeth B

2014-12-16

Runoff from glaciers and ice sheets has been acknowledged as a potential source of bioavailable dissolved organic matter (DOM) to downstream ecosystems. This source may become increasingly significant as glacial melt rates increase in response to future climate change. Recent work has identified significant concentrations of bioavailable carbon and iron in Greenland Ice Sheet (GrIS) runoff. The flux characteristics and export of N-rich DOM are poorly understood. Here, we employed electrospray ionization (ESI) coupled to Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) to determine the elemental compositions of DOM molecules in supraglacial water and subglacial runoff from a large GrIS outlet glacier. We provide the first detailed temporal analysis of the molecular composition of DOM exported over a full melt season. We find that DOM pools in supraglacial and subglacial runoff are compositionally diverse and that N-rich material is continuously exported throughout the melt season, as the snowline retreats further inland. Identification of protein-like compounds and a high proportion of N-rich DOM, accounting for 27-41% of the DOM molecules identified by ESI FT-ICR MS, may suggest a microbial provenance and high bioavailability of glacially exported DOM to downstream microbial communities.

A novel HRM assay for the simultaneous detection and differentiation of eight poxviruses of medical and veterinary importance

PubMed Central

Gelaye, Esayas; Mach, Lukas; Kolodziejek, Jolanta; Grabherr, Reingard; Loitsch, Angelika; Achenbach, Jenna E.; Nowotny, Norbert; Diallo, Adama; Lamien, Charles Euloge

2017-01-01

Poxviruses belonging to the Orthopoxvirus, Capripoxvirus and Parapoxvirus genera share common host species and create a challenge for diagnosis. Here, we developed a novel multiplex PCR method for the simultaneous detection and differentiation of eight poxviruses, belonging to three genera: cowpox virus (CPXV) and camelpox virus (CMLV) [genus Orthopoxvirus]; goatpox virus (GTPV), sheeppox virus (SPPV) and lumpy skin disease virus (LSDV) [genus Capripoxvirus]; orf virus (ORFV), pseudocowpox virus (PCPV) and bovine papular stomatitis virus (BPSV) [genus Parapoxvirus]. The assay is based on high-resolution melting curve analysis (HRMCA) of PCR amplicons produced using genus specific primer pairs and dsDNA binding dye. Differences in fragment size and GC content were used as discriminating power. The assay generated three well separated melting regions for each genus and provided additional intra-genus genotyping allowing the differentiation of the eight poxviruses based on amplicon melting temperature. Out of 271 poxviral DNA samples tested: seven CPXV, 25 CMLV, 42 GTPV, 20 SPPV, 120 LSDV, 33 ORFV, 20 PCPV and two BPSV were detected; two samples presented co-infection with CMLV and PCPV. The assay provides a rapid, sensitive, specific and cost-effective method for the detection of pox diseases in a broad range of animal species and humans. PMID:28216667

Three-dimensional spectral analysis of compositional heterogeneity at Arruntia crater on (4) Vesta using Dawn FC

NASA Astrophysics Data System (ADS)

Thangjam, Guneshwar; Nathues, Andreas; Mengel, Kurt; Schäfer, Michael; Hoffmann, Martin; Cloutis, Edward A.; Mann, Paul; Müller, Christian; Platz, Thomas; Schäfer, Tanja

2016-03-01

We introduce an innovative three-dimensional spectral approach (three band parameter space with polyhedrons) that can be used for both qualitative and quantitative analyzes improving the characterization of surface compositional heterogeneity of (4) Vesta. It is an advanced and more robust methodology compared to the standard two-dimensional spectral approach (two band parameter space). The Dawn Framing Camera (FC) color data obtained during High Altitude Mapping Orbit (resolution ∼ 60 m/pixel) is used. The main focus is on the howardite-eucrite-diogenite (HED) lithologies containing carbonaceous chondritic material, olivine, and impact-melt. The archived spectra of HEDs and their mixtures, from RELAB, HOSERLab and USGS databases as well as our laboratory-measured spectra are used for this study. Three-dimensional convex polyhedrons are defined using computed band parameter values of laboratory spectra. Polyhedrons based on the parameters of Band Tilt (R0.92μm/R0.96μm), Mid Ratio ((R0.75μm/R0.83μm)/(R0.83μm/R0.92μm)) and reflectance at 0.55 μm (R0.55μm) are chosen for the present analysis. An algorithm in IDL programming language is employed to assign FC data points to the respective polyhedrons. The Arruntia region in the northern hemisphere of Vesta is selected for a case study because of its geological and mineralogical importance. We observe that this region is eucrite-dominated howarditic in composition. The extent of olivine-rich exposures within an area of 2.5 crater radii is ∼12% larger than the previous finding (Thangjam, G. et al. [2014]. Meteorit. Planet. Sci. 49, 1831-1850). Lithologies of nearly pure CM2-chondrite, olivine, glass, and diogenite are not found in this region. Although there are no unambiguous spectral features of impact melt, the investigation of morphological features using FC clear filter data from Low Altitude Mapping Orbit (resolution ∼ 18 m/pixel) suggests potential impact-melt features inside and outside of the crater. Our spectral approach can be extended to the entire Vestan surface to study the heterogeneous surface composition and its geology.

Using SSR-HRM to Identify Closely Related Species in Herbal Medicine Products: A Case Study on Licorice.

PubMed

Li, Jingjian; Xiong, Chao; He, Xia; Lu, Zhaocen; Zhang, Xin; Chen, Xiaoyang; Sun, Wei

2018-01-01

Traditional herbal medicines have played important roles in the ways of life of people around the world since ancient times. Despite the advanced medical technology of the modern world, herbal medicines are still used as popular alternatives to synthetic drugs. Due to the increasing demand for herbal medicines, plant species identification has become an important tool to prevent substitution and adulteration. Here we propose a method for biological assessment of the quality of prescribed species in the Chinese Pharmacopoeia by use of high resolution melting (HRM) analysis of microsatellite loci. We tested this method on licorice, a traditional herbal medicine with a long history. Results showed that nine simple sequence repeat (SSR) markers produced distinct melting curve profiles for the five licorice species investigated using HRM analysis. These results were validated by capillary electrophoresis. We applied this protocol to commercially available licorice products, thus enabling the consistent identification of 11 labels with non-declared Glycyrrhiza species. This novel strategy may thus facilitate DNA barcoding as a method of identification of closely related species in herbal medicine products. Based on this study, a brief operating procedure for using the SSR-HRM protocol for herbal authentication is provided.

Using SSR-HRM to Identify Closely Related Species in Herbal Medicine Products: A Case Study on Licorice

PubMed Central

Li, Jingjian; Xiong, Chao; He, Xia; Lu, Zhaocen; Zhang, Xin; Chen, Xiaoyang; Sun, Wei

2018-01-01

Traditional herbal medicines have played important roles in the ways of life of people around the world since ancient times. Despite the advanced medical technology of the modern world, herbal medicines are still used as popular alternatives to synthetic drugs. Due to the increasing demand for herbal medicines, plant species identification has become an important tool to prevent substitution and adulteration. Here we propose a method for biological assessment of the quality of prescribed species in the Chinese Pharmacopoeia by use of high resolution melting (HRM) analysis of microsatellite loci. We tested this method on licorice, a traditional herbal medicine with a long history. Results showed that nine simple sequence repeat (SSR) markers produced distinct melting curve profiles for the five licorice species investigated using HRM analysis. These results were validated by capillary electrophoresis. We applied this protocol to commercially available licorice products, thus enabling the consistent identification of 11 labels with non-declared Glycyrrhiza species. This novel strategy may thus facilitate DNA barcoding as a method of identification of closely related species in herbal medicine products. Based on this study, a brief operating procedure for using the SSR-HRM protocol for herbal authentication is provided. PMID:29740326

High throughput integrated thermal characterization with non-contact optical calorimetry

NASA Astrophysics Data System (ADS)

Hou, Sichao; Huo, Ruiqing; Su, Ming

2017-10-01

Commonly used thermal analysis tools such as calorimeter and thermal conductivity meter are separated instruments and limited by low throughput, where only one sample is examined each time. This work reports an infrared based optical calorimetry with its theoretical foundation, which is able to provide an integrated solution to characterize thermal properties of materials with high throughput. By taking time domain temperature information of spatially distributed samples, this method allows a single device (infrared camera) to determine the thermal properties of both phase change systems (melting temperature and latent heat of fusion) and non-phase change systems (thermal conductivity and heat capacity). This method further allows these thermal properties of multiple samples to be determined rapidly, remotely, and simultaneously. In this proof-of-concept experiment, the thermal properties of a panel of 16 samples including melting temperatures, latent heats of fusion, heat capacities, and thermal conductivities have been determined in 2 min with high accuracy. Given the high thermal, spatial, and temporal resolutions of the advanced infrared camera, this method has the potential to revolutionize the thermal characterization of materials by providing an integrated solution with high throughput, high sensitivity, and short analysis time.

Empirical Retrieval of Surface Melt Magnitude from Coupled MODIS Optical and Thermal Measurements over the Greenland Ice Sheet during the 2001 Ablation Season

PubMed Central

Lampkin, Derrick; Peng, Rui

2008-01-01

Accelerated ice flow near the equilibrium line of west-central Greenland Ice Sheet (GIS) has been attributed to an increase in infiltrated surface melt water as a response to climate warming. The assessment of surface melting events must be more than the detection of melt onset or extent. Retrieval of surface melt magnitude is necessary to improve understanding of ice sheet flow and surface melt coupling. In this paper, we report on a new technique to quantify the magnitude of surface melt. Cloud-free dates of June 10, July 5, 7, 9, and 11, 2001 Moderate Resolution Imaging Spectroradiometer (MODIS) daily reflectance Band 5 (1.230-1.250μm) and surface temperature images rescaled to 1km over western Greenland were used in the retrieval algorithm. An optical-thermal feature space partitioned as a function of melt magnitude was derived using a one-dimensional thermal snowmelt model (SNTHERM89). SNTHERM89 was forced by hourly meteorological data from the Greenland Climate Network (GC-Net) at reference sites spanning dry snow, percolation, and wet snow zones in the Jakobshavn drainage basin in western GIS. Melt magnitude or effective melt (E-melt) was derived for satellite composite periods covering May, June, and July displaying low fractions (0-1%) at elevations greater than 2500m and fractions at or greater than 15% at elevations lower than 1000m assessed for only the upper 5 cm of the snow surface. Validation of E-melt involved comparison of intensity to dry and wet zones determined from QSCAT backscatter. Higher intensities (> 8%) were distributed in wet snow zones, while lower intensities were grouped in dry zones at a first order accuracy of ∼ ±2%. PMID:27873793

Empirical Retrieval of Surface Melt Magnitude from Coupled MODIS Optical and Thermal Measurements over the Greenland Ice Sheet during the 2001 Ablation Season.

PubMed

Lampkin, Derrick; Peng, Rui

2008-08-22

Accelerated ice flow near the equilibrium line of west-central Greenland Ice Sheet (GIS) has been attributed to an increase in infiltrated surface melt water as a response to climate warming. The assessment of surface melting events must be more than the detection of melt onset or extent. Retrieval of surface melt magnitude is necessary to improve understanding of ice sheet flow and surface melt coupling. In this paper, we report on a new technique to quantify the magnitude of surface melt. Cloud-free dates of June 10, July 5, 7, 9, and 11, 2001 Moderate Resolution Imaging Spectroradiometer (MODIS) daily reflectance Band 5 (1.230-1.250μm) and surface temperature images rescaled to 1km over western Greenland were used in the retrieval algorithm. An optical-thermal feature space partitioned as a function of melt magnitude was derived using a one-dimensional thermal snowmelt model (SNTHERM89). SNTHERM89 was forced by hourly meteorological data from the Greenland Climate Network (GC-Net) at reference sites spanning dry snow, percolation, and wet snow zones in the Jakobshavn drainage basin in western GIS. Melt magnitude or effective melt (E-melt) was derived for satellite composite periods covering May, June, and July displaying low fractions (0-1%) at elevations greater than 2500m and fractions at or greater than 15% at elevations lower than 1000m assessed for only the upper 5 cm of the snow surface. Validation of E-melt involved comparison of intensity to dry and wet zones determined from QSCAT backscatter. Higher intensities (> 8%) were distributed in wet snow zones, while lower intensities were grouped in dry zones at a first order accuracy of ~ ±2%.

Estimating stream discharge from a Himalayan Glacier using coupled satellite sensor data

NASA Astrophysics Data System (ADS)

Child, S. F.; Stearns, L. A.; van der Veen, C. J.; Haritashya, U. K.; Tarpanelli, A.

2015-12-01

The 4th IPCC report highlighted our limited understanding of Himalayan glacier behavior and contribution to the region's hydrology. Seasonal snow and glacier melt in the Himalayas are important sources of water, but estimates greatly differ about the actual contribution of melted glacier ice to stream discharge. A more comprehensive understanding of the contribution of glaciers to stream discharge is needed because streams being fed by glaciers affect the livelihoods of a large part of the world's population. Most of the streams in the Himalayas are unmonitored because in situ measurements are logistically difficult and costly. This necessitates the use of remote sensing platforms to obtain estimates of river discharge for validating hydrological models. In this study, we estimate stream discharge using cost-effective methods via repeat satellite imagery from Landsat-8 and SENTINEL-1A sensors. The methodology is based on previous studies, which show that ratio values from optical satellite bands correlate well with measured stream discharge. While similar, our methodology relies on significantly higher resolution imagery (30 m) and utilizes bands that are in the blue and near-infrared spectrum as opposed to previous studies using 250 m resolution imagery and spectral bands only in the near-infrared. Higher resolution imagery is necessary for streams where the source is a glacier's terminus because the width of the stream is often only 10s of meters. We validate our methodology using two rivers in the state of Kansas, where stream gauges are plentiful. We then apply our method to the Bhagirathi River, in the North-Central Himalayas, which is fed by the Gangotri Glacier and has a well monitored stream gauge. The analysis will later be used to couple river discharge and glacier flow and mass balance through an integrated hydrologic model in the Bhagirathi Basin.

Pore architecture of nanoporous gold and titania by hydrogen thermoporometry

DOE PAGES

Johnston, L. T.; Biener, M. M.; Ye, J. C.; ...

2015-07-10

Nanoporous gold (NPG) and materials derived from it by templating have complex pore architecture that determines their technologically relevant physical properties. Here, we apply high-resolution hydrogen thermoporometry to study the pore structure of NPG and NPG-derived titania nanofoam (TNF). Results reveal complex multimodal pore size distributions for NPG and TNF. The freezing–melting hysteresis is pronounced, with freezing and melting scans having entirely different shapes. Experiments involving partial freeze–melt cycles reveal the lack of direct correlation between individual freezing and melting peaks, pointing to phenomena that are beyond the Gibbs-Thomson formalism. The depression of the average freezing temperature scales linearly withmore » the ratio of the internal surface area (measured by gas sorption) and the total pore volume derived from the density of monoliths. In conclusion, thermoporometry yields total pore volumes in good agreement with those derived from monolith densities for both NPG and TNF.« less

Pore architecture of nanoporous gold and titania by hydrogen thermoporometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnston, L. T.; Biener, M. M.; Ye, J. C.

Nanoporous gold (NPG) and materials derived from it by templating have complex pore architecture that determines their technologically relevant physical properties. Here, we apply high-resolution hydrogen thermoporometry to study the pore structure of NPG and NPG-derived titania nanofoam (TNF). Results reveal complex multimodal pore size distributions for NPG and TNF. The freezing–melting hysteresis is pronounced, with freezing and melting scans having entirely different shapes. Experiments involving partial freeze–melt cycles reveal the lack of direct correlation between individual freezing and melting peaks, pointing to phenomena that are beyond the Gibbs-Thomson formalism. The depression of the average freezing temperature scales linearly withmore » the ratio of the internal surface area (measured by gas sorption) and the total pore volume derived from the density of monoliths. In conclusion, thermoporometry yields total pore volumes in good agreement with those derived from monolith densities for both NPG and TNF.« less

Integrating Thermodynamic Models in Geodynamic Simulations: The Example of the Community Software ASPECT

NASA Astrophysics Data System (ADS)

Dannberg, J.; Heister, T.; Grove, R. R.; Gassmoeller, R.; Spiegelman, M. W.; Bangerth, W.

2017-12-01

Earth's surface shows many features whose genesis can only be understood through the interplay of geodynamic and thermodynamic models. This is particularly important in the context of melt generation and transport: Mantle convection determines the distribution of temperature and chemical composition, the melting process itself is then controlled by the thermodynamic relations and in turn influences the properties and the transport of melt. Here, we present our extension of the community geodynamics code ASPECT, which solves the equations of coupled magma/mantle dynamics, and allows to integrate different parametrizations of reactions and phase transitions: They may alternatively be implemented as simple analytical expressions, look-up tables, or computed by a thermodynamics software. As ASPECT uses a variety of numerical methods and solvers, this also gives us the opportunity to compare different approaches of modelling the melting process. In particular, we will elaborate on the spatial and temporal resolution that is required to accurately model phase transitions, and show the potential of adaptive mesh refinement when applied to melt generation and transport. We will assess the advantages and disadvantages of iterating between fluid dynamics and chemical reactions derived from thermodynamic models within each time step, or decoupling them, allowing for different time step sizes. Beyond that, we will expand on the functionality required for an interface between computational thermodynamics and fluid dynamics models from the geodynamics side. Finally, using a simple example of melting of a two-phase, two-component system, we compare different time-stepping and solver schemes in terms of accuracy and efficiency, in dependence of the time scales of fluid flow and chemical reactions relative to each other. Our software provides a framework to integrate thermodynamic models in high resolution, 3d simulations of coupled magma/mantle dynamics, and can be used as a tool to study links between physical processes and geochemical signals in the Earth.

Permeability and 3-Dimensional Melt Distribution in Partially Molten Rocks

NASA Astrophysics Data System (ADS)

Zhu, Wen-Lu; Gaetani, Glenn; Fusseis, Florian

2010-05-01

Quantitative knowledge of the distribution of small amounts of silicate melt in peridotite and of its influence on permeability are critical to our understanding of melt migration and segregation processes in the upper mantle, as well as interpretations of the geochemical and geophysical observations at ocean ridges. For a system containing a single solid phase of isotropic interfacial energy, chemical and mechanical equilibrium requires a constant mean curvature of solid-melt interfaces and a single dihedral angle. Under these conditions, a simple power-law relationship between permeability, grain size and melt fraction, has been derived [e.g., von Bargen and Waff, 1986]. However, microstructural observations on texturally equilibrated, partially molten rocks reveal that the melt distribution is more complex than predicted by the isotropic model. Several factors, such as non-hydrostatic stress, anisotropic interfacial energy, or the presence of a second solid phase, will alter the power-law relationship. Better estimates for the permeability of partially molten rock require an accurate assessment of 3-dimensional melt distribution at the grain-scale. Existing studies of melt distribution, carried out on 2-D slices through experimental charges, have produced divergent models for melt distribution at small melt fractions. While some studies conclude that small amounts of melt are distributed primarily along 3-grain junctions [e.g., Wark et al., 2003], others predict an important role for melt distribution along grain boundaries at low melt fractions [e.g., Faul 1997]. Using X-ray synchrotron microtomography, we have carried out the first high quality non-destructive imaging of 3-dimensional melt distribution in experimentally equilibrated olivine-basalt aggregates [Zhu et al., 2009]. Microtomographic images of melt distribution were obtained on 1 mm cylindrical cores with melt fractions of 0.2, 0.1, and 0.02, at a spatial resolution of 0.7 microns. Textual information such as melt channel size and channel connectivity was determined using AVIZO and MATLAB. Our data indicate that as melt fraction decreases from 0.2 to 0.02, grain size increases slightly whereas melt interconnectivity decreases. Network modeling and the Lattice Boltzmann method provide a quantitative link between the macroscale transport properties and microscale melt distribtution. Incorporating our quantitative 3-D melt distribution data into these models allow us to simulate melt transport and, thereby, calculate the permeability and electrical conductivity of partially molten peridotite, especially at low melt fractions.

Hydrodynamic instabilities in laser pulse-produced melts of metal films

NASA Astrophysics Data System (ADS)

Bostanjoglo, O.; Nink, T.

1996-06-01

The dynamics of melts, as induced by 7 ns laser pulses in Al and Au films, were investigated by in situ time-resolved transmission electron microscopy. Melting, motion of the liquid, and crystallization were observed by tracing the image intensity with a photomultiplier (space/time resolution 100 nm/3 ns) and by streak imaging (streak times 15 ns-4 μs). Films with native oxides/adsorbed atmospheric contaminations and films purified by pulse melting were found to show a completely different behavior of their melts. The melts of purified films either remained almost flat (Al) or revealed a gradual pileup of liquid in cold regions within 500 ns (Au), caused by thermocapillarity with the negative thermal coefficient of the surface tension of pure metals. In contrast, contaminated films showed three distinctly different types of perturbations: (1) a fast expulsion of the melt from the center of the laser spot within 20 ns after the laser pulse; (2) a gradual contraction of liquid at the center within 0.5-1 μs; (3) thickness oscillations with frequencies of 5-10 MHz and time constants of 500 ns. These effects are explained by recoil from evaporating contaminations, by thermocapillary flow with a positive thermal coefficient of the surface tension, caused by surface active impurity atoms, and by thermocapillary waves.

Pressure determination in Hydrothermal Diamond Anvil Cell via laser interferometry: Investigation of hydrothermal melting of haplogranitic glass

NASA Astrophysics Data System (ADS)

Solferino, G.; Anderson, A. J.

2012-12-01

Pressure determination in HDAC experiments of hydrothermal melting of a haplogranitic glass at 130-830 MPa and 600-800 °C were performed employing in-situ visualization of alpha to beta quartz via laser interferometry. Hitherto, Raman spectroscopy of ruby, quartz, 13C and zircon has been used for the same purpose, with a best resolution of 40-50 MPa. Our method average uncertainty is just 3.4 MPa. This augmented precision is critical in estimate of the emplacement depth of mid to upper crustal magmatic bodies, e.g., intermediate-felsic intrusions, or definition of formation conditions of magmatic ores, like rare metal pegmatites. Moreover, thanks to this improved resolution on pressure measurements, we observed that actual run pressure, named Pα/β, is smaller than pressure computed using the equation of state (EOS) of pure water, here labeled PH2O for an ample range of pressures, up to 400 MPa. The absolute value of ΔP = Pα/β- PH2O decrease at higher pressure, and switches from negative to positive at P > 800 MPa. Since dissolution of the glass/melt into the pressure medium (water) leads to increment of the medium compressibility (density), then the medium should be able to impose a larger pressure than pure water for every observed temperature of alpha to beta transition (i.e., steeper isochor). A possible explanation of this discrepancy is found in the differential density between the pressure medium and the melt, and in the change of the volume occupied by the fluid for increasing temperature, as it emerges from a simplified model of dissolution of albite feldspar / albite melt in water, prepared for this study on the base of solubility data available in literature.

Optimization of PCR Condition: The First Study of High Resolution Melting Technique for Screening of APOA1 Variance.

PubMed

Wahyuningsih, Hesty; K Cayami, Ferdy; Bahrudin, Udin; A Sobirin, Mochamad; Ep Mundhofir, Farmaditya; Mh Faradz, Sultana; Hisatome, Ichiro

2017-03-01

High resolution melting (HRM) is a post-PCR technique for variant screening and genotyping based on the different melting points of DNA fragments. The advantages of this technique are that it is fast, simple, and efficient and has a high output, particularly for screening of a large number of samples. APOA1 encodes apolipoprotein A1 (apoA1) which is a major component of high density lipoprotein cholesterol (HDL-C). This study aimed to obtain an optimal quantitative polymerase chain reaction (qPCR)-HRM condition for screening of APOA1 variance. Genomic DNA was isolated from a peripheral blood sample using the salting out method. APOA1 was amplified using the RotorGeneQ 5Plex HRM. The PCR product was visualized with the HRM amplification curve and confirmed using gel electrophoresis. The melting profile was confirmed by looking at the melting curve. Five sets of primers covering the translated region of APOA1 exons were designed with expected PCR product size of 100-400 bps. The amplified segments of DNA were amplicons 2, 3, 4A, 4B, and 4C. Amplicons 2, 3 and 4B were optimized at an annealing temperature of 60 °C at 40 PCR cycles. Amplicon 4A was optimized at an annealing temperature of 62 °C at 45 PCR cycles. Amplicon 4C was optimized at an annealing temperature of 63 °C at 50 PCR cycles. In addition to the suitable procedures of DNA isolation and quantification, primer design and an estimated PCR product size, the data of this study showed that appropriate annealing temperature and PCR cycles were important factors in optimization of HRM technique for variant screening in APOA1 .

Optimization of PCR Condition: The First Study of High Resolution Melting Technique for Screening of APOA1 Variance

PubMed Central

Wahyuningsih, Hesty; K Cayami, Ferdy; Bahrudin, Udin; A Sobirin, Mochamad; EP Mundhofir, Farmaditya; MH Faradz, Sultana; Hisatome, Ichiro

2017-01-01

Background High resolution melting (HRM) is a post-PCR technique for variant screening and genotyping based on the different melting points of DNA fragments. The advantages of this technique are that it is fast, simple, and efficient and has a high output, particularly for screening of a large number of samples. APOA1 encodes apolipoprotein A1 (apoA1) which is a major component of high density lipoprotein cholesterol (HDL-C). This study aimed to obtain an optimal quantitative polymerase chain reaction (qPCR)-HRM condition for screening of APOA1 variance. Methods Genomic DNA was isolated from a peripheral blood sample using the salting out method. APOA1 was amplified using the RotorGeneQ 5Plex HRM. The PCR product was visualized with the HRM amplification curve and confirmed using gel electrophoresis. The melting profile was confirmed by looking at the melting curve. Results Five sets of primers covering the translated region of APOA1 exons were designed with expected PCR product size of 100–400 bps. The amplified segments of DNA were amplicons 2, 3, 4A, 4B, and 4C. Amplicons 2, 3 and 4B were optimized at an annealing temperature of 60 °C at 40 PCR cycles. Amplicon 4A was optimized at an annealing temperature of 62 °C at 45 PCR cycles. Amplicon 4C was optimized at an annealing temperature of 63 °C at 50 PCR cycles. Conclusion In addition to the suitable procedures of DNA isolation and quantification, primer design and an estimated PCR product size, the data of this study showed that appropriate annealing temperature and PCR cycles were important factors in optimization of HRM technique for variant screening in APOA1. PMID:28331418

Uncertainty Quantification for Ice Sheet Science and Sea Level Projections

NASA Astrophysics Data System (ADS)

Boening, C.; Schlegel, N.; Limonadi, D.; Schodlok, M.; Seroussi, H. L.; Larour, E. Y.; Watkins, M. M.

2017-12-01

In order to better quantify uncertainties in global mean sea level rise projections and in particular upper bounds, we aim at systematically evaluating the contributions from ice sheets and potential for extreme sea level rise due to sudden ice mass loss. Here, we take advantage of established uncertainty quantification tools embedded within the Ice Sheet System Model (ISSM) as well as sensitivities to ice/ocean interactions using melt rates and melt potential derived from MITgcm/ECCO2. With the use of these tools, we conduct Monte-Carlo style sampling experiments on forward simulations of the Antarctic ice sheet, by varying internal parameters and boundary conditions of the system over both extreme and credible worst-case ranges. Uncertainty bounds for climate forcing are informed by CMIP5 ensemble precipitation and ice melt estimates for year 2100, and uncertainty bounds for ocean melt rates are derived from a suite of regional sensitivity experiments using MITgcm. Resulting statistics allow us to assess how regional uncertainty in various parameters affect model estimates of century-scale sea level rise projections. The results inform efforts to a) isolate the processes and inputs that are most responsible for determining ice sheet contribution to sea level; b) redefine uncertainty brackets for century-scale projections; and c) provide a prioritized list of measurements, along with quantitative information on spatial and temporal resolution, required for reducing uncertainty in future sea level rise projections. Results indicate that ice sheet mass loss is dependent on the spatial resolution of key boundary conditions - such as bedrock topography and melt rates at the ice-ocean interface. This work is performed at and supported by the California Institute of Technology's Jet Propulsion Laboratory. Supercomputing time is also supported through a contract with the National Aeronautics and Space Administration's Cryosphere program.

Satellite-derived submarine melt rates and mass balance (2011-2015) for Greenland's largest remaining ice tongues

NASA Astrophysics Data System (ADS)

Wilson, Nat; Straneo, Fiammetta; Heimbach, Patrick

2017-12-01

Ice-shelf-like floating extensions at the termini of Greenland glaciers are undergoing rapid changes with potential implications for the stability of upstream glaciers and the ice sheet as a whole. While submarine melting is recognized as a major contributor to mass loss, the spatial distribution of submarine melting and its contribution to the total mass balance of these floating extensions is incompletely known and understood. Here, we use high-resolution WorldView satellite imagery collected between 2011 and 2015 to infer the magnitude and spatial variability of melt rates under Greenland's largest remaining ice tongues - Nioghalvfjerdsbræ (79 North Glacier, 79N), Ryder Glacier (RG), and Petermann Glacier (PG). Submarine melt rates under the ice tongues vary considerably, exceeding 50 m a-1 near the grounding zone and decaying rapidly downstream. Channels, likely originating from upstream subglacial channels, give rise to large melt variations across the ice tongues. We compare the total melt rates to the influx of ice to the ice tongue to assess their contribution to the current mass balance. At Petermann Glacier and Ryder Glacier, we find that the combined submarine and aerial melt approximately balances the ice flux from the grounded ice sheet. At Nioghalvfjerdsbræ the total melt flux (14.2 ± 0.96 km3 a-1 w.e., water equivalent) exceeds the inflow of ice (10.2 ± 0.59 km3 a-1 w.e.), indicating present thinning of the ice tongue.

Simple models for the simulation of submarine melt for a Greenland glacial system model

NASA Astrophysics Data System (ADS)

Beckmann, Johanna; Perrette, Mahé; Ganopolski, Andrey

2018-01-01

Two hundred marine-terminating Greenland outlet glaciers deliver more than half of the annually accumulated ice into the ocean and have played an important role in the Greenland ice sheet mass loss observed since the mid-1990s. Submarine melt may play a crucial role in the mass balance and position of the grounding line of these outlet glaciers. As the ocean warms, it is expected that submarine melt will increase, potentially driving outlet glaciers retreat and contributing to sea level rise. Projections of the future contribution of outlet glaciers to sea level rise are hampered by the necessity to use models with extremely high resolution of the order of a few hundred meters. That requirement in not only demanded when modeling outlet glaciers as a stand alone model but also when coupling them with high-resolution 3-D ocean models. In addition, fjord bathymetry data are mostly missing or inaccurate (errors of several hundreds of meters), which questions the benefit of using computationally expensive 3-D models for future predictions. Here we propose an alternative approach built on the use of a computationally efficient simple model of submarine melt based on turbulent plume theory. We show that such a simple model is in reasonable agreement with several available modeling studies. We performed a suite of experiments to analyze sensitivity of these simple models to model parameters and climate characteristics. We found that the computationally cheap plume model demonstrates qualitatively similar behavior as 3-D general circulation models. To match results of the 3-D models in a quantitative manner, a scaling factor of the order of 1 is needed for the plume models. We applied this approach to model submarine melt for six representative Greenland glaciers and found that the application of a line plume can produce submarine melt compatible with observational data. Our results show that the line plume model is more appropriate than the cone plume model for simulating the average submarine melting of real glaciers in Greenland.

Three dimensional rock microstructures: insights from FIB-SEM tomography

NASA Astrophysics Data System (ADS)

Drury, Martyn; Pennock, Gill; de Winter, Matthijs

2016-04-01

Most studies of rock microstructures investigate two-dimensional sections or thin slices of three dimensional grain structures. With advances of X-ray and electron tomography methods the 3-D microstructure can be(relatively) routinely investigated on scales from a few microns to cm. 3D studies are needed to investigate the connectivity of microstructures and to test the assumptions we use to calculate 3D properties from 2D sections. We have used FIB-SEM tomography to study the topology of melts in synthetic olivine rocks, 3D crystal growth microstructures, pore networks and subgrain structures. The technique uses a focused ion beam to make serial sections with a spacing of tens to hundreds of nanometers. Each section is then imaged or mapped using the electron beam. The 3D geometry of grains and subgrains can be investigated using orientation contrast or EBSD mapping. FIB-SEM tomography of rocks and minerals can be limited by charging of the uncoated surfaces exposed by the ion beam. The newest generation of FIB-SEMs have much improved low voltage imaging capability allowing high resolution charge free imaging. Low kV FIB-SEM tomography is now widely used to study the connectivity of pore networks. In-situ fluids can also be studied using cryo-FIB-SEM on frozen samples, although special freezing techniques are needed to avoid artifacts produced by ice crystallization. FIB-SEM tomography is complementary, in terms of spatial resolution and sampled volume, to TEM tomography and X-ray tomography, and the combination of these methods can cover a wide range of scales. Our studies on melt topology in synthetic olivine rocks with a high melt content show that many grain boundaries are wetted by nanometre scale melt layers that are too thin to resolve by X-ray tomography. A variety of melt layer geometries occur consistent with several mechanisms of melt layer formation. The nature of melt geometries along triple line junctions and quadruple points can be resolved. Quadruple point junctions between four grains cannot be investigated in 2D studies. 3D microstructural studies suggest that triple lines and quadruple points are important sites for the initiation of recrystallization, reaction and fracture.

Analyzing Snowpack Metrics Over Large Spatial Extents Using Calibrated, Enhanced-Resolution Brightness Temperature Data and Long Short Term Memory Artificial Neural Networks

NASA Astrophysics Data System (ADS)

Norris, W.; J Q Farmer, C.

2017-12-01

Snow water equivalence (SWE) is a difficult metric to measure accurately over large spatial extents; snow-tell sites are too localized, and traditional remotely sensed brightness temperature data is at too coarse of a resolution to capture variation. The new Calibrated Enhanced-Resolution Brightness Temperature (CETB) data from the National Snow and Ice Data Center (NSIDC) offers remotely sensed brightness temperature data at an enhanced resolution of 3.125 km versus the original 25 km, which allows for large spatial extents to be analyzed with reduced uncertainty compared to the 25km product. While the 25km brightness temperature data has proved useful in past research — one group found decreasing trends in SWE outweighed increasing trends three to one in North America; other researchers used the data to incorporate winter conditions, like snow cover, into ecological zoning criterion — with the new 3.125 km data, it is possible to derive more accurate metrics for SWE, since we have far more spatial variability in measurements. Even with higher resolution data, using the 37 - 19 GHz frequencies to estimate SWE distorts the data during times of melt onset and accumulation onset. Past researchers employed statistical splines, while other successful attempts utilized non-parametric curve fitting to smooth out spikes distorting metrics. In this work, rather than using legacy curve fitting techniques, a Long Short Term Memory (LSTM) Artificial Neural Network (ANN) was trained to perform curve fitting on the data. LSTM ANN have shown great promise in modeling time series data, and with almost 40 years of data available — 14,235 days — there is plenty of training data for the ANN. LSTM's are ideal for this type of time series analysis because they allow important trends to persist for long periods of time, but ignore short term fluctuations; since LSTM's have poor mid- to short-term memory, they are ideal for smoothing out the large spikes generated in the melt and accumulation onset seasons, while still capturing the overall trends in the data.

Evaporation-induced gas-phase flows at selective laser melting

NASA Astrophysics Data System (ADS)

Zhirnov, I.; Kotoban, D. V.; Gusarov, A. V.

2018-02-01

Selective laser melting is the method for 3D printing from metals. A solid part is built from powder layer-by-layer. A continuum-wave laser beam scans every powder layer to fuse powder. The process is studied with a high-speed CCD camera at the frame rate of 104 fps and the resolution up to 5 µm per pixel. Heat transfer and evaporation in the laser-interaction zone are numerically modeled. Droplets are ejected from the melt pool in the direction around the normal to the melt surface and the powder particles move in the horizontal plane toward the melt pool. A vapor jet is observed in the direction of the normal to the melt surface. The velocities of the droplets, the powder particles, and the jet flow and the mass loss due to evaporation are measured. The gas flow around the vapor jet is calculated by Landau's model of submerged jet. The measured velocities of vapor, droplets, and powder particles correlate with the calculated flow field. The obtained results show the importance of evaporation and the flow of the vapor and the ambient gas. These gas-dynamic phenomena can explain the formation of the denudated zones and the instability at high-energy input.

Surface mass balance of Greenland mountain glaciers and ice caps

NASA Astrophysics Data System (ADS)

Benson, R. J.; Box, J. E.; Bromwich, D. H.; Wahr, J. M.

2009-12-01

Mountain glaciers and ice caps contribute roughly half of eustatic sea-level rise. Greenland has thousands of small mountain glaciers and several ice caps > 1000 sq. km that have not been included in previous mass balance calculations. To include small glaciers and ice caps in our study, we use Polar WRF, a next-generation regional climate data assimilation model is run at grid resolution less than 10 km. WRF provides surface mass balance data at sufficiently high resolution to resolve not only the narrow ice sheet ablation zone, but provides information useful in downscaling melt and accumulation rates on mountain glaciers and ice caps. In this study, we refine Polar WRF to simulate a realistic surface energy budget. Surface melting is calculated in-line from surface energy budget closure. Blowing snow sublimation is computed in-line. Melt water re-freeze is calculated using a revised scheme. Our results are compared with NASA's Gravity Recovery and Climate Experiment (GRACE) and associated error is calculated on a regional and local scale with validation from automated weather stations (AWS), snow pits and ice core data from various regions along the Greenland ice sheet.

Impact of Mutation Type and Amplicon Characteristics on Genetic Diversity Measures Generated Using a High-Resolution Melting Diversity Assay

PubMed Central

Cousins, Matthew M.; Donnell, Deborah; Eshleman, Susan H.

2013-01-01

We adapted high-resolution melting (HRM) technology to measure genetic diversity without sequencing. Diversity is measured as a single numeric HRM score. Herein, we determined the impact of mutation types and amplicon characteristics on HRM diversity scores. Plasmids were generated with single-base changes, insertions, and deletions. Different primer sets were used to vary the position of mutations within amplicons. Plasmids and plasmid mixtures were analyzed to determine the impact of mutation type, position, and concentration on HRM scores. The impact of amplicon length and G/C content on HRM scores was also evaluated. Different mutation types affected HRM scores to varying degrees (1-bp deletion < 1-bp change < 3-bp insertion < 9-bp insertion). The impact of mutations on HRM scores was influenced by amplicon length and the position of the mutation within the amplicon. Mutations were detected at concentrations of 5% to 95%, with the greatest impact at 50%. The G/C content altered melting temperature values of amplicons but had no impact on HRM scores. These data are relevant to the design of assays that measure genetic diversity using HRM technology. PMID:23178437

Experimental and computational analysis of sound absorption behavior in needled nonwovens

NASA Astrophysics Data System (ADS)

Soltani, Parham; Azimian, Mehdi; Wiegmann, Andreas; Zarrebini, Mohammad

2018-07-01

In this paper application of X-ray micro-computed tomography (μCT) together with fluid simulation techniques to predict sound absorption characteristics of needled nonwovens is discussed. Melt-spun polypropylene fibers of different fineness were made on an industrial scale compact melt spinning line. A conventional batt forming-needling line was used to prepare the needled samples. The normal incidence sound absorption coefficients were measured using impedance tube method. Realistic 3D images of samples at micron-level spatial resolution were obtained using μCT. Morphology of fabrics was characterized in terms of porosity, fiber diameter distribution, fiber curliness and pore size distribution from high-resolution realistic 3D images using GeoDict software. In order to calculate permeability and flow resistivity of media, fluid flow was simulated by numerically solving incompressible laminar Newtonian flow through the 3D pore space of realistic structures. Based on the flow resistivity, the frequency-dependent acoustic absorption coefficient of the needled nonwovens was predicted using the empirical model of Delany and Bazley (1970) and its associated modified models. The results were compared and validated with the corresponding experimental results. Based on morphological analysis, it was concluded that for a given weight per unit area, finer fibers yield to presence of higher number of fibers in the samples. This results in formation of smaller and more tortuous pores, which in turn leads to increase in flow resistivity of media. It was established that, among the empirical models, Mechel modification to Delany and Bazley model had superior predictive ability when compared to that of the original Delany and Bazley model at frequency range of 100-5000 Hz and is well suited to polypropylene needled nonwovens.

High-Resolution Melting Analysis as a Powerful Tool to Discriminate and Genotype Pseudomonas savastanoi Pathovars and Strains

PubMed Central

Gori, Andrea; Cerboneschi, Matteo; Tegli, Stefania

2012-01-01

Pseudomonas savastanoi is a serious pathogen of Olive, Oleander, Ash, and several other Oleaceae. Its epiphytic or endophytic presence in asymptomatic plants is crucial for the spread of Olive and Oleander knot disease, as already ascertained for P. savastanoi pv. savastanoi (Psv) on Olive and for pv. nerii (Psn) on Oleander, while no information is available for pv. fraxini (Psf) on Ash. Nothing is known yet about the distribution on the different host plants and the real host range of these pathovars in nature, although cross-infections were observed following artificial inoculations. A multiplex Real-Time PCR assay was recently developed to simultaneously and quantitatively discriminate in vitro and in planta these P. savastanoi pathovars, for routine culture confirmation and for epidemiological and diagnostical studies. Here an innovative High-Resolution Melting Analysis (HRMA)-based assay was set up to unequivocally discriminate Psv, Psn and Psf, according to several single nucleotide polymorphisms found in their Type Three Secretion System clusters. The genetic distances among 56 P. savastanoi strains belonging to these pathovars were also evaluated, confirming and refining data previously obtained by fAFLP. To our knowledge, this is the first time that HRMA is applied to a bacterial plant pathogen, and one of the few multiplex HRMA-based assays developed so far. This protocol provides a rapid, sensitive, specific tool to differentiate and detect Psv, Psn and Psf strains, also in vivo and against other related bacteria, with lower costs than conventional multiplex Real-Time PCR. Its application is particularly suitable for sanitary certification programs for P. savastanoi, aimed at avoiding the spreading of this phytopathogen through asymptomatic plants. PMID:22295075

Comparison of Direct Sequencing, Real-Time PCR-High Resolution Melt (PCR-HRM) and PCR-Restriction Fragment Length Polymorphism (PCR-RFLP) Analysis for Genotyping of Common Thiopurine Intolerant Variant Alleles NUDT15 c.415C>T and TPMT c.719A>G (TPMT*3C).

PubMed

Fong, Wai-Ying; Ho, Chi-Chun; Poon, Wing-Tat

2017-05-12

Thiopurine intolerance and treatment-related toxicity, such as fatal myelosuppression, is related to non-function genetic variants encoding thiopurine S-methyltransferase (TPMT) and Nudix hydrolase 15 (NUDT15). Genetic testing of the common variants NUDT15:NM_018283.2:c.415C>T (Arg139Cys, dbSNP rs116855232 T allele) and TPMT: NM_000367.4:c.719A>G (TPMT*3C, dbSNP rs1142345 G allele) in East Asians including Chinese can potentially prevent treatment-related complications. Two complementary genotyping approaches, real-time PCR-high resolution melt (PCR-HRM) and PCR-restriction fragment length morphism (PCR-RFLP) analysis were evaluated using conventional PCR and Sanger sequencing genotyping as the gold standard. Sixty patient samples were tested, revealing seven patients (11.7%) heterozygous for NUDT15 c.415C>T, one patient homozygous for the variant and one patient heterozygous for the TPMT*3C non-function allele. No patient was found to harbor both variants. In total, nine out of 60 (15%) patients tested had genotypic evidence of thiopurine intolerance, which may require dosage adjustment or alternative medication should they be started on azathioprine, mercaptopurine or thioguanine. The two newly developed assays were more efficient and showed complete concordance (60/60, 100%) compared to the Sanger sequencing results. Accurate and cost-effective genotyping assays by real-time PCR-HRM and PCR-RFLP for NUDT15 c.415C>T and TPMT*3C were successfully developed. Further studies may establish their roles in genotype-informed clinical decision-making in the prevention of morbidity and mortality due to thiopurine intolerance.

High resolution melting (HRM) analysis as a new tool for rapid identification of Salmonella enterica serovar Gallinarum biovars Pullorum and Gallinarum.

PubMed

Ren, Xingxing; Fu, Ying; Xu, Chenggang; Feng, Zhou; Li, Miao; Zhang, Lina; Zhang, Jianmin; Liao, Ming

2017-05-01

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. Therefore, PCR-HRM analyses were used to characterize this gene. A total of 15 reference and 33 clinical isolates of Salmonella and related Gram-negative bacteria were detected using 2 sets of primers. Our PCR-HRM assay could distinguish S. Pullorum from S. Gallinarun and other strains using the primer pair SP-237F/237R. Similarly, S. Gallinarun could be distinguished from S. Pullorum and other strains using primer set SG-598F/598R. These 2 assays showed high specificity (100%) for both S. Pullorum and S. Gallinarun; the sensitivity of these 2 assays was at least 100-fold greater than that of the allele-specific PCR assay. This present study demonstrated that HRM analysis represents a potent, simple, and economic tool for the rapid, specific, and sensitive detection of S. Pullorum and S. Gallinarun. Our approach also may aid efforts for purification of Avian Salmonella disease. © 2016 Poultry Science Association Inc.

Novel Strategy to Evaluate Infectious Salmon Anemia Virus Variants by High Resolution Melting

PubMed Central

Sepúlveda, Dagoberto; Cárdenas, Constanza; Carmona, Marisela; Marshall, Sergio H.

2012-01-01

Genetic variability is a key problem in the prevention and therapy of RNA-based virus infections. Infectious Salmon Anemia virus (ISAv) is an RNA virus which aggressively attacks salmon producing farms worldwide and in particular in Chile. Just as with most of the Orthomyxovirus, ISAv displays high variability in its genome which is reflected by a wider infection potential, thus hampering management and prevention of the disease. Although a number of widely validated detection procedures exist, in this case there is a need of a more complex approach to the characterization of virus variability. We have adapted a procedure of High Resolution Melting (HRM) as a fine-tuning technique to fully differentiate viral variants detected in Chile and projected to other infective variants reported elsewhere. Out of the eight viral coding segments, the technique was adapted using natural Chilean variants for two of them, namely segments 5 and 6, recognized as virulence-associated factors. Our work demonstrates the versatility of the technique as well as its superior resolution capacity compared with standard techniques currently in use as key diagnostic tools. PMID:22719837

Noncontact temperature measurement: Requirements and applications for metals and alloys research

NASA Technical Reports Server (NTRS)

Perepezko, J. H.

1988-01-01

Temperature measurement is an essential capability for almost all areas of metals and alloys research. In the microgravity environment many of the science priorities that have been identified for metals and alloys also require noncontact temperature measurement capability. For example, in order to exploit the full potential of containerless processing, it is critical to have available a suitable noncontact temperature measurement system. This system is needed to track continuously the thermal history, including melt undercooling and rapid recalescence, of relatively small metal spheres during free-fall motion in drop tube systems. During containerless processing with levitation-based equipment, accurate noncontact temperature measurement is required to monitor one or more quasi-static samples with sufficient spatial and thermal resolution to follow the progress of solidification fronts originating in undercooled melts. In crystal growth, thermal migration, coarsening and other experiments high resolution thermal maps would be a valuable asset in the understanding and modeling of solidification processes, fluid flows and microstructure development. The science and applications requirements place several constraints on the spatial resolution, response time and accuracy of suitable instrumentation.

Optical resolution by preferential crystallization of (RS)-2-benzoylamino-2-benzyl-3-hydroxypropanoic acid and its use in synthesizing optically active 2-amino-2-methyl-3-phenylpropanoic acid.

PubMed

Shiraiwa, Tadashi; Suzuki, Masahiro; Sakai, Yoshio; Nagasawa, Hisashi; Takatani, Kazuhiro; Noshi, Daisuke; Yamanashi, Kenji

2002-10-01

To synthesize optically active 2-amino-2-methyl-3-phenylpropanoic acid (1), (RS)-2-benzoylamino-2-benzyl-3-hydroxypropanoic acid [(RS)-2] was first optically resolved using cinchonidine as a resolving agent to yield optically pure (S)- and (R)-2 in yields of about 70%, based on half of the starting amount of (RS)-2. Next, the racemic structure of (RS)-2 was examined based on melting point, solubility, IR spectrum, and binary and ternary phase diagrams, with the aim of optical resolution by preferential crystallization of (RS)-2. Results indicated that the (RS)-2 exists as a conglomerate at room temperature, although it forms a racemic compound at the melting point. The optical resolution by preferential crystallization yielded (S)- and (R)-2 with optical purities of about 90%, which were fully purified by recrystallization. After O-tosylation of (S)- and (R)-2, reduction by zinc powder and sodium iodide gave (R)- and (S)-1, respectively.

Thermal stability of carbon nanotubes probed by anchored tungsten nanoparticles

PubMed Central

Wei, Xianlong; Wang, Ming-Sheng; Bando, Yoshio; Golberg, Dmitri

2011-01-01

The thermal stability of multiwalled carbon nanotubes (CNTs) was studied in high vacuum using tungsten nanoparticles as miniaturized thermal probes. The particles were placed on CNTs inside a high-resolution transmission electron microscope equipped with a scanning tunneling microscope unit. The setup allowed manipulating individual nanoparticles and heating individual CNTs by applying current to them. CNTs were found to withstand high temperatures, up to the melting point of 60-nm-diameter W particles (∼3400 K). The dynamics of W particles on a hot CNT, including particle crystallization, quasimelting, melting, sublimation and intradiffusion, were observed in real time and recorded as a video. Graphite layers reel off CNTs when melted or premelted W particles revolve along the tube axis. PMID:27877413

Impact melting of frozen oceans on the early Earth: implications for the origin of life

NASA Technical Reports Server (NTRS)

Bada, J. L.; Bigham, C.; Miller, S. L.

1994-01-01

Without sufficient greenhouse gases in the atmosphere, the early Earth would have become a permanently frozen planet because the young Sun was less luminous than it is today. Several resolutions to this faint young Sun-frozen Earth paradox have been proposed, with an atmosphere rich in CO2 being the one generally favored. However, these models assume that there were no mechanisms for melting a once frozen ocean. Here we show that bolide impacts between about 3.6 and 4.0 billion years ago could have episodically melted an ice-covered early ocean. Thaw-freeze cycles associated with bolide impacts could have been important for the initiation of abiotic reactions that gave rise to the first living organisms.

Impact melting of frozen oceans on the early Earth: Implications for the origin of life

PubMed Central

Bada, J. L.; Bigham, C.; Miller, S. L.

1994-01-01

Without sufficient greenhouse gases in the atmosphere, the early Earth would have become a permanently frozen planet because the young Sun was less luminous than it is today. Several resolutions to this faint young Sun-frozen Earth paradox have been proposed, with an atmosphere rich in CO2 being the one generally favored. However, these models assume that there were no mechanisms for melting a once frozen ocean. Here we show that bolide impacts between about 3.6 and 4.0 billion years ago could have episodically melted an ice-covered early ocean. Thaw-freeze cycles associated with bolide impacts could have been important for the initiation of abiotic reactions that gave rise to the first living organisms. PMID:11539550

High-resolution Imaging of the Philippine Sea Plate subducting beneath Central Japan

NASA Astrophysics Data System (ADS)

Padhy, S.; Furumura, T.

2016-12-01

Thermal models predict that the oceanic crust of the young (<20 Ma) and warmer Philippine-sea plate (PHP) is more prone to melting. Deriving a high-resolution image of the PHP, including slab melting and other features of the subduction zone, is a key to understand the basics of earthquake occurrence and origin of magma in complex subduction zone like central Japan, where both the PHP and Pacific (PAC) Plates subduct. To this purpose, we analyzed high-resolution waveforms of moderate sized (M 4-6), intermediate-to-deep (>150 km) PAC earthquakes occurring in central Japan and conducted numerical simulation to derive a fine-scale PHP model, which is not constrained in earlier studies. Observations show spindle-shaped seismograms with strong converted phases and extended coda with very slow decay from a group of PAC events occurring in northern part of central Japan and recorded by high-sensitivity seismograph network (Hi-net) stations in the region. We investigate the mechanism of propagation of these anomalous waveforms using the finite difference method (FDM) simulation of wave propagation through the subduction zone. We examine the effects on waveform changes of major subduction zone features, such as the melting of oceanic crust in PHP, serpentinized mantle wedge, hydrated layer on the PAC due to slab dehydration, and anomaly in upper mantle between the PAC and PHP. Simulation results show that the waveform anomaly is primarily explained by strong scattering and absorption of high-frequency energy by the low-velocity anomalous mantle structure, with a strong coda excitation yielding spindle-shaped waveforms. The data are secondarily explained by melting of PHP in the basaltic crust. The location of the mantle anomaly is tightly constrained by the observation and evidence of PAC thinning in the region; these localized low-velocity structures aid in ascending the slab-derived fluids around the slab thinning. We expect that the results of this study will enhance our present understanding on the mechanism of intermediate to deep earthquakes in the region.

Intercomparison of Antarctic ice-shelf, ocean, and sea-ice interactions simulated by MetROMS-iceshelf and FESOM 1.4

NASA Astrophysics Data System (ADS)

Naughten, Kaitlin A.; Meissner, Katrin J.; Galton-Fenzi, Benjamin K.; England, Matthew H.; Timmermann, Ralph; Hellmer, Hartmut H.; Hattermann, Tore; Debernard, Jens B.

2018-04-01

An increasing number of Southern Ocean models now include Antarctic ice-shelf cavities, and simulate thermodynamics at the ice-shelf/ocean interface. This adds another level of complexity to Southern Ocean simulations, as ice shelves interact directly with the ocean and indirectly with sea ice. Here, we present the first model intercomparison and evaluation of present-day ocean/sea-ice/ice-shelf interactions, as simulated by two models: a circumpolar Antarctic configuration of MetROMS (ROMS: Regional Ocean Modelling System coupled to CICE: Community Ice CodE) and the global model FESOM (Finite Element Sea-ice Ocean Model), where the latter is run at two different levels of horizontal resolution. From a circumpolar Antarctic perspective, we compare and evaluate simulated ice-shelf basal melting and sub-ice-shelf circulation, as well as sea-ice properties and Southern Ocean water mass characteristics as they influence the sub-ice-shelf processes. Despite their differing numerical methods, the two models produce broadly similar results and share similar biases in many cases. Both models reproduce many key features of observations but struggle to reproduce others, such as the high melt rates observed in the small warm-cavity ice shelves of the Amundsen and Bellingshausen seas. Several differences in model design show a particular influence on the simulations. For example, FESOM's greater topographic smoothing can alter the geometry of some ice-shelf cavities enough to affect their melt rates; this improves at higher resolution, since less smoothing is required. In the interior Southern Ocean, the vertical coordinate system affects the degree of water mass erosion due to spurious diapycnal mixing, with MetROMS' terrain-following coordinate leading to more erosion than FESOM's z coordinate. Finally, increased horizontal resolution in FESOM leads to higher basal melt rates for small ice shelves, through a combination of stronger circulation and small-scale intrusions of warm water from offshore.

Satellite-derived, melt-season surface temperature of the Greenland Ice Sheet (2000-2005) and its relationship to mass balance

USGS Publications Warehouse

Hall, D.K.; Williams, R.S.; Casey, K.A.; DiGirolamo, N.E.; Wan, Z.

2006-01-01

Mean, clear-sky surface temperature of the Greenland Ice Sheet was measured for each melt season from 2000 to 2005 using Moderate-Resolution Imaging Spectroradiometer (MODIS)–derived land-surface temperature (LST) data-product maps. During the period of most-active melt, the mean, clear-sky surface temperature of the ice sheet was highest in 2002 (−8.29 ± 5.29°C) and 2005 (−8.29 ± 5.43°C), compared to a 6-year mean of −9.04 ± 5.59°C, in agreement with recent work by other investigators showing unusually extensive melt in 2002 and 2005. Surface-temperature variability shows a correspondence with the dry-snow facies of the ice sheet; a reduction in area of the dry-snow facies would indicate a more-negative mass balance. Surface-temperature variability generally increased during the study period and is most pronounced in the 2005 melt season; this is consistent with surface instability caused by air-temperature fluctuations.

Fast and reliable detection of toxic Crotalaria spectabilis Roth. in Thunbergia laurifolia Lindl. herbal products using DNA barcoding coupled with HRM analysis.

PubMed

Singtonat, Sahachat; Osathanunkul, Maslin

2015-05-30

Nowadays, medicinal plants are used as a popular alternative to synthetic drugs. Many medicinal plant products have now been commercialized throughout various markets. These products are commonly sold in processed or modified forms such as powders, dried material and capsules, making it almost impossible to accurately identify the constituent species. The herbal plant known as 'Rang Chuet' in Thai has been widely used as remedies for various ailments. However, two medicinal plants species, Thunbergia laurifolia and Crotalaria spectabilis share this name. Duo to the similarity in nomenclature, the commercial products labeled as 'Rang Chuet' could be any of them. Recently, the evidence of hepatotoxic effects linked to use of C. spectabilis were reported and is now seriously concern. There is a need to find an approach that could help with species identification of these herbal products to ensure the safety and efficacy of the herbal drug. Here DNA barcoding was used in combination with High Resolution Melting analysis (Bar-HRM) to authenticate T. laurifolia species. Four DNA barcodes including matK, rbcL, rpoC and trnL were selected for use in primers design for HRM analysis to produce standard melting profiles of the selected species. Commercial products labeled as 'Rang Chuet' were purchased from Thai markets and authentication by HRM analyses. Melting data from the HRM assay using the designed primers showed that the two 'Rang Chuet' species could easily be distinguished from each other. The melting profiles of the all four region amplicons of each species are clearly separated in all three replicates. The method was then applied to authenticate products in powdered form. HRM curves of all ten test samples indicated that three of the tested products did not only contain the T. laurifolia species. The herbal drugs derived from different plants must be distinguished from each other even they share the same vernacular name. The Bar-HRM method developed here proved useful in the identification and authentication of herbal species in processed samples. In the future, species authentication through Bar-HRM could be used to promote consumer trust, as well as raising the quality of herbal products.

Preparation of optically active (2RS,3SR)-2-amino-3-hydroxy-3-phenylpropanoic acid (threo-beta-phenylserine) via optical resolutions by replacing and preferential crystallization.

PubMed

Shiraiwa, Tadashi; Kawashima, Yuka; Ikaritani, Atsushi; Suganuma, Yumiko; Saijoh, Reiichi

2006-08-01

To obtain optically active threo-2-amino-3-hydroxy-3-phenylpropanoic acid (1) via optical resolutions by replacing and preferential crystallization, the racemic structure of (2RS,3SR)-1 hydrochloride [(2RS,3SR)-1.HCl] was examined based on the melting point, solubility, and infrared spectrum. (2RS,3SR)-1.HCl was indicated to exist as a conglomerate at room temperature, although it forms a racemic compound at the melting point. When, in optical resolution by replacing crystallization, L-phenylalanine methyl ester hydrochloride (L-2) was used as the optically active co-solute, (2R,3S)-1.HCl was preferentially crystallized from the supersaturated racemic solution; the use of D-2 as the co-solute afforded (2S,3R)-1.HCl with an optical purity of 95%. In addition, optical resolution by preferential crystallization was successfully achieved to give successively (2R,3S)- and (2S,3R)-1.HCl with optical purities of 90-92%. The (2R,3S)- and (2S,3R)-1.HCl purified by recrystallization from 1-propanol were treated with triethylamine in methanol to give optically pure (2R,3S)- and (2S,3R)-1.

High Resolution Melting as a rapid, reliable, accurate and cost-effective emerging tool for genotyping pathogenic bacteria and enhancing molecular epidemiological surveillance: a comprehensive review of the literature.

PubMed

Tamburro, M; Ripabelli, G

2017-01-01

Rapid, reliable and accurate molecular typing methods are essential for outbreaks detection and infectious diseases control, for monitoring the evolution and dynamics of microbial populations, and for effective epidemiological surveillance. The introduction of a novel method based on the analysis of melting temperature of amplified products, known as High Resolution Melting (HRM) since 2002, has found applications in epidemiological studies, either for identification of bacterial species or molecular typing, as well as an extensive and increasing use in many research fields. HRM method is based on the use of saturating third generation dyes, advanced real-time PCR platforms, and bioinformatics tools. To describe, by a comphrehensive review of the literature, the use, application and usefulness of HRM for the genotyping of bacterial pathogens in the context of epidemiological surveillance and public health. A literature search was carried out during July-August 2016, by consulting the biomedical databases PubMed/Medline, Scopus, EMBASE, and ISI Web of Science without limits. The search strategy was performed according to the following keywords: high resolution melting analysis and bacteria and genotyping or molecular typing. All the articles evaluating the application of HRM for bacterial pathogen genotyping were selected and reviewed, taking into account the objective of each study, the rationale explaining the use of this technology, and the main results obtained in comparison with gold standards and/or alternative methods, when available. HRM method was extensively used for molecular typing of both Gram-positive and Gram-negative bacterial pathogens, representing a versatile genetic tool: a) to evaluate genetic diversity and subtype at species/subspecies level, based also on allele discrimination/identification and mutation screening; b) to recognize phylogenetic groupings (lineage, sublineage, subgroups); c) to identify antimicrobial resistance; d) to detect and screen for mutations related to drug-resistance; e) to discriminate gene isoforms. HRM method showed, in almost all instances, excellent typeability and discriminatory power, with high concordance of typing results obtained with gold standards or comparable methods. Conversely, for the evaluation of genetic determinants associated to antibiotic-resistance or for screening of associated mutations in key gene fragments, the sensitivity and specificity was not optimal, because the targeted amplicons did not encompass all the crucial mutations. Despite the recent introduction of sequencing-based methods, the HRM method deserves consideration in research fields of infectious diseases, being characterized by low cost, rapidity, flexibility and versatility. However, there are some limitations to HRM assays development, which should be carefully considered. The most common application of HRM for bacterial typing is related to Single Nucleotide Polymorphism (SNP)-based genotyping with the analysis of gene fragments within the multilocus sequence typing (MLST) loci, following an approach termed mini-MLST or Minim typing. Although the resolving power is not totally correspondent to MLST, the Simpson's Index of Diversity provided by HRM method typically >0.95. Furthermore, the cost of this approach is less than MLST, enabling low cost surveillance and rapid response for outbreak control. Hence, the potential of HRM technology can strongly facilitate routine research and diagnostics in the epidemiological studies, as well as advance and streamline the genetic characterization of bacterial pathogens.

Geodetic Imaging and Tsunami Modeling of the 2017 Coupled Landslide-Tsunami Event in Karrat Fjord, West Greenland.

NASA Astrophysics Data System (ADS)

Barba, M.; Willis, M. J.; Tiampo, K. F.; Lynett, P. J.; Mätzler, E.; Thorsøe, K.; Higman, B. M.; Thompson, J. A.; Morin, P. J.

2017-12-01

We use a combination of geodetic imaging techniques and modelling efforts to examine the June 2017 Karrat Fjord, West Greenland, landslide and tsunami event. Our efforts include analysis of pre-cursor motions extracted from Sentinal SAR interferometry that we improved with high-resolution Digital Surface Models derived from commercial imagery and geo-coded Structure from Motion analyses. We produce well constrained estimates of landslide volume through DSM differencing by improving the ArcticDEM coverage of the region, and provide modeled tsunami run-up estimates at villages around the region, constrained with in-situ observations provided by the Greenlandic authorities. Estimates of run-up at unoccupied coasts are derived using a blend of high resolution imagery and elevation models. We further detail post-failure slope stability for areas of interest around the Karrat Fjord region. Warming trends in the region from model and satellite analysis are combined with optical imagery to ascertain whether the influence of melting permafrost and the formation of small springs on a slight bench on the mountainside that eventually failed can be used as indicators of future events.

Constraints on melt content of off-axis magma lenses at the East Pacific Rise from analysis of 3-D seismic amplitude variation with angle of incidence

NASA Astrophysics Data System (ADS)

Aghaei, Omid; Nedimović, Mladen R.; Marjanović, Milena; Carbotte, Suzanne M.; Pablo Canales, J.; Carton, Hélène; Nikić, Nikola

2017-06-01

We use 3-D multichannel seismic data to form partial angle P wave stacks and apply amplitude variation with angle (AVA) crossplotting to assess melt content and melt distribution within two large midcrustal off-axis magma lenses (OAMLs) found along the East Pacific Rise from 9°37.5'N to 9°57'N. The signal envelope of the partial angle stacks suggests that both OAMLs are partially molten with higher average melt content and more uniform melt distribution in the southern OAML than in the northern OAML. For AVA crossplotting, the OAMLs are subdivided into seven 1 km2 analysis windows. The AVA crossplotting results indicate that the OAMLs contain a smaller amount of melt than the axial magma lens (AML). For both OAMLs, a higher melt fraction is detected within analysis windows located close to the ridge axis than within the most distant windows. The highest average melt concentration is interpreted for the central sections of the OAMLs. The overall low OAML melt content could be indicative of melt lost due to recent off-axis eruptions, drainage to the AML, or limited mantle melt supply. Based on the results of this and earlier bathymetric, morphological, geochemical, and geophysical investigations, we propose that the melt-poor OAML state is largely the result of limited melt supply from the underlying mantle source reservoir with smaller contribution attributed to melt leakage to the AML. We hypothesize that the investigated OAMLs have a longer period of melt replenishment, lower eruption recurrence rates, and lower eruption volumes than the AML, though some could be single intrusion events.

Laboratory plant study on the melting process of asbestos waste

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sakai, Shinichi; Terazono, Atsushi; Takatsuki, Hiroshi

The melting process was studied as a method of changing asbestos into non-hazardous waste and recovering it as a reusable resource. In an initial effort, the thermal behaviors of asbestos waste in terms of physical and chemical structure have been studied. Then, 10 kg/h-scale laboratory plant experiments were carried out. By X-ray diffraction analysis, the thermal behaviors of sprayed-on asbestos waste revealed that chrysotile asbestos waste change in crystal structure at around 800 C, and becomes melted slag, mainly composed of magnesium silicate, at around 1,500 C. Laboratory plant experiments on the melting process of sprayed-on asbestos have shown thatmore » melted slag can be obtained. X-ray diffraction analysis of the melted slag revealed crystal structure change, and SEM analysis showed the slag to have a non-fibrous form. And more, TEM analysis proved the very high treatment efficiency of the process, that is, reduction of the asbestos content to 1/10{sup 6} as a weight basis. These analytical results indicate the effectiveness of the melting process for asbestos waste treatment.« less

Cloud screening and melt water detection over melting sea ice using AATSR/SLSTR

NASA Astrophysics Data System (ADS)

Istomina, Larysa; Heygster, Georg

2014-05-01

With the onset of melt in the Arctic Ocean, the fraction of melt water on sea ice, the melt pond fraction, increases. The consequences are: the reduced albedo of sea ice, increased transmittance of sea ice and affected heat balance of the system with more heat passing through the ice into the ocean, which facilitates further melting. The onset of melt, duration of melt season and melt pond fraction are good indicators of the climate state of the Arctic and its change. In the absence of reliable sea ice thickness retrievals in summer, melt pond fraction retrieval from satellite is in demand as input for GCM as an indicator of melt state of the sea ice. The retrieval of melt pond fraction with a moderate resolution radiometer as AATSR is, however, a non-trivial task due to a variety of subpixel surface types with very different optical properties, which give non-unique combinations if mixed. In this work this has been solved by employing additional information on the surface and air temperature of the pixel. In the current work, a concept of melt pond detection on sea ice is presented. The basis of the retrieval is the sensitivity of AATSR reflectance channels 550nm and 860nm to the amount of melt water on sea ice. The retrieval features extensive usage of a database of in situ surface albedo spectra. A tree of decisions is employed to select the feasible family of in situ spectra for the retrieval, depending on the melt stage of the surface. Reanalysis air temperature at the surface and brightness temperature measured by the satellite sensor are analyzed in order to evaluate the melting status of the surface. Case studies for FYI and MYI show plausible retrieved melt pond fractions, characteristic for both of the ice types. The developed retrieval can be used to process the historical AATSR (2002-2012) dataset, as well as for the SLSTR sensor onboard the future Sentinel-3 mission (scheduled for launch in 2015), to keep the continuity and obtain longer time sequence of the product. Cloud detection over melting sea ice is a non-trivial problem as well. The sensitivity of AATSR 3.7 micron band to atmospheric reflectance is used to screen out clouds over melting sea ice.

Resonant absorption induced fast melting studied with mid-IR QCLs.

PubMed

Lu, Jie; Lv, Yankun; Ji, Youxin; Tang, Xiaoliang; Qi, Zeming; Li, Liangbin

2017-02-01

We demonstrate the use of a pump-probe setup based on two mid-infrared quantum cascade lasers (QCLs) to investigate the melting and crystallization of materials through resonant absorption. A combination of pump and probe beams fulfills the two-color synchronous detection. Furthermore, narrow linewidth advances the accuracy of measurements and the character of broad tuning range of QCLs enables wide applications in various sample and multiple structures. 1-Eicosene was selected as a simple model system to verify the feasibility of this method. A pulsed QCL was tuned to the absorption peak of CH 2 bending vibration at 1467 cm -1 to resonantly heat the sample. The other QCL in continuous mode was tuned to 1643 cm -1 corresponding the C=C stretching vibration to follow the fast melting dynamics. By monitoring the transmission intensity variation of pump and probe beams during pump-probe experiments, the resonant absorption induced fast melting and re-crystallization of 1-Eicosene can be studied. Results show that the thermal effect and melting behaviors strongly depend on the pump wavelength (resonant or non-resonant) and energy, as well as the pump time. The realization and detection of melting and recrystallization can be performed in tens of milliseconds, which improves the time resolution of melting process study based on general mid-infrared spectrum by orders of magnitude. The availability of resonant heating and detections based on mid-infrared QCLs is expected to enable new applications in melting study.

High-Resolution Melting-Curve Analysis of obg Gene to Differentiate the Temperature-Sensitive Mycoplasma synoviae Vaccine Strain MS-H from Non-Temperature-Sensitive Strains

PubMed Central

Shahid, Muhammad A.; Markham, Philip F.; Marenda, Marc S.; Agnew-Crumpton, Rebecca; Noormohammadi, Amir H.

2014-01-01

Temperature-sensitive (ts +) vaccine strain MS-H is the only live attenuated M. synoviae vaccine commercially available for use in poultry. With increasing use of this vaccine to control M. synoviae infections, differentiation of MS-H from field M. synoviae strains and from rarely occurring non-temperature-sensitive (ts –) MS-H revertants has become important, especially in countries where local strains are indistinguishable from MS-H by sequence analysis of variable lipoprotein haemagglutinin (vlhA) gene. Single nucleotide polymorphisms (SNPs) in the obg of MS-H have been found to associate with ts phenotype. In this study, four PCRs followed by high-resolution melting (HRM)-curve analysis of the regions encompassing these SNPs were developed and evaluated for their potential to differentiate MS-H from 36 M. synoviae strains/isolates. The nested-obg PCR-HRM differentiated ts + MS-H vaccine not only from field M. synoviae strains/isolates but also from ts – MS-H revertants. The mean genotype confidence percentages, 96.9±3.4 and 8.8±11.2 for ts + and ts – strains, respectively, demonstrated high differentiating power of the nested-obg PCR-HRM. Using a combination of nested-obg and obg-F3R3 PCR-HRM, 97% of the isolates/strains were typed according to their ts phenotype with all MS-H isolates typed as MS-H. A set of respiratory swabs from MS-H vaccinated specific pathogen free chickens and M. synoviae infected commercial chicken flocks were tested using obg PCR-HRM system and results were consistent with those of vlhA genotyping. The PCR-HRM system developed in this study, proved to be a rapid and reliable tool using pure M. synoviae cultures as well as direct clinical specimens. PMID:24643035

Establishment of a simple and rapid identification method for Listeria spp. by using high-resolution melting analysis, and its application in food industry.

PubMed

Ohshima, Chihiro; Takahashi, Hajime; Phraephaisarn, Chirapiphat; Vesaratchavest, Mongkol; Keeratipibul, Suwimon; Kuda, Takashi; Kimura, Bon

2014-01-01

Listeria monocytogenes is the causative bacteria of listeriosis, which has a higher mortality rate than that of other causes of food poisoning. Listeria spp., of which L. monocytogenes is a member, have been isolated from food and manufacturing environments. Several methods have been published for identifying Listeria spp.; however, many of the methods cannot identify newly categorized Listeria spp. Additionally, they are often not suitable for the food industry, owing to their complexity, cost, or time consumption. Recently, high-resolution melting analysis (HRMA), which exploits DNA-sequence differences, has received attention as a simple and quick genomic typing method. In the present study, a new method for the simple, rapid, and low-cost identification of Listeria spp. has been presented using the genes rarA and ldh as targets for HRMA. DNA sequences of 9 Listeria species were first compared, and polymorphisms were identified for each species for primer design. Species specificity of each HRM curve pattern was estimated using type strains of all the species. Among the 9 species, 7 were identified by HRMA using rarA gene, including 3 new species. The remaining 2 species were identified by HRMA of ldh gene. The newly developed HRMA method was then used to assess Listeria isolates from the food industry, and the method efficiency was compared to that of identification by 16S rDNA sequence analysis. The 2 methods were in coherence for 92.6% of the samples, demonstrating the high accuracy of HRMA. The time required for identifying Listeria spp. was substantially low, and the process was considerably simplified, providing a useful and precise method for processing multiple samples per day. Our newly developed method for identifying Listeria spp. is highly valuable; its use is not limited to the food industry, and it can be used for the isolates from the natural environment.

Establishment of a Simple and Rapid Identification Method for Listeria spp. by Using High-Resolution Melting Analysis, and Its Application in Food Industry

PubMed Central

Ohshima, Chihiro; Takahashi, Hajime; Phraephaisarn, Chirapiphat; Vesaratchavest, Mongkol; Keeratipibul, Suwimon; Kuda, Takashi; Kimura, Bon

2014-01-01

Listeria monocytogenes is the causative bacteria of listeriosis, which has a higher mortality rate than that of other causes of food poisoning. Listeria spp., of which L. monocytogenes is a member, have been isolated from food and manufacturing environments. Several methods have been published for identifying Listeria spp.; however, many of the methods cannot identify newly categorized Listeria spp. Additionally, they are often not suitable for the food industry, owing to their complexity, cost, or time consumption. Recently, high-resolution melting analysis (HRMA), which exploits DNA-sequence differences, has received attention as a simple and quick genomic typing method. In the present study, a new method for the simple, rapid, and low-cost identification of Listeria spp. has been presented using the genes rarA and ldh as targets for HRMA. DNA sequences of 9 Listeria species were first compared, and polymorphisms were identified for each species for primer design. Species specificity of each HRM curve pattern was estimated using type strains of all the species. Among the 9 species, 7 were identified by HRMA using rarA gene, including 3 new species. The remaining 2 species were identified by HRMA of ldh gene. The newly developed HRMA method was then used to assess Listeria isolates from the food industry, and the method efficiency was compared to that of identification by 16S rDNA sequence analysis. The 2 methods were in coherence for 92.6% of the samples, demonstrating the high accuracy of HRMA. The time required for identifying Listeria spp. was substantially low, and the process was considerably simplified, providing a useful and precise method for processing multiple samples per day. Our newly developed method for identifying Listeria spp. is highly valuable; its use is not limited to the food industry, and it can be used for the isolates from the natural environment. PMID:24918440

Modeling of subaqueous melting in Petermann Fjord, Northwestern Greenland using an ocean general circulation model

NASA Astrophysics Data System (ADS)

Cai, C.; Rignot, E. J.; Xu, Y.; An, L.; Tinto, K. J.; van den Broeke, M. R.

2014-12-01

Basal melting of the floating tongue of Petermann Glacier, in northwestern Greenland is by far the largest process of mass ablation. Melting of the floating tongue is controlled by the buoyancy of the melt water plume, the pressure-dependence of the melting point of sea ice, and the mixing of warm subsurface water with fresh buoyant subglacial discharge. In prior simulations of this melting process, the role of subglacial discharge has been neglected because in similar configurations (floating ice shelves) in the Antarctic, surface runoff is negligible; this is however not true in Greenland. Here, we use the Mass Institute of Technology general circulation model (MITgcm) at a high spatial resolution (10 m x 10 m) to simulate the melting process of the ice shelf in 2-D. The model is constrained by ice shelf bathymetry and ice thickness (refined model in the immediate vicinity of the grounding line) from NASA Operation IceBridge (2011), ocean temperature/salinity data from Johnson et al. (2011), ocean tide height and current from the Arctic Ocean Tidal Inverse Model (AOTIM-5) by Padman and Erofeeva (2004) and subglacial discharge at the grounding line calculated by the hydrostatic potential of the ice from estimated products of the Regional Atmospheric Climate Model (RACMO) of Royal Netherlands Meteorological Institute (KNMI). We compare the results obtained in winter (no runoff) with summer, and the sensitivity of the results to thermal forcing from the ocean, and to the variation of tide height and current, and to the magnitude of subglacial runoff. We conclude on the impact of the ocean and surface melting on the melting regime of the floating ice tongue of Petermann. The basal melt rate increases ~20% with summer surface runoff. This work is performed under a contract with NASA Cryosphere Program.

Modes of surface premelting in colloidal crystals composed of attractive particles

NASA Astrophysics Data System (ADS)

Li, Bo; Wang, Feng; Zhou, Di; Peng, Yi; Ni, Ran; Han, Yilong

2016-03-01

Crystal surfaces typically melt into a thin liquid layer at temperatures slightly below the melting point of the crystal. Such surface premelting is prevalent in all classes of solids and is important in a variety of metallurgical, geological and meteorological phenomena. Premelting has been studied using X-ray diffraction and differential scanning calorimetry, but the lack of single-particle resolution makes it hard to elucidate the underlying mechanisms. Colloids are good model systems for studying phase transitions because the thermal motions of individual micrometre-sized particles can be tracked directly using optical microscopy. Here we use colloidal spheres with tunable attractions to form equilibrium crystal-vapour interfaces, and study their surface premelting behaviour at the single-particle level. We find that monolayer colloidal crystals exhibit incomplete premelting at their perimeter, with a constant liquid-layer thickness. In contrast, two- and three-layer crystals exhibit conventional complete melting, with the thickness of the surface liquid diverging as the melting point is approached. The microstructures of the surface liquids differ in certain aspects from what would be predicted by conventional premelting theories. Incomplete premelting in the monolayer crystals is triggered by a bulk isostructural solid-solid transition and truncated by a mechanical instability that separately induces homogeneous melting within the bulk. This finding is in contrast to the conventional assumption that two-dimensional crystals melt heterogeneously from their free surfaces (that is, at the solid-vapour interface). The unexpected bulk melting that we observe for the monolayer crystals is accompanied by the formation of grain boundaries, which supports a previously proposed grain-boundary-mediated two-dimensional melting theory. The observed interplay between surface premelting, bulk melting and solid-solid transitions challenges existing theories of surface premelting and two-dimensional melting.

Diagnosis of genetic predisposition for lactose intolerance by high resolution melting analysis.

PubMed

Delacour, Hervé; Leduc, Amandine; Louçano-Perdriat, Andréa; Plantamura, Julie; Ceppa, Franck

2017-02-01

Lactose, the principle sugar in milk, is a disaccharide hydrolyzed by intestinal lactase into glucose and galactose, which are absorbed directly by diffusion in the intestine. The decline of lactase expression (or hypolactasia) in intestinal microvilli after weaning is a normal phenomenon in mammals known as lactase deficiency. It is observed in nearly 75% of the world population and is an inherited autosomal recessive trait with incomplete penetrance. It is caused by SNPs in a regulatory element for lactase gene. In Indo-European, lactase deficiency is associated with rs4982235 SNP (or -13910C>T). The aim of this study is to describe a method based on high resolution melting for rapidly detecting genetic predisposition to lactose intolerance. Analytical performance of the assay was assessed by evaluating within and betwwen-run precision and by comparing the results (n = 50 patients) obtained with the HRM assay to those obtained with the gold standard (Sanger sequencing of the region of interest). In silico prediction of HRM curves was performed to evaluate the potential impact of the other SNPs described within the PCR product on the HRM analytical performances. The assay has good performance (CV <0.2% during the between-run study). A perfect agreement with the gold standard method was observed. The presence of other polymorphisms within the amplified sequence is detected, the misclassification risk is low. This assay can be used for rapidly diagnosing genetic predisposition to lactose intolerance.

The Use of COLD-PCR and High-Resolution Melting Analysis Improves the Limit of Detection of KRAS and BRAF Mutations in Colorectal Cancer

PubMed Central

Mancini, Irene; Santucci, Claudio; Sestini, Roberta; Simi, Lisa; Pratesi, Nicola; Cianchi, Fabio; Valanzano, Rosa; Pinzani, Pamela; Orlando, Claudio

2010-01-01

Fast and reliable tests to detect mutations in human cancers are required to better define clinical samples and orient targeted therapies. KRAS mutations occur in 30–50% of colorectal cancers (CRCs) and represent a marker of clinical resistance to cetuximab therapy. In addition, the BRAF V600E is mutated in about 10% of CRCs, and the development of a specific inhibitor of mutant BRAF kinase has prompted a growing interest in BRAFV600E detection. Traditional methods, such as PCR and direct sequencing, do not detect low-level mutations in cancer, resulting in false negative diagnoses. In this study, we designed a protocol to detect mutations of KRAS and BRAFV600E in 117 sporadic CRCs based on coamplification at lower denaturation temperature PCR (COLD-PCR) and high-resolution melting (HRM). Using traditional PCR and direct sequencing, we found KRAS mutations in 47 (40%) patients and BRAFV600E in 10 (8.5%). The use of COLD-PCR in apparently wild-type samples allowed us to identify 15 newly mutated CRCs (10 for KRAS and 5 for BRAFV600E), raising the percentage of mutated CRCs to 48.7% for KRAS and to 12.8% for BRAFV600E. Therefore, COLD-PCR combined with HRM permits the correct identification of less represented mutations in CRC and better selection of patients eligible for targeted therapies, without requiring expensive and time-consuming procedures. PMID:20616366

Taxonomic Identification of Mediterranean Pines and Their Hybrids Based on the High Resolution Melting (HRM) and trnL Approaches: From Cytoplasmic Inheritance to Timber Tracing

PubMed Central

Ganopoulos, Ioannis; Aravanopoulos, Filippos; Madesis, Panagiotis; Pasentsis, Konstantinos; Bosmali, Irene; Ouzounis, Christos; Tsaftaris, Athanasios

2013-01-01

Fast and accurate detection of plant species and their hybrids using molecular tools will facilitate the assessment and monitoring of local biodiversity in an era of climate and environmental change. Herein, we evaluate the utility of the plastid trnL marker for species identification applied to Mediterranean pines (Pinus spp.). Our results indicate that trnL is a very sensitive marker for delimiting species biodiversity. Furthermore, High Resolution Melting (HRM) analysis was exploited as a molecular fingerprint for fast and accurate discrimination of Pinus spp. DNA sequence variants. The trnL approach and the HRM analyses were extended to wood samples of two species (Pinus nigra and Pinus sylvestris) with excellent results, congruent to those obtained using leaf tissue. Both analyses demonstrate that hybrids from the P. brutia (maternal parent) × P. halepensis (paternal parent) cross, exhibit the P. halepensis profile, confirming paternal plastid inheritance in Group Halepensis pines. Our study indicates that a single one-step reaction method and DNA marker are sufficient for the identification of Mediterranean pines, their hybrids and the origin of pine wood. Furthermore, our results underline the potential for certain DNA regions to be used as novel biological information markers combined with existing morphological characters and suggest a relatively reliable and open taxonomic system that can link DNA variation to phenotype-based species or hybrid assignment status and direct taxa identification from recalcitrant tissues such as wood samples. PMID:23577179

Revisiting surface albedo changes over Greenland since 1980s using satellite data from GLASS, CLARA, MODIS, and Landsat

NASA Astrophysics Data System (ADS)

He, T.; Liang, S.; Zhang, Y.

2017-12-01

Massive melting events over Greenland have been observed over the past few decades. Accompanying the melting events are the surface albedo changes, which had temporal and spatial variations. Albedo changes over Greenland during the past few decades have been reported in previous studies with the help of satellite observations; however, magnitudes and timing in albedo trends differ greatly in those studies. This has limited our understanding of albedo change mechanisms over Greenland. In this study, we present an analysis of surface albedo change over Greenland since 1980s combining four satellite albedo datasets, namely MODIS, GLASS, CLARA, and Landsat. MODIS, GLASS, and CLARA albedo data are publicly available and Landsat albedos were derived in our earlier study trying to bridge the scale difference between coarse resolution data and ground measurements available from early 1980s. Inter-comparisons were made among the satellite albedos and against ground measurements. We have several new findings. First, trends in surface albedo change among the satellite albedo datasets generally agree with each other and with ground measurements. Second, all datasets showed negative albedo trends after 2000, but magnitudes differ greatly. Third, trends before 2000 from coarse resolution data are not significant but Landsat data observed positive albedo changes. Fourth, the turning point of albedo trend was found to be earlier than 2000. Those findings may bring new research topics on timing and magnitude, and an improved understanding mechanisms of the albedo changes over Greenland during the past few decades.

Taxonomic identification of mediterranean pines and their hybrids based on the high resolution melting (HRM) and trnL approaches: from cytoplasmic inheritance to timber tracing.

PubMed

Ganopoulos, Ioannis; Aravanopoulos, Filippos; Madesis, Panagiotis; Pasentsis, Konstantinos; Bosmali, Irene; Ouzounis, Christos; Tsaftaris, Athanasios

2013-01-01

Fast and accurate detection of plant species and their hybrids using molecular tools will facilitate the assessment and monitoring of local biodiversity in an era of climate and environmental change. Herein, we evaluate the utility of the plastid trnL marker for species identification applied to Mediterranean pines (Pinus spp.). Our results indicate that trnL is a very sensitive marker for delimiting species biodiversity. Furthermore, High Resolution Melting (HRM) analysis was exploited as a molecular fingerprint for fast and accurate discrimination of Pinus spp. DNA sequence variants. The trnL approach and the HRM analyses were extended to wood samples of two species (Pinus nigra and Pinus sylvestris) with excellent results, congruent to those obtained using leaf tissue. Both analyses demonstrate that hybrids from the P. brutia (maternal parent) × P. halepensis (paternal parent) cross, exhibit the P. halepensis profile, confirming paternal plastid inheritance in Group Halepensis pines. Our study indicates that a single one-step reaction method and DNA marker are sufficient for the identification of Mediterranean pines, their hybrids and the origin of pine wood. Furthermore, our results underline the potential for certain DNA regions to be used as novel biological information markers combined with existing morphological characters and suggest a relatively reliable and open taxonomic system that can link DNA variation to phenotype-based species or hybrid assignment status and direct taxa identification from recalcitrant tissues such as wood samples.

Diffusion Monte Carlo calculations of Xenon melting under pressure

NASA Astrophysics Data System (ADS)

Shulenburger, L.; Mattsson, T. R.

2011-03-01

The slope of the melting temperature as a function of pressure yields, via the Clausius-Clapeyron equation, important information regarding the changes in density, energy, and entropy. It is therefore crucial to resolve the long-standing differences in melt lines under pressure between Diamond Anvil Cell data (low/flat melt line) and other methods, including density functional theory (DFT) simulations 1 (high/steep melt line). The disagreement for Ta was recently resolved 2 and although a similar situation exists in the literature on Xe,3 the resolution may be quite different. For example, DFT with its lack of van der Waals forces is a prima facie less credible simulation method for Xe, although excellent agreement has been obtained between calculations of the Hugoniot of Xe and experiments.4 We investigate whether this theoretical shortcoming is significant for the melting transition by applying diffusion Monte Carlo. The energy differences obtained in this way are compared to the DFT results in order to address any systematic errors that may be present near the melting transition. 1 Taioli et al. PRB 75, 214103 (2007); 2 Dewaele et al. PRL 104, 255701 (2010); 3 Belonoshko el al. PRB 74, 054114 (2006); 4 Root et al. PRL 105, 085501 (2010) Sandia National Laboratories is a multiprogram laboratory managed and operated by Sandia Corp. for the US Dep. of Energy's National Nuclear Security Administration under Contract DE-AC04-94AL85000.

Development of a Climate-Data Record (CDR) of the Surface Temperature of the Greenland Ice Sheet

NASA Technical Reports Server (NTRS)

Hall, Dorthy K.; Comiso, Josefino C.; Shuman, Christopher A.; DiGirolamo, Nicolo E.; Stock, Larry V.

2010-01-01

Regional "clear sky" surface temperature increases since the early 1980s in the Arctic, measured using Advanced Very High Resolution Radiometer (AVHRR) infrared data, range from 0.57+/-0.02 deg C to 72+/-0.10 deg C per decade. Arctic warming has important implications for ice-sheet mass balance because much of the periphery of the Greenland Ice Sheet is already near 0 deg C during the melt season, and is thus vulnerable to rapid melting if temperatures continue to increase. An increase in melting of the ice sheet would accelerate sea-level rise, an issue affecting potentially billions of people worldwide. To quantify the ice-surface temperature (IST) of the Greenland Ice Sheet, and to provide an IST dataset of Greenland for modelers that provides uncertainties, we are developing a climate-data record (CDR) of daily "clear-sky" IST of the Greenland Ice Sheet, from 1982 to the present using AVHRR (1982 - present) and Moderate-Resolution Imaging Spectroradiometer (MODIS) data (2000 - present) at a resolution of approximately 5 km. Known issues being addressed in the production of the CDR are: time-series bias caused by cloud cover (surface temperatures can be different under clouds vs. clear areas) and cross-calibration in the overlap period between AVHRR instruments, and between AVHRR and MODIS instruments. Because of uncertainties, mainly due to clouds, time-series of satellite IST do not necessarily correspond with actual surface temperatures. The CDR will be validated by comparing results with automatic-weather station data and with satellite-derived surface-temperature products and biases will be calculated.

Experimental research of phase transitions in a melt of high-purity aluminum

NASA Astrophysics Data System (ADS)

Vorontsov, V. B.; Pershin, V. K.

2017-12-01

This scientific work is devoted to the studying of the genetic connection structures of solid and liquid phases. In this paper Fourier analysis of acoustic emission (AE) signals accompanying heating of high purity aluminum from the melting point up to 860 °C was performed. The experimental data allowed to follow the dynamics of disorder zones in the melt with increasing melt temperature up to their complete destruction. The presented results of spectral analysis of the signals were analyzed from the standpoint of the theory of cluster melting metals.

Ice shelf melt rates in Greenland and Antarctica using time-tagged digital imagery from World View and TanDEM-X

NASA Astrophysics Data System (ADS)

Charolais, A.; Rignot, E. J.; Milillo, P.; Scheuchl, B.; Mouginot, J.

2017-12-01

The floating extensions of glaciers, or ice shelves, melt vigorously in contact with ocean waters. Melt is non uniform, with the highest melt taking place in the deepest part of the cavity, where thermal forcing is the greatest because of 1) the pressure dependence of the freezing point of the seawater/ice mixture and 2) subglacial water injects fresh, buoyant, cold melt water to fuel stronger ice-ocean interactions. Melt also forms along preferential channels, which are not stationary, and create lines of weakness in the shelf. Ice shelf melt rates have been successfully measured from space over the entire Antarctic continent and on the ice shelves in Greenland using an Eulerian approach that combines ice thickness, ice velocity vectors, surface mass balance data, and measurements of ice thinning rates. The Eulerian approach is limited by the precision of the thickness gradients, typically of a few km, and requires significant spatial averaging to remove advection effects. A Lagrangian approach has been shown to be robust to advection effects and provides higher resolution details. We implemented a Lagrangian methodology for time-tagged World View DEMs by the Polar Geoscience Center (PGS) at the University of Minnesota and time-tagged TanDEM-X DEMs separated by one year. We derive melt rates on a 300-m grid with a precision of a few m/yr. Melt is strongest along grounding lines and along preferred channels. Channels are non-stationary because melt is not the same on opposite sides of the channels. Examining time series of data and comparing with the time-dependent grounding line positions inferred from satellite radar interferometry, we evaluate the magnitude of melt near the grounding line and even within the grounding zone. A non-zero melt rate in the grounding zone has vast implications for ice sheet modeling. This work is funded by a grant from NASA Cryosphere Program.

Evaluation of a 12-km Satellite-Era Reanalysis of Surface Mass Balance for the Greenland Ice Sheet

NASA Astrophysics Data System (ADS)

Cullather, R. I.; Nowicki, S.; Zhao, B.; Max, S.

2016-12-01

The recent contribution to sea level change from the Greenland Ice Sheet is thought to be strongly driven by surface processes including melt and runoff. Global reanalyses are potential means of reconstructing the historical time series of ice sheet surface mass balance (SMB), but lack spatial resolution needed to resolve ablation areas along the periphery of the ice sheet. In this work, the Modern-Era Retrospective analysis for Research and Applications, version 2 (MERRA-2) is used to examine the spatial and temporal variability of surface melt over the Greenland Ice Sheet. MERRA-2 is produced for the period 1980 to the present at a grid spacing of ½° latitude by ⅝° longitude, and includes snow hydrology processes including compaction, meltwater percolation and refreezing, runoff, and a prognostic surface albedo. The configuration of the MERRA-2 system allows for the background model - the Goddard Earth Observing System model, version 5 (GEOS-5) - to be carried in phase space through analyzed states via the computation of analysis increments, a capability referred to as "replay". Here, a MERRA-2 replay integration is conducted in which atmospheric forcing fields are interpolated and adjusted to sub- atmospheric grid-scale resolution. These adjustments include lapse-rate effects on temperature, humidity, precipitation, and other atmospheric variables that are known to have a strong elevation dependency over ice sheets. The surface coupling is performed such that mass and energy are conserved. The atmospheric forcing influences the surface representation, which operates on land surface tiles with an approximate 12-km spacing. This produces a high-resolution, downscaled SMB which is interactively coupled to the reanalysis model. We compare the downscaled SMB product with other reanalyses, regional climate model values, and a second MERRA-2 replay in which the background model has been replaced with a 12-km, non-hydrostatic version of GEOS-5. The assessment focuses on regional changes in SMB and SMB components, the identification of changes and temporal variability in the SMB equilibrium line, and the relation between SMB and other climate variables related to general circulation.

High Resolution Modeling of the Water Cycle to Refine GRACE Signal Analysis in the Gulf of Alaska Drainage

NASA Astrophysics Data System (ADS)

Beamer, J.; Hill, D. F.; Arendt, A. A.; Luthcke, S. B.; Liston, G. E.

2015-12-01

A comprehensive study of the Gulf of Alaska (GOA) drainage basin was carried out to improve understanding of the coastal freshwater discharge (FWD) and surface mass balance (SMB) of glaciers. Coastal FWD and SMB for all glacier surfaces were modeled using a suite of physically based, spatially distributed weather, energy-balance snow/ice melt, soil water balance, and runoff routing models at a high resolution (1 km horizontal grid; daily time step). A 35 year hind cast was performed, providing complete records of precipitation, runoff, snow water equivalent (SWE) depth, evapotranspiration, coastal FWD and glacier SMB. Meteorological forcing was provided by the North American Regional Reanalysis (NARR), Modern Era Retrospective Analysis for Research and Applications (MERRA), and NCEP Climate Forecast System Reanalysis (CFSR) datasets. A fourth dataset was created by bias-correcting the NARR data to recently-developed monthly weather grids based on PRISM climatologies (NARR-BC). Each weather dataset and model combination was individually calibrated using PRISM climatologies, streamflow, and glacier mass balance measurements from four locations in the study domain. Simulated mean annual FWD into the GOA ranged from 600 km3 yr-1 using NARR to 850 km3 yr-1 from NARR-BC. The CFSR-forced simulations with optimized model parameters produced a simulated regional water storage that compared favorably to data from the NASA/DLR Gravity Recovery and Climate Experiment (GRACE) high resolution mascon solutions (Figure). Glacier runoff, taken as the sum of rainfall, snow and ice melt occurring on glacier surfaces, ranged from 260 km3 yr-1 from MERRA to 400 km3 yr-1 from NARR-BC, approximately one half of the signal from both glaciers and surrounding terrain. The large contribution from non-glacier surfaces to the seasonal water balance is likely not being fully removed from GRACE solutions aimed at isolating the glacier signal alone. We will discuss methods to use our simulations to forward-model the hydrology of the Gulf of Alaska region and minimize uncertainty in the partitioning of the hydrological signal. This study provides significant insight into the linkages between hydrological modeling and gravimetric measurements in mountain environments.

Observations and modeling of ocean-induced melt beneath Petermann Glacier Ice Shelf in northwestern Greenland

NASA Astrophysics Data System (ADS)

Cai, Cilan; Rignot, Eric; Menemenlis, Dimitris; Nakayama, Yoshihiro

2017-08-01

We update observationally based estimates of subaqueous melt, Qm, beneath Petermann Glacier Ice Shelf (PGIS), Greenland, and model its sensitivity to oceanic thermal forcing, TF, and subglacial runoff, Qsg, using the Massachusetts Institute of Technology general circulation model (MITgcm), in a two-dimensional domain, with 20 m vertical and 40 m horizontal resolution at the grounding line. We adjust the drag coefficient to match the observationally based Qm. With the inclusion of Qsg, the maximum melt rate (Qmmax) is 2 times larger in summer and 1/3 larger annually than in winter. Qmmax increases above linear with TF and below linear with Qsg. We estimate that Qmmax increased by 24% (+8.1 m/yr) beneath PGIS from the 1990s to the 2000s from a 0.21°C warming in ocean temperature and a doubling in Qsg, hence contributing to its thinning. If the PGIS is removed, we estimate that the modeled melt rate near the grounding line will increase 13-16 times.

Image analysis of speckle patterns as a probe of melting transitions in laser-heated diamond anvil cell experiments.

PubMed

Salem, Ran; Matityahu, Shlomi; Melchior, Aviva; Nikolaevsky, Mark; Noked, Ori; Sterer, Eran

2015-09-01

The precision of melting curve measurements using laser-heated diamond anvil cell (LHDAC) is largely limited by the correct and reliable determination of the onset of melting. We present a novel image analysis of speckle interference patterns in the LHDAC as a way to define quantitative measures which enable an objective determination of the melting transition. Combined with our low-temperature customized IR pyrometer, designed for measurements down to 500 K, our setup allows studying the melting curve of materials with low melting temperatures, with relatively high precision. As an application, the melting curve of Te was measured up to 35 GPa. The results are found to be in good agreement with previous data obtained at pressures up to 10 GPa.

A probe for neutron activation analysis in a drill hole using 252Cf, and a Ge(Li) detector cooled by a melting cryogen

USGS Publications Warehouse

Tanner, A.B.; Moxham, R.M.; Senftle, F.E.; Baicker, J.A.

1972-01-01

A sonde has been built for high-resolution measurement of natural or neutron-induced gamma rays in boreholes. The sonde is 7.3 cm in diameter and about 2.2 m in length and weighs about 16 kg. The lithium-compensated germanium semiconductor detector is stabilized at -185 to -188??C for as much as ten hours by a cryostatic reservoir containing melting propane. During periods when the sonde is not in use the propane is kept frozen by a gravity-fed trickle of liquid nitrogen from a reservoir temporarily attached to the cryostat section. A 252Cf source, shielded from the detector, may be placed in the bottom section of the sonde for anlysis by measurement of neutron-activation or neutron-capture gamma rays. Stability of the cryostat with changing hydrostatic pressure, absence of vibration, lack of need for power to the cryostat during operation, and freedom of orientation make the method desirable for borehole, undersea, space, and some laboratory applications. ?? 1972.

Application of the SYBR Green real-time HRM PCR technique in the differentiation of the Babesia canis canis protozoa isolated in the areas of eastern Poland.

PubMed

Adaszek, Lukasz; Winiarczyk, Stanisław

2010-04-01

The aim of this study was to determine the usefulness of the real-time polymerised chain reaction (PCR) high-resolution melting (HRM) method in the differentiation of the Babesia canis canis protozoa isolated from dogs in the areas of eastern Poland. The studies involved 20 isolates of B. canis canis qualified depending on the analysis of the 18S RNA gene sequence to group A (EU 622792) and 20 isolates qualified to group B (EU 622793). It was proven with the real-time PCR technique that the melting temperature (Tm) of the obtained products of amplification was 78 degrees C for the representatives of group A and 81 degrees C for the representatives of group B, which proves that the real-time SYBR Green HRM PCR method is a technique allowing for the differentiation of the B. canis isolates which are slightly different with respect to the genetic structure, without the necessity to carry out time-consuming studies, i.e., sequencing and restriction fragment length polymorphism.

New approach on volatile contents determination in silicate melt inclusions: A coupling X-ray microtomography and geochemical approach in Los Humeros caldera complex (Eastern Mexican Volcanic Belt)

NASA Astrophysics Data System (ADS)

Creon, L.; Levresse, G.; Carrasco Nuñez, G.

2016-12-01

Volatile contents and magma degassing behavior are known to affect the style, frequency, and intensity of near-surface magmatic processes. For this reason, much effort have been devoted to characterize the volatile evolution of shallow magmatic systems to better constrain volcanic history. Silicate melt inclusions (SMI) represent samples of melt that were isolated from the bulk magma at depth, thus preserving the PTX conditions of the pre-eruptive material. SMI are often affected by the formation of a bubble after trapping; this is a natural consequence of the PVTX properties of crystal-melt-volatile systems. Previous workers have recognized that bubble formation is an obstacle, which affects the interpretation of SMI trapping conditions based only on analysis of the glass phase. Indeed, they explained that bubbles can contain a significant percentage of the volatiles, particularly for those with low solubility in the melt (e.g. CO2). In this study, we propose to define the pre-eruptive PTX conditions of Los Humeros magma chamber using SMI from the various eruption events within 460 and 30 Ka. An innovative analytical coupling has been used in order to determine: (1) the volume of the SMI glass and bubble, using high resolution 3D X-ray microtomography; (2) the density and composition of the bubbles, using Raman spectroscopy; (3) the volatile element contents in glass, using NanoSIMS; and, (4) the major elements composition of the glass, using EPMA. The recalculated volatile concentrations of the total SMI (glass + bubble), illustrate clearly that the volatile content determinations using only the glass phase, underestimate drastically the total volatile content and therefore induce significant error on the determination of the pre-eruptive volcanic budget and on the constrain on the volcanic and thermal history. This study had moreover highlighted the complex evolution of Los Humeros composite magma chamber and, gave constrains for geothermal exploration purpose.

Melt segregation from partially molten source regions - The importance of melt density and source region size

NASA Technical Reports Server (NTRS)

Stolper, E.; Hager, B. H.; Walker, D.; Hays, J. F.

1981-01-01

An investigation is conducted regarding the changes expected in the density contrast between basic melts and peridotites with increasing pressure using the limited data available on the compressibilities of silicate melts and data on the densities of mantle minerals. It is concluded that since compressibilities of silicate melts are about an order of magnitude greater than those of mantle minerals, the density contrast between basic melts and mantle minerals must diminish significantly with increasing pressure. An earlier analysis regarding the migration of liquid in partially molten source regions conducted by Walker et al. (1978) is extended, giving particular attention to the influence of the diminished density contrast between melt and residual crystals with increasing source region depth and to the influence of source region size. This analysis leads to several generalizations concerning the factors influencing the depths at which magmas will segregate from their source regions and the degrees of partial melting that can be achieved in these source regions before melt segregation occurs.

Sedimentary and crustal thicknesses and Poisson's ratios for the NE Tibetan Plateau and its adjacent regions based on dense seismic arrays

NASA Astrophysics Data System (ADS)

Wang, Weilai; Wu, Jianping; Fang, Lihua; Lai, Guijuan; Cai, Yan

2017-03-01

The sedimentary and crustal thicknesses and Poisson's ratios of the NE Tibetan Plateau and its adjacent regions are estimated by the h- κ stacking and CCP image of receiver functions from the data of 1,317 stations. The horizontal resolution of the obtained results is as high as 0.5° × 0.5°, which can be used for further high resolution model construction in the region. The crustal thicknesses from Airy's equilibrium are smaller than our results in the Sichuan Basin, Qilian tectonic belt, northern Alxa block and Qaidam Basin, which is consistent with the high densities in the mantle lithosphere and may indicate that the high-density lithosphere drags crust down overall. High Poisson's ratios and low velocity zones are found in the mid- and lower crust beneath eastern Qilian tectonic belt and the boundary areas of the Ordos block, indicating that partial melting may exist in these regions. Low Poisson's ratios and low-velocity anomalies are observed in the crust in the NE Tibetan Plateau, implying that the mafic lower crust is thinning or missing and that the mid- and lower crust does not exhibit melting or partial melting in the NE Tibetan Plateau, and weak flow layers are not likely to exist in this region.

Dependence of Snowmelt Simulations on Scaling of the Forcing Processes (Invited)

NASA Astrophysics Data System (ADS)

Winstral, A. H.; Marks, D. G.; Gurney, R. J.

2009-12-01

The spatial organization and scaling relationships of snow distribution in mountain environs is ultimately dependent on the controlling processes. These processes include interactions between weather, topography, vegetation, snow state, and seasonally-dependent radiation inputs. In large scale snow modeling it is vital to know these dependencies to obtain accurate predictions while reducing computational costs. This study examined the scaling characteristics of the forcing processes and the dependency of distributed snowmelt simulations to their scaling. A base model simulation characterized these processes with 10m resolution over a 14.0 km2 basin with an elevation range of 1474 - 2244 masl. Each of the major processes affecting snow accumulation and melt - precipitation, wind speed, solar radiation, thermal radiation, temperature, and vapor pressure - were independently degraded to 1 km resolution. Seasonal and event-specific results were analyzed. Results indicated that scale effects on melt vary by process and weather conditions. The dependence of melt simulations on the scaling of solar radiation fluxes also had a seasonal component. These process-based scaling characteristics should remain static through time as they are based on physical considerations. As such, these results not only provide guidance for current modeling efforts, but are also well suited to predicting how potential climate changes will affect the heterogeneity of mountain snow distributions.

A high-resolution melting (HRM) assay for the differentiation between Israeli field and Neethling vaccine lumpy skin disease viruses.

PubMed

Menasherow, Sophia; Erster, Oran; Rubinstein-Giuni, Marisol; Kovtunenko, Anita; Eyngor, Evgeny; Gelman, Boris; Khinich, Evgeny; Stram, Yehuda

2016-06-01

Lumpy skin disease (LSD) is a constant threat to the Middle East including the State of Israel. During vaccination programs it is essential for veterinary services and farmers to be able to distinguish between animals affected by the cattle-borne virulent viruses and vaccinated animals, subsequently affected by the vaccine strain. This study describes an improved high resolution-melting (HRM) test that exploits a 27 base pair (bp) fragment of the LSDV126 extracellular enveloped virion (EEV) gene that is present in field viruses but is absent from the Neethling vaccine strain. This difference leads to ∼0.5 °C melting point change in the HRM assay, when testing the quantitative PCR (qPCR) products generated from the virulent field viruses compared to the attenuated vaccine. By exploiting this difference, it could be shown using the newly developed HRM assay that virus isolated from vaccinated cattle that developed disease symptoms behave similarly to vaccine virus control, indicating that the vaccine virus can induce disease symptoms. This assay is not only in full agreement with the previously published PCR gradient and restriction fragment length polymorphism (RFLP) tests but it is faster with, fewer steps, cheaper and dependable. Copyright © 2016 Elsevier B.V. All rights reserved.

Massively parallel digital high resolution melt for rapid and absolutely quantitative sequence profiling

NASA Astrophysics Data System (ADS)

Velez, Daniel Ortiz; Mack, Hannah; Jupe, Julietta; Hawker, Sinead; Kulkarni, Ninad; Hedayatnia, Behnam; Zhang, Yang; Lawrence, Shelley; Fraley, Stephanie I.

2017-02-01

In clinical diagnostics and pathogen detection, profiling of complex samples for low-level genotypes represents a significant challenge. Advances in speed, sensitivity, and extent of multiplexing of molecular pathogen detection assays are needed to improve patient care. We report the development of an integrated platform enabling the identification of bacterial pathogen DNA sequences in complex samples in less than four hours. The system incorporates a microfluidic chip and instrumentation to accomplish universal PCR amplification, High Resolution Melting (HRM), and machine learning within 20,000 picoliter scale reactions, simultaneously. Clinically relevant concentrations of bacterial DNA molecules are separated by digitization across 20,000 reactions and amplified with universal primers targeting the bacterial 16S gene. Amplification is followed by HRM sequence fingerprinting in all reactions, simultaneously. The resulting bacteria-specific melt curves are identified by Support Vector Machine learning, and individual pathogen loads are quantified. The platform reduces reaction volumes by 99.995% and achieves a greater than 200-fold increase in dynamic range of detection compared to traditional PCR HRM approaches. Type I and II error rates are reduced by 99% and 100% respectively, compared to intercalating dye-based digital PCR (dPCR) methods. This technology could impact a number of quantitative profiling applications, especially infectious disease diagnostics.

Modeling the Spreading of Glacial Melt Water from the Amundsen and Bellingshausen Seas

NASA Astrophysics Data System (ADS)

Nakayama, Y.; Timmermann, R.; Rodehacke, C. B.; Schröder, M.; Hellmer, H. H.

2014-12-01

The ice shelves and glaciers of the West Antarctic Ice Sheet (WAIS) are rapidly thinning, especially in the Amundsen Sea (AS) and Bellingshausen Sea (BS). The high basal melting of these small ice shelves is caused by relatively warm Circumpolar Deep Water (CDW) that, based on observations, mainly intrudes via two submarine glacial troughs located at the eastern and central AS continental shelf break. When CDW reaches the grounding line of the fringing glaciers, it melts the glaciers and forms buoyant melt water plumes. As the glacial melt becomes part of the AS shelf circulation, it may cause a freshening of the shelf water locally as well as remotely in the Ross Sea (RS). To test whether the observed freshening of the RS is a consequence of the enhanced basal melting of AS ice shelves, we use Finite-Element Sea-ice/ice-shelf/Ocean Model (FESOM) with a horizontal resolution of 2-10 km on the AS and BS continental shelves. The model is forced with 6-hourly atmospheric data from the National Centers for Environmental Prediction Climate Forecast System Reanalysis (NCEP-CFSR) for the period 1979-1988. The model results show bottom temperatures in the AS and BS close to observations, and basal melt rates of AS and BS ice shelves consistent with other observation-based estimates. Using several independent virtual passive tracers to identify pathways of the glacial melt, we find that the melt water from the ice shelves in the AS flows towards the Ross Ice Shelf front. After 10 years of simulation, about half of the melt water in the Ross Sea originates from the Getz Ice Shelf. Further, we investigate the sensitivity of the melt water transport into the RS associated with the strength of the basal melt water flux. When this flux is increased by 30%, the transport of glacial melt into the RS more than doubles, supporting the idea that the basal melting of AS and BS ice shelves is one of the main reasons for the freshening of the RS continental shelf.

Determination of crystal growth rates during rapid solidification of polycrystalline aluminum by nano-scale spatio-temporal resolution in situ transmission electron microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zweiacker, K.; McKeown, J. T.; Liu, C.

In situ investigations of rapid solidification in polycrystalline Al thin films were conducted using nano-scale spatio-temporal resolution dynamic transmission electron microscopy. Differences in crystal growth rates and asymmetries in melt pool development were observed as the heat extraction geometry was varied by controlling the proximity of the laser-pulse irradiation and the associated induced melt pools to the edge of the transmission electron microscopy support grid, which acts as a large heat sink. Experimental parameters have been established to maximize the reproducibility of the material response to the laser-pulse-related heating and to ensure that observations of the dynamical behavior of themore » metal are free from artifacts, leading to accurate interpretations and quantifiable measurements with improved precision. Interface migration rate measurements revealed solidification velocities that increased consistently from ~1.3 m s –1 to ~2.5 m s –1 during the rapid solidification process of the Al thin films. Under the influence of an additional large heat sink, increased crystal growth rates as high as 3.3 m s –1 have been measured. The in situ experiments also provided evidence for development of a partially melted, two-phase region prior to the onset of rapid solidification facilitated crystal growth. As a result, using the experimental observations and associated measurements as benchmarks, finite-element modeling based calculations of the melt pool evolution after pulsed laser irradiation have been performed to obtain estimates of the temperature evolution in the thin films.« less

Determination of crystal growth rates during rapid solidification of polycrystalline aluminum by nano-scale spatio-temporal resolution in situ transmission electron microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zweiacker, K., E-mail: Kai@zweiacker.org; Liu, C.; Wiezorek, J. M. K.

In situ investigations of rapid solidification in polycrystalline Al thin films were conducted using nano-scale spatio-temporal resolution dynamic transmission electron microscopy. Differences in crystal growth rates and asymmetries in melt pool development were observed as the heat extraction geometry was varied by controlling the proximity of the laser-pulse irradiation and the associated induced melt pools to the edge of the transmission electron microscopy support grid, which acts as a large heat sink. Experimental parameters have been established to maximize the reproducibility of the material response to the laser-pulse-related heating and to ensure that observations of the dynamical behavior of themore » metal are free from artifacts, leading to accurate interpretations and quantifiable measurements with improved precision. Interface migration rate measurements revealed solidification velocities that increased consistently from ∼1.3 m s{sup −1} to ∼2.5 m s{sup −1} during the rapid solidification process of the Al thin films. Under the influence of an additional large heat sink, increased crystal growth rates as high as 3.3 m s{sup −1} have been measured. The in situ experiments also provided evidence for development of a partially melted, two-phase region prior to the onset of rapid solidification facilitated crystal growth. Using the experimental observations and associated measurements as benchmarks, finite-element modeling based calculations of the melt pool evolution after pulsed laser irradiation have been performed to obtain estimates of the temperature evolution in the thin films.« less

Determination of crystal growth rates during rapid solidification of polycrystalline aluminum by nano-scale spatio-temporal resolution in situ transmission electron microscopy

DOE PAGES

Zweiacker, K.; McKeown, J. T.; Liu, C.; ...

2016-08-04

In situ investigations of rapid solidification in polycrystalline Al thin films were conducted using nano-scale spatio-temporal resolution dynamic transmission electron microscopy. Differences in crystal growth rates and asymmetries in melt pool development were observed as the heat extraction geometry was varied by controlling the proximity of the laser-pulse irradiation and the associated induced melt pools to the edge of the transmission electron microscopy support grid, which acts as a large heat sink. Experimental parameters have been established to maximize the reproducibility of the material response to the laser-pulse-related heating and to ensure that observations of the dynamical behavior of themore » metal are free from artifacts, leading to accurate interpretations and quantifiable measurements with improved precision. Interface migration rate measurements revealed solidification velocities that increased consistently from ~1.3 m s –1 to ~2.5 m s –1 during the rapid solidification process of the Al thin films. Under the influence of an additional large heat sink, increased crystal growth rates as high as 3.3 m s –1 have been measured. The in situ experiments also provided evidence for development of a partially melted, two-phase region prior to the onset of rapid solidification facilitated crystal growth. As a result, using the experimental observations and associated measurements as benchmarks, finite-element modeling based calculations of the melt pool evolution after pulsed laser irradiation have been performed to obtain estimates of the temperature evolution in the thin films.« less

Product differentiation by analysis of DNA melting curves during the polymerase chain reaction.

PubMed

Ririe, K M; Rasmussen, R P; Wittwer, C T

1997-02-15

A microvolume fluorometer integrated with a thermal cycler was used to acquire DNA melting curves during polymerase chain reaction by fluorescence monitoring of the double-stranded DNA specific dye SYBR Green I. Plotting fluorescence as a function of temperature as the thermal cycler heats through the dissociation temperature of the product gives a DNA melting curve. The shape and position of this DNA melting curve are functions of the GC/AT ratio, length, and sequence and can be used to differentiate amplification products separated by less than 2 degrees C in melting temperature. Desired products can be distinguished from undesirable products, in many cases eliminating the need for gel electrophoresis. Analysis of melting curves can extend the dynamic range of initial template quantification when amplification is monitored with double-stranded DNA specific dyes. Complete amplification and analysis of products can be performed in less than 15 min.

High Spatial Resolution 40Ar/39Ar Geochronology of Lunar Impact Melt Rocks

NASA Astrophysics Data System (ADS)

Mercer, Cameron Mark

Impact cratering has played a key role in the evolution of the solid surfaces of Solar System bodies. While much of Earth’s impact record has been erased, its Moon preserves an extensive history of bombardment. Quantifying the timing of lunar impact events is crucial to understanding how impacts have shaped the evolution of early Earth, and provides the basis for estimating the ages of other cratered surfaces in the Solar System. Many lunar impact melt rocks are complex mixtures of glassy and crystalline “melt” materials and inherited clasts of pre-impact minerals and rocks. If analyzed in bulk, these samples can yield complicated incremental release 40Ar/39Ar spectra, making it challenging to uniquely interpret impact ages. Here, I have used a combination of high-spatial resolution 40Ar/39Ar geochronology and thermal-kinetic modeling to gain new insights into the impact histories recorded by such lunar samples. To compare my data to those of previous studies, I developed a software tool to account for differences in the decay, isotopic, and monitor age parameters used for different published 40Ar/39Ar datasets. Using an ultraviolet laser ablation microprobe (UVLAMP) system I selectively dated melt and clast components of impact melt rocks collected during the Apollo 16 and 17 missions. UVLAMP 40Ar/39Ar data for samples 77135, 60315, 61015, and 63355 show evidence of open-system behavior, and provide new insights into how to interpret some complexities of published incremental heating 40Ar/39Ar spectra. Samples 77115, 63525, 63549, and 65015 have relatively simple thermal histories, and UVLAMP 40Ar/39Ar data for the melt components of these rocks indicate the timing of impact events—spanning hundreds of millions of years—that influenced the Apollo 16 and 17 sites. My modeling and UVLAMP 40Ar/39Ar data for sample 73217 indicate that some impact melt rocks can quantitatively retain evidence for multiple melt-producing impact events, and imply that such polygenetic rocks should be regarded as high-value sampling opportunities during future exploration missions to cratered planetary surfaces. Collectively, my results complement previous incremental heating 40Ar/39Ar studies, and support interpretations that the Moon experienced a prolonged period of heavy bombardment early in its history.

Evolution of Microroughness with Increasing Slip Magnitude on Pseudotachylyte-Bearing Fault Surfaces

NASA Astrophysics Data System (ADS)

Bessey, S.; Resor, P. G.; Di Toro, G.

2013-12-01

High velocity rock friction experiments reproducing seismic slip deformation conditions have shown that there is an initial shear strengthening prior to a significant weakening with slip. This change in shear resistance is inferred to occur due to the development of melt patches, which initially strengthen the fault, and is associated with the evolution of microroughness of the melt-wall rock interface (Hirose and Shimamoto, 2003). Additional melting leads to a continuous layer of melt, allowing easier sliding and weakening. Once there is a balance between formation and extrusion of melt, a steady state shear resistance (and associated effective friction coefficient) is reached (Nielsen et al. 2008). In natural fault zones, the process of frictional melting, slip weakening, and steady state is both recorded and influenced by the microroughness of the fault surface. Our study explores natural faults over a range of slip magnitudes from mm to m of slip, the magnitudes over which this process is most likely to occur during earthquakes. The Gole Larghe fault zone (Italy) is an exhumed strike-slip fault zone in tonalite of the Adamello batholith. The fault zone is characterized by multiple fault strands containing pseudotachylyte or pseudotachylyte overprinting cataclasite. We have sampled several individual faults segments from within the fault zone, with slips ranging from 23 mm to 1.9 m. The smaller scale samples are from pseudotachylyte-only fault strands and therefore probably record single-slip events. The two largest slip faults have pseudotachylyte and cataclasite, indicating that they may have more complicated slip histories. Individual samples consist of cores (2-3.5 cm diameter, 2-6 cm length) drilled parallel to the fault surface and ~perpendicular to the slip. Samples were scanned with an Xradia MicroCT scanner to image the 3D geometry of the fault and wall rocks. Fault surfaces (contact between the pseudotachylyte-bearing slipping zone and the wall rock) were extracted from the CT volume using an edge detection algorithm and their roughness was quantified using Fourier spectral and spatial analysis methods. At very small slip (<30 mm), roughness analysis showed anisotropy in the form of striations with smoothing in the direction of slip coupled with a lack of visible pseudotachylyte (i.e., the volume of pseudotachylyte produced was below the resolution of the MicroCT method), suggesting that the frictional work did not exchange sufficient heat to significantly melt the host rock along the fault surface. With increasing slip (~35mm-310mm), a trend of decreasing anisotropy is in evidence, as is a strong increase in local topography associated with recessed biotite grains. We infer that samples in this range of slip magnitude experienced significant wear due to melting. Microroughness shows a clear, albeit somewhat complicated, relationship with slip and may be used to infer the evolution of shear resistance with seismic slip.

Calculating Freshwater Input from Iceberg Melt in Greenlandic Fjords by Combining In Situ Observations of Iceberg Movement with High Resolution Satellite Imagery

NASA Astrophysics Data System (ADS)

Sulak, D. J.; Sutherland, D.; Stearns, L. A.; Hamilton, G. S.

2015-12-01

Understanding fjord circulation in Greenland's outlet glacial fjords is crucial to explaining recent temporal and spatial variability in glacier dynamics, as well as freshwater transport on the continental shelf. The fjords are commonly assumed to exhibit a plume driven circulation that draws in warmer and saltier Atlantic-origin water toward the glacier at depth. Freshwater input at glacier termini directly drives this circulation and significantly influences water column stratification, which indirectly feeds back on the plume driven circulation. Previous work has focused on freshwater inputs from surface runoff and submarine melting, but the contribution from iceberg melt, a potentially important freshwater source, has not been quantified. Here, we develop a new technique combining in situ observations of movement from iceberg-mounted GPS units with multispectral satellite imagery from Landsat 8. The combination of datasets allows us to examine the details of iceberg movement and quantify mean residence times in a given fjord. We then use common melt rate parameterizations to estimate freshwater input for a given iceberg, utilizing novel satellite-derived iceberg distributions to scale up to a fjord-wide freshwater contribution. We apply this technique to Rink Isbræ and Kangerlussuup Sermia in west Greenland, and Helheim Glacier in southeast Greenland. The analysis can be rapidly expanded to look at other systems as well as seasonal and interannual changes in how icebergs affect the circulation and stratification of Greenland's outlet glacial fjords. Ultimately, this work will lead to a more complete understanding of the wide range of factors that control the observed regional variability in Greenland's glaciers.

When Does the Warmest Water Reach Greenland?

NASA Astrophysics Data System (ADS)

Grist, J. P.; Josey, S. A.; Boehme, L.; Meredith, M. P.; Laidre, K. L.; Heide-Jørgensen, M. P.; Kovacs, K. M.; Lydersen, C.; Davidson, F. J. M.; Stenson, G. B.; Hammill, M. O.; Marsh, R.; Coward, A.

2016-02-01

The warmest water reaching the east and west coast of Greenland is found between 200 and 600 m, in the warm Atlantic Water Layer (WL). Temperature changes within the WL have been highlighted as a possible cause of accelerated melting of tidewater glaciers and therefore are an important consideration for understanding global sea level rise. However, a limited number of winter observations of the WL have prohibited determining its seasonal variability. To address this, temperature data from Argo profiling floats, a range of sources within the World Ocean Database, and unprecedented coverage from marine-mammal borne sensors have been analyzed for the period 2002-2011. A significant seasonal range in temperature ( 1-2°C) is found in the warm layer, in contrast to most of the surrounding ocean. The magnitude of the seasonal cycle is thus comparable with the 1990s warming that was associated with an increased melt rate in a marine terminating glacier of West Greenland. The phase of the seasonal cycle exhibits considerable spatial variability; with high-resolution ocean model trajectory analysis suggesting it is determined by the time taken for waters to be advected from the subduction site in the Irminger Basin. For western Greenland, the annual temperature maximum occurs near or after the turn of the calendar year. This is significant because a recent study suggested that it is in the non-summer months when fjord-shelf exchanges allow the WL to most strongly influence glacier melt rate. However this is also the time of the year when the WL is least well observed. It is therefore clear that year-round subsurface temperature measurements are still required for a complete description of the WL seasonality, and in particular to ensure that the ice-melting potential of the WL is not underestimated.

Investigating ice cliff evolution and contribution to glacier mass-balance using a physically-based dynamic model

NASA Astrophysics Data System (ADS)

Buri, Pascal; Miles, Evan; Ragettli, Silvan; Brun, Fanny; Steiner, Jakob; Pellicciotti, Francesca

2016-04-01

Supraglacial cliffs are a surface feature typical of debris-covered glaciers, affecting surface evolution, glacier downwasting and mass balance by providing a direct ice-atmosphere interface. As a result, melt rates can be very high and ice cliffs may account for a significant portion of the total glacier mass loss. However, their contribution to glacier mass balance has rarely been quantified through physically-based models. Most cliff energy balance models are point scale models which calculate energy fluxes at individual cliff locations. Results from the only grid based model to date accurately reflect energy fluxes and cliff melt, but modelled backwasting patterns are in some cases unrealistic, as the distribution of melt rates would lead to progressive shallowing and disappearance of cliffs. Based on a unique multitemporal dataset of cliff topography and backwasting obtained from high-resolution terrestrial and aerial Structure-from-Motion analysis on Lirung Glacier in Nepal, it is apparent that cliffs exhibit a range of behaviours but most do not rapidly disappear. The patterns of evolution cannot be explained satisfactorily by atmospheric melt alone, and are moderated by the presence of supraglacial ponds at the base of cliffs and by cliff reburial with debris. Here, we document the distinct patterns of evolution including disappearance, growth and stability. We then use these observations to improve the grid-based energy balance model, implementing periodic updates of the cliff geometry resulting from modelled melt perpendicular to the ice surface. Based on a slope threshold, pixels can be reburied by debris or become debris-free. The effect of ponds are taken into account through enhanced melt rates in horizontal direction on pixels selected based on an algorithm considering distance to the water surface, slope and lake level. We use the dynamic model to first study the evolution of selected cliffs for which accurate, high resolution DEMs are available, and then apply the model to the entirety of Lirung and Langtang glaciers to quantify the total contributions of cliffs to glacier mass balance. Observations and model results suggest a strong dependency of the cliffs' life cycle on supraglacial ponds, as the water body keeps the cliff geometry constant through a combination of backwasting and calving at the bottom and maintenance of steep slopes in the lowest sections. The absence of ponds causes the progressive flattening of the cliff, which finally leads to complete disappearance. Modelled volume losses from May to October 2013 range from 2650 to 9415 m3 w.e., in agreement with the estimates with the SfM-approach. Mean error of modelled elevation within the cliff outline ranges from -1.3 to 0.6m. This work sheds light on mechanisms of cliffs' changes by quantifying them for the first time with a physically-based, dynamic model, and presents the first complete estimate of the relevance of supraglacial ice-cliffs to total glacier mass-balance for two distinct glaciers.

Quantifying changes in the contribution of upstream snow and glacier melt to downstream low flows in the River Rhine

NASA Astrophysics Data System (ADS)

Stahl, K.; Kohn, I.; Boehm, M.; Seibert, J.; Freudiger, D.; Gerlinger, K.; Weiler, M.

2016-12-01

Low flows impact river ecosystems and impair water use. In the mid- and downstream reaches of one of the largest rivers in Europe, the River Rhine, low flows can threaten a variety of ecosystem services and direct uses. Low flows in summer and fall are sustained by the snow and ice melt contribution from the glacierized mountain headwaters upstream. This study explores changes in the discharge components of rain, snowmelt and ice melt during extreme low flow events from a downstream perspective. Quantification of the discharge components is based on a novel method of runoff component tracking that was implemented into a model chain, consisting of the HBV model, which includes a glacier mass balance model allowing for areal glacier changes, for the headwaters and the distributed hydrological model LARSIM for the remaining Rhine basin. A transient model run at daily resolution was calibrated to glacier volume change, basin-wide snow cover and snow water equivalent and discharge variability at many gauging stations over the period 1901-2006. The analysis of the resulting discharge components revealed that over the course of the 20th Century, the loss of glacier volume and glacier area in the headwaters appears to have compensated an increasingly negative glacier mass balance, resulting in little long-term change to the ice melt component in summer streamflow - thus showing no clear `peak-water' trend. While the glacier ice melt component was less than two percent of the average annual discharge of the mid and lower reaches of the River Rhine, models suggest its fraction was much higher during extreme low flow events. The low flows of the summers of 1921, 1947, and 2003 were comprised of record daily ice melt fractions of more than one fifth of the daily discharge along the mid and lower reaches from Basel to the mouth. A scenario model run with suppressed glacier area change suggests that the ice melt discharge component would have doubled if the same meteorological event as in 2003 had occurred in the early 1900s when glacier areas were still much larger. Impacts on ecology and water use most likely would have also been less severe. The modeled changes in discharge components thus allow a quantification of the low flow hazard that may loom ahead as the glaciers continue to decline.

Optical resolution by preferential crystallization of (1RS,3RS)-1,2,3,4-tetrahydro-6,7-dihydroxy-1-methyl-3-isoquinolinecarboxylic acid.

PubMed

Shiraiwa, Tadashi; Kiyoe, Ryuuichi

2005-09-01

The racemic structure of (1RS,3RS)-1,2,3,4-tetrahydro-6,7-dihydroxy-1-methyl-3-isoquinolinecarboxylic acid [(1RS,3RS)-1] was examined based on the melting point, solubility, and IR spectrum, with the aim of optical resolution by preferential crystallization. (1RS,3RS)-1 was indicated from these results to exist as a conglomerate. The successive optical resolution by preferential crystallization of (1RS,3RS)-1 yielded (1S,3S)- and (1R,3R)-1 with optical purities of 85--95% at 66--81% degrees of resolution, which were fully purified by recrystallization.

Validation of Suomi-NPP VIIRS sea ice concentration with very high-resolution satellite and airborne camera imagery

NASA Astrophysics Data System (ADS)

Baldwin, Daniel; Tschudi, Mark; Pacifici, Fabio; Liu, Yinghui

2017-08-01

Two independent VIIRS-based Sea Ice Concentration (SIC) products are validated against SIC as estimated from Very High Spatial Resolution Imagery for several VIIRS overpasses. The 375 m resolution VIIRS SIC from the Interface Data Processing Segment (IDPS) SIC algorithm is compared against estimates made from 2 m DigitalGlobe (DG) WorldView-2 imagery and also against estimates created from 10 cm Digital Mapping System (DMS) camera imagery. The 750 m VIIRS SIC from the Enterprise SIC algorithm is compared against DG imagery. The IDPS vs. DG comparisons reveal that, due to algorithm issues, many of the IDPS SIC retrievals were falsely assigned ice-free values when the pixel was clearly over ice. These false values increased the validation bias and RMS statistics. The IDPS vs. DMS comparisons were largely over ice-covered regions and did not demonstrate the false retrieval issue. The validation results show that products from both the IDPS and Enterprise algorithms were within or very close to the 10% accuracy (bias) specifications in both the non-melting and melting conditions, but only products from the Enterprise algorithm met the 25% specifications for the uncertainty (RMS).

Eddy-resolving simulations of the Fimbul Ice Shelf cavity circulation: Basal melting and exchange with open ocean

NASA Astrophysics Data System (ADS)

Hattermann, T.; Smedsrud, L. H.; Nøst, O. A.; Lilly, J. M.; Galton-Fenzi, B. K.

2014-10-01

Melting at the base of floating ice shelves is a dominant term in the overall Antarctic mass budget. This study applies a high-resolution regional ice shelf/ocean model, constrained by observations, to (i) quantify present basal mass loss at the Fimbul Ice Shelf (FIS); and (ii) investigate the oceanic mechanisms that govern the heat supply to ice shelves in the Eastern Weddell Sea. The simulations confirm the low melt rates suggested by observations and show that melting is primarily determined by the depth of the coastal thermocline, regulating deep ocean heat fluxes towards the ice. Furthermore, the uneven distribution of ice shelf area at different depths modulates the melting response to oceanic forcing, causing the existence of two distinct states of melting at the FIS. In the simulated present-day state, only small amounts of Modified Warm Deep Water enter the continental shelf, and ocean temperatures beneath the ice are close to the surface freezing point. The basal mass loss in this so-called state of "shallow melting" is mainly controlled by the seasonal inflow of solar-heated surface water affecting large areas of shallow ice in the upper part of the cavity. This is in contrast to a state of "deep melting", in which the thermocline rises above the shelf break depth, establishing a continuous inflow of Warm Deep Water towards the deep ice. The transition between the two states is found to be determined by a complex response of the Antarctic Slope Front overturning circulation to varying climate forcings. A proper representation of these frontal dynamics in climate models will therefore be crucial when assessing the evolution of ice shelf basal melting along this sector of Antarctica.

Changes in Black Carbon Deposition to Antarctica from Two Ice Core Records, A.D. 1850-2000

NASA Technical Reports Server (NTRS)

Bisiaux, Marion M.; Edward, Ross; McConnell, Joseph R.; Curran, Mark A. J.; VanOmmen, Tas D.; Smith, Andrew M.; Neumann, Thomas A.; Pasteris, Daniel R.; Penner, Joyce E.; Taylor, Kendrick

2012-01-01

Continuous flow analysis was based on a steady sample flow and in-line detection of BC and other chemical substances as described in McConnell et al. (2007). In the cold room, previously cut one meter ice core sticks of 3x3cm, are melted continuously on a heated melter head specifically designed to eliminate contamination from the atmosphere or by the external parts of the ice. The melted ice from the most inner part of the ice stick is continuously pumped by a peristaltic pump and carried to a clean lab by Teflon lines. The recorded signal is continuous, integrating a sample volume of about 0.05 mL, for which the temporal resolution depends on the speed of melting, ice density and snow accumulation rate at the ice core drilling site. For annual accumulation derived from the WAIS and Law Dome ice cores, we assumed 3.1 cm water equivalent uncertainty in each year's accumulation from short scale spatial variability (glaciological noise) which was determined from several measurements of annual accumulation in multiple parallel ice cores notably from the WAIS Divide ice core site (Banta et al., 2008) and from South Pole site (McConnell et al., 1997; McConnell et al., 2000). Refractory black carbon (rBC) concentrations were determined using the same method as in (Bisiaux et al., 2011) and adapted to continuous flow measurements as described by (McConnell et al., 2007). The technique uses a single particle intracavity laser induced incandescence photometer (SP2, Droplet Measurement Technologies, Boulder, Colorado) coupled to an ultrasonic nebulizer/desolvation (CETAC UT5000) Flow Injection Analysis (FIA). All analyses, sample preparation etc, were performed in a class 100 cleanroom using anti contamination "clean techniques". The samples were not acidified.

Identifying and Characterizing Impact Melt Outcrops in the Nectaris Basin

NASA Technical Reports Server (NTRS)

Cohen, B. A.; Lawerence, S. J.; Petro, N. E.; Bart, G. D.; Clegg-Watkins, R. N.; Denevi, B. W.; Ghent, R. R.; Klima, R. L.; Morgan, G. A.; Spudis, P. D.;

An Investigation of Sintering Parameters on Titanium Powder for Electron Beam Melting Processing Optimization.

PubMed

Drescher, Philipp; Sarhan, Mohamed; Seitz, Hermann

2016-12-01

Selective electron beam melting (SEBM) is a relatively new additive manufacturing technology for metallic materials. Specific to this technology is the sintering of the metal powder prior to the melting process. The sintering process has disadvantages for post-processing. The post-processing of parts produced by SEBM typically involves the removal of semi-sintered powder through the use of a powder blasting system. Furthermore, the sintering of large areas before melting decreases productivity. Current investigations are aimed at improving the sintering process in order to achieve better productivity, geometric accuracy, and resolution. In this study, the focus lies on the modification of the sintering process. In order to investigate and improve the sintering process, highly porous titanium test specimens with various scan speeds were built. The aim of this study was to decrease build time with comparable mechanical properties of the components and to remove the residual powder more easily after a build. By only sintering the area in which the melt pool for the components is created, an average productivity improvement of approx. 20% was achieved. Tensile tests were carried out, and the measured mechanical properties show comparatively or slightly improved values compared with the reference.

Refining lunar impact chronology through high spatial resolution (40)Ar/(39)Ar dating of impact melts.

PubMed

Mercer, Cameron M; Young, Kelsey E; Weirich, John R; Hodges, Kip V; Jolliff, Bradley L; Wartho, Jo-Anne; van Soest, Matthijs C

2015-02-01

Quantitative constraints on the ages of melt-forming impact events on the Moon are based primarily on isotope geochronology of returned samples. However, interpreting the results of such studies can often be difficult because the provenance region of any sample returned from the lunar surface may have experienced multiple impact events over the course of billions of years of bombardment. We illustrate this problem with new laser microprobe (40)Ar/(39)Ar data for two Apollo 17 impact melt breccias. Whereas one sample yields a straightforward result, indicating a single melt-forming event at ca. 3.83 Ga, data from the other sample document multiple impact melt-forming events between ca. 3.81 Ga and at least as young as ca. 3.27 Ga. Notably, published zircon U/Pb data indicate the existence of even older melt products in the same sample. The revelation of multiple impact events through (40)Ar/(39)Ar geochronology is likely not to have been possible using standard incremental heating methods alone, demonstrating the complementarity of the laser microprobe technique. Evidence for 3.83 Ga to 3.81 Ga melt components in these samples reinforces emerging interpretations that Apollo 17 impact breccia samples include a significant component of ejecta from the Imbrium basin impact. Collectively, our results underscore the need to quantitatively resolve the ages of different melt generations from multiple samples to improve our current understanding of the lunar impact record, and to establish the absolute ages of important impact structures encountered during future exploration missions in the inner Solar System.

A novel method of multiple nucleic acid detection: Real-time RT-PCR coupled with probe-melting curve analysis.

PubMed

Han, Yang; Hou, Shao-Yang; Ji, Shang-Zhi; Cheng, Juan; Zhang, Meng-Yue; He, Li-Juan; Ye, Xiang-Zhong; Li, Yi-Min; Zhang, Yi-Xuan

2017-11-15

A novel method, real-time reverse transcription PCR (real-time RT-PCR) coupled with probe-melting curve analysis, has been established to detect two kinds of samples within one fluorescence channel. Besides a conventional TaqMan probe, this method employs another specially designed melting-probe with a 5' terminus modification which meets the same label with the same fluorescent group. By using an asymmetric PCR method, the melting-probe is able to detect an extra sample in the melting stage effectively while it almost has little influence on the amplification detection. Thus, this method allows the availability of united employment of both amplification stage and melting stage for detecting samples in one reaction. The further demonstration by simultaneous detection of human immunodeficiency virus (HIV) and hepatitis C virus (HCV) in one channel as a model system is presented in this essay. The sensitivity of detection by real-time RT-PCR coupled with probe-melting analysis was proved to be equal to that detected by conventional real-time RT-PCR. Because real-time RT-PCR coupled with probe-melting analysis can double the detection throughputs within one fluorescence channel, it is expected to be a good solution for the problem of low-throughput in current real-time PCR. Copyright © 2017 Elsevier Inc. All rights reserved.

Geological Mapping of Impact Melt Deposits at Lunar Complex Craters: New Insights into Morphological Diversity, Distribution and the Cratering Process

NASA Astrophysics Data System (ADS)

Dhingra, D.; Head, J. W., III; Pieters, C. M.

2014-12-01

We have completed high resolution geological mapping of impact melt deposits at the young lunar complex craters (<1 billion years) Copernicus, Jackson and Tycho using data from recent missions. Crater floors being the largest repository of impact melt, we have mapped their morphological diversity expressed in terms of varied surface texture, albedo, character and occurrence of boulder units as well as relative differences in floor elevation. Examples of wall and rim impact melt units and their relation to floor units have also been mapped. Among the distinctive features of these impact melt deposits are: 1) Impact Melt Wave Fronts: These are extensive (sometimes several kilometers in length) and we have documented their occurrence and distribution in different parts of the crater floor at Jackson and Tycho. These features emphasize melt mobility and style of emplacement during the modification stage of the craters. 2) Variations in Floor Elevations: Spatially extensive and coherent sections of crater floors have different elevations at all the three craters. The observed elevation differences could be caused by subsidence due to cooling of melt and/or structural failure, together with a contribution from regional slope. 3) Melt-Covered Megablocks: We also observe large blocks/rock-fragments (megablocks) covered in impact melt, which could be sections of collapsed wall or in some cases, subdued sections of central peaks. 4) Melt-Covered Central Peaks: Impact melt has also been mapped on the central peaks but varies in spatial extent among the craters. The presence of melt on peaks must be taken into account when interpreting peak mineralogy as exposures of deeper crust. 5) Boulder Distribution: Interesting trends are observed in the distribution of boulder units of various sizes; some impact melt units have spatially extensive boulders, while boulder distribution is very scarce in other units on the floor. We interpret these distributions to be influenced by a) the differential collapse of the crater walls during the modification stage, and b) the amount of relative melt volume retained in different parts of the crater floor. These observations provide important documentation of the morphological diversity and better understanding of the emplacement and final distribution of impact melt deposits.

Novel Polarization Techniques and Instrumentation for Glacial Melt Pond Laser Bathymetry

NASA Astrophysics Data System (ADS)

Barton-Grimley, R. A.; Gisler, A.; Thayer, J. P.; Stillwell, R. A.; Grigsby, S.; Crowley, G.

2015-12-01

Melt ponds contribute significantly to the feedback processes that serve to amplify the polar response to climate change. A substantial volume of melt water is found in shallow ponds during the Arctic summer on the Greenland Ice Sheet, which have consequences on glacial dynamics and ice loss, however, the water content and subsurface topography of the ponds has proven difficult to measure. The need for instrumentation to provide high-resolution depth measurements in shallow water is addressed by utilizing novel polarization discrimination techniques in a high repetition rate, low power, 532nm photon counting lidar system. Recent advances demonstrate the ability to achieve kHz acquisition rates with a depth precision of 1cm. Use of this technique eliminates the necessity for short laser pulses and high-bandwidth detectors and instead provides a less complex, smaller, and more economical solution to airborne lidar instrumentation. Recent deployment of the lidar system aboard the NASA DC-8 research aircraft, during the 2015 NASA SARP campaign, provided critical engineering data and experience to facilitate further advancement of an airborne bathymetric lidar system for melt pond studies. Signal performance from flight indicates a 50 cm horizontal ground resolution at nominal altitudes below 1000 feet above ground level, and also indicates that maintaining a vertical precision of 1cm is achievable, though these results will be further examined. Results from the DC-8 aircraft deployment are promising, and the modest system size opens up the possibility for future integration into a UAS. This presentation will highlight the measurement capabilities of this novel lidar system, and explore polarization scattering properties of laser light with snow, ice, liquid water. System performance metrics will be evaluated for operating during summer periods in the Polar Regions and discuss the scientific contribution to Cryosphere research - most notably the depth and subsurface ice topography of glacial melt ponds.

Defect Engineering in SrI 2:Eu 2+ Single Crystal Scintillators

DOE PAGES

Wu, Yuntao; Boatner, Lynn A.; Lindsey, Adam C.; ...

2015-06-23

Eu 2+-activated strontium iodide is an excellent single crystal scintillator used for gamma-ray detection and significant effort is currently focused on the development of large-scale crystal growth techniques. A new approach of molten-salt pumping or so-called melt aging was recently applied to optimize the crystal quality and scintillation performance. Nevertheless, a detailed understanding of the underlying mechanism of this technique is still lacking. The main purpose of this paper is to conduct an in-depth study of the interplay between microstructure, trap centers and scintillation efficiency after melt aging treatment. Three SrI 2:2 mol% Eu2+ single crystals with 16 mm diametermore » were grown using the Bridgman method under identical growth conditions with the exception of the melt aging time (e.g. 0, 24 and 72 hours). Using energy-dispersive X-ray spectroscopy, it is found that the matrix composition of the finished crystal after melt aging treatment approaches the stoichiometric composition. The mechanism responsible for the formation of secondary phase inclusions in melt-aged SrI 2:Eu 2+ is discussed. Simultaneous improvement in light yield, energy resolution, scintillation decay-time and afterglow is achieved in melt-aged SrI 2:Eu 2+. The correlation between performance improvement and defect structure is addressed. The results of this paper lead to a better understanding of the effects of defect engineering in control and optimization of metal halide scintillators using the melt aging technique.« less

Object-based Image Classification of Arctic Sea Ice and Melt Ponds through Aerial Photos

NASA Astrophysics Data System (ADS)

Miao, X.; Xie, H.; Li, Z.; Lei, R.

2013-12-01

The last six years have marked the lowest Arctic summer sea ice extents in the modern era, with a new record summer minimum (3.4 million km2) set on 13 September 2012. It has been predicted that the Arctic could be free of summer ice within the next 25-30. The loss of Arctic summer ice could have serious consequences, such as higher water temperature due to the positive feedback of albedo, more powerful and frequent storms, rising sea levels, diminished habitats for polar animals, and more pollution due to fossil fuel exploitation and/ or increased traffic through the Northwest/ Northeast Passage. In these processes, melt ponds play an important role in Earth's radiation balance since they strongly absorb solar radiation rather than reflecting it as snow and ice do. Therefore, it is necessary to develop the ability of predicting the sea ice/ melt pond extents and space-time evolution, which is pivotal to prepare for the variation and uncertainty of the future environment, political, economic, and military needs. A lot of efforts have been put into Arctic sea ice modeling to simulate sea ice processes. However, these sea ice models were initiated and developed based on limited field surveys, aircraft or satellite image data. Therefore, it is necessary to collect high resolution sea ice aerial photo in a systematic way to tune up, validate, and improve models. Currently there are many sea ice aerial photos available, such as Chinese Arctic Exploration (CHINARE 2008, 2010, 2012), SHEBA 1998 and HOTRAX 2005. However, manually delineating of sea ice and melt pond from these images is time-consuming and labor-intensive. In this study, we use the object-based remote sensing classification scheme to extract sea ice and melt ponds efficiently from 1,727 aerial photos taken during the CHINARE 2010. The algorithm includes three major steps as follows. (1) Image segmentation groups the neighboring pixels into objects according to the similarity of spectral and texture information; (2) random forest ensemble classifier can distinguish the following objects: water, submerged ice, shadow, and ice/snow; and (3) polygon neighbor analysis can further separate melt ponds from submerged ice according to the spatial neighboring relationship. Our results illustrate the spatial distribution and morphological characters of melt ponds in different latitudes of the Arctic Pacific sector. This method can be applied to massive photos and images taken in past years and future years, in deriving the detailed sea ice and melt pond distribution and changes through years.

Phase behavior and reactive transport of partial melt in heterogeneous mantle model

NASA Astrophysics Data System (ADS)

Jordan, J.; Hesse, M. A.

2013-12-01

The reactive transport of partial melt is the key process that leads to the chemical and physical differentiation of terrestrial planets and smaller celestial bodies. The essential role of the lithological heterogeneities during partial melting of the mantle is increasingly recognized. How far can enriched melts propagate while interacting with the ambient mantle? Can the melt flow emanating from a fertile heterogeneity be localized through a reactive infiltration feedback in a model without exogenous factors or contrived initial conditions? A full understanding of the role of heterogeneities requires reactive melt transport models that account for the phase behavior of major elements. Previous work on reactive transport in the mantle focuses on trace element partitioning; we present the first nonlinear chromatographic analysis of reactive melt transport in systems with binary solid solution. Our analysis shows that reactive melt transport in systems with binary solid solution leads to the formation of two separate reaction fronts: a slow melting/freezing front along which enthalpy change is dominant and a fast dissolution/precipitation front along which compositional changes are dominated by an ion-exchange process over enthalpy change. An intermediate state forms between these two fronts with a bulk-rock composition and enthalpy that are not necessarily bounded by the bulk-rock composition and enthalpy of either the enriched heterogeneity or the depleted ambient mantle. The formation of this intermediate state makes it difficult to anticipate the porosity changes and hence the stability of reaction fronts. Therefore, we develop a graphical representation for the solution that allows identification of the intermediate state by inspection, for all possible bulk-rock compositions and enthalpies of the heterogeneity and the ambient mantle. We apply the analysis to the partial melting of an enriched heterogeneity. This leads to the formation of moving precipitation front that followes a stationary melting front which creates low porosity intermediate states. Therefore, localization of the melt flow is not observed because the precipitation front is stable and the melting front is always stationary under these conditions. This analysis illustrates the counterintuitive behavior that can arise when the phase behavior is taken into account and is a first step to understanding reactive melt transport and the reactive constraints on channelization in partial melts. ¬¬

Application of high-resolution melting curve analysis for typing of fowl adenoviruses in field cases of inclusion body hepatitis.

PubMed

Steer, P A; O'Rourke, D; Ghorashi, S A; Noormohammadi, A H

2011-05-01

Fowl adenoviruses (FAdVs) cause inclusion body hepatitis (IBH) in chickens. In this study, clinical cases of IBH from Australian broiler flocks were screened for the presence and genotype of FAdVs. Twenty-six IBH cases from commercial poultry farms were screened. Polymerase chain reaction (PCR) coupled with high-resolution melt (HRM) curve analysis (PCR/HRM genotyping) was used to determine the presence and genotype of FAdVs. For comparison, field isolates were also assessed by virus microneutralisation and nucleotide sequence analysis of the hexon loop 1 (Hex L1) gene. PCR detection of chicken anaemia virus (CAV) and infectious bursal disease virus (IBDV) was also employed. FAdV-8b and FAdV-11 were identified in 13 cases each. In one case, FAdV-1 was also identified. Cross-neutralisation was observed between the FAdV-11 field strain and the reference FAdV-2 and 11 antisera, a result also seen with the type 2 and 11 reference FAdVs. Field strains 1 and 8b were neutralised only by their respective type antisera. The FAdV-8b field strain was identical to the Australian FAdV vaccine strain (type 8b) in the Hex L1 region. The Hex L1 sequence of the FAdV-11 field strain had the highest identity to FAdV-11 (93.2%) and FAdV-2 (92.7%) reference strains. In the five cases tested for CAV and IBDV, neither virus was detected. The evidence suggested the presence of sufficient antibodies against CAV and IBD in the parent flocks and there was no indication of immunosuppression caused by these viruses. These results indicate that PCR/HRM genotyping is a reliable diagnostic method for FAdV identification and is more rapid than virus neutralisation and direct sequence analysis. Furthermore, they suggest that IBH in Australian broiler flocks is a primary disease resulting from two alternative FAdV strains from different species. © 2011 The Authors. Australian Veterinary Journal © 2011 Australian Veterinary Association.

High-Throughput Genome Editing and Phenotyping Facilitated by High Resolution Melting Curve Analysis

PubMed Central

Thomas, Holly R.; Percival, Stefanie M.; Yoder, Bradley K.; Parant, John M.

2014-01-01

With the goal to generate and characterize the phenotypes of null alleles in all genes within an organism and the recent advances in custom nucleases, genome editing limitations have moved from mutation generation to mutation detection. We previously demonstrated that High Resolution Melting (HRM) analysis is a rapid and efficient means of genotyping known zebrafish mutants. Here we establish optimized conditions for HRM based detection of novel mutant alleles. Using these conditions, we demonstrate that HRM is highly efficient at mutation detection across multiple genome editing platforms (ZFNs, TALENs, and CRISPRs); we observed nuclease generated HRM positive targeting in 1 of 6 (16%) open pool derived ZFNs, 14 of 23 (60%) TALENs, and 58 of 77 (75%) CRISPR nucleases. Successful targeting, based on HRM of G0 embryos correlates well with successful germline transmission (46 of 47 nucleases); yet, surprisingly mutations in the somatic tail DNA weakly correlate with mutations in the germline F1 progeny DNA. This suggests that analysis of G0 tail DNA is a good indicator of the efficiency of the nuclease, but not necessarily a good indicator of germline alleles that will be present in the F1s. However, we demonstrate that small amplicon HRM curve profiles of F1 progeny DNA can be used to differentiate between specific mutant alleles, facilitating rare allele identification and isolation; and that HRM is a powerful technique for screening possible off-target mutations that may be generated by the nucleases. Our data suggest that micro-homology based alternative NHEJ repair is primarily utilized in the generation of CRISPR mutant alleles and allows us to predict likelihood of generating a null allele. Lastly, we demonstrate that HRM can be used to quickly distinguish genotype-phenotype correlations within F1 embryos derived from G0 intercrosses. Together these data indicate that custom nucleases, in conjunction with the ease and speed of HRM, will facilitate future high-throughput mutation generation and analysis needed to establish mutants in all genes of an organism. PMID:25503746

Effects of Burning Conditions to the Formation of Gold Layer Photograph and Gold Layer Hologram

NASA Astrophysics Data System (ADS)

Kuge, Ken'ichi; Takahashi, Ataru; Harada, Takahito; Doi, Keiji; Sakai, Tomoko

Burning stage from gold nanoparticles to gold layer in the formation process of gold-layer photograph using gold deposition development was investigated. The gelatin layer holding gold nanoparticles is carbonized at about 400°C and burned out until about 500°C. Because gold nanoparticles would be compressed only to vertical direction and then melt to form the gold layer, the gold-layer photograph still holds the high resolution. Gold nanoparaticles do not melt completely even at 900°C, and form continuous clusters of several hundred nm.

Meniscus Imaging for Crystal-Growth Control

NASA Technical Reports Server (NTRS)

Sachs, E. M.

1983-01-01

Silicon crystal growth monitored by new video system reduces operator stress and improves conditions for observation and control of growing process. System optics produce greater magnification vertically than horizontally, so entire meniscus and melt is viewed with high resolution in both width and height dimensions.

In situ Pressure Fluctuations of Polymer Melt Flow Instabilities: Experimental Evidence about their Origin and Dynamics.

PubMed

Palza, Humberto; Naue, Ingo F C; Wilhelm, Manfred

2009-11-02

Despite the practical importance of polymer melt instabilities, there is still a lack of experiments able to characterize in situ the origin and behavior of these phenomena. In this context, a new set-up consisting of high sensitive pressure transducers located inside a slit-die and an advanced mathematical framework to process in situ measurements of polymer melt instabilities, are developed and applied. Our results show for the first time that pressure oscillations can actually be detected inside the die under sharkskin conditions. This originates from a factor of 10(3) and 10(2) improvement in terms of time and pressure resolution. Furthermore, new evidence towards the propagation of the slip phenomena along the die in spurt instabilities are found. Copyright © 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Investigation of the H7 ordinary chondrite, Watson 012: Implications for recognition and classification of Type 7 meteorites

NASA Astrophysics Data System (ADS)

Tait, Alastair W.; Tomkins, Andrew G.; Godel, Bélinda M.; Wilson, Siobhan A.; Hasalova, Pavlina

2014-06-01

Despite the fact that the number of officially classified meteorites is now over 45,000, we lack a clearly defined sequence of samples from a single parent body that records the entire range in metamorphic temperatures from pristine primitive meteorites up to the temperatures required for extensive silicate partial melting. Here, we conduct a detailed analysis of Watson 012, an H7 ordinary chondrite, to generate some clarity on the textural and chemical changes associated with equilibrium-based silicate partial melting in chondritic meteorites. To do this we compare the textures in the meteorite with those preserved in metamorphic contact aureoles on Earth. The most distinctive texture generated by the partial melting that affected Watson 012 is an extensively interconnected plagioclase network, which is clearly observable with a petrographic microscope. Enlarged metal-troilite grains are encapsulated at widenings in this plagioclase network, and this is clearly visible in reflected light. Together with these features, we define a series of other characteristics that can be used to more clearly classify chondritic meteorites as being of petrologic Type 7. To provide comprehensive evidence of silicate partial melting and strengthen the case for using simple petrographic observations to classify similar meteorites, we use high-resolution X-ray computed tomography to demonstrate that the plagioclase network has a high degree of interconnectedness and crystallised as large (cm-scale) skeletal crystals within an olivine-orthopyroxene-clinopyroxene framework, essentially pseudomorphing a melt network. Back-scattered electron imaging and element mapping are used to show that some of the clino- and orthopyroxene in Watson 012 also crystallised from silicate melt, and the order of crystallisation was orthopyroxene → clinopyroxene → plagioclase. X-ray diffraction data, supported by bulk geochemistry, are used to show that plagioclase and ortho- and clinopyroxene were added to the Watson 012 sample by through-flowing basaltic melt. Along with the absence of glass and granophyre, this interconnected network of coarse-grained skeletal plagioclase indicates that the sample cooled slowly at depth within the parent body. The evidence of melt flux indicates that Watson 012 formed in the presence of a gravitational gradient, and thus at significant distance from the centre of the H chondrite parent body (the gravitational gradient at the centre would be zero). Our interpretation is that incipient silicate partial melting in Watson 012 occurred when a region of radiogenically heated H6 material located at considerable depth (possibly at ∼15-20 km from surface) was heated by an additional ca. 200-300 °C in association with a large shock event. Due to insulation at depth within an already hot parent body, the post-shock temperature equilibrated and remained above the solidus long enough for widespread equilibrium-based silicate partial melting, and for melt to migrate. Although the observed melting may have been facilitated by additional heating from an impact event, this is not an example of instantaneous shock melting, which produces thermal disequilibrium at short length scales and distinctly different textures. A small number of H, L and LL chondrites have been previously classified as being of petrologic Type 7; with our new criteria to support that classification, these represent our best opportunity to explore the transition from high temperature sub-solidus metamorphism through the onset of silicate partial melting in three different parent bodies.

Rapid screening of ASXL1, IDH1, IDH2, and c-CBL mutations in de novo acute myeloid leukemia by high-resolution melting.

PubMed

Ibáñez, Mariam; Such, Esperanza; Cervera, José; Luna, Irene; Gómez-Seguí, Inés; López-Pavía, María; Dolz, Sandra; Barragán, Eva; Fuster, Oscar; Llop, Marta; Rodríguez-Veiga, Rebeca; Avaria, Amparo; Oltra, Silvestre; Senent, M Leonor; Moscardó, Federico; Montesinos, Pau; Martínez-Cuadrón, David; Martín, Guillermo; Sanz, Miguel A

2012-11-01

Recently, many novel molecular abnormalities were found to be distinctly associated with acute myeloid leukemia (AML). However, their clinical relevance and prognostic implications are not well established. We developed a new combination of high-resolution melting assays on a LightCycler 480 and direct sequencing to detect somatic mutations of ASXL1 (exon 12), IDH1 (exon 4), IDH2 (exon 4), and c-CBL (exons 8 and 9) genes to know their incidence and prognostic effect in a cohort of 175 patients with de novo AML: 16 patients (9%) carried ASXL1 mutations, 16 patients had IDH variations (3% with IDH1(R132) and 6% with IDH2(R140)), and none had c-CBL mutations. Patients with ASXL1 mutations did not harbor IDH1, [corrected] or CEBPA mutations, and a combination of ASXL1 and IDH2 mutations was found only in one patient. In addition, we did not find IDH1 and FLT3 or CEBPA mutations concurrently or IDH2 with CEBPA. IDH1 and IDH2 mutations were mutually exclusive. Alternatively, NPM1 mutations were concurrently found with ASXL1, IDH1, or IDH2 with a variable incidence. Mutations were not significantly correlated with any of the clinical and biological features studied. High-resolution melting is a reliable, rapid, and efficient screening technique for mutation detection in AML. The incidence for the studied genes was in the range of those previously reported. We were unable to find an effect on the outcome. Copyright © 2012 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Grain-scale alignment of melt in sheared partially molten rocks: implications for viscous anisotropy

NASA Astrophysics Data System (ADS)

Pec, Matej; Quintanilla-Terminel, Alejandra; Holtzman, Benjamin; Zimmerman, Mark; Kohlstedt, David

2016-04-01

Presence of melt significantly influences rheological properties of partially molten rocks by providing fast diffusional pathways. Under stress, melt aligns at the grain scale and this alignment induces viscous anisotropy in the deforming aggregate. One of the consequences of viscous anisotropy is melt segregation into melt-rich sheets oriented at low angle to the shear plane on much larger scales than the grain scale. The magnitude and orientation of viscous anisotropy with respect to the applied stress are important parameters for constitutive models (Takei and Holtzman 2009) that must be constrained by experimental studies. In this contribution, we analyze the shape preferred orientation (SPO) of individual grain-scale melt pockets in deformed partially molten mantle rocks. The starting materials were obtained by isostatically hot-pressing olivine + basalt and olivine + chromite + basalt powders. These partially molten rocks were deformed in general shear or torsion at a confining pressure, Pc = 300 MPa, temperature, T = 1200° - 1250° C, and strain rates of 10-3 - 10-5 s-1to finite shear strains, γ, of 0.5 - 5. After the experiment, high resolution backscattered electron images were obtained using a SEM equipped with a field emission gun. Individual melt pockets were segmented and their SPO analyzed using the paror and surfor methods and Fourier transforms (Heilbronner and Barret 2014). Melt segregation into melt-rich sheets inclined at 15° -20° antithetic with respect to the shear plane occurs in three-phase system (olivine + chromite + basalt) and in two-phase systems (olivine + basalt) twisted to high strain. The SPO of individual melt pockets within the melt-rich bands is moderately strong (b/a ≈ 0.8) and is always steeper (20° -40°) than the average melt-rich band orientation. In the two-phase system (olivine + basalt) sheared to lower strains, no distinct melt-rich sheets are observed. Individual grain-scale melt pockets are oriented at 45° -55° antithetic with respect to the shear plane (i.e., sub-perpendicular to σ3) with a strong SPO (b/a ≈ 0.7) that decreases with increasing finite strain. Our observations of melt alignment at low strains are in agreement with observations performed on analogue materials (borneol, Takei 2010) and provide further constraints for the orientation of viscous anisotropy in the Earth's mantle. The systematic difference in grain-scale melt alignment between samples in which melt segregation did and did not occur - irrespective of the deformation geometry and mineralogy - suggests that melt segregation into bands leads to local stress rotation within the samples.

Significance of Thermal Fluvial Incision and Bedrock Transfer due to Ice Advection on Greenland Ice Sheet Topography

NASA Astrophysics Data System (ADS)

Crozier, J. A.; Karlstrom, L.; Yang, K.

2017-12-01

Ice sheet surface topography reflects a complicated combination of processes that act directly upon the surface and that are products of ice advection. Using recently-available high resolution ice velocity, imagery, ice surface elevation, and bedrock elevation data sets, we seek to determine the domain of significance of two important processes - thermal fluvial incision and transfer of bedrock topography through the ice sheet - on controlling surface topography in the ablation zone. Evaluating such controls is important for understanding how melting of the GIS surface during the melt season may be directly imprinted in topography through supraglacial drainage networks, and indirectly imprinted through its contribution to basal sliding that affects bedrock transfer. We use methods developed by (Karlstrom and Yang, 2016) to identify supraglacial stream networks on the GIS, and use high resolution surface digital elevation models as well as gridded ice velocity and melt rate models to quantify surface processes. We implement a numerically efficient Fourier domain bedrock transfer function (Gudmundsson, 2003) to predict surface topography due to ice advection over bedrock topography obtained from radar. Despite a number of simplifying assumptions, the bedrock transfer function predicts the observed ice sheet surface in most regions of the GIS with ˜90% accuracy, regardless of the presence or absence of supraglacial drainage networks. This supports the hypothesis that bedrock is the most significant driver of ice surface topography on wavelengths similar to ice thickness. Ice surface topographic asymmetry on the GIS is common, with slopes in the direction of ice flow steeper than those faced opposite to ice flow, consistent with bedrock transfer theory. At smaller wavelengths, topography consistent with fluvial erosion by surface hydrologic features is evident. We quantify the effect of ice advection versus fluvial thermal erosion on supraglacial longitudinal stream profiles, as a function of location on the GIS (hence ice thickness and background melt rate) using spectral techniques to quantify longitudinal stream profiles. This work should provide a predictive guide for which processes are responsible for ice sheet topography scales from several m (DEM resolution) up to several ice thicknesses.

Quantifying the Significance of Heterogeneity in Supraglacial Reflectance Characteristics for Meltwater Production in Southwest Greenland

NASA Astrophysics Data System (ADS)

Irvine-Fynn, T. D.; Bunting, P.; Cook, J.; Hardy, A. J.; Hodson, A. J.; Holt, T.; Hubbard, A.; Naegeli, K.; Nilsson, J.; Ryan, J.; Roberts, O.; Tedstone, A.; Tranter, M.; Williamson, C.

2017-12-01

The seasonal melt on the southwestern margin of the Greenland Ice Sheet has been enhanced due to processes affecting the ablation area's ice surface reflectance (albedo). Recent trends in surface reflectance in the region suggest a decline potentially linked to an albedo-feedback associated with regional climate warming, emergence of organic and mineral particulates, and expansion of melt area. However, the heterogeneity of reflectance over bare ice areas in space and time has remained relatively poorly characterised. Numerous surface mass balance models utilise albedo products derived from remote sensing platforms with coarse scale resolution. Such products provide reasonable albedo estimates, but quantification of local variability in reflectance remains lacking. Consequently, there is a need to better define the distribution and representativeness of ice surface reflectance at and below the scale of satellite sensor pixel footprints to facilitate examination of albedo parameterisations. Here, we present reflectance data repeatedly collected in SW Greenland during the 2016 summer melt season over a 0.0625 km2 area proximate to the IMAU K-transect site S6 (67°04.5'N, 49°21.0'W). The Moderate Resolution Imaging Spectrometer (MODIS) albedo product MOD10A1(c6) for the study site was compared to reflectance data from Sentinel-2, centimetre resolution calibrated 12Mpix optical imagery collected using an Unmanned Aerial Vehicle (UAV) flown at a height of 70 m above the ice surface, and ground-based reflectance survey data acquired using a StellarNet Red-Dwarf/Blue-Wave visible-infrared dual system (250-1700nm) at 30 sites distributed over the area of interest. Our data highlight variability in the spatial distribution of ice surface reflectance characteristics over time. Specifically, data demonstrate marked changes in the distribution of reflectance values, despite maintaining a broadly equitable mean and median during July and August. The influence of the varied surface heterogeneity is explored further using surface energy balance modelling to quantify the impact of such changes on melt production. The findings determine the necessity to account for local variability underlying the pixel-averaged values retrieved from remote sensing platforms such as MODIS.

Evaluation of suitable DNA regions for molecular identification of high value medicinal plants in genus Kaempferia.

PubMed

Osathanunkul, Maslin; Dheeranupattana, Srisulak; Rotarayanont, Siriphron; Sookkhee, Siriwoot; Osathanunkul, Khukrit; Madesis, Panagiotis

2017-12-02

DNA barcoding coupled high resolution melting (Bar-HRM) is an emerging method for species discrimination based on DNA dissociation kinetics. The aim of this work was to evaluate the suitability of different primer sets, derived from selected DNA regions, for Bar-HRM analysis of species in Kaempferia (Zingiberaceae). Four primer pairs were evaluated (rbcL, rpoC, trnL and ITS1). It was observed that the ITS1 barcode was the most useful DNA barcoding region overall for species discrimination out of all of the regions and primers assessed. Thus, the primer pair derived from the ITS1 region was the single most effective region for the identification of the tested species, whereas the rbcL primer pair gave the lowest resolution. Our Bar-HRM developed here would not only be useful for identification of Kaempferia plant specimens lacking essential parts for morphological identification but will be useful for authenticating products in powdered form of a high value medicinal species Kaempferia parviflora, in particular.

Testing a common ice-ocean parameterization with laboratory experiments

NASA Astrophysics Data System (ADS)

McConnochie, C. D.; Kerr, R. C.

2017-07-01

Numerical models of ice-ocean interactions typically rely upon a parameterization for the transport of heat and salt to the ice face that has not been satisfactorily validated by observational or experimental data. We compare laboratory experiments of ice-saltwater interactions to a common numerical parameterization and find a significant disagreement in the dependence of the melt rate on the fluid velocity. We suggest a resolution to this disagreement based on a theoretical analysis of the boundary layer next to a vertical heated plate, which results in a threshold fluid velocity of approximately 4 cm/s at driving temperatures between 0.5 and 4°C, above which the form of the parameterization should be valid.

The Origin of the Compositional Diversity of Mercury's Surface Constrained From Experimental Melting of Enstatite Chondrites

NASA Technical Reports Server (NTRS)

Boujibar, A.; Righter, K.; Pando, K.; Danielson, L.

2015-01-01

Mercury is known as an endmember planet as it is the most reduced terrestrial planet with the highest core/mantle ratio. MESSENGER spacecraft has shown that its surface is FeO-poor (2-4 wt%) and Srich (up to 6-7 wt%), which confirms the reducing nature of its silicate mantle. Moreover, high resolution images revealed large volcanic plains and abundant pyroclastic deposits, suggesting important melting stages of the Mercurian mantle. This interpretation was confirmed by the high crustal thickness (up to 100 km) derived from Mercury's gravity field. This is also corroborated by a recent experimental result that showed that Mercurian partial melts are expected to be highly buoyant within the Mercurian mantle and could have risen from depths as high as the core-mantle boundary. In addition MESSENGER spacecraft provided relatively precise data on major elemental compositions of Mercury's surface. These results revealed important chemical and mineralogical heterogeneities that suggested several stages of differentiation and re-melting processes. However, the extent and nature of compositional variations produced by partial melting remains poorly constrained for the particular compositions of Mercury (very reducing conditions, low FeO-contents and high sulfur-contents). Therefore, in this study, we investigated the processes that lead to the various compositions of Mercury's surface. Melting experiments with bulk Mercury-analogue compositions were performed and compared to the compositions measured by MESSENGER.

Impact History on Vesta: Petrographic, Compositional and Future Chronological Studies of Melt Clasts in Howardites

NASA Technical Reports Server (NTRS)

Cartwright, J. A.; Mittlefehldt, D. W.; Hodges, K. V.; Wadhwa, M.

2015-01-01

Howardite meteorites are polymict breccias composed mainly of eucritic and diogenitic material that likely originate from the surface of the Asteroid 4 Vesta. They can be separated into two subtypes: Regolithic, which represent the lithified remains of the active vestan regolith; Fragmental, which represent simpler polymict breccias. Amongst the regolithic features observed in the former, melt clasts are particularly striking for their appearance and compositional variability. They range from glassy spherules to finely crystalline (i.e., devitrified) clasts, and clasts containing only relict mineral grains to those containing only phenocrysts. Glasses can be separated into compositional sub-types including those with low FeO/MgO ratios (less than 5) -low alkali glasses, K-rich (K2O greater than 0.2 wt.%), Na-rich (Na2O greater than 0.6 wt.%) and CaO-rich, and those with high FeO/MgO ratios (greater than 10). There is also a distinction to be made between primary volcanic melt clasts and those produced by impacts. While suggested that a lack of chemical homogeneity among their studied melt clasts ruled out a primary volcanic origin, the low siderophile element contents observed in such clasts suggest less compositional influence from impactors than commonly assumed. Studying the chronology of the impact melt clasts in howardites can help us to better determine the timing of impact events on Vesta and the asteroid belt. In this research, we are launching an investigation into the petrology, composition (major/trace element and noble gas) and chronology of melt clasts in howardites. We have selected a set of howardites known to contain large quantities of melt clasts, and have begun the petrological and compositional studies of these materials. Once the melt clasts have been fully classified, we aim to perform chronological studies of individual clasts using both the Ar-40/Ar-39 and Pb-Pb chronometers, as well as determine the noble gas components present. Of particular note, the study will take advantage of the laser ablation techniques associated with the noble gas facilities at ASU, which will allow high-resolution, in-situ analysis of individual clasts. The broader aim of this work is to ascertain whether the impact flux in the region of the asteroid belt was similar to that on the Moon. Our understanding of impact events in the inner Solar System relies heavily on our analyses of lunar meteorites and returned samples, and there is currently some debate regarding whether there was a "Lunar Cataclysm" event around approx. 3.9 Ga, or the end of an epoch of "Late Heavy Bombardment" (LHB) at this time. New and more comprehensive constraints on howardite melt clast ages may help determine whether the asteroid belt experienced such a cataclysm or LHB.

Towards High Spa-Temporal Resolution Estimates of Surface Radiative Fluxes from Geostationary Satellite Observations for the Tibetan Plateau

NASA Astrophysics Data System (ADS)

Niu, X.; Yang, K.; Tang, W.; Qin, J.

2014-12-01

Surface Solar Radiation (SSR) plays an important role of the hydrological and land process modeling, which particularly contributes more than 90% to the total melt energy for the Tibetan Plateau (TP) ice melting. Neither surface measurement nor existing remote sensing products can meet that requirement in TP. The well-known satellite products (i.e. ISCCP-FD and GEWEX-SRB) are in relatively low spatial resolution (0.5º-2.5º) and temporal resolution (3-hourly, daily, or monthly). The objective of this study is to develop capabilities to improved estimates of SSR in TP based on geostationary satellite observations from the Multi-functional Transport Satellite (MTSAT) with high spatial (0.05º) and temporal (hourly) resolution. An existing physical model, the UMD-SRB (University of Maryland Surface Radiation Budget) which is the basis of the GEWEX-SRB model, is re-visited to improve SSR estimates in TP. The UMD-SRB algorithm transforms TOA radiances into broadband albedos in order to infer atmospheric transmissivity which finally determines the SSR. Specifically, main updates introduced in this study are: implementation at 0.05º spatial resolution at hourly intervals integrated to daily and monthly time scales; and improvement of surface albedo model by introducing the most recently developed Global Land Surface Broadband Albedo Product (GLASS) based on MODIS data. This updated inference scheme will be evaluated against ground observations from China Meteorological Administration (CMA) radiation stations and three TP radiation stations contributed from the Institute of Tibetan Plateau Research.

Fukushima Daiichi Unit 1 Ex-Vessel Prediction: Core-Concrete Interaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Robb, Kevin R.; Farmer, Mitchell T.; Francis, Matthew W.

Lower head failure and corium-concrete interaction were predicted to occur at Fukushima Daiichi Unit 1 (1F1) by several different system-level code analyses, including MELCOR v2.1 and MAAP5. Although these codes capture a wide range of accident phenomena, they do not contain detailed models for ex-vessel core melt behavior. However, specialized codes exist for the analysis of ex-vessel melt spreading (e.g., MELTSPREAD) and long-term debris coolability (e.g., CORQUENCH). On this basis, in this paper an analysis was carried out to further evaluate ex-vessel behavior for 1F1 using MELTSPREAD and CORQUENCH. Best-estimate melt pour conditions predicted by MELCOR v2.1 and MAAP5 weremore » used as input. MELTSPREAD was then used to predict the spatially dependent melt conditions and extent of spreading during relocation from the vessel. The results of the MELTSPREAD analysis are reported in a companion paper. This information was used as input for the long-term debris coolability analysis with CORQUENCH. For the MELCOR-based melt pour scenario, CORQUENCH predicted the melt would readily cool within 2.5 h after the pour, and the sumps would experience limited ablation (approximately 18 cm) under water-flooded conditions. Finally, for the MAAP-based melt pour scenarios, CORQUENCH predicted that the melt would cool in approximately 22.5 h, and the sumps would experience approximately 65 cm of concrete ablation under water-flooded conditions.« less

Fukushima Daiichi Unit 1 Ex-Vessel Prediction: Core-Concrete Interaction

DOE PAGES

Robb, Kevin R.; Farmer, Mitchell T.; Francis, Matthew W.

2016-10-31

Lower head failure and corium-concrete interaction were predicted to occur at Fukushima Daiichi Unit 1 (1F1) by several different system-level code analyses, including MELCOR v2.1 and MAAP5. Although these codes capture a wide range of accident phenomena, they do not contain detailed models for ex-vessel core melt behavior. However, specialized codes exist for the analysis of ex-vessel melt spreading (e.g., MELTSPREAD) and long-term debris coolability (e.g., CORQUENCH). On this basis, in this paper an analysis was carried out to further evaluate ex-vessel behavior for 1F1 using MELTSPREAD and CORQUENCH. Best-estimate melt pour conditions predicted by MELCOR v2.1 and MAAP5 weremore » used as input. MELTSPREAD was then used to predict the spatially dependent melt conditions and extent of spreading during relocation from the vessel. The results of the MELTSPREAD analysis are reported in a companion paper. This information was used as input for the long-term debris coolability analysis with CORQUENCH. For the MELCOR-based melt pour scenario, CORQUENCH predicted the melt would readily cool within 2.5 h after the pour, and the sumps would experience limited ablation (approximately 18 cm) under water-flooded conditions. Finally, for the MAAP-based melt pour scenarios, CORQUENCH predicted that the melt would cool in approximately 22.5 h, and the sumps would experience approximately 65 cm of concrete ablation under water-flooded conditions.« less

Simultaneous Identification of Four "Legal High" Plant Species in a Multiplex PCR High-Resolution Melt Assay.

PubMed

Elkins, Kelly M; Perez, Anjelica C U; Quinn, Alicia A

2017-05-01

The international prevalence of "legal high" drugs necessitates the development of a method for their detection and identification. Herein, we describe the development and validation of a tetraplex multiplex real-time polymerase chain reaction (PCR) assay used to simultaneously identify morning glory, jimson weed, Hawaiian woodrose, and marijuana detected by high-resolution melt using LCGreen Plus ® . The PCR assay was evaluated based on the following: (i) specificity and selectivity-primers were tested on DNA extracted from 30 species and simulated forensic samples, (ii) sensitivity-serial dilutions of the target DNA were prepared, and (iii) reproducibility and reliability-sample replicates were tested and remelted on different days. The assay is ideal for cases in which inexpensive assays are needed to quickly detect and identify trace biological material present on drug paraphernalia that is too compromised for botanical microscopic identification and for which analysts are unfamiliar with the morphology of the emerging "legal high" species. © 2016 American Academy of Forensic Sciences.

Estimates of olivine-basaltic melt electrical conductivity using a digital rock physics approach

NASA Astrophysics Data System (ADS)

Miller, Kevin J.; Montési, Laurent G. J.; Zhu, Wen-lu

2015-12-01

Estimates of melt content beneath fast-spreading mid-ocean ridges inferred from magnetotelluric tomography (MT) vary between 0.01 and 0.10. Much of this variation may stem from a lack of understanding of how the grain-scale melt geometry influences the bulk electrical conductivity of a partially molten rock, especially at low melt fraction. We compute bulk electrical conductivity of olivine-basalt aggregates over 0.02 to 0.20 melt fraction by simulating electric current in experimentally obtained partially molten geometries. Olivine-basalt aggregates were synthesized by hot-pressing San Carlos olivine and high-alumina basalt in a solid-medium piston-cylinder apparatus. Run conditions for experimental charges were 1.5 GPa and 1350 °C. Upon completion, charges were quenched and cored. Samples were imaged using synchrotron X-ray micro-computed tomography (μ-CT). The resulting high-resolution, 3-dimensional (3-D) image of the melt distribution constitutes a digital rock sample, on which numerical simulations were conducted to estimate material properties. To compute bulk electrical conductivity, we simulated a direct current measurement by solving the current continuity equation, assuming electrical conductivities for olivine and melt. An application of Ohm's Law yields the bulk electrical conductivity of the partially molten region. The bulk electrical conductivity values for nominally dry materials follow a power-law relationship σbulk = Cσmeltϕm with fit parameters m = 1.3 ± 0.3 and C = 0.66 ± 0.06. Laminar fluid flow simulations were conducted on the same partially molten geometries to obtain permeability, and the respective pathways for electrical current and fluid flow over the same melt geometry were compared. Our results indicate that the pathways for flow fluid are different from those for electric current. Electrical tortuosity is lower than fluid flow tortuosity. The simulation results are compared to existing experimental data, and the potential influence of volatiles and melt films on electrical conductivity of partially molten rocks is discussed.

The Origin of Mercury's Surface Composition, an Experimental Investigation

NASA Technical Reports Server (NTRS)

Boujibar, A.; Righter, K.; Rapp, J. F.; Ross, D. K.; Pando, K. M.; Danielson, L. R.; Fontaine, E.

2016-01-01

Introduction: Results from MESSENGER spacecraft have confirmed the reduced nature of Mercury, based on its high core/mantle ratio and its FeO-poor and S-rich surface. Moreover, high resolution images revealed large volcanic plains and abundant pyroclastic deposits, suggesting major melting stages of the Mercurian mantle. In addition, MESSENGER has provided the most precise data to date on major elemental compositions of Mercury's surface. These results revealed considerable chemical heterogeneities that suggested several stages of differentiation and re-melting processes. This interpretation was challenged by our experimental previous study, which showed a similar compositional variation in the melting products of enstatite chondrites, which are a possible Mercury analogue. However, these experimental melts were obtained over a limited range of pressure (1 bar to 1 gigapascal) and were not compared to the most recent elemental maps. Therefore, here we extend the experimental dataset to higher pressures and perform a more quantitative comparison with Mercury's surface compositions measured by MESSENGER. In particular, we test whether these chemical heterogeneities result from mixing between polybaric melts. Our experiments and models show that the majority of chemical diversity of Mercury's surface can result from melting of a primitive mantle compositionally similar to enstatite chondrites in composition at various depths and degrees of melting. The high-Mg region's composition is reproduced by melting at high pressure (3 gigapascals) (Tab. 1), which is consistent with previous interpretation as being a large degraded impact basin based on its low elevation and thin average crust. While low-Mg NVP (North Volcanic Plains) are the result of melting at low pressure (1 bar), intermediate-Mg NVP, Caloris Basin and Rachmaninoff result from mixing of a high-pressure (3 gigapascals) and low-pressure components (1 bar for Rachmaninoff and 1 gigapascal for the other regions) (Tab. 1). Moreover, all compositions suggest mixing between low and high degree melts that indicate important differentiation processes.

Development and assessment of multiplex high resolution melting assay as a tool for rapid single-tube identification of five Brucella species.

PubMed

Gopaul, Krishna K; Sells, Jessica; Lee, Robin; Beckstrom-Sternberg, Stephen M; Foster, Jeffrey T; Whatmore, Adrian M

2014-12-11

The zoonosis brucellosis causes economically significant reproductive problems in livestock and potentially debilitating disease of humans. Although the causative agent, organisms from the genus Brucella, can be differentiated into a number of species based on phenotypic characteristics, there are also significant differences in genotype that are concordant with individual species. This paper describes the development of a five target multiplex assay to identify five terrestrial Brucella species using real-time polymerase chain reaction (PCR) and subsequent high resolution melt curve analysis. This technology offers a robust and cost effective alternative to previously described hydrolysis-probe Single Nucleotide Polymorphism (SNP)-based species defining assays. Through the use of Brucella whole genome sequencing five species defining SNPs were identified. Individual HRM assays were developed to these target these changes and, following optimisation of primer concentrations, it was possible to multiplex all five assays in a single tube. In a validation exercise using a panel of 135 Brucella strains of terrestrial and marine origin, it was possible to distinguish the five target species from the other species within this panel. The HRM multiplex offers a number of diagnostic advantages over previously described SNP-based typing approaches. Further, and uniquely for HRM, the successful multiplexing of five assays in a single tube allowing differentiation of five Brucella species in the diagnostic laboratory in a cost-effective and timely manner is described. However there are possible limitations to using this platform on DNA extractions direct from clinical material.

Genetic variation in the urea cycle: a model resource for investigating key candidate genes for common diseases.

PubMed

Mitchell, Sabrina; Ellingson, Clint; Coyne, Thomas; Hall, Lynn; Neill, Meaghan; Christian, Natalie; Higham, Catherine; Dobrowolski, Steven F; Tuchman, Mendel; Summar, Marshall

2009-01-01

The urea cycle is the primary means of nitrogen metabolism in humans and other ureotelic organisms. There are five key enzymes in the urea cycle: carbamoyl-phosphate synthetase 1 (CPS1), ornithine transcarbamylase (OTC), argininosuccinate synthetase (ASS1), argininosuccinate lyase (ASL), and arginase 1 (ARG1). Additionally, a sixth enzyme, N-acetylglutamate synthase (NAGS), is critical for urea cycle function, providing CPS1 with its necessary cofactor. Deficiencies in any of these enzymes result in elevated blood ammonia concentrations, which can have detrimental effects, including central nervous system dysfunction, brain damage, coma, and death. Functional variants, which confer susceptibility for disease or dysfunction, have been described for enzymes within the cycle; however, a comprehensive screen of all the urea cycle enzymes has not been performed. We examined the exons and intron/exon boundaries of the five key urea cycle enzymes, NAGS, and two solute carrier transporter genes (SLC25A13 and SLC25A15) for sequence alterations using single-stranded conformational polymorphism (SSCP) analysis and high-resolution melt profiling. SSCP was performed on a set of DNA from 47 unrelated North American individuals with a mixture of ethnic backgrounds. High-resolution melt profiling was performed on a nonoverlapping DNA set of either 47 or 100 unrelated individuals with a mixture of backgrounds. We identified 33 unarchived polymorphisms in this screen that potentially play a role in the variation observed in urea cycle function. Screening all the genes in the pathway provides a catalog of variants that can be used in investigating candidate diseases. Copyright 2008 Wiley-Liss, Inc.

Evaluation of a DNA-based method for spice/herb authentication, so you do not have to worry about what is in your curry, buon appetito!

PubMed

Osathanunkul, Maslin; Ounjai, Sarawut; Osathanunkul, Rossarin; Madesis, Panagiotis

2017-01-01

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. Then, only four regions (ITS, matK, rbcL and trnH-psbA) were included in the simulated HRM (High-resolution Melting) analysis as the results from previous analysis showed that rpoC and trnL may not be suitable to be used to identify Zingiberaceae species in HRM analysis based on both the percentage of nucleotide variation and GC content. Simulated HRM analysis was performed to test the feasibility of Bar-HRM. We found that ITS2 is the most effective region to be used for identification of the studied species and thus was used in laboratory HRM analysis. All seven tested Zingiberaceae plants were then able to be distinguished using the ITS2 primers in laboratory HRM. Most importantly the melting curves gained from fresh and dried tissue overlapped, which is a crucial outcome for the applicability of the analysis. The method could be used in an authentication test for dried products. In the authentication test, only one of seven store-sold Zingiberaceae products that were tested contained the species listed on their labels, while we found substitution/contamination of the tested purchased products in the rest.

Evaluation of a DNA-based method for spice/herb authentication, so you do not have to worry about what is in your curry, buon appetito!

PubMed Central

Ounjai, Sarawut; Osathanunkul, Rossarin; Madesis, Panagiotis

2017-01-01

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. Then, only four regions (ITS, matK, rbcL and trnH-psbA) were included in the simulated HRM (High-resolution Melting) analysis as the results from previous analysis showed that rpoC and trnL may not be suitable to be used to identify Zingiberaceae species in HRM analysis based on both the percentage of nucleotide variation and GC content. Simulated HRM analysis was performed to test the feasibility of Bar-HRM. We found that ITS2 is the most effective region to be used for identification of the studied species and thus was used in laboratory HRM analysis. All seven tested Zingiberaceae plants were then able to be distinguished using the ITS2 primers in laboratory HRM. Most importantly the melting curves gained from fresh and dried tissue overlapped, which is a crucial outcome for the applicability of the analysis. The method could be used in an authentication test for dried products. In the authentication test, only one of seven store-sold Zingiberaceae products that were tested contained the species listed on their labels, while we found substitution/contamination of the tested purchased products in the rest. PMID:29020084

A Melting Layer Model for Passive/Active Microwave Remote Sensing Applications. Part 1; Model Formulation and Comparison with Observations

NASA Technical Reports Server (NTRS)

Olson, William S.; Bauer, Peter; Viltard, Nicolas F.; Johnson, Daniel E.; Tao, Wei-Kuo

2000-01-01

In this study, a 1-D steady-state microphysical model which describes the vertical distribution of melting precipitation particles is developed. The model is driven by the ice-phase precipitation distributions just above the freezing level at applicable gridpoints of "parent" 3-D cloud-resolving model (CRM) simulations. It extends these simulations by providing the number density and meltwater fraction of each particle in finely separated size categories through the melting layer. The depth of the modeled melting layer is primarily determined by the initial material density of the ice-phase precipitation. The radiative properties of melting precipitation at microwave frequencies are calculated based upon different methods for describing the dielectric properties of mixed phase particles. Particle absorption and scattering efficiencies at the Tropical Rainfall Measuring Mission Microwave Imager frequencies (10.65 to 85.5 GHz) are enhanced greatly for relatively small (approx. 0.1) meltwater fractions. The relatively large number of partially-melted particles just below the freezing level in stratiform regions leads to significant microwave absorption, well-exceeding the absorption by rain at the base of the melting layer. Calculated precipitation backscatter efficiencies at the Precipitation Radar frequency (13.8 GHz) increase in proportion to the particle meltwater fraction, leading to a "bright-band" of enhanced radar reflectivities in agreement with previous studies. The radiative properties of the melting layer are determined by the choice of dielectric models and the initial water contents and material densities of the "seeding" ice-phase precipitation particles. Simulated melting layer profiles based upon snow described by the Fabry-Szyrmer core-shell dielectric model and graupel described by the Maxwell-Garnett water matrix dielectric model lead to reasonable agreement with radar-derived melting layer optical depth distributions. Moreover, control profiles that do not contain mixed-phase precipitation particles yield optical depths that are systematically lower than those observed. Therefore, the use of the melting layer model to extend 3-D CRM simulations appears justified, at least until more realistic spectral methods for describing melting precipitation in high-resolution, 3-D CRM's are implemented.

[Novel Approaches in DNA Methylation Studies - MS-HRM Analysis and Electrochemistry].

PubMed

Bartošík, M; Ondroušková, E

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. MS-HRM is due to its sensitivity and simplicity an interesting alternative to already established techniques, including methylation-specific PCR or bisulfite sequencing. Electrochemistry, when combined with suitable electroactive labels and electrode surfaces, has been applied in several unique strategies for discrimination of cytosines and methylcytosines. Both techniques were successfully tested in analysis of DNA methylation within promoters of important tumor suppressor genes and could thus help in achieving more precise diagnostics and prognostics of cancer. Aberrant methylation of promoters has already been described in hundreds of genes associated with tumorigenesis and could serve as important biomarker if new methods applicable into clinical practice are sufficiently advanced.Key words: DNA methylation - 5-methylcytosine - HRM analysis - melting temperature - DNA duplex - electrochemistry - nucleic acid hybridizationThis work was supported by MEYS - NPS I - LO1413.The authors declare they have no potential conflicts of interest concerning drugs, products, or services used in the study.The Editorial Board declares that the manuscript met the ICMJE recommendation for biomedical papers.Submitted: 6. 5. 2016Accepted: 16. 5. 2016.

Soil Components in Heterogeneous Impact Glass in Martian Meteorite EETA79001

NASA Technical Reports Server (NTRS)

Schrader, C. M.; Cohen, B. A.; Donovan, J. J.; Vicenzi, E. P.

2010-01-01

Martian soil composition can illuminate past and ongoing near-surface processes such as impact gardening [2] and hydrothermal and volcanic activity [3,4]. Though the Mars Exploration Rovers (MER) have analyzed the major-element composition of Martian soils, no soil samples have been returned to Earth for detailed chemical analysis. Rao et al. [1] suggested that Martian meteorite EETA79001 contains melted Martian soil in its impact glass (Lithology C) based on sulfur enrichment of Lithology C relative to the meteorite s basaltic lithologies (A and B) [1,2]. If true, it may be possible to extract detailed soil chemical analyses using this meteoritic sample. We conducted high-resolution (0.3 m/pixel) element mapping of Lithology C in thin section EETA79001,18 by energy dispersive spectrometry (EDS). We use these data for principal component analysis (PCA).

Seismic Velocity Structure of the Pacific Upper Mantle in the NoMelt Region from Finite-Frequency Traveltime Tomography

NASA Astrophysics Data System (ADS)

Hung, S. H.; Lin, P. Y.; Gaherty, J. B.; Russell, J. B.; Jin, G.; Collins, J. A.; Lizarralde, D.; Evans, R. L.; Hirth, G.

2017-12-01

Surface wave dispersion and magnetotelluric survey from the NoMelt Experiment conducted on 70 Ma central Pacific seafloor revealed an electrically resistive, high shear wave velocity lid of 80 km thick underlain by a non-highly conductive, low-velocity layer [Sarafian et al., 2015; Lin et al., 2016]. The vertical structure of the upper mantle consistent with these observational constraints suggests a plausible convection scenario, where the seismically fast, dehydrated lithosphere preserving very strong fossil spreading fabric moves at a constant plate speed over the hydrated, melt-free athenospheric mantle with the presence of either pressure-driven return flow or thermally-driven small scale circulation. To explore 3-D variations in compressional shear wave velocities related to the lithospheric and asthenospheric mantle dynamics, we employ a multichannel cross correlation method to measure relative traveltime residuals based on the vertical P and traverse S waveforms filtered at 10-33 s from telseismic earthquakes at epicentral distance between 30 and 98 degrees. The obtained P and S residuals show on average peak-to-peak variations of ±0.5 s and ±1 s, respectively, across the NoMelt OBS array. Particularly, the P residuals for most of the events display an asymmetrical pattern with respect to an axis oriented nearly N-S to NE-SW through the array. Preliminary ray-based P tomography results reveal similar asymmetric variations in the uppermost 100 km mantle. To verify the resulting structural features, we will further perform both the P and S traveltime tomography and resolution tests based on a multiscale finite-frequency approach which properly takes into account both the 3D off-path sensitivities of the measured residuals and data-adaptive resolution of the model.

Validating SWE reconstruction using Airborne Snow Observatory measurements in the Sierra Nevada

NASA Astrophysics Data System (ADS)

Bair, N.; Rittger, K.; Davis, R. E.; Dozier, J.

2015-12-01

The Airborne Snow Observatory (ASO) program offers high resolution estimates of snow water equivalent (SWE) in several small basins across California during the melt season. Primarily, water managers use this information to model snowmelt runoff into reservoirs. Another, and potentially more impactful, use of ASO SWE measurements is in validating and improving satellite-based SWE estimates which can be used in austere regions with no ground-based snow or water measurements, such as Afghanistan's Hindu Kush. Using the entire ASO dataset to date (2013-2015) which is mostly from the Upper Tuolumne basin, but also includes measurements from 2015 in the Kings, Rush Creek, Merced, and Mammoth Lakes basins, we compare ASO measurements to those from a SWE reconstruction method. Briefly, SWE reconstruction involves downscaling energy balance forcings to compute potential melt energy, then using satellite-derived estimates of fractional snow covered area (fSCA) to estimate snow melt from potential melt. The snowpack can then be built in reverse, given a remotely-sensed date of snow disappearance (fSCA=0). Our model has improvements over previous iterations in that it: uses the full energy balance (compared to a modified degree-day) approach, models bulk and surface snow temperatures, accounts for ephemeral snow, and uses a remotely-sensed snow albedo adjusted for impurities. To check that ASO provides accurate snow measurements, we compare fSCA derived from ASO snow depth at 3 m resolution with fSCA from a spectral unmixing algorithm for LandSAT at 30 m, and from binary SCA estimates from Geoeye at 0.5 m from supervised classification. To conclude, we document how our reconstruction model has evolved over the years and provide specific examples where improvements have been made using ASO and other verification sources.

Iron Supply and Demand in an Antarctic Shelf Ecosystem

NASA Astrophysics Data System (ADS)

McGillicuddy, D. J., Jr.; Sedwick, P.; Dinniman, M. S.; Arrigo, K. R.; Bibby, T. S.; Greenan, B. J. W.; Hofmann, E. E.; Klinck, J. M., II; Smith, W.; Mack, S. L.; Marsay, C. M.; Sohst, B. M.; van Dijken, G.

2016-02-01

The Ross Sea sustains a rich ecosystem and is the most productive sector of the Southern Ocean. Most of this production occurs within a polynya during the November-February period, when the availability of dissolved iron (dFe) is thought to exert the major control on phytoplankton growth. Here we combine new data on the distribution of dFe, high-resolution model simulations of ice melt and regional circulation, and satellite-based estimates of primary production to quantify iron supply and demand over the Ross Sea continental shelf. Our analysis suggests that the largest sources of dFe to the euphotic zone are wintertime mixing and melting sea ice, with a lesser input from intrusions of Circumpolar Deep Water, and a small amount from melting glacial ice. Together these sources are in approximate balance with the annual biological dFe demand inferred from satellite-based productivity algorithms, although both the supply and demand estimates have large uncertainties. Our findings illustrate the complexities of iron cycling in the Southern Ocean, highlighting the heterogeneity of the underlying processes along the Antarctic continental margin. Explicit representation of these complexities, and the temporal variability in both proximate and ultimate sources of iron, will be necessary to understand how a changing climate will affect this important ecosystem and its influence on biogeochemical cycles. Reduction of the present uncertainties in iron supply and demand will require coupled observational and modeling systems capable of resolving the wide range of physical, biological, and chemical processes involved.

Lobate impact melt flows within the extended ejecta blanket of Pierazzo crater

NASA Astrophysics Data System (ADS)

Bray, Veronica J.; Atwood-Stone, Corwin; Neish, Catherine D.; Artemieva, Natalia A.; McEwen, Alfred S.; McElwaine, Jim N.

2018-02-01

Impact melt flows are observed within the continuous and discontinuous ejecta blanket of the 9 km lunar crater Pierazzo, from the crater rim to more than 40 km away from the center of the crater. Our mapping, fractal analysis, and thermal modeling suggest that melt can be emplaced ballistically and, upon landing, can become separated from solid ejecta to form the observed flow features. Our analysis is based on the identification of established melt morphology for these in-ejecta flows and supported by fractal analysis and thermal modeling. We computed the fractal dimension for the flow boundaries and found values of D = 1.05-1.17. These are consistent with terrestrial basaltic lava flows (D = 1.06-1.2) and established lunar impact melt flows (D = 1.06-1.18), but inconsistent with lunar dry granular flows (D = 1.31-1.34). Melt flows within discontinuous ejecta deposits are noted within just 1.5% of the mapping area, suggesting that the surface expression of impact melt in the extended ejecta around craters of this size is rare, most likely due to the efficient mixing of melts with solid ejecta and local target rocks. However, if the ejected fragments (both, molten and solid) are large enough, segregation of melt and its consequent flow is possible. As most of the flows mapped in this work occur on crater-facing slopes, the development of defined melt flows within ejecta deposits might be facilitated by high crater-facing topography restricting the flow of ejecta soon after it makes ground contact, limiting the quenching of molten ejecta through turbulent mixing with solid debris. Our study confirms the idea that impact melt can travel far beyond the continuous ejecta blanket, adding to the lunar regolith over an extensive area.

Antarctic sub-shelf melt rates via SIMPEL

NASA Astrophysics Data System (ADS)

Reese, Ronja; Albrecht, Torsten; Winkelmann, Ricarda

2017-04-01

Ocean-induced melting below ice-shelves is currently suspected to be the dominant cause of mass loss from the Antarctic Ice Sheet (e.g. Depoorter et al. 2013). Although thinning of ice shelves does not directly contribute to sea-level rise, it may have a significant indirect impact through the potential of ice shelves to buttress their adjacent ice sheet. Hence, an appropriate representation of sub-shelf melt rates is essential for modelling the evolution of ice sheets with marine terminating outlet glaciers. Due to computational limits of fully-coupled ice and ocean models, sub-shelf melt rates are often parametrized in large-scale or long-term simulations (e.g. Matin et al. 2011, Pollard & DeConto 2012). These parametrizations usually depend on the depth of the ice shelf base or its local slope but do not include the physical processes in ice shelf cavities. Here, we present the Sub Ice shelf Melt Potsdam modEL (SIMPEL) which mimics the first-order large-scale circulation in ice shelf cavities based on an ocean box model (Olbers & Hellmer, 2010), implemented in the Parallel Ice Sheet Model (Bueler & Brown 2009, Winkelmann et al. 2011, www.pism-docs.org). In SIMPEL, ocean water is transported at depth towards the grounding line where sub-shelf melt rates are highest, and then rises along the shelf base towards the calving front where refreezing can occur. Melt rates are computed by a description of ice-ocean interaction commonly used in high-resolution models (McPhee 1992, Holland & Jenkins 1999). This enables the model to capture a wide-range of melt rates, comparable to the observed range for Antarctic ice shelves (Rignot et al. 2013).

Synthesis, purification and bulk crystal growth of radiation detector materials using melt growth technique

NASA Astrophysics Data System (ADS)

Surabhi, Raja Rahul Reddy

In the past decade, there has been new and increased usage of radiation-detection technologies for applications in homeland security, non-proliferation, and national defense. Most of these applications require a portable device with high gamma-ray energy resolution and detection efficiency, compact size, room-temperature operation, and low cost. Consequently, there is a renewed understanding of the material limitations for these technologies and a great demand to develop next-generation radiation-detection materials that can operate at room temperature. Mercuric iodide (HgI2), Lead iodide (PbI2), and CdZnTe (CZT) are the current leading candidates for radiation detector applications. This is because of their high atomic number and large band gap that makes them particularly well suited for fabrication of high resolution and high efficiency compact devices. PbI2 is a promising material for room temperature nuclear radiation detectors, characterized by its wide band gap (EG=2.32eV) and high-density (rho=6.2g/cm3). It has been reported that PbI2 crystal detectors are able to detect gamma-ray in the range of 1KeV-1MeV, with good energy resolution. However, PbI 2 detectors have not been studied in detail because of non-availability of high quality single crystals. This study presents the synthesis, purification, growth and characterization of PbI2 single crystals grown. In this research, solid-state synthesis technique has been utilized for obtaining PbI2 as a starting material. For the first time, a unique low-temperature purification technique has been developed to obtain high-purity starting material. The crystals were grown using 2-zone Bridgman-Stockbarger (B.S) technique wherein growth rate and temperature gradient at the solid-liquid interface were optimized. Single crystals of PbI2 were successfully grown in quartz glass ampoule under different growth conditions. Material purity was determined by measuring the elemental concentration using the Inductively coupled plasma-optical emission spectroscopy (ICP-OES). ICP-OES is utilized for estimating impurities present in the low-temperature purified material, zone refined material and melt grown PbI2 crystals. The zone-refined material contains no traceable amounts of impurities, whereas the low-temperature purified material and melt grown PbI2 crystals show very low concentration of K (potassium) and Na (sodium) impurities. Crystal characterization has been performed for determining optical properties by UV-VIS spectroscopy. The energy band gap (EG) is an important parameter for materials used for room temperature gamma-ray detector applications. The absorption peak at 530nm is a characteristic of PbI2 and corresponds to the onset of the transitions from the valence band to the exciton level. From this absorption spectrum the calculated indirect band gap of PbI 2 was 2.33+/-0.025 eV at room temperature. For measuring the electrical properties (Dielectric and I-V characteristics) of the crystal, Ag (silver) contacts are applied to both sides of the sample. Dielectric analysis on melt grown PbI2 showed that space charge polarization was dominant at lower frequencies but stabilizes at higher frequencies over different operating temperatures. On the other hand, dielectric analysis for zone-refined material space charge polarization was constant over the operating range resulting in fewer lattice defects. Therefore the low temperature purified material followed by zone-refined purification provides detector grade material with fewer lattice defects. The measured electrical resistivity for melt grown PbI2 and zone-refined material are 3.185 x 10 10 O-cm and 0.754 x 109 O-cm at room temperature along (001) plane respectively.

[Application of melting curve to analyze genotype of Duffy blood group antigen Fy-a/b].

PubMed

Chen, Xue; Zhou, Chang-Hua; Hong, Ying; Gong, Tian-Xiang

2012-12-01

This study was aimed to establish the real-time multiple-PCR with melting curve analysis for Duffy blood group Fy-a/b genotyping. According to the sequence of mRNA coding for β-actin and Fy-a/b, the primers of β-actin and Fy-a/b were synthesized. The real-time multiple-PCR with melting curve analysis for Fy-a/b genotyping was established. The Fy-a/b genotyping of 198 blood donors in Chinese Chengdu area has been investigated by melting curve analysis and PCR-SSP. The results showed that the results of Fy-a/b genotype by melting curve analysis were consistent with PCR-SSP. In all of 198 donors in Chinese Chengdu, 178 were Fy(a) (+) (89.9%), 19 were Fy(a) (+) Fy(b) (+) (9.6%), and 1 was Fy(b) (+) (0.5%). The gene frequency of Fy(a) was 0.947, while that of Fy(b) was 0.053. It is concluded that the genotyping method of Duffy blood group with melting curve analysis is established, which can be used as a high-throughput screening tool for Duffy blood group genotyping; and the Fy(a) genotype is the major of Duffy blood group of donors in Chinese Chengdu area.

MeltMan: Optimization, Evaluation, and Universal Application of a qPCR System Integrating the TaqMan qPCR and Melting Analysis into a Single Assay

PubMed Central

Nagy, Alexander; Černíková, Lenka; Vitásková, Eliška; Křivda, Vlastimil; Dán, Ádám; Dirbáková, Zuzana; Jiřincová, Helena; Procházka, Bohumír; Sedlák, Kamil; Havlíčková, Martina

2016-01-01

In the present work, we optimised and evaluated a qPCR system integrating 6-FAM (6-carboxyfluorescein)-labelled TaqMan probes and melting analysis using the SYTO 82 (S82) DNA binding dye in a single reaction. We investigated the influence of the S82 on various TaqMan and melting analysis parameters and defined its optimal concentration. In the next step, the method was evaluated in 36 different TaqMan assays with a total of 729 paired reactions using various DNA and RNA templates, including field specimens. In addition, the melting profiles of interest were correlated with the electrophoretic patterns. We proved that the S82 is fully compatible with the FAM-TaqMan system. Further, the advantages of this approach in routine diagnostic TaqMan qPCR were illustrated with practical examples. These included solving problems with flat or other atypical amplification curves or even false negativity as a result of probe binding failure. Our data clearly show that the integration of the TaqMan qPCR and melting analysis into a single assay provides an additional control option as well as the opportunity to perform more complex analyses, get more data from the reactions, and obtain analysis results with higher confidence. PMID:27031831

Visualization analysis of tiger-striped flow mark generation phenomena in injection molding

NASA Astrophysics Data System (ADS)

Owada, Shigeru; Yokoi, Hidetoshi

2016-03-01

The generation mechanism of tiger-striped flow marks of polypropylene (PP)/rubber/talc blends in injection molding was investigated by dynamic visualization analysis in a glass-inserted mold. The analysis revealed that the behavior of the melt flow front correlates with the flow mark generation. The cloudy part in the tiger-striped flow marks corresponded to the low transcription rate area of the melt diverging near the cavity wall, while the glossy part corresponded to the high transcription rate area of the melt converging toward the cavity wall side. The melt temperature at the high transcription rate area was slightly lower than that at the low transcription rate area. These phenomena resulted due to the difference in the temperature of the melt front that was caused by the asymmetric fountain flow. These results suggest the followings; At the moment when the melt is broken near the one side of cavity wall due to piling the extensional strains up to a certain level, the melt spurts out near the broken side. It results in generating asymmetric fountain flow temporarily to relax the extensional front surface, which moves toward the opposite side to form the high transcription area.

Vapor-phase infrared spectroscopy on solid organic compounds with a pulsed resonant photoacoustic detection scheme

NASA Astrophysics Data System (ADS)

Bartlome, Richard; Fischer, Cornelia; Sigrist, Markus W.

2005-08-01

There is a great need for a low cost and sensitive method to measure infrared spectra of solid organic compounds in the gas phase. To record such spectra, we propose an optical parametric generator-based photoacoustic spectrometer, which emits in the mid-infrared fingerprint region between 3 and 4 microns. In this system, the sample is heated in a vessel before entering a home built photoacoustic cell, where the gaseous molecules are excited by a tunable laser source with a frequency repetition rate that matches the first longitudinal resonance frequency of the photocaoustic cell. In a first phase, we have focused on low-melting point stimulants such as Nikethamide, Mephentermine sulfate, Methylephedrine, Ephedrine and Pseudoephedrine. The vapor-phase spectra of these doping substances were measured between 2800 and 3100 cm-1, where fundamental C-H stretching vibrations take place. Our spectra show notable differences with commercially available condensed phase spectra. Our scheme enables to measure very low vapor pressures of low-melting point (<160 °C) solid organic compounds. Furthermore, the optical resolution of 8 cm-1 is good enough to distinguish closely related chemical structures such as the Ephedra alkaloids Ephedrine and Methylephedrine, but doesn't allow to differentiate diastereoisomeric pairs such as Ephedrine and Pseudoephedrine, two important neurotransmitters which reveal different biological activities. Therefore, higher resolution and a system capable of measuring organic compounds with higher melting points are required.

The nature and barium partitioning between immiscible melts - A comparison of experimental and natural systems with reference to lunar granite petrogenesis

NASA Technical Reports Server (NTRS)

Neal, C. R.; Taylor, L. A.

1989-01-01

Elemental partitioning between immiscible melts has been studied using experimental liquid-liquid Kds and those determined by analysis of immiscible glasses in basalt mesostases in order to investigate lunar granite petrogenesis. Experimental data show that Ba is partitioned into the basic immiscible melt, while probe analysis results show that Ba is partitioned into the granitic immiscible melt. It is concluded that lunar granite of significant size can only occur in a plutonic or deep hypabyssal environment.

Relaxation of the bulk modulus in partially molten dunite?

NASA Astrophysics Data System (ADS)

Cline, C. J.; Jackson, I.

2016-11-01

To address the possibility of melt-related bulk modulus relaxation, a forced oscillation experiment was conducted at seismic frequencies on a partially molten synthetic dunite specimen (melt fraction = 0.026) utilizing the enhanced capacity of the Australian National University attenuation apparatus to operate in both torsional and flexural oscillation modes. Shear modulus and dissipation data are consistent with those for melt-bearing olivine specimens previously tested in torsion, with a pronounced dissipation peak superimposed on high-temperature background. Flexural data exhibit a monotonic decrease in complex Young's modulus with increasing temperature under transsolidus temperatures. The observed variation of Young's modulus is well described by the relationship 1/E 1/3G, without requiring relaxation of the bulk modulus. At high homologous temperatures, when shear modulus is low, extensional and flexural oscillation measurements have little resolution of bulk modulus, and thus, only pressure oscillation measurements can definitively constrain bulk properties at these conditions.

Electron-Beam Atomic Spectroscopy for In Situ Measurements of Melt Composition for Refractory Metals: Analysis of Fundamental Physics and Plasma Models

NASA Astrophysics Data System (ADS)

Gasper, Paul Joseph; Apelian, Diran

2015-04-01

Electron-beam (EB) melting is used for the processing of refractory metals, such as Ta, Nb, Mo, and W. These metals have high value and are critical to many industries, including the semiconductor, aerospace, and nuclear industries. EB melting can also purify secondary feedstock, enabling the recovery and recycling of these materials. Currently, there is no method for measuring melt composition in situ during EB melting. Optical emission spectroscopy of the plasma generated by EB impact with vapor above the melt, a technique here termed electron-beam atomic spectroscopy, can be used to measure melt composition in situ, allowing for analysis of melt dynamics, facilitating improvement of EB melting processes and aiding recycling and recovery of these critical and high-value metals. This paper reviews the physics of the plasma generation by EB impact by characterizing the densities and energies of electrons, ions, and neutrals, and describing the interactions between them. Then several plasma models are introduced and their suitability to this application analyzed. Lastly, a potential method for calibration-free composition measurement is described and the challenges for implementation addressed.

Refining lunar impact chronology through high spatial resolution 40Ar/39Ar dating of impact melts

PubMed Central

Mercer, Cameron M.; Young, Kelsey E.; Weirich, John R.; Hodges, Kip V.; Jolliff, Bradley L.; Wartho, Jo-Anne; van Soest, Matthijs C.

2015-01-01

Quantitative constraints on the ages of melt-forming impact events on the Moon are based primarily on isotope geochronology of returned samples. However, interpreting the results of such studies can often be difficult because the provenance region of any sample returned from the lunar surface may have experienced multiple impact events over the course of billions of years of bombardment. We illustrate this problem with new laser microprobe 40Ar/39Ar data for two Apollo 17 impact melt breccias. Whereas one sample yields a straightforward result, indicating a single melt-forming event at ca. 3.83 Ga, data from the other sample document multiple impact melt–forming events between ca. 3.81 Ga and at least as young as ca. 3.27 Ga. Notably, published zircon U/Pb data indicate the existence of even older melt products in the same sample. The revelation of multiple impact events through 40Ar/39Ar geochronology is likely not to have been possible using standard incremental heating methods alone, demonstrating the complementarity of the laser microprobe technique. Evidence for 3.83 Ga to 3.81 Ga melt components in these samples reinforces emerging interpretations that Apollo 17 impact breccia samples include a significant component of ejecta from the Imbrium basin impact. Collectively, our results underscore the need to quantitatively resolve the ages of different melt generations from multiple samples to improve our current understanding of the lunar impact record, and to establish the absolute ages of important impact structures encountered during future exploration missions in the inner Solar System. PMID:26601128

MgO melting curve constraints from shock temperature and rarefaction overtake measurements in samples preheated to 2300 K

NASA Astrophysics Data System (ADS)

Fat'yanov, O.; Asimow, P.

2013-06-01

In a continuous effort to determine experimentally the melting curve of MgO at 100-200 GPa, we extended our target preheating capability to 2300 K. The limit was primarily caused by intense sublimation of pure MgO in vacuum above ~2050 K. Completely redesigned Mo capsules holding ~20 mm long MgO crystals with controlled thermal gradients were impacted by thin Ta flyers launched at 6.5 to 7.5 km/s on the Caltech two-stage light-gas gun. Radiative shock temperatures and rarefaction overtake times were measured simultaneously by a 6-channel pyrometer with 3 ns time resolution, over 440-750 nm spectral range. All our experiments showed smooth pressure dependence of MgO sound speed consistent with the solid phase at 204-239 GPa. Observed temperatures are ~1000 K lower than those predicted by the solid phase model, but the plot of measured shock temperature versus pressure exhibits a pattern typical of shock melting at the highest pressure investigated. This may suggest that the Hugoniot of MgO preheated to 2300 K crosses its melting line at 220-240 GPa. Sound speed data indistinguishable from the solid phase model do not exclude the possibility of melting there.

SNP discovery and High Resolution Melting Analysis from massive transcriptome sequencing in the California red abalone Haliotis rufescens.

PubMed

Valenzuela-Muñoz, Valentina; Araya-Garay, José Miguel; Gallardo-Escárate, Cristian

2013-06-01

The California red abalone, Haliotis rufescens that belongs to the Haliotidae family, is the largest species of abalone in the world that has sustained the major fishery and aquaculture production in the USA and Mexico. This native mollusk has not been evaluated or assigned a conservation category even though in the last few decades it was heavily exploited until it disappeared in some areas along the California coast. In Chile, the red abalone was introduced in the 1970s from California wild abalone stocks for the purposes of aquaculture. Considering the number of years that the red abalone has been cultivated in Chile crucial genetic information is scarce and critical issues remain unresolved. This study reports and validates novel single nucleotide polymorphisms (SNP) markers for the red abalone H. rufescens using cDNA pyrosequencing. A total of 622 high quality SNPs were identified in 146 sequences with an estimated frequency of 1 SNP each 1000bp. Forty-five SNPs markers with functional information for gene ontology were selected. Of these, 8 were polymorphic among the individuals screened: Heat shock protein 70 (HSP70), vitellogenin (VTG), lysin, alginate lyase enzyme (AL), Glucose-regulated protein 94 (GRP94), fructose-bisphosphate aldolase (FBA), sulfatase 1A precursor (S1AP) and ornithine decarboxylase antizyme (ODC). Two additional sequences were also identified with polymorphisms but no similarities with known proteins were achieved. To validate the putative SNP markers, High Resolution Melting Analysis (HRMA) was conducted in a wild and hatchery-bred population. Additionally, SNP cross-amplifications were tested in two further native abalone species, Haliotis fulgens and Haliotis corrugata. This study provides novel candidate genes that could be used to evaluate loss of genetic diversity due to hatchery selection or inbreeding effects. Copyright © 2013 Elsevier B.V. All rights reserved.

Duration of convergence at the Pacific-Gondwana plate margin: insights from accessory phase petrochronology of the Alpine Schist, New Zealand

NASA Astrophysics Data System (ADS)

Briggs, S. I.; Cottle, J. M.; Smit, M. A.; Arnush, N. F.

2016-12-01

The timing, duration and along-strike synchroneity of metamorphism and anataxis in the Alpine Schist of New Zealand is a matter of considerable debate. Our preliminary data indicate that metamorphism resulting in garnet growth occurred from 97 - 75 Ma, and anatectic melting occurred from 80 - 51 Ma. These events are contemporaneous with rifting of Zealandia from East Gondwana, and Tasman Sea spreading from 83 - 52 Ma. An important implication of these results is that Late Cretaceous convergence along the Zealandia segment of the Pacific-Gondwana plate margin may have persisted much later than previously thought, and that convergence and extension occurred coevally in adjacent areas. This poses the question: for how long did convergence continue along the Pacific-Gondwana plate margin during East Gondwana breakup? To fully decipher the multiple stages of the complex metamorphic history recorded in the Alpine Schist, we combine Lu-Hf garnet geochronology with U-Th/Pb and REE analyses of zircon and monazite. We use the newly developed `single-shot laser ablation split stream' (SS-LASS) analysis method to obtain depth profiles through 5-10 µm metamorphic zircon overgrowths at 100 nm depth resolution to constrain both the timing and petrological context of discrete metamorphic zircon (re-)crystallization events recorded in the Alpine Schist. We also employ high spatial resolution LASS analysis to target rare 5 - 20 µm monazite in thin section to augment garnet and zircon data. Our multi-accessory phase petrochronology approach is capable of resolving discrete short-duration thermal events, strengthening the geological interpretation of `mean' Lu-Hf garnet ages and discerning between an episodic versus a prolonged history of metamorphism. In addition, comparison with geochronology from anatectic pegmatites clarifies the temporal relationship between metamorphism and melting in the Alpine Schist, while providing direct constraints on the timing and duration of convergence along the Zealandia segment of the Pacific-Gondwana margin.

Identification and Evaluation of Single-Nucleotide Polymorphisms in Allotetraploid Peanut (Arachis hypogaea L.) Based on Amplicon Sequencing Combined with High Resolution Melting (HRM) Analysis.

PubMed

Hong, Yanbin; Pandey, Manish K; Liu, Ying; Chen, Xiaoping; Liu, Hong; Varshney, Rajeev K; Liang, Xuanqiang; Huang, Shangzhi

2015-01-01

The cultivated peanut (Arachis hypogaea L.) is an allotetraploid (AABB) species derived from the A-genome (Arachis duranensis) and B-genome (Arachis ipaensis) progenitors. Presence of two versions of a DNA sequence based on the two progenitor genomes poses a serious technical and analytical problem during single nucleotide polymorphism (SNP) marker identification and analysis. In this context, we have analyzed 200 amplicons derived from expressed sequence tags (ESTs) and genome survey sequences (GSS) to identify SNPs in a panel of genotypes consisting of 12 cultivated peanut varieties and two diploid progenitors representing the ancestral genomes. A total of 18 EST-SNPs and 44 genomic-SNPs were identified in 12 peanut varieties by aligning the sequence of A. hypogaea with diploid progenitors. The average frequency of sequence polymorphism was higher for genomic-SNPs than the EST-SNPs with one genomic-SNP every 1011 bp as compared to one EST-SNP every 2557 bp. In order to estimate the potential and further applicability of these identified SNPs, 96 peanut varieties were genotyped using high resolution melting (HRM) method. Polymorphism information content (PIC) values for EST-SNPs ranged between 0.021 and 0.413 with a mean of 0.172 in the set of peanut varieties, while genomic-SNPs ranged between 0.080 and 0.478 with a mean of 0.249. Total 33 SNPs were used for polymorphism detection among the parents and 10 selected lines from mapping population Y13Zh (Zhenzhuhei × Yueyou13). Of the total 33 SNPs, nine SNPs showed polymorphism in the mapping population Y13Zh, and seven SNPs were successfully mapped into five linkage groups. Our results showed that SNPs can be identified in allotetraploid peanut with high accuracy through amplicon sequencing and HRM assay. The identified SNPs were very informative and can be used for different genetic and breeding applications in peanut.

Quantitative PCR high-resolution melting (qPCR-HRM) curve analysis, a new approach to simultaneously screen point mutations and large rearrangements: application to MLH1 germline mutations in Lynch syndrome.

PubMed

Rouleau, Etienne; Lefol, Cédrick; Bourdon, Violaine; Coulet, Florence; Noguchi, Tetsuro; Soubrier, Florent; Bièche, Ivan; Olschwang, Sylviane; Sobol, Hagay; Lidereau, Rosette

2009-06-01

Several techniques have been developed to screen mismatch repair (MMR) genes for deleterious mutations. Until now, two different techniques were required to screen for both point mutations and large rearrangements. For the first time, we propose a new approach, called "quantitative PCR (qPCR) high-resolution melting (HRM) curve analysis (qPCR-HRM)," which combines qPCR and HRM to obtain a rapid and cost-effective method suitable for testing a large series of samples. We designed PCR amplicons to scan the MLH1 gene using qPCR HRM. Seventy-six patients were fully scanned in replicate, including 14 wild-type patients and 62 patients with known mutations (57 point mutations and five rearrangements). To validate the detected mutations, we used sequencing and/or hybridization on a dedicated MLH1 array-comparative genomic hybridization (array-CGH). All point mutations and rearrangements detected by denaturing high-performance liquid chromatography (dHPLC)+multiplex ligation-dependent probe amplification (MLPA) were successfully detected by qPCR HRM. Three large rearrangements were characterized with the dedicated MLH1 array-CGH. One variant was detected with qPCR HRM in a wild-type patient and was located within the reverse primer. One variant was not detected with qPCR HRM or with dHPLC due to its proximity to a T-stretch. With qPCR HRM, prescreening for point mutations and large rearrangements are performed in one tube and in one step with a single machine, without the need for any automated sequencer in the prescreening process. In replicate, its reagent cost, sensitivity, and specificity are comparable to those of dHPLC+MLPA techniques. However, qPCR HRM outperformed the other techniques in terms of its rapidity and amount of data provided.

Identification of a new genetic marker in Mycoplasma synoviae vaccine strain MS-H and development of a strategy using polymerase chain reaction and high-resolution melting curve analysis for differentiating MS-H from field strains.

PubMed

Zhu, Ling; Konsak, Barbara M; Olaogun, Olusola M; Agnew-Crumptona, Rebecca; Kanci, Anna; Marenda, Marc S; Browning, Glenn F; Noormohammadi, Amir H

2017-10-01

Mycoplasma synoviae (MS) is an economically important avian pathogen worldwide, causing subclinical respiratory tract infection and infectious synovitis in chickens and turkeys. A temperature-sensitive (ts + ) live attenuated vaccine MS-H, derived from the Australian field strain 86079/7NS, is now widely used in many countries to control the disease induced by MS. Differentiation of MS-H vaccine from field strains is crucial for monitoring vaccination programs in commercial poultry. Comparison of genomic sequences of MS-H and its parent strain revealed an adenine deletion at nucleotide position 468 of the MS-H oppF-1 gene. This mutation was shown to be unique to MS-H in further comparative analyses of oppF-1 genes of MS-H re-isolates and field strains from Australia and other countries. Based on this single nucleotide, a combination of nested PCR and high-resolution melting (HRM) curve analysis was used to evaluate its potential for use in differentiation of MS-H from field strains. The mean genotype confidence percentages of 99.27 and 48.20 for MS-H and field strains, respectively, demonstrated the high discriminative power of the newly developed assay (oppF PCR-HRM). A set of 13 tracheal swab samples collected from MS-H vaccinated specific pathogen free birds and commercial chicken flocks infected with MS were tested using the oppF PCR-HRM test and results were totally consistent with those obtained using vlhA genotyping. The nested-PCR HRM method established in this study proved to be a rapid, simple and cost effective tool for discriminating the MS-H vaccine strain from Australian and international strains in pure cultures and on tracheal swabs. Copyright © 2017 Elsevier B.V. All rights reserved.

Detection and discrimination of members of the family Luteoviridae by real-time PCR and SYBR® GreenER™ melting curve analysis.

PubMed

Chomic, Anastasija; Winder, Louise; Armstrong, Karen F; Pearson, Michael N; Hampton, John G

2011-01-01

This study investigated the suitability of a two step real-time RT-PCR melting curve analysis as a tool for the detection and discrimination of nine species in the plant virus family Luteoviridae, being Soybean dwarf virus [SbDV], Bean leafroll virus [BLRV], Beet chlorosis virus [BChV], Beet mild yellowing virus [BMYV], Beet western yellows virus [BWYV], Cereal yellow dwarf virus-RPV [CYDV-RPV], Cucurbit aphid-borne yellows virus [CABYV], Potato leafroll virus [PLRV] and Turnip yellows virus [TuYV]. Melting temperature and shape of the melting peak were analysed for 68 bp and 148 bp coat protein gene amplicons using SYBR® GreenER™ fluorescent dye. Specific melting peaks with unique melting temperature were observed for the various species of the family Luteoviridae using the 68 bp amplicon, but not with the 148 bp amplicon. Due to the high variability of sequences for some members of this family, different melting temperatures were also observed between different isolates of the species CYDV-RPV and TuYV. Nevertheless, discrimination between species was achieved for SbDV, BLRV, BChV, BMYV, CABYV and either PLRV or BWYV. Melting curve analysis, in this study, is a faster and more discriminatory alternative to gel electrophoresis of end-point PCR products for the detection of Luteoviridae infection. Copyright © 2010 Elsevier B.V. All rights reserved.

Development of synthetic nuclear melt glass for forensic analysis.

PubMed

Molgaard, Joshua J; Auxier, John D; Giminaro, Andrew V; Oldham, C J; Cook, Matthew T; Young, Stephen A; Hall, Howard L

A method for producing synthetic debris similar to the melt glass produced by nuclear surface testing is demonstrated. Melt glass from the first nuclear weapon test (commonly referred to as trinitite) is used as the benchmark for this study. These surrogates can be used to simulate a variety of scenarios and will serve as a tool for developing and validating forensic analysis methods.

Challenges in Understanding and Predicting Greenland Lake Drainage Events

NASA Astrophysics Data System (ADS)

Poinar, K.; Andrews, L. C.; Moon, T. A.; Nowicki, S.

2017-12-01

To accurately predict ice flow, an ice-sheet model must resolve the complex spatio-temporal variability of the ice-sheet hydrologic system. For Greenland, this requires understanding rapid lake drainage events, by which moulins deliver water from supraglacial lakes to the ice-sheet base. Critical metrics include the drainage event location and its timing during the melt season. Here, we use multiple remote sensing datasets to investigate whether local principal strain rates control the dates of rapid supraglacial lake drainage events. We identify 359 rapid lake drainage events through a semi-automated analysis of MODIS and Landsat imagery, which we apply to Pâkitsoq, western Greenland, over nine summers (2006-2010 and 2013-2016). We compare these drainage dates to principal strain rates derived from InSAR (MEaSUREs and other products) and Landsat (GoLIVE and other products) satellite data over the same years. The InSAR-derived strain rates have lower uncertainties ( 0.01 yr-1) but capture only a wintertime average; the Landsat-derived strain rates have larger uncertainties ( 0.1 yr-1) but feature higher temporal resolution (≥16 days) and span the entire year, including the melt season. We find that locations with more-tensile wintertime strain rates are associated with earlier draining of supraglacial lakes in the subsequent summer. This is consistent with observations of lake drainage "clusters" or "cascades", where the perturbation from an initial lake drainage event is thought to trigger other lake drainages in the area. Our relation is not statistically significant, however, and any causality is complicated by a stronger correlation with more traditional metrics such as surface elevation and cumulative melt days. We also find that the Landsat-derived summertime strain rates, despite their higher temporal resolution, do not resolve the transient extensional strain rates known from GPS observations to accompany and/or incite rapid lake drainages. Our results highlight the current challenges in observing, at the regional scale, the causes of rapid lake drainage events, which must be better understood in order to parameterize surface-to-bed hydrological connections in ice-sheet models.

Energy balance-based distributed modeling of snow and glacier melt runoff for the Hunza river basin in the Pakistan Karakoram Himalayan region

NASA Astrophysics Data System (ADS)

Shrestha, M.; Wang, L.; Koike, T.; Xue, Y.; Hirabayashi, Y.; Ahmad, S.

2012-12-01

A spatially distributed biosphere hydrological model with energy balance-based multilayer snow physics and multilayer glacier model, including debris free and debris covered surface (enhanced WEB-DHM-S) has been developed and applied to the Hunza river basin in the Pakistan Karakoram Himalayan region, where about 34% of the basin area is covered by glaciers. The spatial distribution of seasonal snow and glacier cover, snow and glacier melt runoff along with rainfall-contributed runoff, and glacier mass balances are simulated. The simulations are carried out at hourly time steps and at 1-km spatial resolution for the two hydrological years (2002-2003) with the use of APHRODITE precipitation dataset, observed temperature, and other atmospheric forcing variables from the Global Land Data Assimilation System (GLDAS). The pixel-to-pixel comparisons for the snow-free and snow-covered grids over the region reveal that the simulation agrees well with the Moderate Resolution Imaging Spectroradiometer (MODIS) eight-day maximum snow-cover extent data (MOD10A2) with an accuracy of 83% and a positive bias of 2.8 %. The quantitative evaluation also shows that the model is able to reproduce the river discharge satisfactorily with Nash efficiency of 0.92. It is found that the contribution of rainfall to total streamflow is small (about 10-12%) while the contribution of snow and glacier is considerably large (35-40% for snowmelt and 50-53% for glaciermelt, respectively). The model simulates the state of snow and glaciers at each model grid prognostically and thus can estimate the net annual mass balance. The net mass balance varies from -2 m to +2 m water equivalent. Additionally, the hypsography analysis for the equilibrium line altitude (ELA) suggests that the average ELA in this region is about 5700 m with substantial variation from glacier to glacier and region to region. This study is the first to adopt a distributed biosphere hydrological model with the energy balance- based multilayer snow and glacier module to estimate the spatial distribution of snow/glacier cover and snow and glacier melt runoff for a river basin in the Karakoram Himalayan region.

Single-cell high resolution melting analysis: A novel, generic, pre-implantation genetic diagnosis (PGD) method applied to cystic fibrosis (HRMA CF-PGD).

PubMed

Destouni, A; Poulou, M; Kakourou, G; Vrettou, C; Tzetis, M; Traeger-Synodinos, J; Kitsiou-Tzeli, S

2016-03-01

Institutions offering CF-PGD face the challenge of developing and optimizing single cell genotyping protocols that should cover for the extremely heterogeneous CF mutation spectrum. Here we report the development and successful clinical application of a generic CF-PGD protocol to facilitate direct detection of any CFTR nucleotide variation(s) by HRMA and simultaneous confirmation of diagnosis through haplotype analysis. A multiplex PCR was optimized supporting co-amplification of any CFTR exon-region, along with 6 closely linked STRs. Single cell genotypes were established through HRM analysis following melting of the 2nd round PCR products and were confirmed by STR haplotype analysis of the 1st PCR products. The protocol was validated pre-clinically, by testing 208 single lymphocytes, isolated from whole blood samples from 4 validation family trios. Fifteen PGD cycles were performed and 103 embryos were biopsied. In 15 clinical PGD cycles, genotypes were achieved in 88/93 (94.6%) embryo biopsy samples, of which 57/88 (64.8%) were deemed genetically suitable for embryo transfer. Amplification failed at all loci for 10/103 blastomeres biopsied from poor quality embryos. Six clinical pregnancies were achieved (2 twin, 4 singletons). PGD genotypes were confirmed following conventional amniocentesis or chorionic villus sampling in all achieved pregnancies. The single cell HRMA CF-PGD protocol described herein is a flexible, generic, low cost and robust genotyping method, which facilitates the analysis of any CFTR genotype combination. Single-cell HRMA can be beneficial to other clinical settings, for example the detection of single nucleotide variants in single cells derived from clinical tumor samples. Copyright © 2015 European Cystic Fibrosis Society. Published by Elsevier B.V. All rights reserved.

Albedo and its relationship with seasonal surface roughness using repeat UAV survey across the Kangerlussuaq sector of the Greenland Ice Sheet

NASA Astrophysics Data System (ADS)

Hubbard, A., II; Ryan, J.; Box, J. E.; Snooke, N.

2015-12-01

Surface albedo is a primary control on absorbed radiation and hence ice surface darkening is a powerful amplifier of melt across the margin of the Greenland ice sheet. To investigate the relationship between ice surface roughness and variations in albedo in space and time at ~dm resolution, a suite of Unmanned Aerial Vehicles (UAVs) were deployed from the margin of Russell Glacier between June and August, 2014. The UAVs were equipped with digital and multispectral cameras, GoPros, fast response broadband pyranometers and temperature and humidity sensors. The primary mission was regular repeat longitudinal transects attaining data from the margin to the equilibrium line 80 km into the ice sheet interior and which were complimented by selected watershed and catchment surveys. The pyranometers reliably measure bare ice surface albedo between 0.34 and 0.58 that correlate well against concurrent MODIS data (where available). Repeat digital photogrammetric analysis enables investigation of relationship between changing meso- and micro-scale albedo and melt processes modulated by ice surface roughness that, in turn, are related to the seasonally evolving surface energy balance recorded at three AWS on the flight path.

A temperature-precipitation-based model of thiry-year mean snowpack accumulation and melt in Oregon, USA

EPA Science Inventory

High-resolution, spatially extensive climate grids can be useful in regional hydrologic applications. However, in regions where precipitation is dominated by snow, snowmelt models are often used to account for timing and magnitude of water delivery. We developed an empirical, non...

MEA/A-1 experiment 81F01 conducted on STS-7 flight, June 1983. Containerless processing of glass forming melts

NASA Technical Reports Server (NTRS)

Day, D. E.; Ray, C. S.

1983-01-01

The space processing of containerless, glassforming melts on board the space shuttle flight STS-7 is investigated. Objectives include; (1) obtain quantitative evidence for the supression of heterogeneous nucleation/crystallization, (2) study melt homogenization without gravity driven convection, (3) procedural development for bubble free, high purity homogeneous melts inmicro-g, (4) comparative analysis of melts on Earth and in micro g, and (5) assess the apparatus for processing multicomponent, glass forming melts in a low gravity environment.

Modelling the response of a Himalayan watershed to climate change: new insights from linking high resolution in-situ data and remote sensing with an advanced simulation model

NASA Astrophysics Data System (ADS)

Ragettli, S.; Pellicciotti, F.; Immerzeel, W.

2014-12-01

In high-elevation watersheds of the Himalayan region the correct representation of the internal states and process dynamics in glacio-hydrological models can often not be verified due to missing in-situ measurements. The aim of this study is to provide a fundamental understanding of the hydrology of a Himalayan watershed through the systematic integration of in-situ data in a glacio-hydrological model. We use ground data from the upper Langtang valley in Nepal combined with high resolution satellite data to understand specific processes and test the application of new model components specifically developed. We apply a new model for ablation under debris that takes into account the varying effect of debris thickness on melt rates. A novel approach is tested to reconstruct spatial fields of debris thickness through combination of energy balance modelling, UAV-derived geodetic mass balance and statistical techniques. The systematic integration of in-situ data for model calibration enables the application of a state-of-the art model with many parameters to model glacier evolution and catchment runoff in spite of the lack of continuous long-term historical records. It allows drawing conclusions on the importance of processes that have been suggested as being relevant but never quantified before. The simulations show that 8.7% of total water inputs originate from sub-debris ice melt. 4.5% originate from melted avalanched snow. These components can be locally much more important, since the spatial variability of processes within the valley is high. The model is then used to simulate the response of the catchment to climate change. We show that climate warming leads to an increase in future icemelt and a peak in glacier runoff by mid-century. The increase in total icemelt is due to higher melt rates and large areas that are currently located above the equilibrium line altitude additionally that will contribute to melt. Catchment runoff will not reach below current levels throughout the 21st century due to precipitation increases. Debris covered glacier area will disappear at a slower pace than non-debris covered area. Still, due to the relative climate insensitivity of melt rates below thick debris, the contribution of sub-debris icemelt to runoff will not exceed 10% at all times.

Theoretical analysis of heat flow in horizontal ribbon growth from a melt. [silicon metal

NASA Technical Reports Server (NTRS)

Zoutendyk, J. A.

1978-01-01

A theoretical heat flow analysis for horizontalribbon growth is presented. Equations are derived relating pull speed, ribbon thickness, thermal gradient in the melt, and melt temperature for limiting cases of heat removal by radiation only and isothermal heat removal from the solid surface over the melt. Geometrical cross sections of the growth zone are shown to be triangular and nearly parabolic for the two respective cases. Theoretical pull speed for silicon ribbon 0.01 cm thick, where the loss of latent heat of fusion is by radiation to ambient temperature (300 K) only, is shown to be 1 cm/sec for horizontal growth extending 2 cm over the melt and with no heat conduction either to or from the melt. Further enhancement of ribbon growth rate by placing cooling blocks adjacent to the top surface is shown to be theoretically possible.

Evolution of ocean-induced ice melt beneath Zachariæ Isstrøm, Northeast Greenland combining observations and an ocean general circulation model from 1978 to present

NASA Astrophysics Data System (ADS)

Cai, C.; Rignot, E. J.; Menemenlis, D.; Millan, R.; Bjørk, A. A.; Khan, S. A.; Charolais, A.

2017-12-01

Zachariæ Isstrøm, a major ice stream in northeast Greenland, lost a large fraction of its ice shelf during the last decade. We study the evolution of subaqueous melting of its floating section from 1978 to present. The ice shelf melt rate depends on thermal forcing from warm, salty, subsurface ocean waters of Atlantic origin (AW), the mixing of AW with fresh, buoyant subglacial discharge at the calving margin, and the shape of the sub-ice-shelf cavity. Subglacial discharge doubled as a result of enhanced ice sheet runoff caused by warmer air temperatures. Ocean thermal forcing has increased due to enhanced advection of AW. Using an Eulerian method, MEaSUREs ice velocity, Operation IceBridge (OIB) ice thickness, and RACMO2.3 surface balance data, we evaluate the ice shelf melt rate in 1978, 1999 and 2010. The melt rate doubled from 1999 to 2010. Using a Lagrangian method with World View imagery, we map the melt rate in detail from 2011 to 2016. We compare the results with 2D simulations from the Massachusetts Institute of Technology general circulation model (MITgcm), at a high spatial resolution (20-m horizontal and 40-m vertical grid spacing), using OIB ice thickness and sub-ice-shelf cavity for years 1978, 1996, 2010 and 2011, combined with in-situ ocean temperature/salinity data from Ocean Melting Greenland (OMG) 2017. We find that winter melt rates are 2 3 times smaller than summer rates and melt rates increase by one order magnitude during the transition from ice shelf termination to near-vertical calving wall termination. As the last remaining bits of floating ice shelf disappear, ice-ocean interaction will therefore play an increasing role in driving the glacier retreat into its marine-based basin. This work was performed under a contract with NASA Cryosphere Program at UC Irvine and Caltech's Jet Propulsion Laboratory.

Receiver function imaging of the onset of melting, implications for volcanism beneath the Afar Rift in contrast to hotspot environments

NASA Astrophysics Data System (ADS)

Rychert, C. A.; Harmon, N.; Hammond, J. O.; Laske, G.; Kendall, J.; Ebinger, C. J.; Shearer, P. M.; Bastow, I. D.; Keir, D.; Ayele, A.; Belachew, M.; Stuart, G. W.

2012-12-01

Heating, melting, and stretching destroy continents at volcanic rifts. Mantle plumes are often invoked to thermally weaken the continental lithosphere and accommodate rifting through the influx of magma. However the relative effects of mechanical stretching vs. melt infiltration and weakening are not well quantified during the evolution of rifting. S-to-p (Sp) imaging beneath the Afar Rift and hotspot regions such as Hawaii provides additional constraints. We use data from the Ethiopia/Kenya Broadband Seismic Experiment (EKBSE), the Ethiopia Afar Geophysical Lithospheric Experiment (EAGLE), a new UK/US led deployment of 46 stations in the Afar depression and surrounding area, and the PLUME experiment. We use two methodologies to investigate structure and locate robust features: 1) binning by conversion point and then simultaneous deconvolution in the frequency domain, and 2) extended multitaper followed by migration and stacking. We image a lithosphere-asthenosphere boundary at ~75 km beneath the flank of the Afar Rift vs. its complete absence beneath the rift, where the mantle lithosphere has been totally destroyed. Instead a strong velocity increase with depth at ~75 km depth matches geodynamic model predictions for a drop in melt percentage at the onset of decompression melting. The shallow depth of the onset of melting is consistent with a mantle potential temperature = 1350 - 1400°C, i.e., typical for adiabatic decompression melting. Therefore although a plume initially destroyed the mantle lithosphere, its influence directly beneath Afar today is minimal. Volcanism continues via adiabatic decompression melting assisted by strong melt buoyancy effects. This contrasts with a similar feature at much deeper depth, ~150 km, just west of Hawaii, where a deep thermal plume is hypothesized to impinge on the lithosphere. Improved high resolution imaging of rifting, ridges, and hotspots in a variety of stages and tectonic settings will increase constraints on the forces sustaining volcanism and the factors that dictate the style of breakup beneath rifts.

Investigation of the effects of melt electrospinning parameters on the direct-writing fiber size using orthogonal design

NASA Astrophysics Data System (ADS)

He, Feng-Li; He, Jin; Deng, Xudong; Li, Da-Wei; Ahmad, Fiaz; Liu, Yang-Yang; Liu, Ya-Li; Ye, Ya-Jing; Zhang, Chen-Yan; Yin, Da-Chuan

2017-10-01

Melt electrospinning is a complex process, and many of the processing parameters can impact the result of fiber formation. In this paper, we conducted a systematic investigation on the impacts of the melt electrospinning parameters (including temperature, needle gauge, flow rate and collector speed) on the fiber diameter via an orthogonal design experiment. The straight single fibers were fabricated using melt electrospinning in a direct-writing way with a diameter varied from 9.68  ±  0.93 µm to 48.55  ±  3.72 µm. The results showed that the fiber diameter changed differently against different parameters: when the temperature or needle gauge increased, the fiber diameter increased first and then decreased; when the flow rate increased, the fiber diameter decreased first and then increased; when the collector speed increased, the fiber diameter decreased monotonously. We also found that the collector speed was the most influential factor while the needle gauge was least important in determining the diameter of the fiber. Moreover, the feasibility of melt electrospinning in a direct-writing way as a novel 3D printing technology had been demonstrated by fabricating both uniform and controllable structures with high accuracy, based on the optimal parameters from the orthogonal experiments. The promising results indicated that melt electrospinning can be developed as a powerful technique for fabricating miniatured parts with high resolution and controllable structures for versatile potential applications.

Steelmaking process control using remote ultraviolet atomic emission spectroscopy

NASA Astrophysics Data System (ADS)

Arnold, Samuel

Steelmaking in North America is a multi-billion dollar industry that has faced tremendous economic and environmental pressure over the past few decades. Fierce competition has driven steel manufacturers to improve process efficiency through the development of real-time sensors to reduce operating costs. In particular, much attention has been focused on end point detection through furnace off gas analysis. Typically, off-gas analysis is done with extractive sampling and gas analyzers such as Non-dispersive Infrared Sensors (NDIR). Passive emission spectroscopy offers a more attractive approach to end point detection as the equipment can be setup remotely. Using high resolution UV spectroscopy and applying sophisticated emission line detection software, a correlation was observed between metal emissions and the process end point during field trials. This correlation indicates a relationship between the metal emissions and the status of a steelmaking melt which can be used to improve overall process efficiency.

Natural Infection of North African Gundi (Ctenodactylus gundi) by Leishmania tropica in the Focus of Cutaneous Leishmaniasis, Southeast Tunisia

PubMed Central

Bousslimi, Nadia; Ben-Ayed, Soumaya; Ben-Abda, Imène; Aoun, Karim; Bouratbine, Aïda

2012-01-01

North African gundis (Ctenodactylus gundi) were trapped in the Leishmania (L.) tropica focus of cutaneous leishmaniasis, situated in southeast Tunisia and evaluated for Leishmania infection by real-time kinetoplast DNA polymerase chain reaction (PCR). Species identification was performed by internal transcribed spacer one (ITS1)-PCR-restriction fragment length polymorphism (RFLP) and high-resolution melting (HRM) analysis of the 7SL RNA gene. Real-time PCR on blood was positive in 6 of 13 (46.2%) tested gundis. Leishmania tropica was identified in five infected gundis and Leishmania major in one specimen. Alignments of the ITS-1 DNA sequences and 7S-HRM curves analysis indicated that similar genotypes were present in humans, a sandfly, and gundis from the same region suggesting a potential role of this rodent as reservoir host of L. tropica in southeast Tunisia. PMID:22665601

Welding bulk metallic glass using nanostructured reactive multilayer foils

NASA Astrophysics Data System (ADS)

Trenkle, Jonathan C.

We have used Al/Ni reactive foils to weld Zr57Ti 5Cu20Ni8Al10 metallic glasses. The welds are a composite morphology comprised of glass ligaments and intermetallic AlNi (the product of the reactive foil). The presence of the presumably brittle intermetallic (in lieu of the glass) is expected to limit the mechanical properties of the welds. Based on fracture toughness measurements and the crack propagation paths, we conclude that virtually all of the toughness can be ascribed to the presence of the metallic glass ligaments. Increasing the pressure applied during welding increases the fraction of the joint made of these ligaments and so increases the fracture toughness as well. To eliminate the intermetallic from the weld altogether, we attempted to fabricate reactive mulitlayer foils that form an amorphous product by melting and cooling rapidly during a self-propagating reaction. We began with reactive foils with overall composition Zr2Ni but quickly determined that the foils did not fully melt. We then attempted to lower the melting temperature and increase the glass forming ability and the heat of mixing by adding Al and Cu. These foils again did not fully melt. Finally we systematically determined that foils of overall compositions Hf37Ni63, Ni 80P20, and Ni60P40, which are all known binary metallic glasses, will potentially melt during a self-propagating reaction. Knowledge of the phase transformations during a self-propagating reaction is necessary to engineer reactive foils for future applications. Furthermore, reactive foils provide an opportunity to study phase transformations under high heating rates not easily achievable. Characterizing the processes in the reaction zone however is challenging, requiring both temporal resolution better than ˜ 100 mus (the time required for the reaction front to pass a fixed location) and spatial resolution of < 100 mum (the approximate width of the reaction zone). Using synchrotron x-ray radiation, we have studied these phase transformations in situ in Al/Ni multilayers. Unlike previous annealing and quenching studies in these multilayers, we observed no metastable or intermediate phases.

Present-day Circum-Antarctic Simulations using the POPSICLES Coupled Ice Sheet-Ocean Model

NASA Astrophysics Data System (ADS)

Asay-Davis, X.; Martin, D. F.; Price, S. F.; Maltrud, M. E.; Collins, W.

2014-12-01

We present POPSICLES simulation results covering the full Antarctic Ice Sheet and the Southern Ocean spanning the period 1990 to 2010. Simulations are performed at 0.1o (~5 km) ocean resolution and with adaptive ice-sheet model resolution as fine as 500 m. We compare time-averaged melt rates below a number of major ice shelves with those reported by Rignot et al. (2013) as well as other recent studies. We also present seasonal variability and decadal trends in submarine melting from several Antarctic regions. Finally, we explore the influence on basal melting and system dynamics resulting from two different choices of climate forcing: a "normal-year" climatology and the CORE v. 2 forcing data (Large and Yeager 2008).POPSICLES couples the POP2x ocean model, a modified version of the Parallel Ocean Program (Smith and Gent, 2002), and the BISICLES ice-sheet model (Cornford et al., 2012). POP2x includes sub-ice-shelf circulation using partial top cells (Losch, 2008) and boundary layer physics following Holland and Jenkins (1999), Jenkins (2001), and Jenkins et al. (2010). Standalone POP2x output compares well with standard ice-ocean test cases (e.g., ISOMIP; Losch, 2008) and other continental-scale simulations and melt-rate observations (Kimura et al., 2013; Rignot et al., 2013). BISICLES makes use of adaptive mesh refinement and a 1st-order accurate momentum balance similar to the L1L2 model of Schoof and Hindmarsh (2009) to accurately model regions of dynamic complexity, such as ice streams, outlet glaciers, and grounding lines. Results of BISICLES simulations have compared favorably to comparable simulations with a Stokes momentum balance in both idealized tests (MISMIP-3D; Pattyn et al., 2013) and realistic configurations (Favier et al. 2014).A companion presentation, "Response of the Antarctic Ice Sheet to ocean forcing using the POPSICLES coupled ice sheet-ocean model" in session C024 covers the ice-sheet response to these melt rates in the coupled simulation. The figure shows eddy activity in the vertically integrated (barotropic) velocity nearly six years into a POPSICLES simulation of the Antarctic region.

Foehn and temperature-based melt patterns over the Larsen C Ice Shelf as simulated by the MAR regional climate model

NASA Astrophysics Data System (ADS)

Datta, R.; Tedesco, M.; Agosta, C.; Fettweis, X.; Kuipers Munneke, P.; van den Broeke, M. R.

2017-12-01

Surface melting has been implicated in the collapse of Antarctic Peninsula ice shelves, most dramatically in the Larsen A (1995) and Larsen B (2002) ice shelves. In July of this year, a rift in the remaining Larsen C ice shelf broke away one of the largest icebergs ever recorded. Ice-shelf retreat is likely related to strong atmospheric warming in this area, by means of hydrofracturing and possibly by the warming atmosphere itself. According the hydrofracture mechanism, meltwater produced during anomalously warm summers infiltrates and deepens pre-existent crevasses, leading to the eventual break-up of the ice shelf. In addition to region-wide warming, melting in the East Antarctic Peninsula can be caused by frequent intrusions of westerly foehn winds. The remaining Larsen C ice shelf, as well as glaciers previously feeding to the former Larsen B ice shelf, are therefore vulnerable to both (a) the atmospheric circulation patterns that influence foehn wind frequency and intensity and (b) regional interannual temperature trends. We discuss spatial patterns of meltwater production in the northeast basin of the Antarctic Peninsula as modeled by the Modèle Atmosphérique Régionale (MAR) at a 10km resolution between 2001 and 2014. The timeseries associated with these patterns are used to identify interannual changes in the frequency of foehn-induced melt, and compare foehn-induced melting to melt associated with regional warming. Melt occurrence in MAR is evaluated against multiple satellite datasets and near-surface automatic weather station data from three sites. Finally, we discuss the seasonal depth to which meltwater percolates into the snowpack (as modeled by MAR) because of the potential influence of meltwater on both warming and densification of the ice shelf.

Impact of fixation artifacts and threshold selection on high resolution melting analysis for KRAS mutation screening.

PubMed

Pérez-Báez, Wendy; García-Latorre, Ethel A; Maldonado-Martínez, Héctor Aquiles; Coronado-Martínez, Iris; Flores-García, Leonardo; Taja-Chayeb, Lucía

2017-10-01

Treatment in metastatic colorectal cancer (mCRC) has expanded with monoclonal antibodies targeting epidermal growth factor receptor, but is restricted to patients with a wild-type (WT) KRAS mutational status. The most sensitive assays for KRAS mutation detection in formalin-fixed paraffin embedded (FFPE) tissues are based on real-time PCR. Among them, high resolution melting analysis (HRMA), is a simple, fast, highly sensitive, specific and cost-effective method, proposed as adjunct for KRAS mutation detection. However the method to categorize WT vs mutant sequences in HRMA is not clearly specified in available studies, besides the impact of FFPE artifacts on HRMA performance hasn't been addressed either. Avowedly adequate samples from 104 consecutive mCRC patients were tested for KRAS mutations by Therascreen™ (FDA Validated test), HRMA, and HRMA with UDG pre-treatment to reverse FFPE fixation artifacts. Comparisons of KRAS status allocation among the three methods were done. Focusing on HRMA as screening test, ROC curve analyses were performed for HRMA and HMRA-UDG against Therascreen™, in order to evaluate their discriminative power and to determine the threshold of profile concordance between WT control and sample for KRAS status determination. Comparing HRMA and HRMA-UDG against Therascreen™ as surrogate gold standard, sensitivity was 1 for both HRMA and HRMA-UDG; and specificity and positive predictive values were respectively 0.838 and 0.939; and 0.777 and 0.913. As evaluated by the McNemar test, HRMA-UDG allocated samples to a WT/mutated genotype in a significatively different way from HRMA (p > 0.001). On the other hand HRMA-UDG did not differ from Therascreen™ (p = 0.125). ROC-curve analysis showed a significant discriminative power for both HRMA and HRMA-UDG against Therascreen™ (respectively, AUC of 0.978, p > 0.0001, CI 95% 0.957-0.999; and AUC of 0.98, p > 0.0001, CI 95% 0.000-1.0). For HRMA as a screening tool, the best threshold (degree of concordance between sample curves and WT control) was attained at 92.14% for HRMA (specificity of 0.887), and at 92.55% for HRMA-UDG (specificity of 0.952). HRMA is a highly sensitive method for KRAS mutation detection, with apparently adequate and statistically significant discriminative power. FFPE sample fixation artifacts have an impact on HRMA results, so for HRMA on FFPE samples pre-treatment with UDG should be strongly suggested. The choice of the threshold for melting curve concordance has also great impact on HRMA performance. A threshold of 93% or greater might be adequate if using HRMA as a screening tool. Further validation of this threshold is required. Copyright © 2017 Elsevier Ltd. All rights reserved.

Fukushima Daiichi Unit 1 ex-vessel prediction: Core melt spreading

DOE Office of Scientific and Technical Information (OSTI.GOV)

Farmer, M. T.; Robb, K. R.; Francis, M. W.

Lower head failure and corium-concrete interaction were predicted to occur at Fukushima Daiichi Unit 1 (1F1) by several different system-level code analyses, including MELCOR v2.1 and MAAP5. Although these codes capture a wide range of accident phenomena, they do not contain detailed models for ex-vessel core melt behavior. However, specialized codes exist for analysis of ex-vessel melt spreading (e.g., MELTSPREAD) and long-term debris coolability (e.g., CORQUENCH). On this basis, an analysis has been carried out to further evaluate ex-vessel behavior for 1F1 using MELTSPREAD and CORQUENCH. Best-estimate melt pour conditions predicted by MELCOR v2.1 and MAAP5 were used as input.more » MELTSPREAD was then used to predict the spatially-dependent melt conditions and extent of spreading during relocation from the vessel. Lastly, this information was then used as input for the long-term debris coolability analysis with CORQUENCH that is reported in a companion paper.« less

Fukushima Daiichi Unit 1 ex-vessel prediction: Core melt spreading

DOE PAGES

Farmer, M. T.; Robb, K. R.; Francis, M. W.

2016-10-31

Lower head failure and corium-concrete interaction were predicted to occur at Fukushima Daiichi Unit 1 (1F1) by several different system-level code analyses, including MELCOR v2.1 and MAAP5. Although these codes capture a wide range of accident phenomena, they do not contain detailed models for ex-vessel core melt behavior. However, specialized codes exist for analysis of ex-vessel melt spreading (e.g., MELTSPREAD) and long-term debris coolability (e.g., CORQUENCH). On this basis, an analysis has been carried out to further evaluate ex-vessel behavior for 1F1 using MELTSPREAD and CORQUENCH. Best-estimate melt pour conditions predicted by MELCOR v2.1 and MAAP5 were used as input.more » MELTSPREAD was then used to predict the spatially-dependent melt conditions and extent of spreading during relocation from the vessel. Lastly, this information was then used as input for the long-term debris coolability analysis with CORQUENCH that is reported in a companion paper.« less

Integrated Assessment and Improvement of the Quality Assurance System for the Cosworth Casting Process

NASA Astrophysics Data System (ADS)

Yousif, Dilon

The purpose of this study was to improve the Quality Assurance (QA) System at the Nemak Windsor Aluminum Plant (WAP). The project used Six Sigma method based on Define, Measure, Analyze, Improve, and Control (DMAIC). Analysis of in process melt at WAP was based on chemical, thermal, and mechanical testing. The control limits for the W319 Al Alloy were statistically recalculated using the composition measured under stable conditions. The "Chemistry Viewer" software was developed for statistical analysis of alloy composition. This software features the Silicon Equivalency (SiBQ) developed by the IRC. The Melt Sampling Device (MSD) was designed and evaluated at WAP to overcome traditional sampling limitations. The Thermal Analysis "Filters" software was developed for cooling curve analysis of the 3XX Al Alloy(s) using IRC techniques. The impact of low melting point impurities on the start of melting was evaluated using the Universal Metallurgical Simulator and Analyzer (UMSA).

Subaqueous melting in Zachariae Isstrom, Northeast Greenland combining observations and an ocean general circulation model

NASA Astrophysics Data System (ADS)

Cai, C.; Rignot, E. J.; Menemenlis, D.; Nakayama, Y.

2016-12-01

Zachariae Isstrom, a major ice stream in northeast Greenland, has lost its entire ice shelf in the past decade. Here, we study the evolution of subaqueous melting of its floating section during the transition. Observations show that the rate of ice shelf melting has doubled during 1999-2010 and is twice higher than that maintaining the ice shelf in a steady state. The ice shelf melt rate depends on the thermal forcing from warm, saline, subsurface ocean water of Atlantic origin (AW), and on the mixing of AW with fresh buoyant subglacial discharge. Subglacial discharge has increased as result of enhanced ice sheet runoff driven by warmer air temperature; ocean thermal forcing has increased due to enhanced advection of AW. Here, we employ the Massachusetts Institute of Technology general circulation model (MITgcm) at a high spatial resolution to simulate the melting process in 3-D. The model is constrained by ice thickness from mass conservation, oceanic bathymetry inverted from gravity data by NASA Operation IceBridge and NASA Ocean Melting Greenland missions, in-situ ocean temperature/salinity data, ocean tide height and current from the Arctic Ocean Tidal Inverse Model (AOTIM-5) and reconstructed seasonal subglacial discharge from the Regional Atmospheric Climate Model (RACMO2). We compare the results in winter (small runoff but not negligible) with summer (maximum runoff) at two different stages with (prior to 2012) and without the ice shelf (after 2012) to subaqueous melt rates deduced from remote sensing observations. We show that ice melting by the ocean has increased by one order of magnitude as a result of the transition from ice shelf terminating to near-vertical calving front terminating. We also find that subglacial discharge has a significant impact on ice shelf melt rates in Greenland. We conclude on the impact of ocean warming and air temperature warming on the melting regime of the ice margin of Zachariae Isstrom, Greenland. This work was performed under a contract with NASA Cryosphere Program at UC Irvine and Caltech's Jet Propulsion Laboratory.

Towards monitoring surface and subsurface lakes on the Greenland Ice Sheet using Sentinel-1 SAR and Landsat-8 OLI imagery

NASA Astrophysics Data System (ADS)

Miles, Katie E.; Willis, Ian C.; Benedek, Corinne L.; Williamson, Andrew G.; Tedesco, Marco

2017-07-01

Supraglacial lakes are an important component of the Greenland Ice Sheet’s mass balance and hydrology, with their drainage affecting ice dynamics. This study uses imagery from the recently launched Sentinel-1A Synthetic Aperture Radar (SAR) satellite to investigate supraglacial lakes in West Greenland. A semi-automated algorithm is developed to detect surface lakes from Sentinel-1 images during the 2015 summer. A combined Landsat-8 and Sentinel-1 dataset, which has a comparable temporal resolution to MODIS (3 days versus daily) but a higher spatial resolution (25-40 m versus 250-500 m), is then used together with a fully-automated lake drainage detection algorithm. Rapid (< 4 days) and slow (> 4 days) drainages are investigated for both small (< 0.125 km2, the minimum size detectable by MODIS) and large (≥ 0.125 km2) lakes through the summer. Drainage events of small lakes occur at lower elevations (mean 159 m), and slightly earlier (mean 4.5 days) in the melt season than those of large lakes. The analysis is extended manually into the early winter to calculate the dates and elevations of lake freeze-through more precisely than is possible with optical imagery (mean 30 August; 1270 m mean elevation). Finally, the Sentinel-1 imagery is used to detect subsurface lakes and, for the first time, their dates of appearance and freeze-through (mean 9 August and 7 October, respectively). These subsurface lakes occur at higher elevations than the surface lakes detected in this study (mean 1593 m and 1185 m, respectively). Sentinel-1 imagery therefore provides great potential for tracking melting, water movement and freezing within both the firn zone and ablation area of the Greenland Ice Sheet.

High-resolution melting PCR assay, applicable for diagnostics and screening studies, allowing detection and differentiation of several Babesia spp. infecting humans and animals.

PubMed

Rozej-Bielicka, Wioletta; Masny, Aleksander; Golab, Elzbieta

2017-10-01

The goal of the study was to design a single tube PCR test for detection and differentiation of Babesia species in DNA samples obtained from diverse biological materials. A multiplex, single tube PCR test was designed for amplification of approximately 400 bp region of the Babesia 18S rRNA gene. Universal primers were designed to match DNA of multiple Babesia spp. and to have low levels of similarity to DNA sequences of other intracellular protozoa and Babesia hosts. The PCR products amplified from Babesia DNA isolated from human, dog, rodent, deer, and tick samples were subjected to high-resolution melting analysis for Babesia species identification. The designed test allowed detection and differentiation of four Babesia species, three zoonotic (B. microti, B. divergens, B. venatorum) and one that is generally not considered zoonotic-Babesia canis. Both detection and identification of all four species were possible based on the HRM curves of the PCR products in samples obtained from the following: humans, dogs, rodents, and ticks. No cross-reactivity with DNA of Babesia hosts or Plasmodium falciparum and Toxoplasma gondii was observed. The lack of cross-reactivity with P. falciparum DNA might allow using the assay in endemic malaria areas. The designed assay is the first PCR-based test for detection and differentiation of several Babesia spp. of medical and veterinary importance, in a single tube reaction. The results of the study show that the designed assay for Babesia detection and identification could be a practical and inexpensive tool for diagnostics and screening studies of diverse biological materials.

Passive microwave derived snowmelt timing: significance, spatial and temporal variability, and potential applications

NASA Astrophysics Data System (ADS)

Semmens, Kathryn Alese

Snow accumulation and melt are dynamic features of the cryosphere indicative of a changing climate. Spring melt and refreeze timing are of particular importance due to the influence on subsequent hydrological and ecological processes, including peak runoff and green-up. To investigate the spatial and temporal variability of melt timing across a sub-arctic region (the Yukon River Basin (YRB), Alaska/Canada) dominated by snow and lacking substantial ground instrumentation, passive microwave remote sensing was utilized to provide daily brightness temperatures (Tb) regardless of clouds and darkness. Algorithms to derive the timing of melt onset and the end of melt-refreeze, a critical transition period where the snowpack melts during the day and refreezes at night, were based on thresholds for Tb and diurnal amplitude variations (day and night difference). Tb data from the Special Sensor Microwave Imager (1988 to 2011) was used for analyzing YRB terrestrial snowmelt timing and for characterizing melt regime patterns for icefields in Alaska and Patagonia. Tb data from the Advanced Microwave Scanning Radiometer for EOS (2003 to 2010) was used for determining the occurrence of early melt events (before melt onset) associated with fog or rain on snow, for investigating the correlation between melt timing and forest fires, and for driving a flux-based snowmelt runoff model. From the SSM/I analysis: the melt-refreeze period lengthened for the majority of the YRB with later end of melt-refreeze and earlier melt onset; and positive Tb anomalies were found in recent years from glacier melt dynamics. From the AMSR-E analysis: early melt events throughout the YRB were most often associated with warm air intrusions and reflect a consistent spatial distribution; years and areas of earlier melt onset and refreeze had more forest fire occurrences suggesting melt timing's effects extend to later seasons; and satellite derived melt timing served as an effective input for model simulation of discharge in remote, ungauged snow-dominated basins. The melt detection methodology and results present a new perspective on the changing cryosphere, provide an understanding of melt's influence on other earth system processes, and develop a baseline from which to assess and evaluate future change. The temporal and spatial variability conveyed through the regional context of this research may be useful to communities in climate change adaptation planning.

Multi-platform observations on melt pond in Arctic summer 2010

NASA Astrophysics Data System (ADS)

Wang, Y.; Huang, W.; Lu, P.; Li, Z.

2011-12-01

Melt ponds play an important role in sea ice surface albedo and further affect the heat budget between ice-air interface. The overall reductions of Arctic sea ice extend and thickness especially in recent years is considered to be enhanced partly by the melt ponds, and understanding of melt ponds on how they change the heat and mass balance of sea ice through the ice surface albedo decrease is urgently required. Although satellite remote sensing is a general tool to observe sea ice surface features on a large scale, the small scale information with higher spatial and temporal resolution is more helpful to understand the physical mechanism in the evolution of melt ponds. Arctic summer in 2010 is special because of an obvious trans-polar melting, during which the multi-year ice in the central Arctic was seriously melted, and formed a trans-polar zone with ice concentration less than 80% stretching from the Chukchi Sea to the Greenland Sea. It provided a fantastic opportunity to observe melt ponds especially at the high latitude. The Fourth Chinese National Arctic Research Expedition in 2010 (CHINARE-2010) was carried out from July 1 to September 20, 2010. As R/V Xuelong sailing in the ice-infested seas, a multi-platform observation was conducted to investigate the evolution of melt ponds on Arctic sea ice. Among which, aerial photography provided a downward-looking snapshot of the ice surface by using the camera installed on a helicopter, and melt pond information on a 100-meter scale can be obtained. Shipboard photography gave an inclined inspection on the ice conditions beside the ship using the camera installed on the vessel, and melt pond information on a 10-meter scale can be determined. Ground-based photography was similar to the shipboard photography, but the camera with tilt angle was installed on the top of a vertical lifting device fixed on the ice, and melt pond information on a 1-meter scale can be observed. Over 10,000 sea ice images from different platforms were collected during the cruise, and the survey area covered the regions 140°W-180°W, 70°N-88°N. An image processing technique based on difference in colors of the surface features was used to divide each image into three components: snow-covered ice floes, melt ponds and leads. And then geometric features of melt ponds, such as area, perimeter, and roundness, could be extracted from the aerial images. These data can enrich our knowledge on the distribution of melt pond on different spatial scale, especially those in the high latitude regions where summer melting was never so serious in previous years.

Imaging the Chicxulub central crater zone from large scale seismic acoustic wave propagation and gravity modeling

NASA Astrophysics Data System (ADS)

Fucugauchi, J. U.; Ortiz-Aleman, C.; Martin, R.

2017-12-01

Large complex craters are characterized by central uplifts that represent large-scale differential movement of deep basement from the transient cavity. Here we investigate the central sector of the large multiring Chicxulub crater, which has been surveyed by an array of marine, aerial and land-borne geophysical methods. Despite high contrasts in physical properties,contrasting results for the central uplift have been obtained, with seismic reflection surveys showing lack of resolution in the central zone. We develop an integrated seismic and gravity model for the main structural elements, imaging the central basement uplift and melt and breccia units. The 3-D velocity model built from interpolation of seismic data is validated using perfectly matched layer seismic acoustic wave propagation modeling, optimized at grazing incidence using shift in the frequency domain. Modeling shows significant lack of illumination in the central sector, masking presence of the central uplift. Seismic energy remains trapped in an upper low velocity zone corresponding to the sedimentary infill, melt/breccias and surrounding faulted blocks. After conversion of seismic velocities into a volume of density values, we use massive parallel forward gravity modeling to constrain the size and shape of the central uplift that lies at 4.5 km depth, providing a high-resolution image of crater structure.The Bouguer anomaly and gravity response of modeled units show asymmetries, corresponding to the crater structure and distribution of post-impact carbonates, breccias, melt and target sediments

EOS Aqua AMSR-E Sea Ice Validation Program: Meltpond2000 Flight Report

NASA Technical Reports Server (NTRS)

Cavalieri, Donald J.

2000-01-01

This flight report describes the field component of Meltpond2000, the first in a series of Arctic and Antarctic aircraft campaigns planned as part of NASA's Earth Observing System Aqua sea ice validation program for the Advanced Microwave Scanning Radiometer (AMSR-E). This prelaunch Arctic field campaign was carried out between June 25 and July 6, 2000 from Thule, Greenland, with the objective of quantifying the errors incurred by the AMSR-E sea ice algorithms resulting from the presence of melt ponds. A secondary objective of the mission was to develop a microwave capability to discriminate between melt ponds and seawater using low-frequency microwave radiometers. Meltpond2000 was a multiagency effort involving personnel from the Navy, NOAA, and NASA. The field component of the mission consisted of making five 8-hour flights from Thule Air Base with a Naval Air Warfare Center P-3 aircraft over portions of Baffin Bay and the Canadian Arctic. The aircraft sensors were provided and operated by the Microwave Radiometry Group of NOAA's Environmental TechnologyLaboratory. A Navy ice observer from the National Ice Center provided visual documentation of surface ice conditions during each of the flights. Two of the five flights were coordinated with Canadian scientists making surface measurements of melt ponds at an ice camp located near Resolute Bay, Canada. Coordination with the Canadians will provide additional information on surface characteristics and will be of great value in the interpretation of the aircraft and high-resolution satellite data sets.