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Sample records for thermal stability sequence-tagged-sites

  1. Poly(A)-tag deep sequencing data processing to extract poly(A) sites.

    Science.gov (United States)

    Wu, Xiaohui; Ji, Guoli; Li, Qingshun Quinn

    2015-01-01

    Polyadenylation [poly(A)] is an essential posttranscriptional processing step in the maturation of eukaryotic mRNA. The advent of next-generation sequencing (NGS) technology has offered feasible means to generate large-scale data and new opportunities for intensive study of polyadenylation, particularly deep sequencing of the transcriptome targeting the junction of 3'-UTR and the poly(A) tail of the transcript. To take advantage of this unprecedented amount of data, we present an automated workflow to identify polyadenylation sites by integrating NGS data cleaning, processing, mapping, normalizing, and clustering. In this pipeline, a series of Perl scripts are seamlessly integrated to iteratively map the single- or paired-end sequences to the reference genome. After mapping, the poly(A) tags (PATs) at the same genome coordinate are grouped into one cleavage site, and the internal priming artifacts removed. Then the ambiguous region is introduced to parse the genome annotation for cleavage site clustering. Finally, cleavage sites within a close range of 24 nucleotides and from different samples can be clustered into poly(A) clusters. This procedure could be used to identify thousands of reliable poly(A) clusters from millions of NGS sequences in different tissues or treatments.

  2. Expressed sequence tags (ESTs) and single nucleotide ...

    African Journals Online (AJOL)

    SERVER

    2008-02-19

    Feb 19, 2008 ... the discovery of the DNA, a new area of modern plant biotechnology begun. In plant ... Marker Assisted Breeding and Sequence Tagged Sites. (STS) are all in use in modern ...... and behaviour in the honey bee. Genome Res.

  3. Novel expressed sequence tag- simple sequence repeats (EST ...

    African Journals Online (AJOL)

    Using different bioinformatic criteria, the SUCEST database was used to mine for simple sequence repeat (SSR) markers. Among 42,189 clusters, 1,425 expressed sequence tag- simple sequence repeats (EST-SSRs) were identified in silico. Trinucleotide repeats were the most abundant SSRs detected. Of 212 primer pairs ...

  4. Random Tagging Genotyping by Sequencing (rtGBS, an Unbiased Approach to Locate Restriction Enzyme Sites across the Target Genome.

    Directory of Open Access Journals (Sweden)

    Elena Hilario

    Full Text Available Genotyping by sequencing (GBS is a restriction enzyme based targeted approach developed to reduce the genome complexity and discover genetic markers when a priori sequence information is unavailable. Sufficient coverage at each locus is essential to distinguish heterozygous from homozygous sites accurately. The number of GBS samples able to be pooled in one sequencing lane is limited by the number of restriction sites present in the genome and the read depth required at each site per sample for accurate calling of single-nucleotide polymorphisms. Loci bias was observed using a slight modification of the Elshire et al.some restriction enzyme sites were represented in higher proportions while others were poorly represented or absent. This bias could be due to the quality of genomic DNA, the endonuclease and ligase reaction efficiency, the distance between restriction sites, the preferential amplification of small library restriction fragments, or bias towards cluster formation of small amplicons during the sequencing process. To overcome these issues, we have developed a GBS method based on randomly tagging genomic DNA (rtGBS. By randomly landing on the genome, we can, with less bias, find restriction sites that are far apart, and undetected by the standard GBS (stdGBS method. The study comprises two types of biological replicates: six different kiwifruit plants and two independent DNA extractions per plant; and three types of technical replicates: four samples of each DNA extraction, stdGBS vs. rtGBS methods, and two independent library amplifications, each sequenced in separate lanes. A statistically significant unbiased distribution of restriction fragment size by rtGBS showed that this method targeted 49% (39,145 of BamH I sites shared with the reference genome, compared to only 14% (11,513 by stdGBS.

  5. EnTagRec : an enhanced tag recommendation system for software information sites

    NARCIS (Netherlands)

    Wang, S.; Lo, D.; Vasilescu, B.N.; Serebrenik, A.

    2014-01-01

    Software engineers share experiences with modern technologies by means of software information sites, such as STACK OVERFLOW. These sites allow developers to label posted content, referred to as software objects, with short descriptions, known as tags. However, tags assigned to objects tend to be

  6. Sequence tagging reveals unexpected modifications in toxicoproteomics

    Science.gov (United States)

    Dasari, Surendra; Chambers, Matthew C.; Codreanu, Simona G.; Liebler, Daniel C.; Collins, Ben C.; Pennington, Stephen R.; Gallagher, William M.; Tabb, David L.

    2010-01-01

    Toxicoproteomic samples are rich in posttranslational modifications (PTMs) of proteins. Identifying these modifications via standard database searching can incur significant performance penalties. Here we describe the latest developments in TagRecon, an algorithm that leverages inferred sequence tags to identify modified peptides in toxicoproteomic data sets. TagRecon identifies known modifications more effectively than the MyriMatch database search engine. TagRecon outperformed state of the art software in recognizing unanticipated modifications from LTQ, Orbitrap, and QTOF data sets. We developed user-friendly software for detecting persistent mass shifts from samples. We follow a three-step strategy for detecting unanticipated PTMs in samples. First, we identify the proteins present in the sample with a standard database search. Next, identified proteins are interrogated for unexpected PTMs with a sequence tag-based search. Finally, additional evidence is gathered for the detected mass shifts with a refinement search. Application of this technology on toxicoproteomic data sets revealed unintended cross-reactions between proteins and sample processing reagents. Twenty five proteins in rat liver showed signs of oxidative stress when exposed to potentially toxic drugs. These results demonstrate the value of mining toxicoproteomic data sets for modifications. PMID:21214251

  7. Establishing nursery estuary otolith geochemical tags for Sea Bass (Dicentrarchus labrax): Is temporal stability estuary dependent?

    Science.gov (United States)

    Ryan, Diarmuid; Wögerbauer, Ciara; Roche, William

    2016-12-01

    The ability to determine connectivity between juveniles in nursery estuaries and adult populations is an important tool for fisheries management. Otoliths of juvenile fish contain geochemical tags, which reflect the variation in estuarine elemental chemistry, and allow discrimination of their natal and/or nursery estuaries. These tags can be used to investigate connectivity patterns between juveniles and adults. However, inter-annual variability of geochemical tags may limit the accuracy of nursery origin determinations. Otolith elemental composition was used to assign a single cohort of 0-group sea bass Dicentrarchus labrax to their nursery estuary thus establishing an initial baseline for stocks in waters around Ireland. Using a standard LDFA model, high classification accuracies to nursery sites (80-88%) were obtained. Temporal stability of otolith geochemical tags was also investigated to assess if annual sampling is required for connectivity studies. Geochemical tag stability was found to be strongly estuary dependent.

  8. An evaluation of sequence tagged microsatellite site markers for genetic analysis within Citrus and related species.

    Science.gov (United States)

    Kijas, J M; Fowler, J C; Thomas, M R

    1995-04-01

    Microsatellites, also called sequence tagged microsatellite sites (STMSs), have become important markers for genome analysis but are currently little studied in plants. To assess the value of STMSs for analysis within the Citrus plant species, two example STMSs were isolated from an intergeneric cross between rangpur lime (Citrus x limonia Osbeck) and trifoliate orange (Poncirus trifoliata (L.) Raf.). Unique flanking primers were constructed for polymerase chain reaction amplification both within the test cross and across a broad range of citrus and related species. Both loci showed length variation between test cross parents with alleles segregating in a Mendelian fashion to progeny. Amplification across species showed the STMS flanking primers to be conserved in every genome tested. The traits of polymorphism, inheritance, and conservation across species mean that STMS markers are ideal for genome mapping within Citrus, which contains high levels of genetic variability.

  9. In silico Analysis of 3′-End-Processing Signals in Aspergillus oryzae Using Expressed Sequence Tags and Genomic Sequencing Data

    Science.gov (United States)

    Tanaka, Mizuki; Sakai, Yoshifumi; Yamada, Osamu; Shintani, Takahiro; Gomi, Katsuya

    2011-01-01

    To investigate 3′-end-processing signals in Aspergillus oryzae, we created a nucleotide sequence data set of the 3′-untranslated region (3′ UTR) plus 100 nucleotides (nt) sequence downstream of the poly(A) site using A. oryzae expressed sequence tags and genomic sequencing data. This data set comprised 1065 sequences derived from 1042 unique genes. The average 3′ UTR length in A. oryzae was 241 nt, which is greater than that in yeast but similar to that in plants. The 3′ UTR and 100 nt sequence downstream of the poly(A) site is notably U-rich, while the region located 15–30 nt upstream of the poly(A) site is markedly A-rich. The most frequently found hexanucleotide in this A-rich region is AAUGAA, although this sequence accounts for only 6% of all transcripts. These data suggested that A. oryzae has no highly conserved sequence element equivalent to AAUAAA, a mammalian polyadenylation signal. We identified that putative 3′-end-processing signals in A. oryzae, while less well conserved than those in mammals, comprised four sequence elements: the furthest upstream U-rich element, A-rich sequence, cleavage site, and downstream U-rich element flanking the cleavage site. Although these putative 3′-end-processing signals are similar to those in yeast and plants, some notable differences exist between them. PMID:21586533

  10. Mining of expressed sequence tag libraries of cacao

    Indian Academy of Sciences (India)

    Expressed sequence tags (ESTs) provide researchers with a quick and inexpensive route for discovering new genes, data on gene expression and regulation, and also provide genic markers that help in constructing genome maps. Cacao is an important perennial crop of humid tropics. Cacao EST sequences, as available ...

  11. Mining microsatellite markers from public expressed sequence tag

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 91; Issue 3. Mining microsatellite markers from public expressed sequence tag sequences for genetic diversity analysis in pomegranate. Zai-Hai Jian Xin-She Liu Jian-Bin Hu Yan-Hui Chen Jian-Can Feng. Research Note Volume 91 Issue 3 December 2012 pp 353-358 ...

  12. TagDust2: a generic method to extract reads from sequencing data.

    Science.gov (United States)

    Lassmann, Timo

    2015-01-28

    Arguably the most basic step in the analysis of next generation sequencing data (NGS) involves the extraction of mappable reads from the raw reads produced by sequencing instruments. The presence of barcodes, adaptors and artifacts subject to sequencing errors makes this step non-trivial. Here I present TagDust2, a generic approach utilizing a library of hidden Markov models (HMM) to accurately extract reads from a wide array of possible read architectures. TagDust2 extracts more reads of higher quality compared to other approaches. Processing of multiplexed single, paired end and libraries containing unique molecular identifiers is fully supported. Two additional post processing steps are included to exclude known contaminants and filter out low complexity sequences. Finally, TagDust2 can automatically detect the library type of sequenced data from a predefined selection. Taken together TagDust2 is a feature rich, flexible and adaptive solution to go from raw to mappable NGS reads in a single step. The ability to recognize and record the contents of raw reads will help to automate and demystify the initial, and often poorly documented, steps in NGS data analysis pipelines. TagDust2 is freely available at: http://tagdust.sourceforge.net .

  13. OSIRIS-REx Touch-And-Go (TAG) Navigation Performance

    Science.gov (United States)

    Berry, Kevin; Antreasian, Peter; Moreau, Michael C.; May, Alex; Sutter, Brian

    2015-01-01

    The Origins Spectral Interpretation Resource identification Security Regolith Explorer (OSIRIS-REx) mission is a NASA New Frontiers mission launching in 2016 to rendezvous with the near-Earth asteroid (101955) Bennu in late 2018. Following an extensive campaign of proximity operations activities to characterize the properties of Bennu and select a suitable sample site, OSIRIES-REx will fly a Touch-And-Go (TAG) trajectory to the asteroid's surface to obtain a regolith sample. The paper summarizes the mission design of the TAG sequence, the propulsive required to achieve the trajectory, and the sequence of events leading up to the TAG event. The paper will summarize the Monte-Carlo simulation of the TAG sequence and present analysis results that demonstrate the ability to conduct the TAG within 25 meters of the selected sample site and +-2 cms of the targeted contact velocity. The paper will describe some of the challenges associated with conducting precision navigation operations and ultimately contacting a very small asteroid.

  14. OSIRI-REx Touch and Go (TAG) Navigation Performance

    Science.gov (United States)

    Berry, Kevin; Antreasian, Peter; Moreau, Michael C.; May, Alex; Sutter, Brian

    2015-01-01

    The Origins Spectral Interpretation Resource Identification Security Regolith Explorer (OSIRIS-REx) mission is a NASA New Frontiers mission launching in 2016 to rendezvous with the near-Earth asteroid (101955) Bennu in late 2018. Following an extensive campaign of proximity operations activities to characterize the properties of Bennu and select a suitable sample site, OSIRIS-REx will fly a Touch-And-Go (TAG) trajectory to the asteroid's surface to obtain a regolith sample. The paper summarizes the mission design of the TAG sequence, the propulsive maneuvers required to achieve the trajectory, and the sequence of events leading up to the TAG event. The paper also summarizes the Monte-Carlo simulation of the TAG sequence and presents analysis results that demonstrate the ability to conduct the TAG within 25 meters of the selected sample site and 2 cm/s of the targeted contact velocity. The paper describes some of the challenges associated with conducting precision navigation operations and ultimately contacting a very small asteroid.

  15. Rapid in silico cloning of genes using expressed sequence tags (ESTs).

    Science.gov (United States)

    Gill, R W; Sanseau, P

    2000-01-01

    Expressed sequence tags (ESTs) are short single-pass DNA sequences obtained from either end of cDNA clones. These ESTs are derived from a vast number of cDNA libraries obtained from different species. Human ESTs are the bulk of the data and have been widely used to identify new members of gene families, as markers on the human chromosomes, to discover polymorphism sites and to compare expression patterns in different tissues or pathologies states. Information strategies have been devised to query EST databases. Since most of the analysis is performed with a computer, the term "in silico" strategy has been coined. In this chapter we will review the current status of EST databases, the pros and cons of EST-type data and describe possible strategies to retrieve meaningful information.

  16. Sequence-indexed mutations in maize using the UniformMu transposon-tagging population

    Directory of Open Access Journals (Sweden)

    Baier John

    2007-05-01

    Full Text Available Abstract Background Gene knockouts are a critical resource for functional genomics. In Arabidopsis, comprehensive knockout collections were generated by amplifying and sequencing genomic DNA flanking insertion mutants. These Flanking Sequence Tags (FSTs map each mutant to a specific locus within the genome. In maize, FSTs have been generated using DNA transposons. Transposable elements can generate unstable insertions that are difficult to analyze for simple knockout phenotypes. Transposons can also generate somatic insertions that fail to segregate in subsequent generations. Results Transposon insertion sites from 106 UniformMu FSTs were tested for inheritance by locus-specific PCR. We confirmed 89% of the FSTs to be germinal transposon insertions. We found no evidence for somatic insertions within the 11% of insertion sites that were not confirmed. Instead, this subset of insertion sites had errors in locus-specific primer design due to incomplete or low-quality genomic sequences. The locus-specific PCR assays identified a knockout of a 6-phosphogluconate dehydrogenase gene that co-segregates with a seed mutant phenotype. The mutant phenotype linked to this knockout generates novel hypotheses about the role for the plastid-localized oxidative pentose phosphate pathway during grain-fill. Conclusion We show that FSTs from the UniformMu population identify stable, germinal insertion sites in maize. Moreover, we show that these sequence-indexed mutations can be readily used for reverse genetic analysis. We conclude from these data that the current collection of 1,882 non-redundant insertion sites from UniformMu provide a genome-wide resource for reverse genetics.

  17. Thermal precipitation fluorescence assay for protein stability screening.

    Science.gov (United States)

    Fan, Junping; Huang, Bo; Wang, Xianping; Zhang, Xuejun C

    2011-09-01

    A simple and reliable method of protein stability assessment is desirable for high throughput expression screening of recombinant proteins. Here we described an assay termed thermal precipitation fluorescence (TPF) which can be used to compare thermal stabilities of recombinant protein samples directly from cell lysate supernatants. In this assay, target membrane proteins are expressed as recombinant fusions with a green fluorescence protein tag and solubilized with detergent, and the fluorescence signals are used to report the quantity of the fusion proteins in the soluble fraction of the cell lysate. After applying a heat shock, insoluble protein aggregates are removed by centrifugation. Subsequently, the amount of remaining protein in the supernatant is quantified by in-gel fluorescence analysis and compared to samples without a heat shock treatment. Over 60 recombinant membrane proteins from Escherichia coli were subject to this screening in the presence and absence of a few commonly used detergents, and the results were analyzed. Because no sophisticated protein purification is required, this TPF technique is suitable to high throughput expression screening of recombinant membrane proteins as well as soluble ones and can be used to prioritize target proteins based on their thermal stabilities for subsequent large scale expression and structural studies. Copyright © 2011 Elsevier Inc. All rights reserved.

  18. Exploiting sequence and stability information for directing nanobody stability engineering.

    Science.gov (United States)

    Kunz, Patrick; Flock, Tilman; Soler, Nicolas; Zaiss, Moritz; Vincke, Cécile; Sterckx, Yann; Kastelic, Damjana; Muyldermans, Serge; Hoheisel, Jörg D

    2017-09-01

    Variable domains of camelid heavy-chain antibodies, commonly named nanobodies, have high biotechnological potential. In view of their broad range of applications in research, diagnostics and therapy, engineering their stability is of particular interest. One important aspect is the improvement of thermostability, because it can have immediate effects on conformational stability, protease resistance and aggregation propensity of the protein. We analyzed the sequences and thermostabilities of 78 purified nanobody binders. From this data, potentially stabilizing amino acid variations were identified and studied experimentally. Some mutations improved the stability of nanobodies by up to 6.1°C, with an average of 2.3°C across eight modified nanobodies. The stabilizing mechanism involves an improvement of both conformational stability and aggregation behavior, explaining the variable degree of stabilization in individual molecules. In some instances, variations predicted to be stabilizing actually led to thermal destabilization of the proteins. The reasons for this contradiction between prediction and experiment were investigated. The results reveal a mutational strategy to improve the biophysical behavior of nanobody binders and indicate a species-specificity of nanobody architecture. This study illustrates the potential and limitations of engineering nanobody thermostability by merging sequence information with stability data, an aspect that is becoming increasingly important with the recent development of high-throughput biophysical methods. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  19. Construction of stabilized and tagged foot-and-mouth disease virus.

    Science.gov (United States)

    Park, Jeong-Nam; Ko, Mi-Kyeong; Kim, Rae-Hyung; Park, Min-Eun; Lee, Seo-Yong; Yoon, Ji-Eun; Choi, Joo-Hyung; You, Su-Hwa; Park, Jung-Won; Lee, Kwang-Nyeong; Chun, Ji-Eun; Kim, Su-Mi; Tark, Dongseob; Lee, Hyang-Sim; Ko, Young-Joon; Kim, Byounghan; Lee, Myoung-Heon; Park, Jong-Hyeon

    2016-11-01

    Foot-and-mouth disease (FMD) is a highly contagious and economically devastating disease that affects cloven-hoofed animals worldwide. Construction and purification of stable antigen for vaccine are necessary but technically difficult and laborious. Here, we have tried to investigate an alternative method by inserting a hexa-histidine tag (6xHIS) in the VP1 C-terminal for easy purification and replacing two amino acids of VP1/VP2 to enhance the stability of the capsid of the FMD virus (FMDV) Asia1/MOG/05. In addition, infectious 6xHIS-tagged stable (S/T) FMDVs were maintained under acidic conditions (pH 6.0) and were readily purified from small-scale cultures using a commercial metal-affinity column. The groups vaccinated with the S/T FMDV antigen showed complete protection comparing to low survival rate in the group vaccinated with non-S/T FMDV against lethal challenge with Asia1 Shamir in mice. Therefore, the present findings indicate that the stabilized and tagged antigen offers an alternative to using the current methods for antigen purification and enhancement of stability and has potential for the development of a new FMD vaccine. Copyright © 2016 Elsevier B.V. All rights reserved.

  20. Effect of Si additions on thermal stability and the phase transition sequence of sputtered amorphous alumina thin films

    International Nuclear Information System (INIS)

    Bolvardi, H.; Baben, M. to; Nahif, F.; Music, D.; Schnabel, V.; Shaha, K. P.; Mráz, S.; Schneider, J. M.; Bednarcik, J.; Michalikova, J.

    2015-01-01

    Si-alloyed amorphous alumina coatings having a silicon concentration of 0 to 2.7 at. % were deposited by combinatorial reactive pulsed DC magnetron sputtering of Al and Al-Si (90-10 at. %) split segments in Ar/O 2 atmosphere. The effect of Si alloying on thermal stability of the as-deposited amorphous alumina thin films and the phase formation sequence was evaluated by using differential scanning calorimetry and X-ray diffraction. The thermal stability window of the amorphous phase containing 2.7 at. % of Si was increased by more than 100 °C compared to that of the unalloyed phase. A similar retarding effect of Si alloying was also observed for the α-Al 2 O 3 formation temperature, which increased by more than 120 °C. While for the latter retardation, the evidence for the presence of SiO 2 at the grain boundaries was presented previously, this obviously cannot explain the stability enhancement reported here for the amorphous phase. Based on density functional theory molecular dynamics simulations and synchrotron X-ray diffraction experiments for amorphous Al 2 O 3 with and without Si incorporation, we suggest that the experimentally identified enhanced thermal stability of amorphous alumina with addition of Si is due to the formation of shorter and stronger Si–O bonds as compared to Al–O bonds

  1. Effect of Si additions on thermal stability and the phase transition sequence of sputtered amorphous alumina thin films

    Energy Technology Data Exchange (ETDEWEB)

    Bolvardi, H.; Baben, M. to; Nahif, F.; Music, D., E-mail: music@mch.rwth-aachen.de; Schnabel, V.; Shaha, K. P.; Mráz, S.; Schneider, J. M. [Materials Chemistry, RWTH Aachen University, Kopernikusstr. 10, D-52074 Aachen (Germany); Bednarcik, J.; Michalikova, J. [Deutsches Elektronen Synchrotron DESY, FS-PE group, Notkestrasse 85, D-22607 Hamburg (Germany)

    2015-01-14

    Si-alloyed amorphous alumina coatings having a silicon concentration of 0 to 2.7 at. % were deposited by combinatorial reactive pulsed DC magnetron sputtering of Al and Al-Si (90-10 at. %) split segments in Ar/O{sub 2} atmosphere. The effect of Si alloying on thermal stability of the as-deposited amorphous alumina thin films and the phase formation sequence was evaluated by using differential scanning calorimetry and X-ray diffraction. The thermal stability window of the amorphous phase containing 2.7 at. % of Si was increased by more than 100 °C compared to that of the unalloyed phase. A similar retarding effect of Si alloying was also observed for the α-Al{sub 2}O{sub 3} formation temperature, which increased by more than 120 °C. While for the latter retardation, the evidence for the presence of SiO{sub 2} at the grain boundaries was presented previously, this obviously cannot explain the stability enhancement reported here for the amorphous phase. Based on density functional theory molecular dynamics simulations and synchrotron X-ray diffraction experiments for amorphous Al{sub 2}O{sub 3} with and without Si incorporation, we suggest that the experimentally identified enhanced thermal stability of amorphous alumina with addition of Si is due to the formation of shorter and stronger Si–O bonds as compared to Al–O bonds.

  2. Peptides derivatized with bicyclic quaternary ammonium ionization tags. Sequencing via tandem mass spectrometry.

    Science.gov (United States)

    Setner, Bartosz; Rudowska, Magdalena; Klem, Ewelina; Cebrat, Marek; Szewczuk, Zbigniew

    2014-10-01

    Improving the sensitivity of detection and fragmentation of peptides to provide reliable sequencing of peptides is an important goal of mass spectrometric analysis. Peptides derivatized by bicyclic quaternary ammonium ionization tags: 1-azabicyclo[2.2.2]octane (ABCO) or 1,4-diazabicyclo[2.2.2]octane (DABCO), are characterized by an increased detection sensitivity in electrospray ionization mass spectrometry (ESI-MS) and longer retention times on the reverse-phase (RP) chromatography columns. The improvement of the detection limit was observed even for peptides dissolved in 10 mM NaCl. Collision-induced dissociation tandem mass spectrometry of quaternary ammonium salts derivatives of peptides showed dominant a- and b-type ions, allowing facile sequencing of peptides. The bicyclic ionization tags are stable in collision-induced dissociation experiments, and the resulted fragmentation pattern is not significantly influenced by either acidic or basic amino acid residues in the peptide sequence. Obtained results indicate the general usefulness of the bicyclic quaternary ammonium ionization tags for ESI-MS/MS sequencing of peptides. Copyright © 2014 John Wiley & Sons, Ltd.

  3. A new RF tagging pulse based on the Frank poly-phase perfect sequence

    DEFF Research Database (Denmark)

    Laustsen, Christoffer; Greferath, Marcus; Ringgaard, Steffen

    2014-01-01

    Radio frequency (RF) spectrally selective multiband pulses or tagging pulses, are applicable in a broad range of magnetic resonance methods. We demonstrate through simulations and experiments a new phase-modulation-only RF pulse for RF tagging based on the Frank poly-phase perfect sequence...

  4. Expressed sequence tags as a tool for phylogenetic analysis of placental mammal evolution.

    Directory of Open Access Journals (Sweden)

    Morgan Kullberg

    Full Text Available BACKGROUND: We investigate the usefulness of expressed sequence tags, ESTs, for establishing divergences within the tree of placental mammals. This is done on the example of the established relationships among primates (human, lagomorphs (rabbit, rodents (rat and mouse, artiodactyls (cow, carnivorans (dog and proboscideans (elephant. METHODOLOGY/PRINCIPAL FINDINGS: We have produced 2000 ESTs (1.2 mega bases from a marsupial mouse and characterized the data for their use in phylogenetic analysis. The sequences were used to identify putative orthologous sequences from whole genome projects. Although most ESTs stem from single sequence reads, the frequency of potential sequencing errors was found to be lower than allelic variation. Most of the sequences represented slowly evolving housekeeping-type genes, with an average amino acid distance of 6.6% between human and mouse. Positive Darwinian selection was identified at only a few single sites. Phylogenetic analyses of the EST data yielded trees that were consistent with those established from whole genome projects. CONCLUSIONS: The general quality of EST sequences and the general absence of positive selection in these sequences make ESTs an attractive tool for phylogenetic analysis. The EST approach allows, at reasonable costs, a fast extension of data sampling from species outside the genome projects.

  5. Thermal stability engineering of Glomerella cingulata cutinase.

    Science.gov (United States)

    Chin, Iuan-Sheau; Abdul Murad, Abdul Munir; Mahadi, Nor Muhammad; Nathan, Sheila; Abu Bakar, Farah Diba

    2013-05-01

    Cutinase has been ascertained as a biocatalyst for biotechnological and industrial bioprocesses. The Glomerella cingulata cutinase was genetically modified to enhance its enzymatic performance to fulfill industrial requirements. Two sites were selected for mutagenesis with the aim of altering the surface electrostatics as well as removing a potentially deamidation-prone asparagine residue. The N177D cutinase variant was affirmed to be more resilient to temperature increase with a 2.7-fold increase in half-life at 50°C as compared with wild-type enzyme, while, the activity at 25°C is not compromised. Furthermore, the increase in thermal tolerance of this variant is accompanied by an increase in optimal temperature. Another variant, the L172K, however, exhibited higher enzymatic performance towards phenyl ester substrates of longer carbon chain length, yet its thermal stability is inversely affected. In order to restore the thermal stability of L172K, we constructed a L172K/N177D double variant and showed that these two mutations yield an improved variant with enhanced activity towards phenyl ester substrates and enhanced thermal stability. Taken together, our study may provide valuable information for enhancing catalytic performance and thermal stability in future engineering endeavors.

  6. Dissecting the salt dependence of the Tus-Ter protein-DNA complexes by high-throughput differential scanning fluorimetry of a GFP-tagged Tus.

    Science.gov (United States)

    Moreau, Morgane J J; Schaeffer, Patrick M

    2013-12-01

    The analysis of the salt dependence of protein-DNA complexes provides useful information about the non-specific electrostatic and sequence-specific parameters driving complex formation and stability. The differential scanning fluorimetry of GFP-tagged protein (DSF-GTP) assay has been geared with an automatic Tm peak recognition system and was applied for the high-throughput (HT) determination of salt-induced effects on the GFP-tagged DNA replication protein Tus in complex with various Ter and Ter-lock sequences. The system was designed to generate two-dimensional heat map profiles of Tus-GFP protein stability allowing for a comparative study of the effect of eight increasing salt concentrations on ten different Ter DNA species at once. The data obtained with the new HT DSF-GTP allowed precise dissection of the non-specific electrostatic and sequence-specific parameters driving Tus-Ter and Tus-Ter-lock complex formation and stability. The major factor increasing the thermal resistance of Tus-Ter-lock complexes in high-salt is the formation of the TT-lock, e.g. a 10-fold higher Kspe was obtained for Tus-GFP:Ter-lockB than for Tus-GFP:TerB. It is anticipated that the system can be easily adapted for the study of other protein-DNA complexes.

  7. Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags

    Science.gov (United States)

    de Souza, Sandro J.; Camargo, Anamaria A.; Briones, Marcelo R. S.; Costa, Fernando F.; Nagai, Maria Aparecida; Verjovski-Almeida, Sergio; Zago, Marco A.; Andrade, Luis Eduardo C.; Carrer, Helaine; El-Dorry, Hamza F. A.; Espreafico, Enilza M.; Habr-Gama, Angelita; Giannella-Neto, Daniel; Goldman, Gustavo H.; Gruber, Arthur; Hackel, Christine; Kimura, Edna T.; Maciel, Rui M. B.; Marie, Suely K. N.; Martins, Elizabeth A. L.; Nóbrega, Marina P.; Paçó-Larson, Maria Luisa; Pardini, Maria Inês M. C.; Pereira, Gonçalo G.; Pesquero, João Bosco; Rodrigues, Vanderlei; Rogatto, Silvia R.; da Silva, Ismael D. C. G.; Sogayar, Mari C.; de Fátima Sonati, Maria; Tajara, Eloiza H.; Valentini, Sandro R.; Acencio, Marcio; Alberto, Fernando L.; Amaral, Maria Elisabete J.; Aneas, Ivy; Bengtson, Mário Henrique; Carraro, Dirce M.; Carvalho, Alex F.; Carvalho, Lúcia Helena; Cerutti, Janete M.; Corrêa, Maria Lucia C.; Costa, Maria Cristina R.; Curcio, Cyntia; Gushiken, Tsieko; Ho, Paulo L.; Kimura, Elza; Leite, Luciana C. C.; Maia, Gustavo; Majumder, Paromita; Marins, Mozart; Matsukuma, Adriana; Melo, Analy S. A.; Mestriner, Carlos Alberto; Miracca, Elisabete C.; Miranda, Daniela C.; Nascimento, Ana Lucia T. O.; Nóbrega, Francisco G.; Ojopi, Élida P. B.; Pandolfi, José Rodrigo C.; Pessoa, Luciana Gilbert; Rahal, Paula; Rainho, Claudia A.; da Ro's, Nancy; de Sá, Renata G.; Sales, Magaly M.; da Silva, Neusa P.; Silva, Tereza C.; da Silva, Wilson; Simão, Daniel F.; Sousa, Josane F.; Stecconi, Daniella; Tsukumo, Fernando; Valente, Valéria; Zalcberg, Heloisa; Brentani, Ricardo R.; Reis, Luis F. L.; Dias-Neto, Emmanuel; Simpson, Andrew J. G.

    2000-01-01

    Transcribed sequences in the human genome can be identified with confidence only by alignment with sequences derived from cDNAs synthesized from naturally occurring mRNAs. We constructed a set of 250,000 cDNAs that represent partial expressed gene sequences and that are biased toward the central coding regions of the resulting transcripts. They are termed ORF expressed sequence tags (ORESTES). The 250,000 ORESTES were assembled into 81,429 contigs. Of these, 1,181 (1.45%) were found to match sequences in chromosome 22 with at least one ORESTES contig for 162 (65.6%) of the 247 known genes, for 67 (44.6%) of the 150 related genes, and for 45 of the 148 (30.4%) EST-predicted genes on this chromosome. Using a set of stringent criteria to validate our sequences, we identified a further 219 previously unannotated transcribed sequences on chromosome 22. Of these, 171 were in fact also defined by EST or full length cDNA sequences available in GenBank but not utilized in the initial annotation of the first human chromosome sequence. Thus despite representing less than 15% of all expressed human sequences in the public databases at the time of the present analysis, ORESTES sequences defined 48 transcribed sequences on chromosome 22 not defined by other sequences. All of the transcribed sequences defined by ORESTES coincided with DNA regions predicted as encoding exons by genscan. (http://genes.mit.edu/GENSCAN.html). PMID:11070084

  8. Cloning and Expression of Ontak Immunotoxin Using Intein Tag

    Directory of Open Access Journals (Sweden)

    SA Moosavizadeh

    2016-06-01

    Full Text Available Introduction: Inteins (INT are internal parts of a number of proteins in yeast and some other unicellular eukaryotes, which can be separated from the immature protein during protein splicing process. After identifying the mechanism of intein action, applications of these sequences are be considered in the single- step purification of recombinant proteins and different intein tags were developed. The most important advantage of using intein tags in purification of recombinant proteins than other affinity tags is no requirement of expensive protease enzymes and following additional steps to remove protease that make intein tags economically are considered more important. In the present study, denileukin diftitox immunotoxin (brand name Ontak, be fused with an intein tag and it was inserted in pTXB1 plasmid. Methods: In this study, with respect to multiple cloning sites (MCS of pTXB1, specific primers were designed. Polymerase Chain Reaction (PCR was performed and encoding sequence of ONTAK was cloned using restriction sites of NdeI and SapI. Recombinant vector (PTX-IDZ was transformed into E. coli strain ER2566 and expression of gene was studied. Results: The accuracy of recombinant construct was confirmed by PCR and enzymatic digestion. The produced recombinant proteins were confirmed by SDS-PAGE and Western blotting. Conclusion: Restriction site of SapI guarantees no additional residues incorporate in primary protein sequence. Also, the expression of this construct was analyzed in compare with fused protein to poly-His tag. According to the appropriate expression of fused protein in both constructs it was expected that one step- purification of considered drug protein will be success in the following steps.

  9. 40 CFR 35.4040 - How many groups can receive a TAG at one Superfund site?

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 1 2010-07-01 2010-07-01 false How many groups can receive a TAG at one Superfund site? 35.4040 Section 35.4040 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Eligible? § 35.4040 How many groups can receive a TAG at one Superfund site? (a) Only one TAG may be...

  10. SEQUENCING OF FLAX LIS-1 INSERTION SITE IN THE ALBIDUM GENOTYPE

    Directory of Open Access Journals (Sweden)

    Jana Žiarovská

    2012-12-01

    Full Text Available The paper presents a methodology of identifying the insertion site of LIS-1-1 (Linum Insertion Sequence 1 element in flax Albidum variety when growing under the in vitro combined with environmental stress conditions. Abiotic stress was induced by a reduced nutrient content in a growth medium. The LIS-1 insertion site amplification was reaLIS-1ed using the forward LIS-L: 5'-GGG CAG TTT AAC TGT AAC GAA - 3 'and revers LIS-R: 5'-GCT TGG ATT TAG ACT TGG CAA C - 3' primers by PCR. PCR product was sequenced by direct sequencing method to proove the nucleotide sequence for matching with database LIS-1 sequence. A comparison has been matched with the sequence of the amplified segment in the database for all nucleotides except the 11-position in the 5'-3 ' direction, where instead of the three adenine pair is a couple in the Albidum variety. Changes caused by mobile elements or insertion sequences result in common flax in variability that can be used for the purposes of development of effective marker identification or environment based markers development.

  11. MR colonography with fecal tagging: comparison between 2D turbo FLASH and 3D FLASH sequences

    International Nuclear Information System (INIS)

    Papanikolaou, Nickolas; Grammatikakis, John; Maris, Thomas; Prassopoulos, Panos; Gourtsoyiannis, Nicholas; Lauenstein, Thomas

    2003-01-01

    The objective of this study was to compare inversion recovery turbo 2D fast low-angle shot (FLASH) and 3D FLASH sequences for fecal-tagged MR colonography studies. Fifteen consecutive patients with indications for colonoscopy underwent MR colonography with fecal tagging. An inversion recovery turbo-FLASH sequence was applied and compared in terms of artifacts presence, efficiency for masking residual stool, and colonic wall conspicuity with a fat-saturated 3D FLASH sequence. Both sequences were acquired following administration of paramagnetic contrast agent. Contrast-to-noise ratio and relative contrast between colonic wall and lumen were calculated and compared for both sequences. Turbo 2D FLASH provided fewer artifacts, higher efficiency for masking the residual stool, and colonic wall conspicuity equivalent to 3D FLASH. An inversion time of 10 ms provided homogeneously low signal intensity of the colonic lumen. Contrast to noise between colonic wall and lumen was significantly higher in the 3D FLASH images, whereas differences in relative contrast were not statistically significant. An optimized inversion-recovery 2D turbo-FLASH sequence provides better fecal tagging results and should be added to the 3D FLASH sequence when designing dark-lumen MR colonography examination protocols. (orig.)

  12. Improved i-motif thermal stability by insertion of anthraquinone monomers

    DEFF Research Database (Denmark)

    Gouda, Alaa S; Amine, Mahasen S.; Pedersen, Erik Bjerregaard

    2017-01-01

    In order to gain insight into how to improve thermal stability of i-motifs when used in the context of biomedical and nanotechnological applications, novel anthraquinone-modified i-motifs were synthesized by insertion of 1,8-, 1,4-, 1,5- and 2,6-disubstituted anthraquinone monomers into the TAA...... loops of a 22mer cytosine-rich human telomeric DNA sequence. The influence of the four anthraquinone linkers on the i-motif thermal stability was investigated at 295 nm and pH 5.5. Anthraquinone monomers modulate the i-motif stability in a position-depending manner and the modulation also depends...... unlocked nucleic acid monomers or twisted intercalating nucleic acid. The 2,6-disubstituted anthraquinone linker replacing T10 enabled a significant increase of i-motif thermal melting by 8.2 °C. A substantial increase of 5.0 °C in i-motif thermal melting was recorded when both A6 and T16 were modified...

  13. Genomic analysis of expressed sequence tags in American black bear Ursus americanus

    Science.gov (United States)

    2010-01-01

    Background Species of the bear family (Ursidae) are important organisms for research in molecular evolution, comparative physiology and conservation biology, but relatively little genetic sequence information is available for this group. Here we report the development and analyses of the first large scale Expressed Sequence Tag (EST) resource for the American black bear (Ursus americanus). Results Comprehensive analyses of molecular functions, alternative splicing, and tissue-specific expression of 38,757 black bear EST sequences were conducted using the dog genome as a reference. We identified 18 genes, involved in functions such as lipid catabolism, cell cycle, and vesicle-mediated transport, that are showing rapid evolution in the bear lineage Three genes, Phospholamban (PLN), cysteine glycine-rich protein 3 (CSRP3) and Troponin I type 3 (TNNI3), are related to heart contraction, and defects in these genes in humans lead to heart disease. Two genes, biphenyl hydrolase-like (BPHL) and CSRP3, contain positively selected sites in bear. Global analysis of evolution rates of hibernation-related genes in bear showed that they are largely conserved and slowly evolving genes, rather than novel and fast-evolving genes. Conclusion We provide a genomic resource for an important mammalian organism and our study sheds new light on the possible functions and evolution of bear genes. PMID:20338065

  14. Genomic analysis of expressed sequence tags in American black bear Ursus americanus.

    Science.gov (United States)

    Zhao, Sen; Shao, Chunxuan; Goropashnaya, Anna V; Stewart, Nathan C; Xu, Yichi; Tøien, Øivind; Barnes, Brian M; Fedorov, Vadim B; Yan, Jun

    2010-03-26

    Species of the bear family (Ursidae) are important organisms for research in molecular evolution, comparative physiology and conservation biology, but relatively little genetic sequence information is available for this group. Here we report the development and analyses of the first large scale Expressed Sequence Tag (EST) resource for the American black bear (Ursus americanus). Comprehensive analyses of molecular functions, alternative splicing, and tissue-specific expression of 38,757 black bear EST sequences were conducted using the dog genome as a reference. We identified 18 genes, involved in functions such as lipid catabolism, cell cycle, and vesicle-mediated transport, that are showing rapid evolution in the bear lineage Three genes, Phospholamban (PLN), cysteine glycine-rich protein 3 (CSRP3) and Troponin I type 3 (TNNI3), are related to heart contraction, and defects in these genes in humans lead to heart disease. Two genes, biphenyl hydrolase-like (BPHL) and CSRP3, contain positively selected sites in bear. Global analysis of evolution rates of hibernation-related genes in bear showed that they are largely conserved and slowly evolving genes, rather than novel and fast-evolving genes. We provide a genomic resource for an important mammalian organism and our study sheds new light on the possible functions and evolution of bear genes.

  15. Expressed sequence tag-derived microsatellite markers of perennial ryegrass (Lolium perenne L.)

    DEFF Research Database (Denmark)

    Studer, Bruno; Asp, Torben; Frei, Ursula

    2008-01-01

    An expressed sequence tag (EST) library of the key grassland species perennial ryegrass (Lolium perenne L.) has been exploited as a resource for microsatellite marker development. Out of 955 simple sequence repeat (SSR) containing ESTs, 744 were used for primer design. Primer amplification was te...

  16. CREST--classification resources for environmental sequence tags.

    Directory of Open Access Journals (Sweden)

    Anders Lanzén

    Full Text Available Sequencing of taxonomic or phylogenetic markers is becoming a fast and efficient method for studying environmental microbial communities. This has resulted in a steadily growing collection of marker sequences, most notably of the small-subunit (SSU ribosomal RNA gene, and an increased understanding of microbial phylogeny, diversity and community composition patterns. However, to utilize these large datasets together with new sequencing technologies, a reliable and flexible system for taxonomic classification is critical. We developed CREST (Classification Resources for Environmental Sequence Tags, a set of resources and tools for generating and utilizing custom taxonomies and reference datasets for classification of environmental sequences. CREST uses an alignment-based classification method with the lowest common ancestor algorithm. It also uses explicit rank similarity criteria to reduce false positives and identify novel taxa. We implemented this method in a web server, a command line tool and the graphical user interfaced program MEGAN. Further, we provide the SSU rRNA reference database and taxonomy SilvaMod, derived from the publicly available SILVA SSURef, for classification of sequences from bacteria, archaea and eukaryotes. Using cross-validation and environmental datasets, we compared the performance of CREST and SilvaMod to the RDP Classifier. We also utilized Greengenes as a reference database, both with CREST and the RDP Classifier. These analyses indicate that CREST performs better than alignment-free methods with higher recall rate (sensitivity as well as precision, and with the ability to accurately identify most sequences from novel taxa. Classification using SilvaMod performed better than with Greengenes, particularly when applied to environmental sequences. CREST is freely available under a GNU General Public License (v3 from http://apps.cbu.uib.no/crest and http://lcaclassifier.googlecode.com.

  17. Thermal stability of substitutional ag in CdTe

    NARCIS (Netherlands)

    Jahn, SG; Hofsass, H; Restle, M; Ronning, C; Quintel, H; BharuthRam, K; Wahl, U

    The thermal stability of substitutional Ag in CdTe was deduced from lattice location measurements at different temperatures. Substitutional Ag probe atoms were generated via transmutation doping from radioactive Cd isotopes. The lattice sites of Ag isotopes were determined by measuring the

  18. Dispersion stability of thermal nanofluids

    Directory of Open Access Journals (Sweden)

    Fan Yu

    2017-10-01

    Full Text Available Thermal nanofluids, the engineered fluids with dispersed functional nanoparticles, have exhibited extraordinary thermophysical properties and added functionalities, and thus have enabled a broad range of important applications. The poor dispersion stability of thermal nanofluids, however, has been considered as a long-existing issue that limits their further development and practical application. This review overviews the recent efforts and progresses in improving the dispersion stability of thermal nanofluids such as mechanistic understanding of dispersion behavior of nanofluids, examples of both water-based and oil-based nanofluids, strategies to stabilize nanofluids, and characterization techniques for dispersion behavior of nanofluids. Finally, on-going research needs, and possible solutions to research challenges and future research directions in exploring stably dispersed thermal nanofluids are discussed. Keywords: Thermal nanofluids, Dispersion, Aggregation, Electrostatic stabilization, Steric stabilization

  19. The feasibility of surgical site tagging with CT virtual reality of the paranasal sinuses.

    Science.gov (United States)

    Hopper, K D; Iyriboz, A T; Wise, S W; Fornadley, J A

    1999-01-01

    The purpose of this work was to evaluate the feasibility of tagging (highlighting) surgical sites using volumetric CT virtual reality of the paranasal sinuses in the planning for endoscopic sinus surgery. Twenty-five patients with significant paranasal sinus disease had a planned surgical site marked on 2D coronal images. This planned surgical site was then tagged and included on CT volumetric virtual reality imaging. Each case was evaluated as to the ability of the CT virtual reality to demonstrate the planned surgical site and its orientation with respect to adjacent superficial anatomy. For all 25 planned surgeries, the virtual images showed the entire surgical site marked on the 2D coronal images. In all 25 cases, the orientation of the planned surgical site to adjacent normal anatomy was well demonstrated. For surgery into the maxillary sinuses, tagging and electronic removal of the middle turbinates and uncinate processes mimicked the actual surgery and allowed complete visualization of the infundibulum and the planned surgical site. Planned endoscopic paranasal sinus surgical sites can be easily and reliably highlighted using CT virtual reality techniques with respect to the patient's normal endoscopic anatomy.

  20. Application of an E. coli signal sequence as a versatile inclusion body tag.

    Science.gov (United States)

    Jong, Wouter S P; Vikström, David; Houben, Diane; van den Berg van Saparoea, H Bart; de Gier, Jan-Willem; Luirink, Joen

    2017-03-21

    Heterologous protein production in Escherichia coli often suffers from bottlenecks such as proteolytic degradation, complex purification procedures and toxicity towards the expression host. Production of proteins in an insoluble form in inclusion bodies (IBs) can alleviate these problems. Unfortunately, the propensity of heterologous proteins to form IBs is variable and difficult to predict. Hence, fusing the target protein to an aggregation prone polypeptide or IB-tag is a useful strategy to produce difficult-to-express proteins in an insoluble form. When screening for signal sequences that mediate optimal targeting of heterologous proteins to the periplasmic space of E. coli, we observed that fusion to the 39 amino acid signal sequence of E. coli TorA (ssTorA) did not promote targeting but rather directed high-level expression of the human proteins hEGF, Pla2 and IL-3 in IBs. Further analysis revealed that ssTorA even mediated IB formation of the highly soluble endogenous E. coli proteins TrxA and MBP. The ssTorA also induced aggregation when fused to the C-terminus of target proteins and appeared functional as IB-tag in E. coli K-12 as well as B strains. An additive effect on IB-formation was observed upon fusion of multiple ssTorA sequences in tandem, provoking almost complete aggregation of TrxA and MBP. The ssTorA-moiety was successfully used to produce the intrinsically unstable hEGF and the toxic fusion partner SymE, demonstrating its applicability as an IB-tag for difficult-to-express and toxic proteins. We present proof-of-concept for the use of ssTorA as a small, versatile tag for robust E. coli-based expression of heterologous proteins in IBs.

  1. Tub-Tag Labeling; Chemoenzymatic Incorporation of Unnatural Amino Acids.

    Science.gov (United States)

    Helma, Jonas; Leonhardt, Heinrich; Hackenberger, Christian P R; Schumacher, Dominik

    2018-01-01

    Tub-tag labeling is a chemoenzymatic method that enables the site-specific labeling of proteins. Here, the natural enzyme tubulin tyrosine ligase incorporates noncanonical tyrosine derivatives to the terminal carboxylic acid of proteins containing a 14-amino acid recognition sequence called Tub-tag. The tyrosine derivative carries a unique chemical reporter allowing for a subsequent bioorthogonal modification of proteins with a great variety of probes. Here, we describe the Tub-tag protein modification protocol in detail and explain its utilization to generate labeled proteins for advanced applications in cell biology, imaging, and diagnostics.

  2. PASSIOMA: Exploring Expressed Sequence Tags during Flower Development in Passiflora spp.

    Directory of Open Access Journals (Sweden)

    Lucas Cutri

    2012-01-01

    Full Text Available The genus Passiflora provides a remarkable example of floral complexity and diversity. The extreme variation of Passiflora flower morphologies allowed a wide range of interactions with pollinators to evolve. We used the analysis of expressed sequence tags (ESTs as an approach for the characterization of genes expressed during Passiflora reproductive development. Analyzing the Passiflora floral EST database (named PASSIOMA, we found sequences showing significant sequence similarity to genes known to be involved in reproductive development such as MADS-box genes. Some of these sequences were studied using RT-PCR and in situ hybridization confirming their expression during Passiflora flower development. The detection of these novel sequences can contribute to the development of EST-based markers for important agronomic traits as well as to the establishment of genomic tools to study the naturally occurring floral diversity among Passiflora species.

  3. Quantum tagging for tags containing secret classical data

    International Nuclear Information System (INIS)

    Kent, Adrian

    2011-01-01

    Various authors have considered schemes for quantum tagging, that is, authenticating the classical location of a classical tagging device by sending and receiving quantum signals from suitably located distant sites, in an environment controlled by an adversary whose quantum information processing and transmitting power is potentially unbounded. All of the schemes proposed elsewhere in the literature assume that the adversary is able to inspect the interior of the tagging device. All of these schemes have been shown to be breakable if the adversary has unbounded predistributed entanglement. We consider here the case in which the tagging device contains a finite key string shared with distant sites but kept secret from the adversary, and show this allows the location of the tagging device to be authenticated securely and indefinitely. Our protocol relies on quantum key distribution between the tagging device and at least one distant site, and demonstrates a new practical application of quantum key distribution. It also illustrates that the attainable security in position-based cryptography can depend crucially on apparently subtle details in the security scenario considered.

  4. Thermal Stability of Rhodopsin and Progression of Retinitis Pigmentosa

    Science.gov (United States)

    Liu, Monica Yun; Liu, Jian; Mehrotra, Devi; Liu, Yuting; Guo, Ying; Baldera-Aguayo, Pedro A.; Mooney, Victoria L.; Nour, Adel M.; Yan, Elsa C. Y.

    2013-01-01

    Over 100 point mutations in the rhodopsin gene have been associated with retinitis pigmentosa (RP), a family of inherited visual disorders. Among these, we focused on characterizing the S186W mutation. We compared the thermal properties of the S186W mutant with another RP-causing mutant, D190N, and with WT rhodopsin. To assess thermal stability, we measured the rate of two thermal reactions contributing to the thermal decay of rhodopsin as follows: thermal isomerization of 11-cis-retinal and hydrolysis of the protonated Schiff base linkage between the 11-cis-retinal chromophore and opsin protein. We used UV-visible spectroscopy and HPLC to examine the kinetics of these reactions at 37 and 55 °C for WT and mutant rhodopsin purified from HEK293 cells. Compared with WT rhodopsin and the D190N mutant, the S186W mutation dramatically increases the rates of both thermal isomerization and dark state hydrolysis of the Schiff base by 1–2 orders of magnitude. The results suggest that the S186W mutant thermally destabilizes rhodopsin by disrupting a hydrogen bond network at the receptor's active site. The decrease in the thermal stability of dark state rhodopsin is likely to be associated with higher levels of dark noise that undermine the sensitivity of rhodopsin, potentially accounting for night blindness in the early stages of RP. Further studies of the thermal stability of additional pathogenic rhodopsin mutations in conjunction with clinical studies are expected to provide insight into the molecular mechanism of RP and test the correlation between rhodopsin's thermal stability and RP progression in patients. PMID:23625926

  5. Evaluation of early systolic flow pattern in left ventricle by tagging cine MRI in normal volunteers

    International Nuclear Information System (INIS)

    Sakakura, Kazuyoshi; Anno, Naoko; Kondo, Takeshi

    1992-01-01

    The tagging method is a new technique, which permits to apply discretionary lines (tags) on MR images. To evaluate intra left ventricular (LV) flow pattern, we performed ECG-gated gradient field echo cine MRI using tagging method in five normal male volunteers, aged 22-42 years. The horizontal long axis view of LV was imaged by multiphasic field echo pulse sequence. The three parallel tags (basal, middle and apical portion) were established on the horizontal long axis view of LV just after the triggered QRS waves. And the initial two images (70 ms and 120 ms after the triggered QRS waves) were analyzed. On the two tags (middle and apical portion) of these three tags, we measured the distance of displacement of the tags on three points (the near site of IVS, middle portion and the near site of free wall) respectively. At 70 ms after the trigger point, the only tagged blood at the near site of free wall flowed toward the apex. At 120 ms after the trigger point, all the tagged blood flowed toward the outflow tract of LV. And the maximum blood flow velocity was observed at the near site of IVS on middle portion of LV (166.0 mm/s). These results coincided with earlier studies by Doppler echocardiography. But we could not observe intra LV blood flow patterns throughout one cardiac cycle in this pulse sequence, because the tags had flowed out from LV and had become unclear due to spin relaxation and mixing. We concluded that the tagging method was useful to evaluate intra left ventricular blood flow patterns in early systolic phase. (author)

  6. Experimental and numerical study of the stability of phyllosilicates in a strong thermal gradient. Test in the geothermal site of Soultz-sous-Forets

    International Nuclear Information System (INIS)

    Baldeyrou-Bailly, A.

    2003-01-01

    Thermodynamic data of hydrated phyllosilicates, in particular clay minerals are not well known. The stability fields of these minerals are not well determined; following some authors they even do not exist. We have developed an experimental approach, in which a sequence of local equilibrium states between a fluid and minerals take place in a closed gold cell along a strong thermal gradient. The experiments were conducted in the chemical systems: Mg-Al-Si-H 2 O (MASH), K-Al-Si-H 2 O (KASH), and K-Mg-Al-Si-H 2 O (KMASH). The sequences of crystallization observed along the thermal gradient are the same if one exchanges the position of the cells containing the initial reacting materials with respect to the thermal gradient end-members. The crystallization sequences correspond to local equilibrium states. Following the temperature increase (from 200 to 350 C) one observes the following sequences: di-octahedral smectite? tri-octahedral smectite; kaolinite? donbassite? tri-octahedral chlorite; smectite? illite? muscovite; or even kaolinite? illite + smectite? donbassite; commonly observed in hydrothermal systems. They allow to develop a thermodynamic model for hydrated phyllosilicates, taking into account their hydration state as a function of temperature. This model shows the stability fields of clay minerals between 200 and 350 C.The chemical and mineralogical dynamics showed in these experimental systems has been applied to predict the possible dissolutions and/or precipitations which may take place between the circulated hot fluid and the geothermal granitic reservoir in the geothermal system at Soultz-sous-Forets. These processes may affect the duration of the geothermal reservoir, as a function of evolution in the morphology of the porosity. Our experimental approach shows that feldspars and smectites are forming the major part of the total volume of silicates which may precipitate in addition to carbonates already described in previous studies. (author)

  7. An expressed sequence tag (EST) data mining strategy succeeding in the discovery of new G-protein coupled receptors.

    Science.gov (United States)

    Wittenberger, T; Schaller, H C; Hellebrand, S

    2001-03-30

    We have developed a comprehensive expressed sequence tag database search method and used it for the identification of new members of the G-protein coupled receptor superfamily. Our approach proved to be especially useful for the detection of expressed sequence tag sequences that do not encode conserved parts of a protein, making it an ideal tool for the identification of members of divergent protein families or of protein parts without conserved domain structures in the expressed sequence tag database. At least 14 of the expressed sequence tags found with this strategy are promising candidates for new putative G-protein coupled receptors. Here, we describe the sequence and expression analysis of five new members of this receptor superfamily, namely GPR84, GPR86, GPR87, GPR90 and GPR91. We also studied the genomic structure and chromosomal localization of the respective genes applying in silico methods. A cluster of six closely related G-protein coupled receptors was found on the human chromosome 3q24-3q25. It consists of four orphan receptors (GPR86, GPR87, GPR91, and H963), the purinergic receptor P2Y1, and the uridine 5'-diphosphoglucose receptor KIAA0001. It seems likely that these receptors evolved from a common ancestor and therefore might have related ligands. In conclusion, we describe a data mining procedure that proved to be useful for the identification and first characterization of new genes and is well applicable for other gene families. Copyright 2001 Academic Press.

  8. Movement patterns of juvenile whale sharks tagged at an aggregation site in the Red Sea.

    Directory of Open Access Journals (Sweden)

    Michael L Berumen

    Full Text Available Conservation efforts aimed at the whale shark, Rhincodon typus, remain limited by a lack of basic information on most aspects of its ecology, including global population structure, population sizes and movement patterns. Here we report on the movements of 47 Red Sea whale sharks fitted with three types of satellite transmitting tags from 2009-2011. Most of these sharks were tagged at a single aggregation site near Al-Lith, on the central coast of the Saudi Arabian Red Sea. Individuals encountered at this site were all juveniles based on size estimates ranging from 2.5-7 m total length with a sex ratio of approximately 1∶1. All other known aggregation sites for juvenile whale sharks are dominated by males. Results from tagging efforts showed that most individuals remained in the southern Red Sea and that some sharks returned to the same location in subsequent years. Diving data were recorded by 37 tags, revealing frequent deep dives to at least 500 m and as deep as 1360 m. The unique temperature-depth profiles of the Red Sea confirmed that several whale sharks moved out of the Red Sea while tagged. The wide-ranging horizontal movements of these individuals highlight the need for multinational, cooperative efforts to conserve R. typus populations in the Red Sea and Indian Ocean.

  9. Movement patterns of juvenile whale sharks tagged at an aggregation site in the Red Sea.

    Science.gov (United States)

    Berumen, Michael L; Braun, Camrin D; Cochran, Jesse E M; Skomal, Gregory B; Thorrold, Simon R

    2014-01-01

    Conservation efforts aimed at the whale shark, Rhincodon typus, remain limited by a lack of basic information on most aspects of its ecology, including global population structure, population sizes and movement patterns. Here we report on the movements of 47 Red Sea whale sharks fitted with three types of satellite transmitting tags from 2009-2011. Most of these sharks were tagged at a single aggregation site near Al-Lith, on the central coast of the Saudi Arabian Red Sea. Individuals encountered at this site were all juveniles based on size estimates ranging from 2.5-7 m total length with a sex ratio of approximately 1∶1. All other known aggregation sites for juvenile whale sharks are dominated by males. Results from tagging efforts showed that most individuals remained in the southern Red Sea and that some sharks returned to the same location in subsequent years. Diving data were recorded by 37 tags, revealing frequent deep dives to at least 500 m and as deep as 1360 m. The unique temperature-depth profiles of the Red Sea confirmed that several whale sharks moved out of the Red Sea while tagged. The wide-ranging horizontal movements of these individuals highlight the need for multinational, cooperative efforts to conserve R. typus populations in the Red Sea and Indian Ocean.

  10. Movement patterns of juvenile whale sharks tagged at an aggregation site in the Red Sea

    KAUST Repository

    Berumen, Michael L.

    2014-07-30

    Conservation efforts aimed at the whale shark, Rhincodon typus, remain limited by a lack of basic information on most aspects of its ecology, including global population structure, population sizes and movement patterns. Here we report on the movements of 47 Red Sea whale sharks fitted with three types of satellite transmitting tags from 2009-2011. Most of these sharks were tagged at a single aggregation site near Al-Lith, on the central coast of the Saudi Arabian Red Sea. Individuals encountered at this site were all juveniles based on size estimates ranging from 2.5-7 m total length with a sex ratio of approximately 1:1. All other known aggregation sites for juvenile whale sharks are dominated by males. Results from tagging efforts showed that most individuals remained in the southern Red Sea and that some sharks returned to the same location in subsequent years. Diving data were recorded by 37 tags, revealing frequent deep dives to at least 500 m and as deep as 1360 m. The unique temperature-depth profiles of the Red Sea confirmed that several whale sharks moved out of the Red Sea while tagged. The wide-ranging horizontal movements of these individuals highlight the need for multinational, cooperative efforts to conserve R. typus populations in the Red Sea and Indian Ocean. © 2014 Berumen et al.

  11. Tags in Domain-Specific Sites - New Information?

    DEFF Research Database (Denmark)

    Steinhauer, Jeremy; Delcambre, Lois M.L.; Maier, David

    2011-01-01

    If researchers use tags in retrieval applications they might assume, implicitly, that tags represent novel information, e.g., when they attribute performance improvement in their retrieval algorithm(s) to the use of tags. In this work, we investigate whether this assumption is true. We focus on t...

  12. Modeling ChIP sequencing in silico with applications.

    Directory of Open Access Journals (Sweden)

    Zhengdong D Zhang

    2008-08-01

    Full Text Available ChIP sequencing (ChIP-seq is a new method for genomewide mapping of protein binding sites on DNA. It has generated much excitement in functional genomics. To score data and determine adequate sequencing depth, both the genomic background and the binding sites must be properly modeled. To develop a computational foundation to tackle these issues, we first performed a study to characterize the observed statistical nature of this new type of high-throughput data. By linking sequence tags into clusters, we show that there are two components to the distribution of tag counts observed in a number of recent experiments: an initial power-law distribution and a subsequent long right tail. Then we develop in silico ChIP-seq, a computational method to simulate the experimental outcome by placing tags onto the genome according to particular assumed distributions for the actual binding sites and for the background genomic sequence. In contrast to current assumptions, our results show that both the background and the binding sites need to have a markedly nonuniform distribution in order to correctly model the observed ChIP-seq data, with, for instance, the background tag counts modeled by a gamma distribution. On the basis of these results, we extend an existing scoring approach by using a more realistic genomic-background model. This enables us to identify transcription-factor binding sites in ChIP-seq data in a statistically rigorous fashion.

  13. The Biotechnological Applications of Recombinant Single-Domain Antibodies are Optimized by the C-Terminal Fusion to the EPEA Sequence (C Tag

    Directory of Open Access Journals (Sweden)

    Selma Djender

    2014-04-01

    Full Text Available We designed a vector for the bacterial expression of recombinant antibodies fused to a double tag composed of 6xHis and the EPEA amino acid sequence. EPEA sequence (C tag is tightly bound by a commercial antibody when expressed at the C-term end of a polypeptide. The antigen is released in the presence of 2 M MgCl2. Consequently, constructs fused to the 6xHis-C tags can be purified by two successive and orthogonal affinity steps. Single-domain antibodies were produced either in the periplasmic or in the cytoplasmic space of E. coli. Surprisingly, the first affinity purification step performed using the EPEA-binding resin already yielded homogeneous proteins. The presence of the C tag did not interfere with the binding activity of the antibodies, as assessed by FACS and SPR analyses, and the C tag was extremely effective for immunoprecipitating HER2 receptor. Finally, the Alexa488-coupled anti-C tag allowed for simplification of FACS and IF analyses. These results show that a tag of minimal dimensions can be effectively used to improve the applicability of recombinant antibodies as reagents. In our hands, C tag was superior to His-tag in affinity purification and pull-down experiments, and practical in any other standard immune technique.

  14. Development of expressed sequence tag-simple sequence repeat markers for genetic characterization and population structure analysis of Praxelis clematidea (Asteraceae).

    Science.gov (United States)

    Wang, Q Z; Huang, M; Downie, S R; Chen, Z X

    2016-05-23

    Invasive plants tend to spread aggressively in new habitats and an understanding of their genetic diversity and population structure is useful for their management. In this study, expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed for the invasive plant species Praxelis clematidea (Asteraceae) from 5548 Stevia rebaudiana (Asteraceae) expressed sequence tags (ESTs). A total of 133 microsatellite-containing ESTs (2.4%) were identified, of which 56 (42.1%) were hexanucleotide repeat motifs and 50 (37.6%) were trinucleotide repeat motifs. Of the 24 primer pairs designed from these 133 ESTs, 7 (29.2%) resulted in significant polymorphisms. The number of alleles per locus ranged from 5 to 9. The relatively high genetic diversity (H = 0.2667, I = 0.4212, and P = 100%) of P. clematidea was related to high gene flow (Nm = 1.4996) among populations. The coefficient of population differentiation (GST = 0.2500) indicated that most genetic variation occurred within populations. A Mantel test suggested that there was significant correlation between genetic distance and geographical distribution (r = 0.3192, P = 0.012). These results further support the transferability of EST-SSR markers between closely related genera of the same family.

  15. Stability-class determination: a comparison for one site

    International Nuclear Information System (INIS)

    Bowen, B.M.; Dewart, J.M.; Chen, A.I.

    1983-01-01

    The Pasquill method of determining stability class at a site with irregular terrain with other commonly used methods: vertical temperature difference (#betta#T); Richardson number (Ri) and Bulk Richardson number (Ri/sub B/); and horizontal standard deviation of wind and vertical standard deviation of wind. Also, the indirect methods of measuring turbulence, such as the Pasquill method, are compared to direct measures of turbulence. The various methods for determining stability class are analyzed and compared with the Pasquill classification scheme at 2 sites with irregular terrain. The Pasquill categories were estimated objectively and compared with other stability indicators for 15-minute periods over a year. The results show that near-surface #betta#T distinguishes the neutral category very well. However, it does not differentiate the specific stable and unstable categories very well. Both the Ri and Ri/sub B/, indicators of both thermal and mechanical turbulence, correlate very well with and distinguish the different stability categories. Due to the irregular terrain, the various methods of determining stability may be even better indicators of turbulence and diffusion if the wind direction were taken into account. It is suggested that further study investigate the methods by wind direction

  16. Analysis of expressed sequence tags from Prunus mume flower and fruit and development of simple sequence repeat markers

    Directory of Open Access Journals (Sweden)

    Gao Zhihong

    2010-07-01

    Full Text Available Abstract Background Expressed Sequence Tag (EST has been a cost-effective tool in molecular biology and represents an abundant valuable resource for genome annotation, gene expression, and comparative genomics in plants. Results In this study, we constructed a cDNA library of Prunus mume flower and fruit, sequenced 10,123 clones of the library, and obtained 8,656 expressed sequence tag (EST sequences with high quality. The ESTs were assembled into 4,473 unigenes composed of 1,492 contigs and 2,981 singletons and that have been deposited in NCBI (accession IDs: GW868575 - GW873047, among which 1,294 unique ESTs were with known or putative functions. Furthermore, we found 1,233 putative simple sequence repeats (SSRs in the P. mume unigene dataset. We randomly tested 42 pairs of PCR primers flanking potential SSRs, and 14 pairs were identified as true-to-type SSR loci and could amplify polymorphic bands from 20 individual plants of P. mume. We further used the 14 EST-SSR primer pairs to test the transferability on peach and plum. The result showed that nearly 89% of the primer pairs produced target PCR bands in the two species. A high level of marker polymorphism was observed in the plum species (65% and low in the peach (46%, and the clustering analysis of the three species indicated that these SSR markers were useful in the evaluation of genetic relationships and diversity between and within the Prunus species. Conclusions We have constructed the first cDNA library of P. mume flower and fruit, and our data provide sets of molecular biology resources for P. mume and other Prunus species. These resources will be useful for further study such as genome annotation, new gene discovery, gene functional analysis, molecular breeding, evolution and comparative genomics between Prunus species.

  17. Chemical and thermal stability of insulin

    DEFF Research Database (Denmark)

    Huus, Kasper; Havelund, Svend; Olsen, Helle B

    2006-01-01

    To study the correlation between the thermal and chemical stability of insulin formulations with various insulin hexamer ligands.......To study the correlation between the thermal and chemical stability of insulin formulations with various insulin hexamer ligands....

  18. The role of glycosylation and domain interactions in the thermal stability of human angiotensin-converting enzyme.

    Science.gov (United States)

    O'Neill, Hester G; Redelinghuys, Pierre; Schwager, Sylva L U; Sturrock, Edward D

    2008-09-01

    The N and C domains of somatic angiotensin-converting enzyme (sACE) differ in terms of their substrate specificity, inhibitor profiling, chloride dependency and thermal stability. The C domain is thermally less stable than sACE or the N domain. Since both domains are heavily glycosylated, the effect of glycosylation on their thermal stability was investigated by assessing their catalytic and physicochemical properties. Testis ACE (tACE) expressed in mammalian cells, mammalian cells in the presence of a glucosidase inhibitor and insect cells yielded proteins with altered catalytic and physicochemical properties, indicating that the more complex glycans confer greater thermal stabilization. Furthermore, a decrease in tACE and N-domain N-glycans using site-directed mutagenesis decreased their thermal stability, suggesting that certain N-glycans have an important effect on the protein's thermodynamic properties. Evaluation of the thermal stability of sACE domain swopover and domain duplication mutants, together with sACE expressed in insect cells, showed that the C domain contained in sACE is less dependent on glycosylation for thermal stabilization than a single C domain, indicating that stabilizing interactions between the two domains contribute to the thermal stability of sACE and are decreased in a C-domain-duplicating mutant.

  19. Expressed sequence tags from heat-shocked seagrass Zostera noltii (Hornemann) from its southern distribution range

    NARCIS (Netherlands)

    Massa, Sonia I.; Pearson, Gareth A.; Aires, Tania; Kube, Michael; Olsen, Jeanine L.; Reinhardt, Richard; Serrao, Ester A.; Arnaud-Haond, Sophie

    Predicted global climate change threatens the distributional ranges of species worldwide. We identified genes expressed in the intertidal seagrass Zostera midi during recovery from a simulated low tide heat-shock exposure. Five Expressed Sequence Tag (EST) libraries were compared, corresponding to

  20. Monitoring System for Slope Stability under Rainfall by using MEMS Acceleration Sensor IC tags

    International Nuclear Information System (INIS)

    Murakami, S; Dairaku, A; Komine, H; Saito, O; Sakai, N; Isizawa, T; Maruyama, I

    2013-01-01

    Real-time warning system for slope failure under rainfall is available to disaster prevention and mitigation. Monitoring of multi-point and wireless measurements is effective because it is difficult to conclude the most dangerous part in a slope. The purpose of this study is to propose a method of monitoring system with multi-point and wireless measurements for a slope stability using MEMS acceleration sensor IC tags. MEMS acceleration sensor IC tag is an acceleration sensor microminiaturized by a technology of Micro Electro Mechanical Systems on board IC tag. Especially, low cost of the sensor will yield to the realization of the system. In order to investigate the applicability of the proposed system, a large-scale model test of artificial slope subjected to rainfall has been performed. MEMS acceleration sensor IC tags has been located on the slope and ground acceleration caused by forced vibration has been measured until the model slope collapses. The experimental results show that the MEMS acceleration sensor IC tag is comfortably available under rainfall, the characteristics of ground accelerations varies with changing the condition of the slope subjected to rainfall, and the proposed method can be applied to a real-time monitoring system for slope failure under rainfall.

  1. trieFinder: an efficient program for annotating Digital Gene Expression (DGE) tags.

    Science.gov (United States)

    Renaud, Gabriel; LaFave, Matthew C; Liang, Jin; Wolfsberg, Tyra G; Burgess, Shawn M

    2014-10-13

    Quantification of a transcriptional profile is a useful way to evaluate the activity of a cell at a given point in time. Although RNA-Seq has revolutionized transcriptional profiling, the costs of RNA-Seq are still significantly higher than microarrays, and often the depth of data delivered from RNA-Seq is in excess of what is needed for simple transcript quantification. Digital Gene Expression (DGE) is a cost-effective, sequence-based approach for simple transcript quantification: by sequencing one read per molecule of RNA, this technique can be used to efficiently count transcripts while obviating the need for transcript-length normalization and reducing the total numbers of reads necessary for accurate quantification. Here, we present trieFinder, a program specifically designed to rapidly map, parse, and annotate DGE tags of various lengths against cDNA and/or genomic sequence databases. The trieFinder algorithm maps DGE tags in a two-step process. First, it scans FASTA files of RefSeq, UniGene, and genomic DNA sequences to create a database of all tags that can be derived from a predefined restriction site. Next, it compares the experimental DGE tags to this tag database, taking advantage of the fact that the tags are stored as a prefix tree, or "trie", which allows for linear-time searches for exact matches. DGE tags with mismatches are analyzed by recursive calls in the data structure. We find that, in terms of alignment speed, the mapping functionality of trieFinder compares favorably with Bowtie. trieFinder can quickly provide the user an annotation of the DGE tags from three sources simultaneously, simplifying transcript quantification and novel transcript detection, delivering the data in a simple parsed format, obviating the need to post-process the alignment results. trieFinder is available at http://research.nhgri.nih.gov/software/trieFinder/.

  2. Thermal stabilization of uranium mill tailings

    International Nuclear Information System (INIS)

    Dreesen, D.R.; Williams, J.M.; Cokal, E.J.

    1981-01-01

    The sintering of tailings at high temperatures (1200 0 C) has shown promise as a conditioning approach that greatly reduces the 222 Rn emanation of uranium mill tailings. The structure of thermally stabilized tailings has been appreciably altered producing a material that will have minimal management requirements and will be applicable to on-site processing and disposal. The mineralogy of untreated tailings is presented to define the structure of the original materials. Quartz predominates in most tailings samples; however, appreciable quantities of gypsum, clay, illite, or albites are found in some tailings. Samples from the Durango and Shiprock sites have plagioclase-type aluminosilicates and non-aluminum silicates as major components. The iron-rich vanadium tailings from the Salt Lake City site contain appreciable quantities of α-hematite and chloroapatite. The reduction in radon emanation power and changes in mineralogy as a function of sintering temperature are presented

  3. Citrus plastid-related gene profiling based on expressed sequence tag analyses

    Directory of Open Access Journals (Sweden)

    Tercilio Calsa Jr.

    2007-01-01

    Full Text Available Plastid-related sequences, derived from putative nuclear or plastome genes, were searched in a large collection of expressed sequence tags (ESTs and genomic sequences from the Citrus Biotechnology initiative in Brazil. The identified putative Citrus chloroplast gene sequences were compared to those from Arabidopsis, Eucalyptus and Pinus. Differential expression profiling for plastid-directed nuclear-encoded proteins and photosynthesis-related gene expression variation between Citrus sinensis and Citrus reticulata, when inoculated or not with Xylella fastidiosa, were also analyzed. Presumed Citrus plastome regions were more similar to Eucalyptus. Some putative genes appeared to be preferentially expressed in vegetative tissues (leaves and bark or in reproductive organs (flowers and fruits. Genes preferentially expressed in fruit and flower may be associated with hypothetical physiological functions. Expression pattern clustering analysis suggested that photosynthesis- and carbon fixation-related genes appeared to be up- or down-regulated in a resistant or susceptible Citrus species after Xylella inoculation in comparison to non-infected controls, generating novel information which may be helpful to develop novel genetic manipulation strategies to control Citrus variegated chlorosis (CVC.

  4. Site-Specific, Covalent Immobilization of Dehalogenase ST2570 Catalyzed by Formylglycine-Generating Enzymes and Its Application in Batch and Semi-Continuous Flow Reactors

    Directory of Open Access Journals (Sweden)

    Hui Jian

    2016-07-01

    Full Text Available Formylglycine-generating enzymes can selectively recognize and oxidize cysteine residues within the sulfatase sub motif at the terminus of proteins to form aldehyde-bearing formylglycine (FGly residues, and are normally used in protein labeling. In this study, an aldehyde tag was introduced to proteins using formylglycine-generating enzymes encoded by a reconstructed set of the pET28a plasmid system for enzyme immobilization. The haloacid dehalogenase ST2570 from Sulfolobus tokodaii was used as a model enzyme. The C-terminal aldehyde-tagged ST2570 (ST2570CQ exhibited significant enzymological properties, such as new free aldehyde groups, a high level of protein expression and improved enzyme activity. SBA-15 has widely been used as an immobilization support for its large surface and excellent thermal and chemical stability. It was functionalized with amino groups by aminopropyltriethoxysilane. The C-terminal aldehyde-tagged ST2570 was immobilized to SBA-15 by covalent binding. The site-specific immobilization of ST2570 avoided the chemical denaturation that occurs in general covalent immobilization and resulted in better fastening compared to physical adsorption. The site-specific immobilized ST2570 showed 3-fold higher thermal stability, 1.2-fold higher catalytic ability and improved operational stability than free ST2570. The site-specific immobilized ST2570 retained 60% of its original activity after seven cycles of batch operation, and it was superior to the ST2570 immobilized to SBA-15 by physical adsorption, which loses 40% of its original activity when used for the second time. It is remarkable that the site-specific immobilized ST2570 still retained 100% of its original activity after 10 cycles of reuse in the semi-continuous flow reactor. Overall, these results provide support for the industrial-scale production and application of site-specific, covalently immobilized ST2570.

  5. Conformation and stability of intramolecular telomeric G-quadruplexes: sequence effects in the loops.

    Directory of Open Access Journals (Sweden)

    Giovanna Sattin

    Full Text Available Telomeres are guanine-rich sequences that protect the ends of chromosomes. These regions can fold into G-quadruplex structures and their stabilization by G-quadruplex ligands has been employed as an anticancer strategy. Genetic analysis in human telomeres revealed extensive allelic variation restricted to loop bases, indicating that the variant telomeric sequences maintain the ability to fold into G-quadruplex. To assess the effect of mutations in loop bases on G-quadruplex folding and stability, we performed a comprehensive analysis of mutant telomeric sequences by spectroscopic techniques, molecular dynamics simulations and gel electrophoresis. We found that when the first position in the loop was mutated from T to C or A the resulting structure adopted a less stable antiparallel topology; when the second position was mutated to C or A, lower thermal stability and no evident conformational change were observed; in contrast, substitution of the third position from A to C induced a more stable and original hybrid conformation, while mutation to T did not significantly affect G-quadruplex topology and stability. Our results indicate that allelic variations generate G-quadruplex telomeric structures with variable conformation and stability. This aspect needs to be taken into account when designing new potential anticancer molecules.

  6. Parallel Sequencing of Expressed Sequence Tags from Two Complementary DNA Libraries for High and Low Phosphorus Adaptation in Common Beans

    Directory of Open Access Journals (Sweden)

    Matthew W. Blair

    2011-11-01

    Full Text Available Expressed sequence tags (ESTs have proven useful for gene discovery in many crops. In this work, our objective was to construct complementary DNA (cDNA libraries from root tissues of common beans ( L. grown under low and high P hydroponic conditions and to conduct EST sequencing and comparative analyses of the libraries. Expressed sequence tag analysis of 3648 clones identified 2372 unigenes, of which 1591 were annotated as known genes while a total of 465 unigenes were not associated with any known gene. Unigenes with hits were categorized according to biological processes, molecular function, and cellular compartmentalization. Given the young tissue used to make the root libraries, genes for catalytic activity and binding were highly expressed. Comparisons with previous root EST sequencing and between the two libraries made here resulted in a set of genes to study further for differential gene expression and adaptation to low P, such as a 14 kDa praline-rich protein, a metallopeptidase, tonoplast intrinsic protein, adenosine triphosphate (ATP citrate synthase, and cell proliferation genes expressed in the low P treated plants. Given that common beans are often grown on acid soils of the tropics and subtropics that are usually low in P these genes and the two parallel libraries will be useful for selection for better uptake of this essential macronutrient. The importance of EST generation for common bean root tissues under low P and other abiotic soil stresses is also discussed.

  7. System design description PFP thermal stabilization

    International Nuclear Information System (INIS)

    RISENMAY, H.R.

    1998-01-01

    The purpose of this document is to provide a system design description and design basis for the Plutonium Finishing P1ant (PFP) Thermal Stabilization project. The sources of material for this project are residues scraped from glovebox floors and materials already stored in vault storage that need further stabilizing to meet the 3013 storage requirements. Stabilizing this material will promote long term storage and reduced worker exposure. This document addresses: function design, equipment, and safety requirements for thermal stabilization of plutonium residues and oxides

  8. SSH analysis of endosperm transcripts and characterization of heat stress regulated expressed sequence tags in bread wheat

    Directory of Open Access Journals (Sweden)

    Suneha Goswami

    2016-08-01

    Full Text Available Heat stress is one of the major problems in agriculturally important cereal crops, especially wheat. Here, we have constructed a subtracted cDNA library from the endosperm of HS-treated (42°C for 2 h wheat cv. HD2985 by suppression subtractive hybridization (SSH. We identified ~550 recombinant clones ranging from 200 to 500 bp with an average size of 300 bp. Sanger’s sequencing was performed with 205 positive clones to generate the differentially expressed sequence tags (ESTs. Most of the ESTs were observed to be localized on the long arm of chromosome 2A and associated with heat stress tolerance and metabolic pathways. Identified ESTs were BLAST search using Ensemble, TriFLD and TIGR databases and the predicted CDS were translated and aligned with the protein sequences available in pfam and InterProScan 5 databases to predict the differentially expressed proteins (DEPs. We observed eight different types of post-translational modifications (PTMs in the DEPs corresponds to the cloned ESTs—147 sites with phosphorylation, 21 sites with sumoylation, 237 with palmitoylation, 96 sites with S-nitrosylation, 3066 calpain cleavage sites, and 103 tyrosine nitration sites, predicted to sense the heat stress and regulate the expression of stress genes. Twelve DEPs were observed to have transmembrane helixes (TMH in their structure, predicted to play the role of sensors of HS. Quantitative Real-Time PCR of randomly selected ESTs showed very high relative expression of HSP17 under HS; up-regulation was observed more in wheat cv. HD2985 (thermotolerant, as compared to HD2329 (thermosusceptible during grain-filling. The abundance of transcripts was further validated through northern blot analysis. The ESTs and their corresponding DEPs can be used as molecular marker for screening or targeted precision breeding program. PTMs identified in the DEPs can be used to elucidate the thermotolerance mechanism of wheat – a novel step towards the development of

  9. Survey of transposable elements in sugarcane expressed sequence tags (ESTs

    Directory of Open Access Journals (Sweden)

    Rossi Magdalena

    2001-01-01

    Full Text Available The sugarcane expressed sequence tag (SUCEST project has produced a large number of cDNA sequences from several plant tissues submitted or not to different conditions of stress. In this paper we report the result of a search for transposable elements (TEs revealing a surprising amount of expressed TEs homologues. Of the 260,781 sequences grouped in 81,223 fragment assembly program (Phrap clusters, a total of 276 clones showed homology to previously reported TEs using a stringent cut-off value of e-50 or better. Homologous clones to Copia/Ty1 and Gypsy/Ty3 groups of long terminal repeat (LTR retrotransposons were found but no non-LTR retroelements were identified. All major transposon families were represented in sugarcane including Activator (Ac, Mutator (MuDR, Suppressor-mutator (En/Spm and Mariner. In order to compare the TE diversity in grasses genomes, we carried out a search for TEs described in sugarcane related species O.sativa, Z. mays and S. bicolor. We also present preliminary results showing the potential use of TEs insertion pattern polymorphism as molecular markers for cultivar identification.

  10. Improving the thermal stability of cellobiohydrolase Cel7A from Hypocrea jecorina by directed evolution.

    Science.gov (United States)

    Goedegebuur, Frits; Dankmeyer, Lydia; Gualfetti, Peter; Karkehabadi, Saeid; Hansson, Henrik; Jana, Suvamay; Huynh, Vicky; Kelemen, Bradley R; Kruithof, Paulien; Larenas, Edmund A; Teunissen, Pauline J M; Ståhlberg, Jerry; Payne, Christina M; Mitchinson, Colin; Sandgren, Mats

    2017-10-20

    Secreted mixtures of Hypocrea jecorina cellulases are able to efficiently degrade cellulosic biomass to fermentable sugars at large, commercially relevant scales. H. jecorina Cel7A, cellobiohydrolase I, from glycoside hydrolase family 7, is the workhorse enzyme of the process. However, the thermal stability of Cel7A limits its use to processes where temperatures are no higher than 50 °C. Enhanced thermal stability is desirable to enable the use of higher processing temperatures and to improve the economic feasibility of industrial biomass conversion. Here, we enhanced the thermal stability of Cel7A through directed evolution. Sites with increased thermal stability properties were combined, and a Cel7A variant (FCA398) was obtained, which exhibited a 10.4 °C increase in T m and a 44-fold greater half-life compared with the wild-type enzyme. This Cel7A variant contains 18 mutated sites and is active under application conditions up to at least 75 °C. The X-ray crystal structure of the catalytic domain was determined at 2.1 Å resolution and showed that the effects of the mutations are local and do not introduce major backbone conformational changes. Molecular dynamics simulations revealed that the catalytic domain of wild-type Cel7A and the FCA398 variant exhibit similar behavior at 300 K, whereas at elevated temperature (475 and 525 K), the FCA398 variant fluctuates less and maintains more native contacts over time. Combining the structural and dynamic investigations, rationales were developed for the stabilizing effect at many of the mutated sites. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  11. System evaluation of improved thermal stability jet fuels

    Energy Technology Data Exchange (ETDEWEB)

    Binns, K.E.; Dieterle, G.L.; Williams, T. [Univ. of Dayton Research Institute, OH (United States)

    1995-05-01

    A single-pass, single-tube heat exchanger device called the Phoenix rig and a single-pass, dual-heat exchanger system called the Extended Duration Thermal Stability Test system are specific devices/systems developed for evaluating jet fuel thermal stability. They have been used extensively in the evaluation of various jet fuels and thermal stability additives. The test results have indicated that additives can substantially improve the thermal stability of conventional jet fuels. Relationships of oxygen consumption, residence time, bulk, and wetted wall temperatures on coking deposits that form in the heated tubes have also been investigated.

  12. Generation and analysis of expressed sequence tags from Botrytis cinerea

    Directory of Open Access Journals (Sweden)

    EVELYN SILVA

    2006-01-01

    Full Text Available Botrytis cinerea is a filamentous plant pathogen of a wide range of plant species, and its infection may cause enormous damage both during plant growth and in the post-harvest phase. We have constructed a cDNA library from an isolate of B. cinerea and have sequenced 11,482 expressed sequence tags that were assembled into 1,003 contigs sequences and 3,032 singletons. Approximately 81% of the unigenes showed significant similarity to genes coding for proteins with known functions: more than 50% of the sequences code for genes involved in cellular metabolism, 12% for transport of metabolites, and approximately 10% for cellular organization. Other functional categories include responses to biotic and abiotic stimuli, cell communication, cell homeostasis, and cell development. We carried out pair-wise comparisons with fungal databases to determine the B. cinerea unisequence set with relevant similarity to genes in other fungal pathogenic counterparts. Among the 4,035 non-redundant B. cinerea unigenes, 1,338 (23% have significant homology with Fusarium verticillioides unigenes. Similar values were obtained for Saccharomyces cerevisiae and Aspergillus nidulans (22% and 24%, respectively. The lower percentages of homology were with Magnaporthe grisae and Neurospora crassa (13% and 19%, respectively. Several genes involved in putative and known fungal virulence and general pathogenicity were identified. The results provide important information for future research on this fungal pathogen

  13. Thermal Stabilization of Biologics with Photoresponsive Hydrogels.

    Science.gov (United States)

    Sridhar, Balaji V; Janczy, John R; Hatlevik, Øyvind; Wolfson, Gabriel; Anseth, Kristi S; Tibbitt, Mark W

    2018-03-12

    Modern medicine, biological research, and clinical diagnostics depend on the reliable supply and storage of complex biomolecules. However, biomolecules are inherently susceptible to thermal stress and the global distribution of value-added biologics, including vaccines, biotherapeutics, and Research Use Only (RUO) proteins, requires an integrated cold chain from point of manufacture to point of use. To mitigate reliance on the cold chain, formulations have been engineered to protect biologics from thermal stress, including materials-based strategies that impart thermal stability via direct encapsulation of the molecule. While direct encapsulation has demonstrated pronounced stabilization of proteins and complex biological fluids, no solution offers thermal stability while enabling facile and on-demand release from the encapsulating material, a critical feature for broad use. Here we show that direct encapsulation within synthetic, photoresponsive hydrogels protected biologics from thermal stress and afforded user-defined release at the point of use. The poly(ethylene glycol) (PEG)-based hydrogel was formed via a bioorthogonal, click reaction in the presence of biologics without impact on biologic activity. Cleavage of the installed photolabile moiety enabled subsequent dissolution of the network with light and release of the encapsulated biologic. Hydrogel encapsulation improved stability for encapsulated enzymes commonly used in molecular biology (β-galactosidase, alkaline phosphatase, and T4 DNA ligase) following thermal stress. β-galactosidase and alkaline phosphatase were stabilized for 4 weeks at temperatures up to 60 °C, and for 60 min at 85 °C for alkaline phosphatase. T4 DNA ligase, which loses activity rapidly at moderately elevated temperatures, was protected during thermal stress of 40 °C for 24 h and 60 °C for 30 min. These data demonstrate a general method to employ reversible polymer networks as robust excipients for thermal stability of complex

  14. Tracking Cell Surface GABAB Receptors Using an α-Bungarotoxin Tag*

    Science.gov (United States)

    Wilkins, Megan E.; Li, Xinyan; Smart, Trevor G.

    2008-01-01

    GABAB receptors mediate slow synaptic inhibition in the central nervous system and are important for synaptic plasticity as well as being implicated in disease. Located at pre- and postsynaptic sites, GABAB receptors will influence cell excitability, but their effectiveness in doing so will be dependent, in part, on their trafficking to, and stability on, the cell surface membrane. To examine the dynamic behavior of GABAB receptors in GIRK cells and neurons, we have devised a method that is based on tagging the receptor with the binding site components for the neurotoxin, α-bungarotoxin. By using the α-bungarotoxin binding site-tagged GABAB R1a subunit (R1aBBS), co-expressed with the R2 subunit, we can track receptor mobility using the small reporter, α-bungarotoxin-conjugated rhodamine. In this way, the rates of internalization and membrane insertion for these receptors could be measured with fixed and live cells. The results indicate that GABAB receptors rapidly turnover in the cell membrane, with the rate of internalization affected by the state of receptor activation. The bungarotoxin-based method of receptor-tagging seems ideally suited to follow the dynamic regulation of other G-protein-coupled receptors. PMID:18812318

  15. Analyses of an expressed sequence tag library from Taenia solium, Cysticerca.

    Directory of Open Access Journals (Sweden)

    Jonas Lundström

    Full Text Available BACKGROUND: Neurocysticercosis is a disease caused by the oral ingestion of eggs from the human parasitic worm Taenia solium. Although drugs are available they are controversial because of the side effects and poor efficiency. An expressed sequence tag (EST library is a method used to describe the gene expression profile and sequence of mRNA from a specific organism and stage. Such information can be used in order to find new targets for the development of drugs and to get a better understanding of the parasite biology. METHODS AND FINDINGS: Here an EST library consisting of 5760 sequences from the pig cysticerca stage has been constructed. In the library 1650 unique sequences were found and of these, 845 sequences (52% were novel to T. solium and not identified within other EST libraries. Furthermore, 918 sequences (55% were of unknown function. Amongst the 25 most frequently expressed sequences 6 had no relevant similarity to other sequences found in the Genbank NR DNA database. A prediction of putative signal peptides was also performed and 4 among the 25 were found to be predicted with a signal peptide. Proposed vaccine and diagnostic targets T24, Tsol18/HP6 and Tso31d could also be identified among the 25 most frequently expressed. CONCLUSIONS: An EST library has been produced from pig cysticerca and analyzed. More than half of the different ESTs sequenced contained a sequence with no suggested function and 845 novel EST sequences have been identified. The library increases the knowledge about what genes are expressed and to what level. It can also be used to study different areas of research such as drug and diagnostic development together with parasite fitness via e.g. immune modulation.

  16. Reliable Refuge: Two Sky Island Scorpion Species Select Larger, Thermally Stable Retreat Sites.

    Science.gov (United States)

    Becker, Jamie E; Brown, Christopher A

    2016-01-01

    Sky island scorpions shelter under rocks and other surface debris, but, as with other scorpions, it is unclear whether these species select retreat sites randomly. Furthermore, little is known about the thermal preferences of scorpions, and no research has been done to identify whether reproductive condition might influence retreat site selection. The objectives were to (1) identify physical or thermal characteristics for retreat sites occupied by two sky island scorpions (Vaejovis cashi Graham 2007 and V. electrum Hughes 2011) and those not occupied; (2) determine whether retreat site selection differs between the two study species; and (3) identify whether thermal selection differs between species and between gravid and non-gravid females of the same species. Within each scorpion's habitat, maximum dimensions of rocks along a transect line were measured and compared to occupied rocks to determine whether retreat site selection occurred randomly. Temperature loggers were placed under a subset of occupied and unoccupied rocks for 48 hours to compare the thermal characteristics of these rocks. Thermal gradient trials were conducted before parturition and after dispersal of young in order to identify whether gravidity influences thermal preference. Vaejovis cashi and V. electrum both selected larger retreat sites that had more stable thermal profiles. Neither species appeared to have thermal preferences influenced by reproductive condition. However, while thermal selection did not differ among non-gravid individuals, gravid V. electrum selected warmer temperatures than its gravid congener. Sky island scorpions appear to select large retreat sites to maintain thermal stability, although biotic factors (e.g., competition) could also be involved in this choice. Future studies should focus on identifying the various biotic or abiotic factors that could influence retreat site selection in scorpions, as well as determining whether reproductive condition affects thermal

  17. Expressed sequence tags of differential genes in the radioresistant mice and their parental mice

    International Nuclear Information System (INIS)

    Wang Qin; Yue Jingyin; Li Jin; Song Li; Liu Qiang; Mu Chuanjie; Wu Hongying

    2009-01-01

    Objective: To explore radioresistance correlative genes in IRM-2 inbred mouse. Methods: The total RNA was extracted from spleen cells of IRM-2 and their parent 615 and ICR/JCL mouse. The mRNA differential display technique was used to analyze gene expression differences. Each differential bands were amplified by PCR, cloned and sequenced. Results: There were 75 differential expression bands appearing in IRM-2 mouse but not in 615 and ICR/JCL mouse. Fifty-two pieces of cDNA sequences were got by sequencing. Twenty-one expressed sequence tags (EST) that were not the same as known mice genes were found and registered by comparing with GenBank database. Conclusion: Twenty-one EST denote that radioresistance correlative genes may be in IRM-2 mouse, which have laid a foundation for isolating and identifying radioresistance correlative genes in further study. (authors)

  18. Expressed sequence tags from Atta laevigata and identification of candidate genes for the control of pest leaf-cutting ants

    Directory of Open Access Journals (Sweden)

    Henrique-Silva Flávio

    2011-06-01

    Full Text Available Abstract Background Leafcutters are the highest evolved within Neotropical ants in the tribe Attini and model systems for studying caste formation, labor division and symbiosis with microorganisms. Some species of leafcutters are agricultural pests controlled by chemicals which affect other animals and accumulate in the environment. Aiming to provide genetic basis for the study of leafcutters and for the development of more specific and environmentally friendly methods for the control of pest leafcutters, we generated expressed sequence tag data from Atta laevigata, one of the pest ants with broad geographic distribution in South America. Results The analysis of the expressed sequence tags allowed us to characterize 2,006 unique sequences in Atta laevigata. Sixteen of these genes had a high number of transcripts and are likely positively selected for high level of gene expression, being responsible for three basic biological functions: energy conservation through redox reactions in mitochondria; cytoskeleton and muscle structuring; regulation of gene expression and metabolism. Based on leafcutters lifestyle and reports of genes involved in key processes of other social insects, we identified 146 sequences potential targets for controlling pest leafcutters. The targets are responsible for antixenobiosis, development and longevity, immunity, resistance to pathogens, pheromone function, cell signaling, behavior, polysaccharide metabolism and arginine kynase activity. Conclusion The generation and analysis of expressed sequence tags from Atta laevigata have provided important genetic basis for future studies on the biology of leaf-cutting ants and may contribute to the development of a more specific and environmentally friendly method for the control of agricultural pest leafcutters.

  19. Expressed sequence tags from Atta laevigata and identification of candidate genes for the control of pest leaf-cutting ants.

    Science.gov (United States)

    Rodovalho, Cynara M; Ferro, Milene; Fonseca, Fernando Pp; Antonio, Erik A; Guilherme, Ivan R; Henrique-Silva, Flávio; Bacci, Maurício

    2011-06-17

    Leafcutters are the highest evolved within Neotropical ants in the tribe Attini and model systems for studying caste formation, labor division and symbiosis with microorganisms. Some species of leafcutters are agricultural pests controlled by chemicals which affect other animals and accumulate in the environment. Aiming to provide genetic basis for the study of leafcutters and for the development of more specific and environmentally friendly methods for the control of pest leafcutters, we generated expressed sequence tag data from Atta laevigata, one of the pest ants with broad geographic distribution in South America. The analysis of the expressed sequence tags allowed us to characterize 2,006 unique sequences in Atta laevigata. Sixteen of these genes had a high number of transcripts and are likely positively selected for high level of gene expression, being responsible for three basic biological functions: energy conservation through redox reactions in mitochondria; cytoskeleton and muscle structuring; regulation of gene expression and metabolism. Based on leafcutters lifestyle and reports of genes involved in key processes of other social insects, we identified 146 sequences potential targets for controlling pest leafcutters. The targets are responsible for antixenobiosis, development and longevity, immunity, resistance to pathogens, pheromone function, cell signaling, behavior, polysaccharide metabolism and arginine kynase activity. The generation and analysis of expressed sequence tags from Atta laevigata have provided important genetic basis for future studies on the biology of leaf-cutting ants and may contribute to the development of a more specific and environmentally friendly method for the control of agricultural pest leafcutters.

  20. Biochemical Characterization, Thermal Stability, and Partial Sequence of a Novel Exo-Polygalacturonase from the Thermophilic Fungus Rhizomucor pusillus A13.36 Obtained by Submerged Cultivation

    Directory of Open Access Journals (Sweden)

    Lucas Vinícius Trindade

    2016-01-01

    Full Text Available This work reports the production of an exo-polygalacturonase (exo-PG by Rhizomucor pusillus A13.36 in submerged cultivation (SmC in a shaker at 45°C for 96 h. A single pectinase was found and purified in order to analyze its thermal stability, by salt precipitation and hydrophobic interaction chromatography. The pectinase has an estimated Mw of approximately 43.5–47 kDa and optimum pH of 4.0 but is stable in pH ranging from 3.5 to 9.5 and has an optimum temperature of 61°C. It presents thermal stability between 30 and 60°C, has 70% activation in the presence of Ca2+, and was tested using citrus pectin with a degree of methyl esterification (DE of 26%. Ea(d for irreversible denaturation was 125.5 kJ/mol with positive variations of entropy and enthalpy for that and ΔG(d values were around 50 kJ/mol. The hydrolysis of polygalacturonate was analyzed by capillary electrophoresis which displayed a pattern of sequential hydrolysis (exo. The partial identification of the primary sequence was done by MS MALDI-TOF and a comparison with data banks showed the highest identity of the sequenced fragments of exo-PG from R. pusillus with an exo-pectinase from Aspergillus fumigatus. Pectin hydrolysis showed a sigmoidal curve for the Michaelis-Menten plot.

  1. Identifying novel genes in C. elegans using SAGE tags

    Directory of Open Access Journals (Sweden)

    Chen Nansheng

    2010-12-01

    Full Text Available Abstract Background Despite extensive efforts devoted to predicting protein-coding genes in genome sequences, many bona fide genes have not been found and many existing gene models are not accurate in all sequenced eukaryote genomes. This situation is partly explained by the fact that gene prediction programs have been developed based on our incomplete understanding of gene feature information such as splicing and promoter characteristics. Additionally, full-length cDNAs of many genes and their isoforms are hard to obtain due to their low level or rare expression. In order to obtain full-length sequences of all protein-coding genes, alternative approaches are required. Results In this project, we have developed a method of reconstructing full-length cDNA sequences based on short expressed sequence tags which is called sequence tag-based amplification of cDNA ends (STACE. Expressed tags are used as anchors for retrieving full-length transcripts in two rounds of PCR amplification. We have demonstrated the application of STACE in reconstructing full-length cDNA sequences using expressed tags mined in an array of serial analysis of gene expression (SAGE of C. elegans cDNA libraries. We have successfully applied STACE to recover sequence information for 12 genes, for two of which we found isoforms. STACE was used to successfully recover full-length cDNA sequences for seven of these genes. Conclusions The STACE method can be used to effectively reconstruct full-length cDNA sequences of genes that are under-represented in cDNA sequencing projects and have been missed by existing gene prediction methods, but their existence has been suggested by short sequence tags such as SAGE tags.

  2. STUDY OF THERMAL AND ACID STABILITY OF BENTONITE CLAY

    Directory of Open Access Journals (Sweden)

    Karna Wijaya

    2010-06-01

    Full Text Available The thermal and acid stability of the bentonite clays (Na- and Ca-bentonite have been tested. The thermal stability testing has been carried out by heating 5 gram of the clays  for five hours at 200, 300 and 500 °C respectively, meanwhile acid stability testing was performed by immersing 5 gram clays into 100 mL sulphuric acid 1M, 2M and 3M for 24 hours. The tested clays, then were characterized by means of X-Ray difractometry and IR-spectroscopy methods. The characterization results showed that upon heating, both Ca- and Na-bentonites indicated same thermal stability. However, upon acid treatment, Na-bentonite was found relatively stabiler and more resistance then Ca-bentonite.   Keywords: bentonite, clay, thermal stability, acid stability.

  3. Studies on thermal properties and thermal control effectiveness of a new shape-stabilized phase change material with high thermal conductivity

    International Nuclear Information System (INIS)

    Cheng Wenlong; Liu Na; Wu Wanfan

    2012-01-01

    In order to overcome the difficulty of conventional phase change materials (PCMs) in packaging, the shape-stabilized PCMs are proposed to be used in the electronic device thermal control. However, the conventional shape-stabilized PCMs have the drawback of lower thermal conductivity, so a new shape-stabilized PCM with high thermal conductivity, which is suitable for thermal control of electronic devices, is prepared. The thermal properties of n-octadecane-based shape-stabilized PCM are tested and analyzed. The heat storage/release performance is studied by numerical simulation. Its thermal control effect for electronic devices is also discussed. The results show that the expanded graphite (EG) can greatly improve the thermal conductivity of the material with little effect on latent heat and phase change temperature. When the mass fraction of EG is 5%, thermal conductivity has reached 1.76 W/(m K), which is over 4 times than that of the original one. Moreover, the material has larger latent heat and good thermal stability. The simulation results show that the material can have good heat storage/release performance. The analysis of the effect of thermal parameters on thermal control effect for electronic devices provides references to the design of phase change thermal control unit. - Highlights: ► A new shape-stabilized PCM with higher thermal conductivity is prepared. ► The material overcomes the packaging difficulty of traditional PCMs used in thermal control unit. ► The EG greatly improves thermal conductivity with little effect on latent heat. ► The material has high thermal stability and good heat storage/release performance. ► The effectiveness of the material for electronic device thermal control is proved.

  4. Cardiac MR tagging: optimization of sequence parameters and comparison at 1.5 T and 3.0 T in a volunteer study

    International Nuclear Information System (INIS)

    Kramer, U.; Fenchel, M.; Klumpp, B.; Claussen, C.D.; Miller, S.; Deshpande, V.; Laub, G.; Finn, J.P.

    2006-01-01

    Purpose: The aim of this study was the optimization of a gradient echo (GRE) MR tagging sequence at 3.0 T in comparison to 1.5 T in order to obtain the best image contrast between the myocardium, tag lines and blood signal. Theoretically expected improvements of signal-to-noise (SNR) and contrast-to-noise ratios (CNR) were also calculated. Materials and methods: 14 healthy volunteers (8 male, 6 female; mean age 43.4±10.3 years) were scanned using a 3.0 T as well as a 1.5 T whole-body system. A GRE flash-2 D tagging sequence was evaluated (midventricular short axis view) by varying the flip angle (8-16 ), slice thickness (4-8 mm; fixed flip angle 1.5/3.0 T: 12 /8 , tag size 8 mm) and tag size (4-8 mm, fixed flip angle 1.5/3.0 T: 12 /8 , slice thickness 6 mm). The field of view, acquisition time and temporal resolution (45 ms) were kept constant. Qualitative and quantitative image analysis was performed by calculating the SNR, CNR tag as well as the relative contrast between the myocardium and tag lines (RCMT). Results: Based on individual comparison, the best imaging protocol was found at a slice thickness of 6 mm, tag size of 8 mm, optimized flip angle of 8 (3.0 T) and 12 (1.5 T), respectively. Compared to 1.5 T, a significantly higher overall image score was determined (mean±sd; 3.2±0.2 vs 2.7±0.4) and a strong correlation between the CNR tag and RCMT for flip angle α and the slice thickness was found. A higher field strength resulted in an 80% increase in the CNR tag compared to 1.5 T (mean 10.7/6.1). Furthermore, the SNR was improved by 35% (mean 20.6/15.3) and the RCMT by 35% (mean 0.47/0.35). Conclusion: Myocardial tagging at 3.0 T has shown superior image quality in comparison to 1.5 T due to a higher baseline SNR and an improved CNR as well as RCMT. The suppressed fading of the tags enables the accessibility to the diastolic phase of the cardiac cycle. (orig.)

  5. Thermal equilibrium, stability and burn control

    International Nuclear Information System (INIS)

    Cohn, D.

    1982-01-01

    A number of aspects of the thermal stability and equilibrium control of ignited tokamak plasma have been investigated. Examined approaches were passive control (the effect of radial motion, the effect of radial motion and small additional transport loss), active control (the compression and decompression of plasma, subignited operation with small amount of variable external heating, and density control), and thermal equilibrium control (additional power loss from impurity radiation and enhanced transport from increased ripple). One-D calculation has been made on thermal instability eigen-modes. It was found that for electron thermal induction loss given by Alcator scaling and for neoclassical ion transport, there was at most one unstable mode with a temperature profile which maintains the temperature profile at thermal equilibrium. The effect of the coupling of temperature fluctuation and the fluctuation in major radius was investigated. Temperature driven radial motion combined with a small amount of ripple transport loss was found to be a very effective mechanism for passive thermal stability control. (Kato, T.)

  6. Expressed sequence tag-derived polymorphic SSR markers for Fucus serratus and amplification in other species of Fucus

    NARCIS (Netherlands)

    Coyer, J. A.; Hoarau, G.; Beszteri, B.; Pearson, G.; Olsen, J. L.

    The seaweed genus Fucus is a dominant component of intertidal shores throughout the North Atlantic and North Pacific and has been the focus of considerable developmental, ecological, and evolutionary research for the past century. Here, we present details of 21 expressed sequence tag-derived simple

  7. Tracking cell surface GABAB receptors using an alpha-bungarotoxin tag.

    Science.gov (United States)

    Wilkins, Megan E; Li, Xinyan; Smart, Trevor G

    2008-12-12

    GABA(B) receptors mediate slow synaptic inhibition in the central nervous system and are important for synaptic plasticity as well as being implicated in disease. Located at pre- and postsynaptic sites, GABA(B) receptors will influence cell excitability, but their effectiveness in doing so will be dependent, in part, on their trafficking to, and stability on, the cell surface membrane. To examine the dynamic behavior of GABA(B) receptors in GIRK cells and neurons, we have devised a method that is based on tagging the receptor with the binding site components for the neurotoxin, alpha-bungarotoxin. By using the alpha-bungarotoxin binding site-tagged GABA(B) R1a subunit (R1a(BBS)), co-expressed with the R2 subunit, we can track receptor mobility using the small reporter, alpha-bungarotoxin-conjugated rhodamine. In this way, the rates of internalization and membrane insertion for these receptors could be measured with fixed and live cells. The results indicate that GABA(B) receptors rapidly turnover in the cell membrane, with the rate of internalization affected by the state of receptor activation. The bungarotoxin-based method of receptor-tagging seems ideally suited to follow the dynamic regulation of other G-protein-coupled receptors.

  8. Analysis and functional annotation of expressed sequence tags from the fall armyworm Spodoptera frugiperda

    Science.gov (United States)

    Deng, Youping; Dong, Yinghua; Thodima, Venkata; Clem, Rollie J; Passarelli, A Lorena

    2006-01-01

    Background Little is known about the genome sequences of lepidopteran insects, although this group of insects has been studied extensively in the fields of endocrinology, development, immunity, and pathogen-host interactions. In addition, cell lines derived from Spodoptera frugiperda and other lepidopteran insects are routinely used for baculovirus foreign gene expression. This study reports the results of an expressed sequence tag (EST) sequencing project in cells from the lepidopteran insect S. frugiperda, the fall armyworm. Results We have constructed an EST database using two cDNA libraries from the S. frugiperda-derived cell line, SF-21. The database consists of 2,367 ESTs which were assembled into 244 contigs and 951 singlets for a total of 1,195 unique sequences. Conclusion S. frugiperda is an agriculturally important pest insect and genomic information will be instrumental for establishing initial transcriptional profiling and gene function studies, and for obtaining information about genes manipulated during infections by insect pathogens such as baculoviruses. PMID:17052344

  9. Unexpected observations after mapping LongSAGE tags to the human genome

    Directory of Open Access Journals (Sweden)

    Duret Laurent

    2007-05-01

    Full Text Available Abstract Background SAGE has been used widely to study the expression of known transcripts, but much less to annotate new transcribed regions. LongSAGE produces tags that are sufficiently long to be reliably mapped to a whole-genome sequence. Here we used this property to study the position of human LongSAGE tags obtained from all public libraries. We focused mainly on tags that do not map to known transcripts. Results Using a published error rate in SAGE libraries, we first removed the tags likely to result from sequencing errors. We then observed that an unexpectedly large number of the remaining tags still did not match the genome sequence. Some of these correspond to parts of human mRNAs, such as polyA tails, junctions between two exons and polymorphic regions of transcripts. Another non-negligible proportion can be attributed to contamination by murine transcripts and to residual sequencing errors. After filtering out our data with these screens to ensure that our dataset is highly reliable, we studied the tags that map once to the genome. 31% of these tags correspond to unannotated transcripts. The others map to known transcribed regions, but many of them (nearly half are located either in antisense or in new variants of these known transcripts. Conclusion We performed a comprehensive study of all publicly available human LongSAGE tags, and carefully verified the reliability of these data. We found the potential origin of many tags that did not match the human genome sequence. The properties of the remaining tags imply that the level of sequencing error may have been under-estimated. The frequency of tags matching once the genome sequence but not in an annotated exon suggests that the human transcriptome is much more complex than shown by the current human genome annotations, with many new splicing variants and antisense transcripts. SAGE data is appropriate to map new transcripts to the genome, as demonstrated by the high rate of cross

  10. Optimal use of tandem biotin and V5 tags in ChIP assays

    Directory of Open Access Journals (Sweden)

    Krpic Sanja

    2009-02-01

    Full Text Available Abstract Background Chromatin immunoprecipitation (ChIP assays coupled to genome arrays (Chip-on-chip or massive parallel sequencing (ChIP-seq lead to the genome wide identification of binding sites of chromatin associated proteins. However, the highly variable quality of antibodies and the availability of epitopes in crosslinked chromatin can compromise genomic ChIP outcomes. Epitope tags have often been used as more reliable alternatives. In addition, we have employed protein in vivo biotinylation tagging as a very high affinity alternative to antibodies. In this paper we describe the optimization of biotinylation tagging for ChIP and its coupling to a known epitope tag in providing a reliable and efficient alternative to antibodies. Results Using the biotin tagged erythroid transcription factor GATA-1 as example, we describe several optimization steps for the application of the high affinity biotin streptavidin system in ChIP. We find that the omission of SDS during sonication, the use of fish skin gelatin as blocking agent and choice of streptavidin beads can lead to significantly improved ChIP enrichments and lower background compared to antibodies. We also show that the V5 epitope tag performs equally well under the conditions worked out for streptavidin ChIP and that it may suffer less from the effects of formaldehyde crosslinking. Conclusion The combined use of the very high affinity biotin tag with the less sensitive to crosslinking V5 tag provides for a flexible ChIP platform with potential implications in ChIP sequencing outcomes.

  11. Optimal use of tandem biotin and V5 tags in ChIP assays

    Science.gov (United States)

    Kolodziej, Katarzyna E; Pourfarzad, Farzin; de Boer, Ernie; Krpic, Sanja; Grosveld, Frank; Strouboulis, John

    2009-01-01

    Background Chromatin immunoprecipitation (ChIP) assays coupled to genome arrays (Chip-on-chip) or massive parallel sequencing (ChIP-seq) lead to the genome wide identification of binding sites of chromatin associated proteins. However, the highly variable quality of antibodies and the availability of epitopes in crosslinked chromatin can compromise genomic ChIP outcomes. Epitope tags have often been used as more reliable alternatives. In addition, we have employed protein in vivo biotinylation tagging as a very high affinity alternative to antibodies. In this paper we describe the optimization of biotinylation tagging for ChIP and its coupling to a known epitope tag in providing a reliable and efficient alternative to antibodies. Results Using the biotin tagged erythroid transcription factor GATA-1 as example, we describe several optimization steps for the application of the high affinity biotin streptavidin system in ChIP. We find that the omission of SDS during sonication, the use of fish skin gelatin as blocking agent and choice of streptavidin beads can lead to significantly improved ChIP enrichments and lower background compared to antibodies. We also show that the V5 epitope tag performs equally well under the conditions worked out for streptavidin ChIP and that it may suffer less from the effects of formaldehyde crosslinking. Conclusion The combined use of the very high affinity biotin tag with the less sensitive to crosslinking V5 tag provides for a flexible ChIP platform with potential implications in ChIP sequencing outcomes. PMID:19196479

  12. Comparative Genomics in Switchgrass Using 61,585 High-Quality Expressed Sequence Tags

    Directory of Open Access Journals (Sweden)

    Christian M. Tobias

    2008-11-01

    Full Text Available The development of genomic resources for switchgrass ( L., a perennial NAD-malic enzyme type C grass, is required to enable molecular breeding and biotechnological approaches for improving its value as a forage and bioenergy crop. Expressed sequence tag (EST sequencing is one method that can quickly sample gene inventories and produce data suitable for marker development or analysis of tissue-specific patterns of expression. Toward this goal, three cDNA libraries from callus, crown, and seedling tissues of ‘Kanlow’ switchgrass were end-sequenced to generate a total of 61,585 high-quality ESTs from 36,565 separate clones. Seventy-three percent of the assembled consensus sequences could be aligned with the sorghum [ (L. Moench] genome at a -value of <1 × 10, indicating a high degree of similarity. Sixty-five percent of the ESTs matched with gene ontology molecular terms, and 3.3% of the sequences were matched with genes that play potential roles in cell-wall biogenesis. The representation in the three libraries of gene families known to be associated with C photosynthesis, cellulose and β-glucan synthesis, phenylpropanoid biosynthesis, and peroxidase activity indicated likely roles for individual family members. Pairwise comparisons of synonymous codon substitutions were used to assess genome sequence diversity and indicated an overall similarity between the two genome copies present in the tetraploid. Identification of EST–simple sequence repeat markers and amplification on two individual parents of a mapping population yielded an average of 2.18 amplicons per individual, and 35% of the markers produced fragment length polymorphisms.

  13. An active ac/ds transposon system for activation tagging in tomato cultivar m82 using clonal propagation.

    Science.gov (United States)

    Carter, Jared D; Pereira, Andy; Dickerman, Allan W; Veilleux, Richard E

    2013-05-01

    Tomato (Solanum lycopersicum) is a model organism for Solanaceae in both molecular and agronomic research. This project utilized Agrobacterium tumefaciens transformation and the transposon-tagging construct Activator (Ac)/Dissociator (Ds)-ATag-Bar_gosGFP to produce activation-tagged and knockout mutants in the processing tomato cultivar M82. The construct carried hygromycin resistance (hyg), green fluorescent protein (GFP), and the transposase (TPase) of maize (Zea mays) Activator major transcript X054214.1 on the stable Ac element, along with a 35S enhancer tetramer and glufosinate herbicide resistance (BAR) on the mobile Ds-ATag element. An in vitro propagation strategy was used to produce a population of 25 T0 plants from a single transformed plant regenerated in tissue culture. A T1 population of 11,000 selfed and cv M82 backcrossed progeny was produced from the functional T0 line. This population was screened using glufosinate herbicide, hygromycin leaf painting, and multiplex polymerase chain reaction (PCR). Insertion sites of transposed Ds-ATag elements were identified through thermal asymmetric interlaced PCR, and resulting product sequences were aligned to the recently published tomato genome. A population of 509 independent, Ds-only transposant lines spanning all 12 tomato chromosomes has been developed. Insertion site analysis demonstrated that more than 80% of these lines harbored Ds insertions conducive to activation tagging. The capacity of the Ds-ATag element to alter transcription was verified by quantitative real-time reverse transcription-PCR in two mutant lines. The transposon-tagged lines have been immortalized in seed stocks and can be accessed through an online database, providing a unique resource for tomato breeding and analysis of gene function in the background of a commercial tomato cultivar.

  14. Building Tag Clouds in Perl and PHP

    CERN Document Server

    Bumgardner, Jim

    2006-01-01

    Tag clouds are everywhere on the web these days. First popularized by the web sites Flickr, Technorati, and del.icio.us, these amorphous clumps of words now appear on a slew of web sites as visual evidence of their membership in the elite corps of "Web 2.0." This PDF analyzes what is and isn't a tag cloud, offers design tips for using them effectively, and then goes on to show how to collect tags and display them in the tag cloud format. Scripts are provided in Perl and PHP. Yes, some have said tag clouds are a fad. But as you will see, tag clouds, when used properly, have real merits. More

  15. APE1 incision activity at abasic sites in tandem repeat sequences.

    Science.gov (United States)

    Li, Mengxia; Völker, Jens; Breslauer, Kenneth J; Wilson, David M

    2014-05-29

    Repetitive DNA sequences, such as those present in microsatellites and minisatellites, telomeres, and trinucleotide repeats (linked to fragile X syndrome, Huntington disease, etc.), account for nearly 30% of the human genome. These domains exhibit enhanced susceptibility to oxidative attack to yield base modifications, strand breaks, and abasic sites; have a propensity to adopt non-canonical DNA forms modulated by the positions of the lesions; and, when not properly processed, can contribute to genome instability that underlies aging and disease development. Knowledge on the repair efficiencies of DNA damage within such repetitive sequences is therefore crucial for understanding the impact of such domains on genomic integrity. In the present study, using strategically designed oligonucleotide substrates, we determined the ability of human apurinic/apyrimidinic endonuclease 1 (APE1) to cleave at apurinic/apyrimidinic (AP) sites in a collection of tandem DNA repeat landscapes involving telomeric and CAG/CTG repeat sequences. Our studies reveal the differential influence of domain sequence, conformation, and AP site location/relative positioning on the efficiency of APE1 binding and strand incision. Intriguingly, our data demonstrate that APE1 endonuclease efficiency correlates with the thermodynamic stability of the DNA substrate. We discuss how these results have both predictive and mechanistic consequences for understanding the success and failure of repair protein activity associated with such oxidatively sensitive, conformationally plastic/dynamic repetitive DNA domains. Published by Elsevier Ltd.

  16. Discharge residence of TLD tagged fish

    International Nuclear Information System (INIS)

    Romberg, G.P.; Prepejchal, W.

    1974-01-01

    Although visual observations suggested that fish remained in the discharge for considerable periods, temperature-sensitive tags indicated the majority of fish spend less than 50 hr or 10 percent of the time at discharge temperatures. During 1974 a second fish tagging study was conducted, using temperature-sensitive tags to yield discharge residence times of Lake Michigan salmonids at Point Beach thermal discharge. Preliminary results revealed that many fish tag values were close to Unit I line indicating that calculated maximum discharge residence times for these fish will be nearly 100 percent of the elapsed time

  17. Sorting of a HaloTag protein that has only a signal peptide sequence into exocrine secretory granules without protein aggregation.

    Science.gov (United States)

    Fujita-Yoshigaki, Junko; Matsuki-Fukushima, Miwako; Yokoyama, Megumi; Katsumata-Kato, Osamu

    2013-11-15

    The mechanism involved in the sorting and accumulation of secretory cargo proteins, such as amylase, into secretory granules of exocrine cells remains to be solved. To clarify that sorting mechanism, we expressed a reporter protein HaloTag fused with partial sequences of salivary amylase protein in primary cultured parotid acinar cells. We found that a HaloTag protein fused with only the signal peptide sequence (Met(1)-Ala(25)) of amylase, termed SS25H, colocalized well with endogenous amylase, which was confirmed by immunofluorescence microscopy. Percoll-density gradient centrifugation of secretory granule fractions shows that the distributions of amylase and SS25H were similar. These results suggest that SS25H is transported to secretory granules and is not discriminated from endogenous amylase by the machinery that functions to remove proteins other than granule cargo from immature granules. Another reporter protein, DsRed2, that has the same signal peptide sequence also colocalized with amylase, suggesting that the sorting to secretory granules is not dependent on a characteristic of the HaloTag protein. Whereas Blue Native PAGE demonstrates that endogenous amylase forms a high-molecular-weight complex, SS25H does not participate in the complex and does not form self-aggregates. Nevertheless, SS25H was released from cells by the addition of a β-adrenergic agonist, isoproterenol, which also induces amylase secretion. These results indicate that addition of the signal peptide sequence, which is necessary for the translocation in the endoplasmic reticulum, is sufficient for the transportation and storage of cargo proteins in secretory granules of exocrine cells.

  18. Creation and structure determination of an artificial protein with three complete sequence repeats

    Energy Technology Data Exchange (ETDEWEB)

    Adachi, Motoyasu, E-mail: adachi.motoyasu@jaea.go.jp; Shimizu, Rumi; Kuroki, Ryota [Japan Atomic Energy Agency, Shirakatashirane 2-4, Nakagun Tokaimura, Ibaraki 319-1195 (Japan); Blaber, Michael [Japan Atomic Energy Agency, Shirakatashirane 2-4, Nakagun Tokaimura, Ibaraki 319-1195 (Japan); Florida State University, Tallahassee, FL 32306-4300 (United States)

    2013-11-01

    An artificial protein with three complete sequence repeats was created and the structure was determined by X-ray crystallography. The structure showed threefold symmetry even though there is an amino- and carboxy-terminal. The artificial protein with threefold symmetry may be useful as a scaffold to capture small materials with C3 symmetry. Symfoil-4P is a de novo protein exhibiting the threefold symmetrical β-trefoil fold designed based on the human acidic fibroblast growth factor. First three asparagine–glycine sequences of Symfoil-4P are replaced with glutamine–glycine (Symfoil-QG) or serine–glycine (Symfoil-SG) sequences protecting from deamidation, and His-Symfoil-II was prepared by introducing a protease digestion site into Symfoil-QG so that Symfoil-II has three complete repeats after removal of the N-terminal histidine tag. The Symfoil-QG and SG and His-Symfoil-II proteins were expressed in Eschericha coli as soluble protein, and purified by nickel affinity chromatography. Symfoil-II was further purified by anion-exchange chromatography after removing the HisTag by proteolysis. Both Symfoil-QG and Symfoil-II were crystallized in 0.1 M Tris-HCl buffer (pH 7.0) containing 1.8 M ammonium sulfate as precipitant at 293 K; several crystal forms were observed for Symfoil-QG and II. The maximum diffraction of Symfoil-QG and II crystals were 1.5 and 1.1 Å resolution, respectively. The Symfoil-II without histidine tag diffracted better than Symfoil-QG with N-terminal histidine tag. Although the crystal packing of Symfoil-II is slightly different from Symfoil-QG and other crystals of Symfoil derivatives having the N-terminal histidine tag, the refined crystal structure of Symfoil-II showed pseudo-threefold symmetry as expected from other Symfoils. Since the removal of the unstructured N-terminal histidine tag did not affect the threefold structure of Symfoil, the improvement of diffraction quality of Symfoil-II may be caused by molecular characteristics of

  19. Myocardial tagging by Cardiovascular Magnetic Resonance: evolution of techniques--pulse sequences, analysis algorithms, and applications

    Directory of Open Access Journals (Sweden)

    Ibrahim El-Sayed H

    2011-07-01

    Full Text Available Abstract Cardiovascular magnetic resonance (CMR tagging has been established as an essential technique for measuring regional myocardial function. It allows quantification of local intramyocardial motion measures, e.g. strain and strain rate. The invention of CMR tagging came in the late eighties, where the technique allowed for the first time for visualizing transmural myocardial movement without having to implant physical markers. This new idea opened the door for a series of developments and improvements that continue up to the present time. Different tagging techniques are currently available that are more extensive, improved, and sophisticated than they were twenty years ago. Each of these techniques has different versions for improved resolution, signal-to-noise ratio (SNR, scan time, anatomical coverage, three-dimensional capability, and image quality. The tagging techniques covered in this article can be broadly divided into two main categories: 1 Basic techniques, which include magnetization saturation, spatial modulation of magnetization (SPAMM, delay alternating with nutations for tailored excitation (DANTE, and complementary SPAMM (CSPAMM; and 2 Advanced techniques, which include harmonic phase (HARP, displacement encoding with stimulated echoes (DENSE, and strain encoding (SENC. Although most of these techniques were developed by separate groups and evolved from different backgrounds, they are in fact closely related to each other, and they can be interpreted from more than one perspective. Some of these techniques even followed parallel paths of developments, as illustrated in the article. As each technique has its own advantages, some efforts have been made to combine different techniques together for improved image quality or composite information acquisition. In this review, different developments in pulse sequences and related image processing techniques are described along with the necessities that led to their invention

  20. Thermal Stabilization FY 1999 blend plan

    Energy Technology Data Exchange (ETDEWEB)

    RISENMAY, H.R.

    1999-02-23

    This Blend Plan documents the alternate feed material items for the thermal stabilization process that will be used in place of the metal items that were originally planned to be processed. Problems with resolution of the safety basis for the metal items resulted in the decision to run material that already had an established safety basis. Various in process and scrap recovery items stored in gloveboxes, plutonium oxide and plutonium oxide mixed with uranium oxide stored in 2736-Z vaults will be processed through the stabilization furnaces until the safety basis for the metal items has been resolved. The purpose of thermal stabilization is to heat the material to 1000 degrees Celsius to drive off all volatile materials and leave the plutonium and/or uranium as oxides. The stabilized material will be sampled to determine the Loss On Ignition (LOI). The stabilized material must meet LOI of less than 0.5% to be acceptable for storage under DOE-STD-3013-94 specifications. Out of specification material will be recycled through the furnaces until the LOI limits are met.

  1. Thermal Stabilization FY 1999 blend plan

    International Nuclear Information System (INIS)

    RISENMAY, H.R.

    1999-01-01

    This Blend Plan documents the alternate feed material items for the thermal stabilization process that will be used in place of the metal items that were originally planned to be processed. Problems with resolution of the safety basis for the metal items resulted in the decision to run material that already had an established safety basis. Various in process and scrap recovery items stored in gloveboxes, plutonium oxide and plutonium oxide mixed with uranium oxide stored in 2736-Z vaults will be processed through the stabilization furnaces until the safety basis for the metal items has been resolved. The purpose of thermal stabilization is to heat the material to 1000 degrees Celsius to drive off all volatile materials and leave the plutonium and/or uranium as oxides. The stabilized material will be sampled to determine the Loss On Ignition (LOI). The stabilized material must meet LOI of less than 0.5% to be acceptable for storage under DOE-STD-3013-94 specifications. Out of specification material will be recycled through the furnaces until the LOI limits are met

  2. Thermal stabilization FY 1999 blend plan

    International Nuclear Information System (INIS)

    RISENMAY, H.R.

    1999-01-01

    This Blend Plan documents the alternate feed material items for the thermal stabilization process that will be used in place of the metal items that were originally planned to be processed. Problems with resolution of the safety basis for the metal items resulted in the decision to run material that already had an established safety basis. Various in process and scrap recovery items stored in gloveboxes, plutonium oxide and plutonium oxide mixed with uranium oxide stored in 2736-2 vaults will be processed through the stabilization furnaces until the safety basis for the metal items has been resolved. The purpose of thermal stabilization is to heat the material to 1000 degrees Celsius to drive off all volatile materials and leave the plutonium and/or uranium as oxides. The stabilized material will be sampled to determine the Loss On Ignition (LOI). The stabilized material must meet LOI of less than 0.5% to be acceptable for storage under DOE-STD-3013-94 specifications. Out of specification material will be recycled through the furnaces until the LOI limits are met

  3. Thermal stabilization FY 1999 blend plan

    Energy Technology Data Exchange (ETDEWEB)

    RISENMAY, H.R.

    1999-06-01

    This Blend Plan documents the alternate feed material items for the thermal stabilization process that will be used in place of the metal items that were originally planned to be processed. Problems with resolution of the safety basis for the metal items resulted in the decision to run material that already had an established safety basis. Various in process and scrap recovery items stored in gloveboxes, plutonium oxide and plutonium oxide mixed with uranium oxide stored in 2736-2 vaults will be processed through the stabilization furnaces until the safety basis for the metal items has been resolved. The purpose of thermal stabilization is to heat the material to 1000 degrees Celsius to drive off all volatile materials and leave the plutonium and/or uranium as oxides. The stabilized material will be sampled to determine the Loss On Ignition (LOI). The stabilized material must meet LOI of less than 0.5% to be acceptable for storage under DOE-STD-3013-94 specifications. Out of specification material will be recycled through the furnaces until the LOI limits are met.

  4. Synthesis, thermal properties and recrystallization of ball-milled high Tc superconductors. (Topological stabilization of metastable phases)

    International Nuclear Information System (INIS)

    Schulz, R.; Lanteigne, J.; Simoneau, M.; Tessier, P.; Neste, A. van; Strom Olsen, J.O.

    1995-01-01

    Amorphous and nanocrystalline phases have been formed by ball-milling Y-Ba-Cu-O and Bi-Ca-Sr-Cu-O. The strong mechanical deformations induce disorder on the oxygen sublattice and on the cation sites. These order-disorder transformations often produce simple cubic perovskite structures. During recrystallization, the chemical order is restored. Small ordered regions nucleate, grow and produce particular metastable configurations which minimize the total elastic strain energy. The sequence of events giving rise to the various metastable phases has been followed by x-ray diffraction and differential scanning calorimetry and is explained in terms of free energy diagrams. The stress and strain fields associated with the Y-Ba disorder are calculated using the elastic properties of the Y-Ba-Cu-O superconductor. A simple model is proposed to explain the stability of the structures observed after thermal treatments. (orig.)

  5. Thermal stability of polyvinyl alcohol/nanocrystalline cellulose composites.

    Science.gov (United States)

    Voronova, Marina I; Surov, Oleg V; Guseinov, Sabir S; Barannikov, Vladimir P; Zakharov, Anatoly G

    2015-10-05

    Thermal stability of polyvinyl alcohol/cellulose nanocrystals (PVA/CNCs) composites prepared with solution casting technique was studied. The PVA/CNCs composites were characterized by Fourier transform infrared spectrometry, X-ray diffraction, differential scanning calorimeter (DSC) and thermogravimetric (TG) analysis. Due to the presence of CNCs nanoparticles, thermal degradation of the composites occurs at much higher temperatures compared to that of the neat PVA. Thermal stability of the PVA/CNCs composites is maximally enhanced with CNCs content of 8-12 wt%. Some thermal degradation products of the PVA/CNCs composites were identified by mass spectrometric analysis. TG measurements with synchronous recording of mass spectra revealed that the thermal degradation of both CNCs and PVA in the composites with CNCs content of 8-12 wt% occurs simultaneously at a much higher temperature than that of CNCs or the neat PVA. However, with increasing CNCs content more than 12 wt% the thermal stability of the composites decreases. In this case, the degradation of CNCs comes first followed by the degradation of PVA. Copyright © 2015 Elsevier Ltd. All rights reserved.

  6. Methyl-CpG island-associated genome signature tags

    Science.gov (United States)

    Dunn, John J

    2014-05-20

    Disclosed is a method for analyzing the organismic complexity of a sample through analysis of the nucleic acid in the sample. In the disclosed method, through a series of steps, including digestion with a type II restriction enzyme, ligation of capture adapters and linkers and digestion with a type IIS restriction enzyme, genome signature tags are produced. The sequences of a statistically significant number of the signature tags are determined and the sequences are used to identify and quantify the organisms in the sample. Various embodiments of the invention described herein include methods for using single point genome signature tags to analyze the related families present in a sample, methods for analyzing sequences associated with hyper- and hypo-methylated CpG islands, methods for visualizing organismic complexity change in a sampling location over time and methods for generating the genome signature tag profile of a sample of fragmented DNA.

  7. Development of thermal stability additive packages for JP-8

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, S.D.; Harrison, W.E. III; Edwards, T.; Morris, R.W.; Shouse, D.T. [USAF Wright Lab., Wright-Paterson AFB, OH (United States)

    1995-05-01

    Advanced military aircraft use fuel as the primary heat sink to cool engine and airframe components. As the fuel is thermally stressed, thermal oxidative reactions take place that result in the formation of deposits. These deposits degrade aircraft performance and ultimately lead to premature servicing of the affected components. The frequency of these incidents, coupled with the projected cooling requirements for future systems, demonstrates that current thermal stability limits are inadequate. In response to this situation, the United States Air Force (USAF) has embarked on a program to improve thermal stability using specially formulated additive packages. Results indicate that additives offer significant thermal stability improvement. This paper describes the USAF program to develop and deploy an improved JP-8 for fleet-wide use by 1998.

  8. Research of thermal stability of ion exchangers

    International Nuclear Information System (INIS)

    Stuchlik, S.; Srnkova, J.

    1983-01-01

    Prior to the fixation of radioactive ion exchangers into bitumen these exchangers have to be dried. The resulting gaseous products may generate explosive mixtures. An analysis was made of the thermal stability of two types of ion exchangers, the cation exchanger KU-2-8 cS and the anion exchanger AV-17-8 cS which are used in the V-1 nuclear power plant at Jaslovske Bohunice. The thermal stability of the anion exchangers was monitored using gas chromatography at temperatures of 100, 120, 140, 160 and 180 degC and by measuring weight loss by kiln-drying at temperatures of 120, 140, 160 and 180 degC. The ion exchanger was heated for 6 hours and samples were taken continuously at one hour intervals. The thermal stability of the cation exchanger was monitored by measuring the weight loss. Gas chromatography showed the release of trimethylamine from the anion exchanger in direct dependence on temperature. The measurement of weight losses, however, only showed higher losses of released products which are explained by the release of other thermally unstable products. The analysis of the thermal stability of the cation exchanger showed the release of SO 2 and the weight loss (following correction for water content) was found only after the fourth hour of decomposition. The experiment showed that the drying of anion exchanger AV-17-8 cS may cause the formation of explosive mixtures. (J.P.)

  9. Expressed Sequence Tag-Simple Sequence Repeat (EST-SSR Marker Resources for Diversity Analysis of Mango (Mangifera indica L.

    Directory of Open Access Journals (Sweden)

    Natalie L. Dillon

    2014-01-01

    Full Text Available In this study, a collection of 24,840 expressed sequence tags (ESTs generated from five mango (Mangifera indica L. cDNA libraries was mined for EST-based simple sequence repeat (SSR markers. Over 1,000 ESTs with SSR motifs were detected from more than 24,000 EST sequences with di- and tri-nucleotide repeat motifs the most abundant. Of these, 25 EST-SSRs in genes involved in plant development, stress response, and fruit color and flavor development pathways were selected, developed into PCR markers and characterized in a population of 32 mango selections including M. indica varieties, and related Mangifera species. Twenty-four of the 25 EST-SSR markers exhibited polymorphisms, identifying a total of 86 alleles with an average of 5.38 alleles per locus, and distinguished between all Mangifera selections. Private alleles were identified for Mangifera species. These newly developed EST-SSR markers enhance the current 11 SSR mango genetic identity panel utilized by the Australian Mango Breeding Program. The current panel has been used to identify progeny and parents for selection and the application of this extended panel will further improve and help to design mango hybridization strategies for increased breeding efficiency.

  10. Comparison of methods for genomic localization of gene trap sequences

    Directory of Open Access Journals (Sweden)

    Ferrin Thomas E

    2006-09-01

    Full Text Available Abstract Background Gene knockouts in a model organism such as mouse provide a valuable resource for the study of basic biology and human disease. Determining which gene has been inactivated by an untargeted gene trapping event poses a challenging annotation problem because gene trap sequence tags, which represent sequence near the vector insertion site of a trapped gene, are typically short and often contain unresolved residues. To understand better the localization of these sequences on the mouse genome, we compared stand-alone versions of the alignment programs BLAT, SSAHA, and MegaBLAST. A set of 3,369 sequence tags was aligned to build 34 of the mouse genome using default parameters for each algorithm. Known genome coordinates for the cognate set of full-length genes (1,659 sequences were used to evaluate localization results. Results In general, all three programs performed well in terms of localizing sequences to a general region of the genome, with only relatively subtle errors identified for a small proportion of the sequence tags. However, large differences in performance were noted with regard to correctly identifying exon boundaries. BLAT correctly identified the vast majority of exon boundaries, while SSAHA and MegaBLAST missed the majority of exon boundaries. SSAHA consistently reported the fewest false positives and is the fastest algorithm. MegaBLAST was comparable to BLAT in speed, but was the most susceptible to localizing sequence tags incorrectly to pseudogenes. Conclusion The differences in performance for sequence tags and full-length reference sequences were surprisingly small. Characteristic variations in localization results for each program were noted that affect the localization of sequence at exon boundaries, in particular.

  11. 2-Methoxypyridine as a Thymidine Mimic in Watson-Crick Base Pairs of DNA and PNA: Synthesis, Thermal Stability, and NMR Structural Studies.

    Science.gov (United States)

    Novosjolova, Irina; Kennedy, Scott D; Rozners, Eriks

    2017-11-02

    The development of nucleic acid base-pair analogues that use new modes of molecular recognition is important both for fundamental research and practical applications. The goal of this study was to evaluate 2-methoxypyridine as a cationic thymidine mimic in the A-T base pair. The hypothesis was that including protonation in the Watson-Crick base pairing scheme would enhance the thermal stability of the DNA double helix without compromising the sequence selectivity. DNA and peptide nucleic acid (PNA) sequences containing the new 2-methoxypyridine nucleobase (P) were synthesized and studied by using UV thermal melting and NMR spectroscopy. Introduction of P nucleobase caused a loss of thermal stability of ≈10 °C in DNA-DNA duplexes and ≈20 °C in PNA-DNA duplexes over a range of mildly acidic to neutral pH. Despite the decrease in thermal stability, the NMR structural studies showed that P-A formed the expected protonated base pair at pH 4.3. Our study demonstrates the feasibility of cationic unnatural base pairs; however, future optimization of such analogues will be required. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Simple sequence repeat marker development from bacterial artificial chromosome end sequences and expressed sequence tags of flax (Linum usitatissimum L.).

    Science.gov (United States)

    Cloutier, Sylvie; Miranda, Evelyn; Ward, Kerry; Radovanovic, Natasa; Reimer, Elsa; Walichnowski, Andrzej; Datla, Raju; Rowland, Gordon; Duguid, Scott; Ragupathy, Raja

    2012-08-01

    Flax is an important oilseed crop in North America and is mostly grown as a fibre crop in Europe. As a self-pollinated diploid with a small estimated genome size of ~370 Mb, flax is well suited for fast progress in genomics. In the last few years, important genetic resources have been developed for this crop. Here, we describe the assessment and comparative analyses of 1,506 putative simple sequence repeats (SSRs) of which, 1,164 were derived from BAC-end sequences (BESs) and 342 from expressed sequence tags (ESTs). The SSRs were assessed on a panel of 16 flax accessions with 673 (58 %) and 145 (42 %) primer pairs being polymorphic in the BESs and ESTs, respectively. With 818 novel polymorphic SSR primer pairs reported in this study, the repertoire of available SSRs in flax has more than doubled from the combined total of 508 of all previous reports. Among nucleotide motifs, trinucleotides were the most abundant irrespective of the class, but dinucleotides were the most polymorphic. SSR length was also positively correlated with polymorphism. Two dinucleotide (AT/TA and AG/GA) and two trinucleotide (AAT/ATA/TAA and GAA/AGA/AAG) motifs and their iterations, different from those reported in many other crops, accounted for more than half of all the SSRs and were also more polymorphic (63.4 %) than the rest of the markers (42.7 %). This improved resource promises to be useful in genetic, quantitative trait loci (QTL) and association mapping as well as for anchoring the physical/genetic map with the whole genome shotgun reference sequence of flax.

  13. Colour interceptions, thermal stability and surface morphology of polyester metal complexes

    International Nuclear Information System (INIS)

    Zohdy, M.H.

    2005-01-01

    Chelating copolymers via grafting of acrylic acid (AAc) and acrylamide (AAm/AAc) comonomer mixture onto polyester micro fiber fabrics (PETMF) using gamma-radiation technique were prepared. The prepared graft chains (PETMF-g-AAc) and (PETMF-g-PAAc/PAAm) acted as chelating sites for some selected transition metal ions. The prepared graft copolymers and their metal complexes were characterized using thermogravimetric analysis (TGA), colour parameters and surface morphology measurements. The colour interception and strength measurements showed that the metal complexation is homogeneously distributed. The results showed that the thermal stability of PETMF was improved after graft copolymerization and metal complexes. Moreover, the degree of grafting enhanced the thermal stability values of the grafted and complexed copolymers up to 25% of magnitude, on the other hand the activation energy of the grafted-copolymer with acrylic acid increased up to 80%. The SEM observation gives further supports to the homogenous distribution of grafting and metal complexation

  14. The rescue and evaluation of FLAG and HIS epitope-tagged Asia 1 type foot-and-mouth disease viruses.

    Science.gov (United States)

    Yang, Bo; Yang, Fan; Zhang, Yan; Liu, Huanan; Jin, Ye; Cao, Weijun; Zhu, Zixiang; Zheng, Haixue; Yin, Hong

    2016-02-02

    The VP1 G-H loop of the foot-and-mouth disease virus (FMDV) contains the primary antigenic site, as well as an Arg-Gly-Asp (RGD) binding motif for the αv-integrin family of cell surface receptors. We anticipated that introducing a foreign epitope tag sequence downstream of the RGD motif would be tolerated by the viral capsid and would not destroy the antigenic site of FMDV. In this study, we have designed, generated, and characterized two recombinant FMDVs with a FLAG tag or histidine (HIS) inserted in the VP1 G-H loop downstream of the RGD motif +9 position. The tagged viruses were genetically stable and exhibited similar growth properties with their parental virus. What is more, the recombinant viruses rFMDV-FLAG and rFMDV-HIS showed neutralization sensitivity to FMDV type Asia1-specific mAbs, as well as to polyclonal antibodies. Additionally, the r1 values of the recombinant viruses were similar to that of the parental virus, indicating that the insertion of FLAG or HIS tag sequences downstream of the RGD motif +9 position do not eradicate the antigenic site of FMDV and do not affect its antigenicity. These results indicated that the G-H loop of Asia1 FMDV is able to effectively display the foreign epitopes, making this a potential approach for novel FMDV vaccines development. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. Mining and gene ontology based annotation of SSR markers from expressed sequence tags of Humulus lupulus

    Science.gov (United States)

    Singh, Swati; Gupta, Sanchita; Mani, Ashutosh; Chaturvedi, Anoop

    2012-01-01

    Humulus lupulus is commonly known as hops, a member of the family moraceae. Currently many projects are underway leading to the accumulation of voluminous genomic and expressed sequence tag sequences in public databases. The genetically characterized domains in these databases are limited due to non-availability of reliable molecular markers. The large data of EST sequences are available in hops. The simple sequence repeat markers extracted from EST data are used as molecular markers for genetic characterization, in the present study. 25,495 EST sequences were examined and assembled to get full-length sequences. Maximum frequency distribution was shown by mononucleotide SSR motifs i.e. 60.44% in contig and 62.16% in singleton where as minimum frequency are observed for hexanucleotide SSR in contig (0.09%) and pentanucleotide SSR in singletons (0.12%). Maximum trinucleotide motifs code for Glutamic acid (GAA) while AT/TA were the most frequent repeat of dinucleotide SSRs. Flanking primer pairs were designed in-silico for the SSR containing sequences. Functional categorization of SSRs containing sequences was done through gene ontology terms like biological process, cellular component and molecular function. PMID:22368382

  16. Thermal stability of novel polyurethane adhesives investigated by TGA

    Directory of Open Access Journals (Sweden)

    Mariusz Mamiński

    2014-05-01

    Full Text Available The objective of the work was an assessment of thermal stability of novel polyurethane wood adhesives by means of TGA. Hyperbranched polyglycerols of various structures were used as polyol components cured with polymeric methylenediphenyldiisocyanate (PMDI or polymeric hexamethylenediisocyanate (PHDI. Resultant adhesives were thermally degraded in temperature range 20 - 500ºC. Performance of polyurethane based on fully aliphatic polyglycerol was inferior to those based on polyglycerols bearing aromatic moieties. The differences in 50%-weight loss temperature achieving 27 - 39°C as well as residual weights at 480 ºC indicate the contribution of aromatic units presence within the macromonomer structure to increased thermal stability of polyurethane upon thermal degradation. Furthermore, temperature of 50% weight loss revealed that thermal stability of the developed hyperbranched polyglycerol-based adhesives was comparable to that of the commercial PUR adhesive.

  17. Electronic archival tags provide first glimpse of bathythermal habitat use by free-ranging adult lake sturgeon Acipenser fulvescens

    Science.gov (United States)

    Briggs, Andrew S.; Hondorp, Darryl W.; Quinlan, Henry R.; Boase, James C.; Mohr, Lloyd C.

    2016-01-01

    Information on lake sturgeon (Acipenser fulvescens) depth and thermal habitat use during non-spawning periods is unavailable due to the difficulty of observing lake sturgeon away from shallow water spawning sites. In 2002 and 2003, lake sturgeon captured in commercial trap nets near Sarnia, Ontario were implanted with archival tags and released back into southern Lake Huron. Five of the 40 tagged individuals were recaptured and were at large for 32, 57, 286, 301, and 880 days. Temperatures and depths recorded by archival tags ranged from 0 to 23.5 ºC and 0.1 to 42.4 m, respectively. For the three lake sturgeon that were at large for over 200 days, temperatures occupied emulated seasonal fluctuations. Two of these fish occupied deeper waters during winter than summer while the other occupied similar depths during non-spawning periods. This study provides important insight into depth and thermal habitat use of lake sturgeon throughout the calendar year along with exploring the feasibility of using archival tags to obtain important physical habitat attributes during non-spawning periods.

  18. Abiotic Stress-Related Expressed Sequence Tags from the Diploid Strawberry Fragaria vesca f. semperflorens

    Directory of Open Access Journals (Sweden)

    Maximo. Rivarola

    2011-03-01

    Full Text Available Strawberry ( spp. is a eudicotyledonous plant that belongs to the Rosaceae family, which includes other agronomically important plants such as raspberry ( L. and several tree-fruit species. Despite the vital role played by cultivated strawberry in agriculture, few stress-related gene expression characterizations of this crop are available. To increase the diversity of available transcriptome sequence, we produced 41,430 L. expressed sequence tags (ESTs from plants growing under water-, temperature-, and osmotic-stress conditions as well as a combination of heat and osmotic stresses that is often found in irrigated fields. Clustering and assembling of the ESTs resulted in a total of 11,836 contigs and singletons that were annotated using Gene Ontology (GO terms. Furthermore, over 1200 sequences with no match to available Rosaceae ESTs were found, including six that were assigned the “response to stress” GO category. Analysis of EST frequency provided an estimate of steady state transcript levels, with 91 sequences exhibiting at least a 20-fold difference between treatments. This EST collection represents a useful resource to advance our understanding of the abiotic stress-response mechanisms in strawberry. The sequence information may be translated to valuable tree crops in the Rosaceae family, where whole-plant treatments are not as simple or practical.

  19. Intraclade heterogeneity in nitrogen utilization by marine prokaryotes revealed using stable isotope probing coupled with tag sequencing (Tag-SIP

    Directory of Open Access Journals (Sweden)

    Michael Morando

    2016-12-01

    Full Text Available Nitrogen can greatly influence the structure and productivity of microbial communities through its relative availability and form. However, roles of specific organisms in the uptake of different nitrogen species remain poorly characterized. Most studies seeking to identify agents of assimilation have been correlative, indirectly linking activity measurements (e.g., nitrate uptake with the presence or absence of biological markers, particularly functional genes and their transcripts. Evidence is accumulating of previously underappreciated functional diversity in major microbial subpopulations, which may confer physiological advantages under certain environmental conditions leading to ecotype divergence. This microdiversity further complicates our view of genetic variation in environmental samples requiring the development of more targeted approaches. Here, next-generation tag sequencing was successfully coupled with stable isotope probing (Tag-SIP to assess the ability of individual phylotypes to assimilate a particular N source. Our results provide the first direct evidence of nitrate utilization by organisms thought to lack the genes required for this process including the heterotrophic clades SAR11 and the Archaeal Marine Group II (MG-II. We also provide new direct evidence of in situ nitrate utilization by the cyanobacterium Prochlorococcus in support of recent findings. Furthermore, these results revealed widespread functional heterogeneity, i.e. different levels of N assimilation within clades, likely reflecting niche partitioning by ecotypes. The addition of nitrate utilization to ecosystem and ecosystem models by these globally dominant clades will likely improve the mechanistic accuracy of these models.

  20. Thermal stability and phase transformations of martensitic Ti–Nb alloys

    Directory of Open Access Journals (Sweden)

    Matthias Bönisch, Mariana Calin, Thomas Waitz, Ajit Panigrahi, Michael Zehetbauer, Annett Gebert, Werner Skrotzki and Jürgen Eckert

    2013-01-01

    Full Text Available Aiming at understanding the governing microstructural phenomena during heat treatments of Ni-free Ti-based shape memory materials for biomedical applications, a series of Ti–Nb alloys with Nb concentrations up to 29 wt% was produced by cold-crucible casting, followed by homogenization treatment and water quenching. Despite the large amount of literature available concerning the thermal stability and ageing behavior of Ti–Nb alloys, only few studies were performed dealing with the isochronal transformation behavior of initially martensitic Ti–Nb alloys. In this work, the formation of martensites (α' and α'' and their stability under different thermal processing conditions were investigated by a combination of x-ray diffraction, differential scanning calorimetry, dilatometry and electron microscopy. The effect of Nb additions on the structural competition in correlation with stable and metastable phase diagrams was also studied. Alloys with 24 wt% Nb or less undergo a transformation sequence on heating from room temperature to 1155 K. In alloys containing >24 wt% Nb α'' martensitically reverts back to β0, which is highly unstable against chemical demixing by formation of isothermal ωiso. During slow cooling from the single phase β domain α precipitates and only very limited amounts of α'' martensite form.

  1. Thermal-Stability and Reconstitution Ability of Listeria Phages P100 and A511

    Directory of Open Access Journals (Sweden)

    Hanie Ahmadi

    2017-12-01

    Full Text Available The study evaluated the thermal-stability of Listeria phages P100 and A511 at temperatures simulating the preparation of ready-to-eat meats. The phage infectivity after heating to 71°C and holding for a minimum of 30 s, before eventually cooling to 4°C were examined. Higher temperatures of 75, 80, and 85°C were also tested to evaluate their effect on phages thermal-stability. This study found that despite minor differences in the amino acid sequences of their structural proteins, the two phages responded differently to high temperatures. P100 activity declined at least 10 log (PFU mL-1 with exposure to 71°C (30 s and falling below the limit of detection (1 log PFU mL-1 while, A511 dropped from 108 to 105 PFU mL-1. Cooling resulted in partial reconstitution of P100 phage particles to 103 PFU mL-1. Exposure to 75°C (30 s abolished A511 activity (8 log PFU mL-1 and both phages showed reconstitution during cooling phase after exposure to 75°C. P100 exhibited reconstitution after treatment at 80°C (30 s, conversely A511 showed no reconstitution activity. Heating P100 to 85°C abolished the reconstitution potential. Substantial differences were found in thermal-stability and reconstitution of the examined phages showing A511 to be more thermo-stable than P100, while P100 exhibited reconstitution during cooling after treatment at 80°C which was absent in A511. The differences in predicted melting temperatures of structural proteins of P100 and A511 were consistent with the observed differences in thermal stability and morphological changes observed with transmission electron microscopy.

  2. Stability of thermal HFB and dissipative thermal RPA

    CERN Document Server

    Tanabe, K

    1999-01-01

    It is shown that, as for a Nilsson + pairing model, the extended stability condition of the thermal Hartree-Fock-Bogoliubov (THFB) solution coincides with the one of the thermal RPA (TRPA) solution unless the pairing constant G is too large. As possible extensions of the TRPA equation in alternative ways describing thermal fluctuation effect, the extended TRPA (ETRPA) and the dissipative TRPA (DTRPA) are discussed. Furthermore, the general microscopic framework of the TRPA predicts the saturation and decrease of giant resonance width in high temperature limit, i.e. the fragmentation width GAMMA sub f propor to(kT) sup ( sup - sup 3 sup ( sup 2 sup ) sup ) and the spreading width GAMMA suparrow down propor to(kT) sup ( sup - sup 1 sup ( sup 2 sup ) sup ).

  3. Hanford Site radioactive mixed waste thermal treatment initiative

    International Nuclear Information System (INIS)

    Place, B.G.; Riddelle, J.G.

    1993-03-01

    This paper is a progress report of current Westinghouse Hanford Company engineering activities related to the implementation of a program for the thermal treatment of the Hanford Site radioactive mixed waste. Topics discussed include a site-specific engineering study, the review of private sector capability in thermal treatment, and thermal treatment of some of the Hanford Site radioactive mixed waste at other US Department of Energy sites

  4. Stabilizing the thermal lattice Boltzmann method by spatial filtering.

    Science.gov (United States)

    Gillissen, J J J

    2016-10-01

    We propose to stabilize the thermal lattice Boltzmann method by filtering the second- and third-order moments of the collision operator. By means of the Chapman-Enskog expansion, we show that the additional numerical diffusivity diminishes in the low-wavnumber limit. To demonstrate the enhanced stability, we consider a three-dimensional thermal lattice Boltzmann system involving 33 discrete velocities. Filtering extends the linear stability of this thermal lattice Boltzmann method to 10-fold smaller transport coefficients. We further demonstrate that the filtering does not compromise the accuracy of the hydrodynamics by comparing simulation results to reference solutions for a number of standardized test cases, including natural convection in two dimensions.

  5. Cloning, analysis and functional annotation of expressed sequence tags from the Earthworm Eisenia fetida

    Science.gov (United States)

    Pirooznia, Mehdi; Gong, Ping; Guan, Xin; Inouye, Laura S; Yang, Kuan; Perkins, Edward J; Deng, Youping

    2007-01-01

    Background Eisenia fetida, commonly known as red wiggler or compost worm, belongs to the Lumbricidae family of the Annelida phylum. Little is known about its genome sequence although it has been extensively used as a test organism in terrestrial ecotoxicology. In order to understand its gene expression response to environmental contaminants, we cloned 4032 cDNAs or expressed sequence tags (ESTs) from two E. fetida libraries enriched with genes responsive to ten ordnance related compounds using suppressive subtractive hybridization-PCR. Results A total of 3144 good quality ESTs (GenBank dbEST accession number EH669363–EH672369 and EL515444–EL515580) were obtained from the raw clone sequences after cleaning. Clustering analysis yielded 2231 unique sequences including 448 contigs (from 1361 ESTs) and 1783 singletons. Comparative genomic analysis showed that 743 or 33% of the unique sequences shared high similarity with existing genes in the GenBank nr database. Provisional function annotation assigned 830 Gene Ontology terms to 517 unique sequences based on their homology with the annotated genomes of four model organisms Drosophila melanogaster, Mus musculus, Saccharomyces cerevisiae, and Caenorhabditis elegans. Seven percent of the unique sequences were further mapped to 99 Kyoto Encyclopedia of Genes and Genomes pathways based on their matching Enzyme Commission numbers. All the information is stored and retrievable at a highly performed, web-based and user-friendly relational database called EST model database or ESTMD version 2. Conclusion The ESTMD containing the sequence and annotation information of 4032 E. fetida ESTs is publicly accessible at . PMID:18047730

  6. Tag-to-Tag Interference Suppression Technique Based on Time Division for RFID

    Directory of Open Access Journals (Sweden)

    Grishma Khadka

    2017-01-01

    Full Text Available Radio-frequency identification (RFID is a tracking technology that enables immediate automatic object identification and rapid data sharing for a wide variety of modern applications using radio waves for data transmission from a tag to a reader. RFID is already well established in technical areas, and many companies have developed corresponding standards and measurement techniques. In the construction industry, effective monitoring of materials and equipment is an important task, and RFID helps to improve monitoring and controlling capabilities, in addition to enabling automation for construction projects. However, on construction sites, there are many tagged objects and multiple RFID tags that may interfere with each other’s communications. This reduces the reliability and efficiency of the RFID system. In this paper, we propose an anti-collision algorithm for communication between multiple tags and a reader. In order to suppress interference signals from multiple neighboring tags, the proposed algorithm employs the time-division (TD technique, where tags in the interrogation zone are assigned a specific time slot so that at every instance in time, a reader communicates with tags using the specific time slot. We present representative computer simulation examples to illustrate the performance of the proposed anti-collision technique for multiple RFID tags.

  7. ConiferEST: an integrated bioinformatics system for data reprocessing and mining of conifer expressed sequence tags (ESTs).

    Science.gov (United States)

    Liang, Chun; Wang, Gang; Liu, Lin; Ji, Guoli; Fang, Lin; Liu, Yuansheng; Carter, Kikia; Webb, Jason S; Dean, Jeffrey F D

    2007-05-29

    With the advent of low-cost, high-throughput sequencing, the amount of public domain Expressed Sequence Tag (EST) sequence data available for both model and non-model organism is growing exponentially. While these data are widely used for characterizing various genomes, they also present a serious challenge for data quality control and validation due to their inherent deficiencies, particularly for species without genome sequences. ConiferEST is an integrated system for data reprocessing, visualization and mining of conifer ESTs. In its current release, Build 1.0, it houses 172,229 loblolly pine EST sequence reads, which were obtained from reprocessing raw DNA sequencer traces using our software--WebTraceMiner. The trace files were downloaded from NCBI Trace Archive. ConiferEST provides biologists unique, easy-to-use data visualization and mining tools for a variety of putative sequence features including cloning vector segments, adapter sequences, restriction endonuclease recognition sites, polyA and polyT runs, and their corresponding Phred quality values. Based on these putative features, verified sequence features such as 3' and/or 5' termini of cDNA inserts in either sense or non-sense strand have been identified in-silico. Interestingly, only 30.03% of the designated 3' ESTs were found to have an authenticated 5' terminus in the non-sense strand (i.e., polyT tails), while fewer than 5.34% of the designated 5' ESTs had a verified 5' terminus in the sense strand. Such previously ignored features provide valuable insight for data quality control and validation of error-prone ESTs, as well as the ability to identify novel functional motifs embedded in large EST datasets. We found that "double-termini adapters" were effective indicators of potential EST chimeras. For all sequences with in-silico verified termini/terminus, we used InterProScan to assign protein domain signatures, results of which are available for in-depth exploration using our biologist

  8. ConiferEST: an integrated bioinformatics system for data reprocessing and mining of conifer expressed sequence tags (ESTs

    Directory of Open Access Journals (Sweden)

    Carter Kikia

    2007-05-01

    Full Text Available Abstract Background With the advent of low-cost, high-throughput sequencing, the amount of public domain Expressed Sequence Tag (EST sequence data available for both model and non-model organism is growing exponentially. While these data are widely used for characterizing various genomes, they also present a serious challenge for data quality control and validation due to their inherent deficiencies, particularly for species without genome sequences. Description ConiferEST is an integrated system for data reprocessing, visualization and mining of conifer ESTs. In its current release, Build 1.0, it houses 172,229 loblolly pine EST sequence reads, which were obtained from reprocessing raw DNA sequencer traces using our software – WebTraceMiner. The trace files were downloaded from NCBI Trace Archive. ConiferEST provides biologists unique, easy-to-use data visualization and mining tools for a variety of putative sequence features including cloning vector segments, adapter sequences, restriction endonuclease recognition sites, polyA and polyT runs, and their corresponding Phred quality values. Based on these putative features, verified sequence features such as 3' and/or 5' termini of cDNA inserts in either sense or non-sense strand have been identified in-silico. Interestingly, only 30.03% of the designated 3' ESTs were found to have an authenticated 5' terminus in the non-sense strand (i.e., polyT tails, while fewer than 5.34% of the designated 5' ESTs had a verified 5' terminus in the sense strand. Such previously ignored features provide valuable insight for data quality control and validation of error-prone ESTs, as well as the ability to identify novel functional motifs embedded in large EST datasets. We found that "double-termini adapters" were effective indicators of potential EST chimeras. For all sequences with in-silico verified termini/terminus, we used InterProScan to assign protein domain signatures, results of which are available

  9. Large-scale Identification of Expressed Sequence Tags (ESTs from Nicotianatabacum by Normalized cDNA Library Sequencing

    Directory of Open Access Journals (Sweden)

    Alvarez S Perez

    2014-12-01

    Full Text Available An expressed sequence tags (EST resource for tobacco plants (Nicotianatabacum was established using high-throughput sequencing of randomly selected clones from one cDNA library representing a range of plant organs (leaf, stem, root and root base. Over 5000 ESTs were generated from the 3’ ends of 8000 clones, analyzed by BLAST searches and categorized functionally. All annotated ESTs were classified into 18 functional categories, unique transcripts involved in energy were the largest group accounting for 831 (32.32% of the annotated ESTs. After excluding 2450 non-significant tentative unique transcripts (TUTs, 100 unique sequences (1.67% of total TUTs were identified from the N. tabacum database. In the array result two genes strongly related to the tobacco mosaic virus (TMV were obtained, one basic form of pathogenesis-related protein 1 precursor (TBT012G08 and ubiquitin (TBT087G01. Both of them were found in the variety Hongda, some other important genes were classified into two groups, one of these implicated in plant development like those genes related to a photosynthetic process (chlorophyll a-b binding protein, photosystem I, ferredoxin I and III, ATP synthase and a further group including genes related to plant stress response (ubiquitin, ubiquitin-like protein SMT3, glycine-rich RNA binding protein, histones and methallothionein. The interesting finding in this study is that two of these genes have never been reported before in N. tabacum (ubiquitin-like protein SMT3 and methallothionein. The array results were confirmed using quantitative PCR.

  10. Screening of hydrocarbons as supercritical ORCs working fluids by thermal stability

    International Nuclear Information System (INIS)

    Dai, Xiaoye; Shi, Lin; An, Qingsong; Qian, Weizhong

    2016-01-01

    Highlights: • A rapid evaluation method for thermal stability of hydrocarbons for ORCs. • Methane and hydrogen are confirmed to be decomposition indicators. • The decomposition temperatures for some hydrocarbons using the rapid method. • Long carbon chain hydrocarbons are not suitable for supercritical ORCs. - Abstract: Organic Rankine Cycle (ORC) systems are widely used for industrial waste heat recovery and renewable energy utilization. The supercritical ORC is currently one of the main development directions due to its low exergy loss, high thermal efficiency and high work output. The thermal stability is the major limitation of organic working fluid selection with high temperature heat sources. This paper presents a rapid experimental method for assessing the thermal stability of hydrocarbons for ORCs. The fluids were tested in a high temperature reactor with methane and hydrogen theoretically and experimentally confirmed to be the indicators of thermal decomposition. The thermal decomposition temperatures were obtained for n-hexane, n-pentane, isopentane, cyclopentane, n-butane and isobutane using the rapid experimental method. The results show that cycloalkanes are not the good choices by thermal stability and long carbon chain hydrocarbons (longer than C6) are not suitable for supercritical ORCs due to the thermal stability limitation.

  11. A simple, flexible and efficient PCR-fusion/Gateway cloning procedure for gene fusion, site-directed mutagenesis, short sequence insertion and domain deletions and swaps

    Directory of Open Access Journals (Sweden)

    Etchells J Peter

    2009-10-01

    Full Text Available Abstract Background The progress and completion of various plant genome sequencing projects has paved the way for diverse functional genomic studies that involve cloning, modification and subsequent expression of target genes. This requires flexible and efficient procedures for generating binary vectors containing: gene fusions, variants from site-directed mutagenesis, addition of protein tags together with domain swaps and deletions. Furthermore, efficient cloning procedures, ideally high throughput, are essential for pyramiding of multiple gene constructs. Results Here, we present a simple, flexible and efficient PCR-fusion/Gateway cloning procedure for construction of binary vectors for a range of gene fusions or variants with single or multiple nucleotide substitutions, short sequence insertions, domain deletions and swaps. Results from selected applications of the procedure which include ORF fusion, introduction of Cys>Ser mutations, insertion of StrepII tag sequence and domain swaps for Arabidopsis secondary cell wall AtCesA genes are demonstrated. Conclusion The PCR-fusion/Gateway cloning procedure described provides an elegant, simple and efficient solution for a wide range of diverse and complicated cloning tasks. Through streamlined cloning of sets of gene fusions and modification variants into binary vectors for systematic functional studies of gene families, our method allows for efficient utilization of the growing sequence and expression data.

  12. Generation and analysis of expressed sequence tags from the ciliate protozoan parasite Ichthyophthirius multifiliis

    Directory of Open Access Journals (Sweden)

    Arias Covadonga

    2007-06-01

    Full Text Available Abstract Background The ciliate protozoan Ichthyophthirius multifiliis (Ich is an important parasite of freshwater fish that causes 'white spot disease' leading to significant losses. A genomic resource for large-scale studies of this parasite has been lacking. To study gene expression involved in Ich pathogenesis and virulence, our goal was to generate expressed sequence tags (ESTs for the development of a powerful microarray platform for the analysis of global gene expression in this species. Here, we initiated a project to sequence and analyze over 10,000 ESTs. Results We sequenced 10,368 EST clones using a normalized cDNA library made from pooled samples of the trophont, tomont, and theront life-cycle stages, and generated 9,769 sequences (94.2% success rate. Post-sequencing processing led to 8,432 high quality sequences. Clustering analysis of these ESTs allowed identification of 4,706 unique sequences containing 976 contigs and 3,730 singletons. These unique sequences represent over two million base pairs (~10% of Plasmodium falciparum genome, a phylogenetically related protozoan. BLASTX searches produced 2,518 significant (E-value -5 hits and further Gene Ontology (GO analysis annotated 1,008 of these genes. The ESTs were analyzed comparatively against the genomes of the related protozoa Tetrahymena thermophila and P. falciparum, allowing putative identification of additional genes. All the EST sequences were deposited by dbEST in GenBank (GenBank: EG957858–EG966289. Gene discovery and annotations are presented and discussed. Conclusion This set of ESTs represents a significant proportion of the Ich transcriptome, and provides a material basis for the development of microarrays useful for gene expression studies concerning Ich development, pathogenesis, and virulence.

  13. Generation and analysis of a barcode-tagged insertion mutant library in the fission yeast Schizosaccharomyces pombe

    Science.gov (United States)

    2012-01-01

    Background Barcodes are unique DNA sequence tags that can be used to specifically label individual mutants. The barcode-tagged open reading frame (ORF) haploid deletion mutant collections in the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe allow for high-throughput mutant phenotyping because the relative growth of mutants in a population can be determined by monitoring the proportions of their associated barcodes. While these mutant collections have greatly facilitated genome-wide studies, mutations in essential genes are not present, and the roles of these genes are not as easily studied. To further support genome-scale research in S. pombe, we generated a barcode-tagged fission yeast insertion mutant library that has the potential of generating viable mutations in both essential and non-essential genes and can be easily analyzed using standard molecular biological techniques. Results An insertion vector containing a selectable ura4+ marker and a random barcode was used to generate a collection of 10,000 fission yeast insertion mutants stored individually in 384-well plates and as six pools of mixed mutants. Individual barcodes are flanked by Sfi I recognition sites and can be oligomerized in a unique orientation to facilitate barcode sequencing. Independent genetic screens on a subset of mutants suggest that this library contains a diverse collection of single insertion mutations. We present several approaches to determine insertion sites. Conclusions This collection of S. pombe barcode-tagged insertion mutants is well-suited for genome-wide studies. Because insertion mutations may eliminate, reduce or alter the function of essential and non-essential genes, this library will contain strains with a wide range of phenotypes that can be assayed by their associated barcodes. The design of the barcodes in this library allows for barcode sequencing using next generation or standard benchtop cloning approaches. PMID:22554201

  14. Generation and analysis of a barcode-tagged insertion mutant library in the fission yeast Schizosaccharomyces pombe

    Directory of Open Access Journals (Sweden)

    Chen Bo-Ruei

    2012-05-01

    Full Text Available Abstract Background Barcodes are unique DNA sequence tags that can be used to specifically label individual mutants. The barcode-tagged open reading frame (ORF haploid deletion mutant collections in the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe allow for high-throughput mutant phenotyping because the relative growth of mutants in a population can be determined by monitoring the proportions of their associated barcodes. While these mutant collections have greatly facilitated genome-wide studies, mutations in essential genes are not present, and the roles of these genes are not as easily studied. To further support genome-scale research in S. pombe, we generated a barcode-tagged fission yeast insertion mutant library that has the potential of generating viable mutations in both essential and non-essential genes and can be easily analyzed using standard molecular biological techniques. Results An insertion vector containing a selectable ura4+ marker and a random barcode was used to generate a collection of 10,000 fission yeast insertion mutants stored individually in 384-well plates and as six pools of mixed mutants. Individual barcodes are flanked by Sfi I recognition sites and can be oligomerized in a unique orientation to facilitate barcode sequencing. Independent genetic screens on a subset of mutants suggest that this library contains a diverse collection of single insertion mutations. We present several approaches to determine insertion sites. Conclusions This collection of S. pombe barcode-tagged insertion mutants is well-suited for genome-wide studies. Because insertion mutations may eliminate, reduce or alter the function of essential and non-essential genes, this library will contain strains with a wide range of phenotypes that can be assayed by their associated barcodes. The design of the barcodes in this library allows for barcode sequencing using next generation or standard benchtop cloning

  15. Exploration of porous SiC nanostructures as thermal insulator with high thermal stability and low thermal conductivity

    Institute of Scientific and Technical Information of China (English)

    Peng; WAN; Jingyang; WANG

    2016-01-01

    The crucial challenge for current nanoscale thermal insulation materials,such as Al2O3 and SiO2 aerogel composites,is to solve the trade-off between extremely low thermal conductivity and unsatisfied thermal stability.Typical high-temperature ceramic SiC possesses excellent mechanical properties and

  16. An active site–tail interaction in the structure of hexahistidine-tagged Thermoplasma acidophilum citrate synthase

    Energy Technology Data Exchange (ETDEWEB)

    Murphy, Jesse R.; Donini, Stefano; Kappock, T. Joseph, E-mail: kappock@purdue.edu [Purdue University, 175 South University Street, West Lafayette, IN 47907-2063 (United States)

    2015-09-23

    Citrate synthase from the thermophilic euryarchaeon T. acidophilum fused to a hexahistidine tag was purified and biochemically characterized. The structure of the unliganded enzyme at 2.2 Å resolution contains tail–active site contacts in half of the active sites. Citrate synthase (CS) plays a central metabolic role in aerobes and many other organisms. The CS reaction comprises two half-reactions: a Claisen aldol condensation of acetyl-CoA (AcCoA) and oxaloacetate (OAA) that forms citryl-CoA (CitCoA), and CitCoA hydrolysis. Protein conformational changes that ‘close’ the active site play an important role in the assembly of a catalytically competent condensation active site. CS from the thermoacidophile Thermoplasma acidophilum (TpCS) possesses an endogenous Trp fluorophore that can be used to monitor the condensation reaction. The 2.2 Å resolution crystal structure of TpCS fused to a C-terminal hexahistidine tag (TpCSH6) reported here is an ‘open’ structure that, when compared with several liganded TpCS structures, helps to define a complete path for active-site closure. One active site in each dimer binds a neighboring His tag, the first nonsubstrate ligand known to occupy both the AcCoA and OAA binding sites. Solution data collectively suggest that this fortuitous interaction is stabilized by the crystalline lattice. As a polar but almost neutral ligand, the active site–tail interaction provides a new starting point for the design of bisubstrate-analog inhibitors of CS.

  17. An active site–tail interaction in the structure of hexahistidine-tagged Thermoplasma acidophilum citrate synthase

    International Nuclear Information System (INIS)

    Murphy, Jesse R.; Donini, Stefano; Kappock, T. Joseph

    2015-01-01

    Citrate synthase from the thermophilic euryarchaeon T. acidophilum fused to a hexahistidine tag was purified and biochemically characterized. The structure of the unliganded enzyme at 2.2 Å resolution contains tail–active site contacts in half of the active sites. Citrate synthase (CS) plays a central metabolic role in aerobes and many other organisms. The CS reaction comprises two half-reactions: a Claisen aldol condensation of acetyl-CoA (AcCoA) and oxaloacetate (OAA) that forms citryl-CoA (CitCoA), and CitCoA hydrolysis. Protein conformational changes that ‘close’ the active site play an important role in the assembly of a catalytically competent condensation active site. CS from the thermoacidophile Thermoplasma acidophilum (TpCS) possesses an endogenous Trp fluorophore that can be used to monitor the condensation reaction. The 2.2 Å resolution crystal structure of TpCS fused to a C-terminal hexahistidine tag (TpCSH6) reported here is an ‘open’ structure that, when compared with several liganded TpCS structures, helps to define a complete path for active-site closure. One active site in each dimer binds a neighboring His tag, the first nonsubstrate ligand known to occupy both the AcCoA and OAA binding sites. Solution data collectively suggest that this fortuitous interaction is stabilized by the crystalline lattice. As a polar but almost neutral ligand, the active site–tail interaction provides a new starting point for the design of bisubstrate-analog inhibitors of CS

  18. Disruption of the Putative Vascular Leak Peptide Sequence in the Stabilized Ricin Vaccine Candidate RTA1-33/44-198

    Directory of Open Access Journals (Sweden)

    Charles B. Millard

    2013-01-01

    Full Text Available Vitetta and colleagues identified and characterized a putative vascular leak peptide (VLP consensus sequence in recombinant ricin toxin A-chain (RTA that contributed to dose-limiting human toxicity when RTA was administered intravenously in large quantities during chemotherapy. We disrupted this potentially toxic site within the more stable RTA1-33/44-198 vaccine immunogen and determined the impact of these mutations on protein stability, structure and protective immunogenicity using an experimental intranasal ricin challenge model in BALB/c mice to determine if the mutations were compatible. Single amino acid substitutions at the positions corresponding with RTA D75 (to A, or N and V76 (to I, or M had minor effects on the apparent protein melting temperature of RTA1-33/44-198 but all four variants retained greater apparent stability than the parent RTA. Moreover, each VLP(− variant tested provided protection comparable with that of RTA1-33/44-198 against supralethal intranasal ricin challenge as judged by animal survival and several biomarkers. To understand better how VLP substitutions and mutations near the VLP site impact epitope structure, we introduced a previously described thermal stabilizing disulfide bond (R48C/T77C along with the D75N or V76I substitutions in RTA1-33/44-198. The D75N mutation was compatible with the adjacent stabilizing R48C/T77C disulfide bond and the Tm was unaffected, whereas the V76I mutation was less compatible with the adjacent disulfide bond involving C77. A crystal structure of the RTA1-33/44-198 R48C/T77C/D75N variant showed that the structural integrity of the immunogen was largely conserved and that a stable immunogen could be produced from E. coli. We conclude that it is feasible to disrupt the VLP site in RTA1-33/44-198 with little or no impact on apparent protein stability or protective efficacy in mice and such variants can be stabilized further by introduction of a disulfide bond.

  19. Engineering [Ln(DPA){sub 3}]{sup 3-} binding sites in proteins: a widely applicable method for tagging proteins with lanthanide ions

    Energy Technology Data Exchange (ETDEWEB)

    Jia Xinying; Yagi, Hiromasa; Su Xuncheng; Stanton-Cook, Mitchell; Huber, Thomas; Otting, Gottfried, E-mail: gottfried.otting@anu.edu.au [Australian National University, Research School of Chemistry (Australia)

    2011-08-15

    Paramagnetic relaxation enhancements from unpaired electrons observed in nuclear magnetic resonance (NMR) spectra present powerful long-range distance restraints. The most frequently used paramagnetic tags, however, are tethered to the protein via disulfide bonds, requiring proteins with single cysteine residues for covalent attachment. Here we present a straightforward strategy to tag proteins site-specifically with paramagnetic lanthanides without a tether and independent of cysteine residues. It relies on preferential binding of the complex between three dipicolinic acid molecules (DPA) and a lanthanide ion (Ln{sup 3+}), [Ln(DPA){sub 3}]{sup 3-}, to a pair of positively charged amino acids whose charges are not compensated by negatively charged residues nearby. This situation rarely occurs in wild-type proteins, allowing the creation of specific binding sites simply by introduction of positively charged residues that are positioned far from glutamate or aspartate residues. The concept is demonstrated with the hnRNPLL RRM1 domain. In addition, we show that histidine- and arginine-tags present binding sites for [Ln(DPA){sub 3}]{sup 3-}.

  20. An Ambystoma mexicanum EST sequencing project: analysis of 17,352 expressed sequence tags from embryonic and regenerating blastema cDNA libraries

    Science.gov (United States)

    Habermann, Bianca; Bebin, Anne-Gaelle; Herklotz, Stephan; Volkmer, Michael; Eckelt, Kay; Pehlke, Kerstin; Epperlein, Hans Henning; Schackert, Hans Konrad; Wiebe, Glenis; Tanaka, Elly M

    2004-01-01

    Background The ambystomatid salamander, Ambystoma mexicanum (axolotl), is an important model organism in evolutionary and regeneration research but relatively little sequence information has so far been available. This is a major limitation for molecular studies on caudate development, regeneration and evolution. To address this lack of sequence information we have generated an expressed sequence tag (EST) database for A. mexicanum. Results Two cDNA libraries, one made from stage 18-22 embryos and the other from day-6 regenerating tail blastemas, generated 17,352 sequences. From the sequenced ESTs, 6,377 contigs were assembled that probably represent 25% of the expressed genes in this organism. Sequence comparison revealed significant homology to entries in the NCBI non-redundant database. Further examination of this gene set revealed the presence of genes involved in important cell and developmental processes, including cell proliferation, cell differentiation and cell-cell communication. On the basis of these data, we have performed phylogenetic analysis of key cell-cycle regulators. Interestingly, while cell-cycle proteins such as the cyclin B family display expected evolutionary relationships, the cyclin-dependent kinase inhibitor 1 gene family shows an unusual evolutionary behavior among the amphibians. Conclusions Our analysis reveals the importance of a comprehensive sequence set from a representative of the Caudata and illustrates that the EST sequence database is a rich source of molecular, developmental and regeneration studies. To aid in data mining, the ESTs have been organized into an easily searchable database that is freely available online. PMID:15345051

  1. Thermal stability of biodiesel and its blends: A review

    Energy Technology Data Exchange (ETDEWEB)

    Jain, Siddharth; Sharma, M.P. [Biofuel Research Laboratory, Alternate Hydro Energy Centre, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667 (India)

    2011-01-15

    The vegetable oil, fats and their biodiesel suffer with the drawback of deterioration of its quality during long term storage unlike petroleum diesel due to large number of environmental and other factors making the fuel stability and quality questionable. There are various types of stabilities like oxidation, storage and thermal, playing key roles in making the fuel unstable. The present paper is an attempt to review the work done so far on the thermal stability of biodiesel and their blends with diesel under different conditions. The mechanism of thermal deterioration of vegetable oils, various methods of stability measurement including a new proposed method based on Karl Fischer coulometer, an alternative to conventional Rancimat test has been discussed. No correlations have been found in the literature among the results of various methods used. The effect of antioxidants on the stability parameters has also been discussed. TGA/DTA has been found as an effective method to check the deterioration of oil with respect to temperature using activation energy and order of reaction as the parameter to monitor the deterioration of oil. (author)

  2. Expression sequence tag library derived from peripheral blood mononuclear cells of the chlorocebus sabaeus

    Directory of Open Access Journals (Sweden)

    Tchitchek Nicolas

    2012-06-01

    Full Text Available Abstract Background African Green Monkeys (AGM are amongst the most frequently used nonhuman primate models in clinical and biomedical research, nevertheless only few genomic resources exist for this species. Such information would be essential for the development of dedicated new generation technologies in fundamental and pre-clinical research using this model, and would deliver new insights into primate evolution. Results We have exhaustively sequenced an Expression Sequence Tag (EST library made from a pool of Peripheral Blood Mononuclear Cells from sixteen Chlorocebus sabaeus monkeys. Twelve of them were infected with the Simian Immunodeficiency Virus. The mononuclear cells were or not stimulated in vitro with Concanavalin A, with lipopolysacharrides, or through mixed lymphocyte reaction in order to generate a representative and broad library of expressed sequences in immune cells. We report here 37,787 sequences, which were assembled into 14,410 contigs representing an estimated 12% of the C. sabaeus transcriptome. Using data from primate genome databases, 9,029 assembled sequences from C. sabaeus could be annotated. Sequences have been systematically aligned with ten cDNA references of primate species including Homo sapiens, Pan troglodytes, and Macaca mulatta to identify ortholog transcripts. For 506 transcripts, sequences were quasi-complete. In addition, 6,576 transcript fragments are potentially specific to the C. sabaeus or corresponding to not yet described primate genes. Conclusions The EST library we provide here will prove useful in gene annotation efforts for future sequencing of the African Green Monkey genomes. Furthermore, this library, which particularly well represents immunological and hematological gene expression, will be an important resource for the comparative analysis of gene expression in clinically relevant nonhuman primate and human research.

  3. Study on the effect of shape-stabilized phase change materials on spacecraft thermal control in extreme thermal environment

    International Nuclear Information System (INIS)

    Wu, Wan-fan; Liu, Na; Cheng, Wen-long; Liu, Yi

    2013-01-01

    Highlights: ► A shape-stabilized PCM is used to protect the spacecraft attacked by high energy. ► Taking a satellite as example, it proves the solution given in the work is feasible. ► Low thermal conductivity makes the material above its thermal stability limit. ► It provides guidance on how to choose the shape-stabilized PCM for similar problems. - Abstract: In space, the emergencies such as short-term high heat flux is prone to cause spacecraft thermal control system faults, resulting in temperature anomalies of electronic equipment of the spacecraft and even failures in them. In order to protect the spacecraft attacked by the high energy, a new guard method is proposed. A shape-stabilized phase change material (PCM), which has high thermal conductivity and does not require being tightly packaged, is proposed to be used on the spacecraft. To prove the feasibility of using the material on spacecraft attacked by high energy, the thermal responses for spacecraft with shape-stabilized PCM are investigated in situations of normal and short-term high heat flux, in contrast to that with conventional thermal control system. The results indicate that the shape-stabilized PCM can effectively absorb the heat to prevent the thermal control system faults when the spacecraft’s outer heat flux changes dramatically and has no negative effect on spacecraft in normal heat flux. Additionally the effect of thermal conductivity of PCM on its application effectiveness is discussed

  4. The contribution of 700,000 ORF sequence tags to the definition of the human transcriptome

    Science.gov (United States)

    Camargo, Anamaria A.; Samaia, Helena P. B.; Dias-Neto, Emmanuel; Simão, Daniel F.; Migotto, Italo A.; Briones, Marcelo R. S.; Costa, Fernando F.; Aparecida Nagai, Maria; Verjovski-Almeida, Sergio; Zago, Marco A.; Andrade, Luis Eduardo C.; Carrer, Helaine; El-Dorry, Hamza F. A.; Espreafico, Enilza M.; Habr-Gama, Angelita; Giannella-Neto, Daniel; Goldman, Gustavo H.; Gruber, Arthur; Hackel, Christine; Kimura, Edna T.; Maciel, Rui M. B.; Marie, Suely K. N.; Martins, Elizabeth A. L.; Nóbrega, Marina P.; Paçó-Larson, Maria Luisa; Pardini, Maria Inês M. C.; Pereira, Gonçalo G.; Pesquero, João Bosco; Rodrigues, Vanderlei; Rogatto, Silvia R.; da Silva, Ismael D. C. G.; Sogayar, Mari C.; Sonati, Maria de Fátima; Tajara, Eloiza H.; Valentini, Sandro R.; Alberto, Fernando L.; Amaral, Maria Elisabete J.; Aneas, Ivy; Arnaldi, Liliane A. T.; de Assis, Angela M.; Bengtson, Mário Henrique; Bergamo, Nadia Aparecida; Bombonato, Vanessa; de Camargo, Maria E. R.; Canevari, Renata A.; Carraro, Dirce M.; Cerutti, Janete M.; Corrêa, Maria Lucia C.; Corrêa, Rosana F. R.; Costa, Maria Cristina R.; Curcio, Cyntia; Hokama, Paula O. M.; Ferreira, Ari J. S.; Furuzawa, Gilberto K.; Gushiken, Tsieko; Ho, Paulo L.; Kimura, Elza; Krieger, José E.; Leite, Luciana C. C.; Majumder, Paromita; Marins, Mozart; Marques, Everaldo R.; Melo, Analy S. A.; Melo, Monica; Mestriner, Carlos Alberto; Miracca, Elisabete C.; Miranda, Daniela C.; Nascimento, Ana Lucia T. O.; Nóbrega, Francisco G.; Ojopi, Élida P. B.; Pandolfi, José Rodrigo C.; Pessoa, Luciana G.; Prevedel, Aline C.; Rahal, Paula; Rainho, Claudia A.; Reis, Eduardo M. R.; Ribeiro, Marcelo L.; da Rós, Nancy; de Sá, Renata G.; Sales, Magaly M.; Sant'anna, Simone Cristina; dos Santos, Mariana L.; da Silva, Aline M.; da Silva, Neusa P.; Silva, Wilson A.; da Silveira, Rosana A.; Sousa, Josane F.; Stecconi, Daniella; Tsukumo, Fernando; Valente, Valéria; Soares, Fernando; Moreira, Eloisa S.; Nunes, Diana N.; Correa, Ricardo G.; Zalcberg, Heloisa; Carvalho, Alex F.; Reis, Luis F. L.; Brentani, Ricardo R.; Simpson, Andrew J. G.; de Souza, Sandro J.

    2001-01-01

    Open reading frame expressed sequences tags (ORESTES) differ from conventional ESTs by providing sequence data from the central protein coding portion of transcripts. We generated a total of 696,745 ORESTES sequences from 24 human tissues and used a subset of the data that correspond to a set of 15,095 full-length mRNAs as a means of assessing the efficiency of the strategy and its potential contribution to the definition of the human transcriptome. We estimate that ORESTES sampled over 80% of all highly and moderately expressed, and between 40% and 50% of rarely expressed, human genes. In our most thoroughly sequenced tissue, the breast, the 130,000 ORESTES generated are derived from transcripts from an estimated 70% of all genes expressed in that tissue, with an equally efficient representation of both highly and poorly expressed genes. In this respect, we find that the capacity of the ORESTES strategy both for gene discovery and shotgun transcript sequence generation significantly exceeds that of conventional ESTs. The distribution of ORESTES is such that many human transcripts are now represented by a scaffold of partial sequences distributed along the length of each gene product. The experimental joining of the scaffold components, by reverse transcription–PCR, represents a direct route to transcript finishing that may represent a useful alternative to full-length cDNA cloning. PMID:11593022

  5. The contribution of 700,000 ORF sequence tags to the definition of the human transcriptome.

    Science.gov (United States)

    Camargo, A A; Samaia, H P; Dias-Neto, E; Simão, D F; Migotto, I A; Briones, M R; Costa, F F; Nagai, M A; Verjovski-Almeida, S; Zago, M A; Andrade, L E; Carrer, H; El-Dorry, H F; Espreafico, E M; Habr-Gama, A; Giannella-Neto, D; Goldman, G H; Gruber, A; Hackel, C; Kimura, E T; Maciel, R M; Marie, S K; Martins, E A; Nobrega, M P; Paco-Larson, M L; Pardini, M I; Pereira, G G; Pesquero, J B; Rodrigues, V; Rogatto, S R; da Silva, I D; Sogayar, M C; Sonati, M F; Tajara, E H; Valentini, S R; Alberto, F L; Amaral, M E; Aneas, I; Arnaldi, L A; de Assis, A M; Bengtson, M H; Bergamo, N A; Bombonato, V; de Camargo, M E; Canevari, R A; Carraro, D M; Cerutti, J M; Correa, M L; Correa, R F; Costa, M C; Curcio, C; Hokama, P O; Ferreira, A J; Furuzawa, G K; Gushiken, T; Ho, P L; Kimura, E; Krieger, J E; Leite, L C; Majumder, P; Marins, M; Marques, E R; Melo, A S; Melo, M B; Mestriner, C A; Miracca, E C; Miranda, D C; Nascimento, A L; Nobrega, F G; Ojopi, E P; Pandolfi, J R; Pessoa, L G; Prevedel, A C; Rahal, P; Rainho, C A; Reis, E M; Ribeiro, M L; da Ros, N; de Sa, R G; Sales, M M; Sant'anna, S C; dos Santos, M L; da Silva, A M; da Silva, N P; Silva, W A; da Silveira, R A; Sousa, J F; Stecconi, D; Tsukumo, F; Valente, V; Soares, F; Moreira, E S; Nunes, D N; Correa, R G; Zalcberg, H; Carvalho, A F; Reis, L F; Brentani, R R; Simpson, A J; de Souza, S J; Melo, M

    2001-10-09

    Open reading frame expressed sequences tags (ORESTES) differ from conventional ESTs by providing sequence data from the central protein coding portion of transcripts. We generated a total of 696,745 ORESTES sequences from 24 human tissues and used a subset of the data that correspond to a set of 15,095 full-length mRNAs as a means of assessing the efficiency of the strategy and its potential contribution to the definition of the human transcriptome. We estimate that ORESTES sampled over 80% of all highly and moderately expressed, and between 40% and 50% of rarely expressed, human genes. In our most thoroughly sequenced tissue, the breast, the 130,000 ORESTES generated are derived from transcripts from an estimated 70% of all genes expressed in that tissue, with an equally efficient representation of both highly and poorly expressed genes. In this respect, we find that the capacity of the ORESTES strategy both for gene discovery and shotgun transcript sequence generation significantly exceeds that of conventional ESTs. The distribution of ORESTES is such that many human transcripts are now represented by a scaffold of partial sequences distributed along the length of each gene product. The experimental joining of the scaffold components, by reverse transcription-PCR, represents a direct route to transcript finishing that may represent a useful alternative to full-length cDNA cloning.

  6. Thermal stability of manganese-stabilized stainless steels

    International Nuclear Information System (INIS)

    Klueh, R.L.; Kenik, E.A.

    1993-01-01

    Previous work on a series of experimental high-manganese reduced-activation austenitic stainless steels demonstrated that they have improved tensile properties relative to type 316 stainless steel in both the annealed and 20% cold-worked conditions. Steels were tested with an Fe-20Mn-12Cr-0.25C (in weight percent) base composition, to which various combinations of Ti, W, V, P, and B were added. Tensile tests have now been completed on these steels after thermal aging at 600 degrees C. Thermal stability varied with composition, but the alloys were as stable or more stable than type 316 stainless steel. the strength of the annealed steels increased slightly after aging to 5000 h, while a strength decrease occurred for the cold worked steel. In both conditions, a steel containing a combination of all the alloying elements was most stable and had the best strength after thermal aging 5000 h at 600 degrees C. Despite having much higher strength than 316 stainless steel after aging, the ductility of the strongest experimental alloy was still as good as that of 316 stainless steel

  7. Thermal Site Descriptive Model. A strategy for the model development during site investigations. Version 1.0

    International Nuclear Information System (INIS)

    Sundberg, Jan

    2003-04-01

    Site investigations are in progress for the siting of a deep repository for spent nuclear fuel. As part of the planning work, strategies are developed for site descriptive modelling regarding different disciplines, amongst them the thermal conditions. The objective of the strategy for a thermal site descriptive model is to guide the practical implementation of evaluating site specific data during the site investigations. It is understood that further development may be needed. The model describes the thermal properties and other thermal parameters of intact rock, fractures and fracture zones, and of the rock mass. The methodology is based on estimation of thermal properties of intact rock and discontinuities, using both empirical and theoretical/numerical approaches, and estimation of thermal processes using mathematical modelling. The methodology will be used and evaluated for the thermal site descriptive modelling at the Aespoe Hard Rock Laboratory

  8. Social tagging in support of cancer patients’ information interaction

    DEFF Research Database (Denmark)

    Ådland, Marit Kristine; Lykke, Marianne

    2012-01-01

    Purpose: The purpose of this paper is to explore whether and how social tagging can be useful in an information website for cancer patients and their relatives. Methodology/approach: Three studies have been carried out in order to investigate the research questions. Firstly, we reviewed and analy......Purpose: The purpose of this paper is to explore whether and how social tagging can be useful in an information website for cancer patients and their relatives. Methodology/approach: Three studies have been carried out in order to investigate the research questions. Firstly, we reviewed...... and analyzed literature about cancer patients’ information needs and seeking behavior, and about social tagging and patient terminology. Secondly, we analyzed tags applied to blog postings at Blogomkraeft.dk, a blog site at the Danish information web site Cancer.dk. The tags were compared with the formal...... browsing structure of Cancer.dk. Results from the two studies were used to develop a prototype for social tagging at Cancer.dk. Thus thirdly, we evaluated the prototype in a usability study. Findings: We found that tags have the potential to describe and provide access to web site content from the users...

  9. Structural changes and thermal stability of charged LiNixMnyCozO₂ cathode materials studied by combined in situ time-resolved XRD and mass spectroscopy.

    Science.gov (United States)

    Bak, Seong-Min; Hu, Enyuan; Zhou, Yongning; Yu, Xiqian; Senanayake, Sanjaya D; Cho, Sung-Jin; Kim, Kwang-Bum; Chung, Kyung Yoon; Yang, Xiao-Qing; Nam, Kyung-Wan

    2014-12-24

    Thermal stability of charged LiNixMnyCozO2 (NMC, with x + y + z = 1, x:y:z = 4:3:3 (NMC433), 5:3:2 (NMC532), 6:2:2 (NMC622), and 8:1:1 (NMC811)) cathode materials is systematically studied using combined in situ time-resolved X-ray diffraction and mass spectroscopy (TR-XRD/MS) techniques upon heating up to 600 °C. The TR-XRD/MS results indicate that the content of Ni, Co, and Mn significantly affects both the structural changes and the oxygen release features during heating: the more Ni and less Co and Mn, the lower the onset temperature of the phase transition (i.e., thermal decomposition) and the larger amount of oxygen release. Interestingly, the NMC532 seems to be the optimized composition to maintain a reasonably good thermal stability, comparable to the low-nickel-content materials (e.g., NMC333 and NMC433), while having a high capacity close to the high-nickel-content materials (e.g., NMC811 and NMC622). The origin of the thermal decomposition of NMC cathode materials was elucidated by the changes in the oxidation states of each transition metal (TM) cations (i.e., Ni, Co, and Mn) and their site preferences during thermal decomposition. It is revealed that Mn ions mainly occupy the 3a octahedral sites of a layered structure (R3̅m) but Co ions prefer to migrate to the 8a tetrahedral sites of a spinel structure (Fd3̅m) during the thermal decomposition. Such element-dependent cation migration plays a very important role in the thermal stability of NMC cathode materials. The reasonably good thermal stability and high capacity characteristics of the NMC532 composition is originated from the well-balanced ratio of nickel content to manganese and cobalt contents. This systematic study provides insight into the rational design of NMC-based cathode materials with a desired balance between thermal stability and high energy density.

  10. Characteristics of the Lotus japonicus gene repertoire deduced from large-scale expressed sequence tag (EST) analysis.

    Science.gov (United States)

    Asamizu, Erika; Nakamura, Yasukazu; Sato, Shusei; Tabata, Satoshi

    2004-02-01

    To perform a comprehensive analysis of genes expressed in a model legume, Lotus japonicus, a total of 74472 3'-end expressed sequence tags (EST) were generated from cDNA libraries produced from six different organs. Clustering of sequences was performed with an identity criterion of 95% for 50 bases, and a total of 20457 non-redundant sequences, 8503 contigs and 11954 singletons were generated. EST sequence coverage was analyzed by using the annotated L. japonicus genomic sequence and 1093 of the 1889 predicted protein-encoding genes (57.9%) were hit by the EST sequence(s). Gene content was compared to several plant species. Among the 8503 contigs, 471 were identified as sequences conserved only in leguminous species and these included several disease resistance-related genes. This suggested that in legumes, these genes may have evolved specifically to resist pathogen attack. The rate of gene sequence divergence was assessed by comparing similarity level and functional category based on the Gene Ontology (GO) annotation of Arabidopsis genes. This revealed that genes encoding ribosomal proteins, as well as those related to translation, photosynthesis, and cellular structure were more abundantly represented in the highly conserved class, and that genes encoding transcription factors and receptor protein kinases were abundantly represented in the less conserved class. To make the sequence information and the cDNA clones available to the research community, a Web database with useful services was created at http://www.kazusa.or.jp/en/plant/lotus/EST/.

  11. Evaluation of gamma ray durability and its application of shielded RF tags

    International Nuclear Information System (INIS)

    Teraura, Nobuyuki; Ito, Kunio; Kobayashi, Daisuke; Sakurai, Kouichi

    2015-01-01

    In this study, the RF (Radio Frequency) tag with radiation shield is developed and its gamma ray durability is evaluated. RFID (RF Identification) is a radio-wave-based identification technology that can be used for various items. RF tags find use in many applications, including item tracing, access control, etc. RF tags can be classified as active RF tags, which have inbuilt voltaic cells, and passive RF tags without these cells. Passive RF tags, known for their low price and durability, are used in various fields. For instance, they are used for equipment maintenance in factories and thermal power plants. Several frequencies are used for RF tags. Further, RF tagging on the UHF (Ultra High Frequency) frequencies allows a communication range of approximately 10 m, and thus, remote reading is possible. When used in radiation environments such as in nuclear power plants, remote reading can contribute to the reduction of radiation exposure. However, because semiconductors are the primary elements used in the manufacture of RF tags, they can be damaged by radiation, and operational errors can occur. Therefore, this technology has not been used in environments affected by relatively high radiation levels. Therefore, in nuclear power plants, the use of RF tags is limited in areas of low radiation levels. In our study, we develop and manufacture a new RF tag with a radiation shield cover that provides error correction functionality. It is expected that radiation shielded RF tags will improve the radiation-proof feature, and its application range will be expanded. Using the radiation-proof RF tag, we have conducted radiation durability tests. These tests are of two types: one using low energy gamma ray, and the other using high-energy gamma ray. Experimental results are then analyzed. The number of applications for radiation shielded RF tags is considerably increasing, because it can be used in various radiation environments other than nuclear power plants as well, such as

  12. Cap stabilization for reclaimed uranium sites

    International Nuclear Information System (INIS)

    Abt, S.R.; Nelson, J.D.; Johnson, T.L.; Hawkins, E.F.

    1989-01-01

    The reclamation and stabilization of uranium-mill tailings sites requires engineering designs to protect against the disruption of tailings and the potential release of radioactive materials. The reclamation design is to be effective for 200-1000 years. This paper presents recently developed or refined techniques and methodologies used to evaluate uranium-tailings-reclamation plans designed to provide long-term stability against failure modes. Specific cap-design aspects presented include design flood selection, influence of fluvial geomorphology on site stabilization, stable slope prediction, slope stabilization using riprap, and riprap selection relative to rock quality and durability. Design relationships are presented for estimating flow through riprap, sizing riprap, and estimating riprap flow resistance for overtopping conditions. Guidelines for riprap-layer thickness and gradation are presented. A riprap-rating procedure for estimating rock quality and durability is also presented

  13. Thermal stability analysis and modelling of advanced perpendicular magnetic tunnel junctions

    Science.gov (United States)

    Van Beek, Simon; Martens, Koen; Roussel, Philippe; Wu, Yueh Chang; Kim, Woojin; Rao, Siddharth; Swerts, Johan; Crotti, Davide; Linten, Dimitri; Kar, Gouri Sankar; Groeseneken, Guido

    2018-05-01

    STT-MRAM is a promising non-volatile memory for high speed applications. The thermal stability factor (Δ = Eb/kT) is a measure for the information retention time, and an accurate determination of the thermal stability is crucial. Recent studies show that a significant error is made using the conventional methods for Δ extraction. We investigate the origin of the low accuracy. To reduce the error down to 5%, 1000 cycles or multiple ramp rates are necessary. Furthermore, the thermal stabilities extracted from current switching and magnetic field switching appear to be uncorrelated and this cannot be explained by a macrospin model. Measurements at different temperatures show that self-heating together with a domain wall model can explain these uncorrelated Δ. Characterizing self-heating properties is therefore crucial to correctly determine the thermal stability.

  14. DNA repair-related genes in sugarcane expressed sequence tags (ESTs

    Directory of Open Access Journals (Sweden)

    R.M.A. Costa

    2001-12-01

    Full Text Available There is much interest in the identification and characterization of genes involved in DNA repair because of their importance in the maintenance of the genome integrity. The high level of conservation of DNA repair genes means that these genetic elements may be used in phylogenetic studies as a source of information on the genetic origin and evolution of species. The mechanisms by which damaged DNA is repaired are well understood in bacteria, yeast and mammals, but much remains to be learned as regards plants. We identified genes involved in DNA repair mechanisms in sugarcane using a similarity search of the Brazilian Sugarcane Expressed Sequence Tag (SUCEST database against known sequences deposited in other public databases (National Center of Biotechnology Information (NCBI database and the Munich Information Center for Protein Sequences (MIPS Arabidopsis thaliana database. This search revealed that most of the various proteins involved in DNA repair in sugarcane are similar to those found in other eukaryotes. However, we also identified certain intriguing features found only in plants, probably due to the independent evolution of this kingdom. The DNA repair mechanisms investigated include photoreactivation, base excision repair, nucleotide excision repair, mismatch repair, non-homologous end joining, homologous recombination repair and DNA lesion tolerance. We report the main differences found in the DNA repair machinery in plant cells as compared to other organisms. These differences point to potentially different strategies plants employ to deal with DNA damage, that deserve further investigation.A identificação e caracterização de genes envolvidos com reparo de DNA são de grande interesse, dada a sua importância na manutenção da integridade genômica. Além disso, a alta conservação dos genes de reparo de DNA faz com que possam ser utilizados como fonte de informação no que diz respeito à origem e evolução das esp

  15. Genetic stability of attenuated mengovirus vectors with duplicate primary cleavage sequences

    International Nuclear Information System (INIS)

    Binder, J.J.; Hoffman, M.A.; Palmenberg, A.C.

    2003-01-01

    Short poly(C)-tract Mengoviruses have proven vaccine efficacy in many species of animals. A novel vector for the delivery of foreign proteins was created by insertion of a second autoproteolytic primary cleavage cassette linked to a multiple cloning site (MCS) into an attenuated variant of Mengo. Nineteen cDNAs from foreign sequences that ranged from 39 to 1653 bases were cloned into the MCS. The viral reading frame was maintained and translation resulted in dual, autocatalytic excision of the foreign peptides without disruption of any Mengo proteins. All cDNAs except those with the largest insertions produced viable virus. Active proteins such as GFP, CAT, and SIV p27 were expressed within infected cells. Relative to parental Mengo, the growth kinetics and genetic stability of each vector was inversely proportional to the size of the inserted sequence. While segments up to 1000 bases could be carried, inserts greater than 500-600 bases were usually reduced in size during serial passage. The limit on carrying capacity was probably due to difficulties in virion assembly or particle stability. Yet for inserts less than 500-600 bases, the Mengo vectors provided an effective system for the delivery of foreign epitopes into cells and mice

  16. Thermal and mechanical stability of zeolitic imidazolate frameworks polymorphs

    Directory of Open Access Journals (Sweden)

    Lila Bouëssel du Bourg

    2014-12-01

    Full Text Available Theoretical studies on the experimental feasibility of hypothetical Zeolitic Imidazolate Frameworks (ZIFs have focused so far on relative energy of various polymorphs by energy minimization at the quantum chemical level. We present here a systematic study of stability of 18 ZIFs as a function of temperature and pressure by molecular dynamics simulations. This approach allows us to better understand the limited stability of some experimental structures upon solvent or guest removal. We also find that many of the hypothetical ZIFs proposed in the literature are not stable at room temperature. Mechanical and thermal stability criteria thus need to be considered for the prediction of new MOF structures. Finally, we predict a variety of thermal expansion behavior for ZIFs as a function of framework topology, with some materials showing large negative volume thermal expansion.

  17. Development and application of sequence-tagged microsatellite site (STMS) markers in chickpea (Cicer arietinum), banana (Musa spp.) and their major pathogens, Ascochyta rabiei and Mycosphaerella fijiensis

    International Nuclear Information System (INIS)

    Winter, P.; Kaemmer, D.; Paff, T.; Geistlinger, J.; Neu, C.; Kahl, G.

    2001-01-01

    DNA markers of various kinds have found widespread application in many facets of plant breeding and plant pathogen control. Yet another marker type, sequence-tagged microsatellite (STMS) markers, provides the markers of choice for nearly every crop because of their co-dominant nature, reliability, ease of application and high polymorphic information content. We report here on the development of a whole set of STMS markers and the respective, selected primer sequences for two important crops, chickpea (Cicer arietinum L.) and banana (Musa acuminata), and for their most devastating fungal pathogens, Ascochyta rabiei and Mycosphaerella fijiensis, respectively. These markers were generated either by direct screening of size-selected genomic libraries with microsatellite-complementary oligonucleotides, or by enrichment of DNA fragments containing microsatellite sequences. A total of 69 markers for chickpea, 15 markers for M. acuminata, 19 markers for A rabiei and 11 markers for M. fijiensis, selected on the basis of their high information content and ease of use are presented here. These can be applied for mapping of the respective genomes, for various population studies, and cultivar and isolate identification. We further demonstrate that several of these markers can potentially be applied across species boundaries and thus could increase the marker repertoire also for other species of the genus Cicer, Musa and for Ascochyta-type pathogens of bean, and potentially also of lentil and pea. (author)

  18. PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality

    Directory of Open Access Journals (Sweden)

    Rooman Marianne

    2011-05-01

    Full Text Available Abstract Background The rational design of modified proteins with controlled stability is of extreme importance in a whole range of applications, notably in the biotechnological and environmental areas, where proteins are used for their catalytic or other functional activities. Future breakthroughs in medical research may also be expected from an improved understanding of the effect of naturally occurring disease-causing mutations on the molecular level. Results PoPMuSiC-2.1 is a web server that predicts the thermodynamic stability changes caused by single site mutations in proteins, using a linear combination of statistical potentials whose coefficients depend on the solvent accessibility of the mutated residue. PoPMuSiC presents good prediction performances (correlation coefficient of 0.8 between predicted and measured stability changes, in cross validation, after exclusion of 10% outliers. It is moreover very fast, allowing the prediction of the stability changes resulting from all possible mutations in a medium size protein in less than a minute. This unique functionality is user-friendly implemented in PoPMuSiC and is particularly easy to exploit. Another new functionality of our server concerns the estimation of the optimality of each amino acid in the sequence, with respect to the stability of the structure. It may be used to detect structural weaknesses, i.e. clusters of non-optimal residues, which represent particularly interesting sites for introducing targeted mutations. This sequence optimality data is also expected to have significant implications in the prediction and the analysis of particular structural or functional protein regions. To illustrate the interest of this new functionality, we apply it to a dataset of known catalytic sites, and show that a much larger than average concentration of structural weaknesses is detected, quantifying how these sites have been optimized for function rather than stability. Conclusion The

  19. Lanthanide phosphonates: Synthesis, thermal stability and magnetic characterization

    Energy Technology Data Exchange (ETDEWEB)

    Amghouz, Z., E-mail: amghouz.uo@uniovi.es [Departamentos de Quimica Fisica y Analitica y Quimica Organica e Inorganica, Universidad de Oviedo - CINN, 33006 Oviedo (Spain); Garcia, J.R.; Garcia-Granda, S. [Departamentos de Quimica Fisica y Analitica y Quimica Organica e Inorganica, Universidad de Oviedo - CINN, 33006 Oviedo (Spain); Clearfield, A. [Department of Chemistry, Texas A and M University, College Station, TX 77842-3012 (United States); Rodriguez Fernandez, J.; Pedro, I. de [CITIMAC, Facultad de Ciencias, Universidad de Cantabria, 39005 Santander (Spain); Blanco, J.A. [Departamento de Fisica, Universidad de Oviedo, 33007 Oviedo (Spain)

    2012-09-25

    Highlights: Black-Right-Pointing-Pointer Report of the complete series of lanthanide 1,4-phenylbis(phosphonate). Black-Right-Pointing-Pointer Synthesis under conventional hydrothermal synthesis or microwave-assisted hydrothermal synthesis. Black-Right-Pointing-Pointer Cation size is the key factor for the structural and particles size variations. Black-Right-Pointing-Pointer Thermal behaviour is characterized by unusual very high thermal stability. - Abstract: Series of novel organic-inorganic hybrids materials based on trivalent lanthanides (Ln = Y, La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu) and 1,4-phenylbis(phosphonate) obtained under hydrothermal conditions either by oven heat or microwave irradiation. The anhydrous compounds containing La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, and Ho, are isostructural. However, the compounds based on Y, Er, Tm, Yb, and Lu are hydrated and their structures have not yet been solved. The series of compounds are characterized by PXRD, TEM, SEM-EDX and thermal analyses (TG-MS and DSC). TEM study show a variable particles size with a minimum mean-particle size of ca. 30 nm. These compounds exhibit unusual very high thermal stability. The size of particles and the thermal stability are depending on lanthanide(III) cation features. All the investigated materials show paramagnetic behaviour. The magnetic susceptibility data follow a Curie-Weiss laws with paramagnetic effective moments in good agreement with those expected for Ln{sup 3+} free ions.

  20. Thermal stability of ultrasoft Fe-Zr-N films

    NARCIS (Netherlands)

    Chechenin, NG; van Veen, A; Schut, H; Chezan, AR; Boerma, D; Vystavel, T; De Hosson, JTM

    2003-01-01

    The thermal stability of nanocrystalline ultrasoft magnetic (Fe98Zr2)(1-x)N-x films with x = 0.10-0.25 was studied using thermal desorption spectrometry, positron beam analysis and high resolution transmission electron microscopy. The results demonstrate that grain growth during the heat treatment

  1. Estudio comparativo de la estructura del bacterioplancton en aguas del Mar Argentino mediante el método de pirosecuenciación 454 tag A comparative study of bacterioplankton structure in Argentinian Sea waters by the 454 - tag pyrosequencing method

    Directory of Open Access Journals (Sweden)

    S. R. Peressutti

    2010-12-01

    higher differences among Bacteria rather than among Archaea in both studied sites. The dominant phylotypes in marine environment were Bacteroidetes Flavobacteriaceae, Proteobacteria Gammaproteobacteria, Proteobacteria Rhodobacteraceae and Proteobacteria Rickettsiales SAR11; and Pseudoalteromonadaceae Pseudoalteromonas, Proteobacteria Gammaproteobacteria, Proteobacteria Shewanella, Proteobacteria Rickettsiales SAR11 in the estuary sampling site. Archaea Euryarchaeota and Archaea Crenarchaeota were the major archaeal phylotypes found. The most abundant tag sequences included previously characterized taxa, although we also retrieved a large number of highly diverse, low-abundant phylotypes which constitute a largely unexplored "rare" biosphere. These microorganisms could have a crucial ecological role.

  2. Expressed sequence tags from heat-shocked seagrass Zostera noltii (Hornemann) from its southern distribution range.

    Science.gov (United States)

    Massa, Sónia I; Pearson, Gareth A; Aires, Tânia; Kube, Michael; Olsen, Jeanine L; Reinhardt, Richard; Serrão, Ester A; Arnaud-Haond, Sophie

    2011-09-01

    Predicted global climate change threatens the distributional ranges of species worldwide. We identified genes expressed in the intertidal seagrass Zostera noltii during recovery from a simulated low tide heat-shock exposure. Five Expressed Sequence Tag (EST) libraries were compared, corresponding to four recovery times following sub-lethal temperature stress, and a non-stressed control. We sequenced and analyzed 7009 sequence reads from 30min, 2h, 4h and 24h after the beginning of the heat-shock (AHS), and 1585 from the control library, for a total of 8594 sequence reads. Among 51 Tentative UniGenes (TUGs) exhibiting significantly different expression between libraries, 19 (37.3%) were identified as 'molecular chaperones' and were over-expressed following heat-shock, while 12 (23.5%) were 'photosynthesis TUGs' generally under-expressed in heat-shocked plants. A time course analysis of expression showed a rapid increase in expression of the molecular chaperone class, most of which were heat-shock proteins; which increased from 2 sequence reads in the control library to almost 230 in the 30min AHS library, followed by a slow decrease during further recovery. In contrast, 'photosynthesis TUGs' were under-expressed 30min AHS compared with the control library, and declined progressively with recovery time in the stress libraries, with a total of 29 sequence reads 24h AHS, compared with 125 in the control. A total of 4734 TUGs were screened for EST-Single Sequence Repeats (EST-SSRs) and 86 microsatellites were identified. Copyright © 2011 Elsevier B.V. All rights reserved.

  3. A self-adaptive thermal switch array for rapid temperature stabilization under various thermal power inputs

    International Nuclear Information System (INIS)

    Geng, Xiaobao; Patel, Pragnesh; Narain, Amitabh; Meng, Dennis Desheng

    2011-01-01

    A self-adaptive thermal switch array (TSA) based on actuation by low-melting-point alloy droplets is reported to stabilize the temperature of a heat-generating microelectromechanical system (MEMS) device at a predetermined range (i.e. the optimal working temperature of the device) with neither a control circuit nor electrical power consumption. When the temperature is below this range, the TSA stays off and works as a thermal insulator. Therefore, the MEMS device can quickly heat itself up to its optimal working temperature during startup. Once this temperature is reached, TSA is automatically turned on to increase the thermal conductance, working as an effective thermal spreader. As a result, the MEMS device tends to stay at its optimal working temperature without complex thermal management components and the associated parasitic power loss. A prototype TSA was fabricated and characterized to prove the concept. The stabilization temperatures under various power inputs have been studied both experimentally and theoretically. Under the increment of power input from 3.8 to 5.8 W, the temperature of the device increased only by 2.5 °C due to the stabilization effect of TSA

  4. Thermal stability of PMMA–clay hybrids

    Indian Academy of Sciences (India)

    Administrator

    Thermal stability of PMMA–clay hybrids. TANUSHREE CHOUDHURY* and NIRENDRA M MISRA. Department of Applied Chemistry, Indian School of Mines University, Dhanbad 826 004, India. MS received 9 December 2008. Abstract. Materials with small particle size are being extensively used in composites and hybrid ...

  5. A suite of standard post-tagging evaluation metrics can help assess tag retention for field-based fish telemetry research

    Science.gov (United States)

    Gerber, Kayla M.; Mather, Martha E.; Smith, Joseph M.

    2017-01-01

    Telemetry can inform many scientific and research questions if a context exists for integrating individual studies into the larger body of literature. Creating cumulative distributions of post-tagging evaluation metrics would allow individual researchers to relate their telemetry data to other studies. Widespread reporting of standard metrics is a precursor to the calculation of benchmarks for these distributions (e.g., mean, SD, 95% CI). Here we illustrate five types of standard post-tagging evaluation metrics using acoustically tagged Blue Catfish (Ictalurus furcatus) released into a Kansas reservoir. These metrics included: (1) percent of tagged fish detected overall, (2) percent of tagged fish detected daily using abacus plot data, (3) average number of (and percent of available) receiver sites visited, (4) date of last movement between receiver sites (and percent of tagged fish moving during that time period), and (5) number (and percent) of fish that egressed through exit gates. These metrics were calculated for one to three time periods: early ( 5 days early in the study. On average, tagged Blue Catfish visited 9 (50%) and 13 (72%) of 18 within-reservoir receivers early and at the end of the study, respectively. At the end of the study, 73% of all tagged fish were detected moving between receivers. Creating statistical benchmarks for individual metrics can provide useful reference points. In addition, combining multiple metrics can inform ecology and research design. Consequently, individual researchers and the field of telemetry research can benefit from widespread, detailed, and standard reporting of post-tagging detection metrics.

  6. A suite of standard post-tagging evaluation metrics can help assess tag retention for field-based fish telemetry research

    Science.gov (United States)

    Gerber, Kayla M.; Mather, Martha E.; Smith, Joseph M.

    2017-01-01

    Telemetry can inform many scientific and research questions if a context exists for integrating individual studies into the larger body of literature. Creating cumulative distributions of post-tagging evaluation metrics would allow individual researchers to relate their telemetry data to other studies. Widespread reporting of standard metrics is a precursor to the calculation of benchmarks for these distributions (e.g., mean, SD, 95% CI). Here we illustrate five types of standard post-tagging evaluation metrics using acoustically tagged Blue Catfish (Ictalurus furcatus) released into a Kansas reservoir. These metrics included: (1) percent of tagged fish detected overall, (2) percent of tagged fish detected daily using abacus plot data, (3) average number of (and percent of available) receiver sites visited, (4) date of last movement between receiver sites (and percent of tagged fish moving during that time period), and (5) number (and percent) of fish that egressed through exit gates. These metrics were calculated for one to three time periods: early (of the study (5 months). Over three-quarters of our tagged fish were detected early (85%) and at the end (85%) of the study. Using abacus plot data, all tagged fish (100%) were detected at least one day and 96% were detected for > 5 days early in the study. On average, tagged Blue Catfish visited 9 (50%) and 13 (72%) of 18 within-reservoir receivers early and at the end of the study, respectively. At the end of the study, 73% of all tagged fish were detected moving between receivers. Creating statistical benchmarks for individual metrics can provide useful reference points. In addition, combining multiple metrics can inform ecology and research design. Consequently, individual researchers and the field of telemetry research can benefit from widespread, detailed, and standard reporting of post-tagging detection metrics.

  7. The use of tags and tag clouds to discern credible content in online health message forums.

    Science.gov (United States)

    O'Grady, Laura; Wathen, C Nadine; Charnaw-Burger, Jill; Betel, Lisa; Shachak, Aviv; Luke, Robert; Hockema, Stephen; Jadad, Alejandro R

    2012-01-01

    Web sites with health-oriented content are potentially harmful if inaccurate or inappropriate medical information is used to make health-related decisions. Checklists, rating systems and guidelines have been developed to help people determine what is credible, but recent Internet technologies emphasize applications that are collaborative in nature, including tags and tag clouds, where site users 'tag' or label online content, each using their own labelling system. Concepts such as the date, reference, author, testimonial and quotations are considered predictors of credible content. An understanding of these descriptive tools, how they relate to the depiction of credibility and how this relates to overall efforts to label data in relation to the semantic web has yet to emerge. This study investigates how structured (pre-determined) and unstructured (user-generated) tags and tag clouds with a multiple word search feature are used by participants to assess credibility of messages posted in online message forums. The targeted respondents were those using web sites message forums for disease self-management. We also explored the relevancy of our findings to the labelling or indexing of data in the context of the semantic web. Diabetes was chosen as the content area in this study, since (a) this is a condition with increasing prevalence and (b) diabetics have been shown to actively use the Internet to manage their condition. From January to March 2010 participants were recruited using purposive sampling techniques. A screening instrument was used to determine eligibility. The study consisted of a demographic and computer usage survey, a series of usability tests and an interview. We tested participants (N=22) on two scenarios, each involving tasks that assessed their ability to tag content and search using a tag cloud that included six structured credibility terms (statistics, date, reference, author, testimonial and quotations). MORAE Usability software (version 3

  8. Sequence specific electronic conduction through polyion-stabilized double-stranded DNA in nanoscale break junctions

    International Nuclear Information System (INIS)

    Mahapatro, Ajit K; Jeong, Kyung J; Lee, Gil U; Janes, David B

    2007-01-01

    This paper presents a study of sequence specific electronic conduction through short (15-base-pair) double-stranded (ds) DNA molecules, measured by immobilizing 3 ' -thiol-derivatized DNAs in nanometre scale gaps between gold electrodes. The polycation spermidine was used to stabilize the ds-DNA structure, allowing electrical measurements to be performed in a dry state. For specific sequences, the conductivity was observed to scale with the surface density of immobilized DNA, which can be controlled by the buffer concentration. A series of 15-base DNA oligonucleotide pairs, in which the centre sequence of five base pairs was changed from G:C to A:T pairs, has been studied. The conductivity per molecule is observed to decrease exponentially with the number of adjacent A:T pairs replacing G:C pairs, consistent with a barrier at the A:T sites. Conductance-based devices for short DNA sequences could provide sensing approaches with direct electrical readout, as well as label-free detection

  9. Dual-mode fluorophore-doped nickel nitrilotriacetic acid-modified silica nanoparticles combine histidine-tagged protein purification with site-specific fluorophore labeling.

    Science.gov (United States)

    Kim, Sung Hoon; Jeyakumar, M; Katzenellenbogen, John A

    2007-10-31

    We present the first example of a fluorophore-doped nickel chelate surface-modified silica nanoparticle that functions in a dual mode, combining histidine-tagged protein purification with site-specific fluorophore labeling. Tetramethylrhodamine (TMR)-doped silica nanoparticles, estimated to contain 700-900 TMRs per ca. 23 nm particle, were surface modified with nitrilotriacetic acid (NTA), producing TMR-SiO2-NTA-Ni2+. Silica-embedded TMR retains very high quantum yield, is resistant to quenching by buffer components, and is modestly quenched and only to a certain depth (ca. 2 nm) by surface-attached Ni2+. When exposed to a bacterial lysate containing estrogen receptor alpha ligand binding domain (ERalpha) as a minor component, these beads showed very high specificity binding, enabling protein purification in one step. The capacity and specificity of these beads for binding a his-tagged protein were characterized by electrophoresis, radiometric counting, and MALDI-TOF MS. ERalpha, bound to TMR-SiO2-NTA-Ni++ beads in a site-specific manner, exhibited good activity for ligand binding and for ligand-induced binding to coactivators in solution FRET experiments and protein microarray fluorometric and FRET assays. This dual-mode type TMR-SiO2-NTA-Ni2+ system represents a powerful combination of one-step histidine-tagged protein purification and site-specific labeling with multiple fluorophore species.

  10. A robust, simple genotyping-by-sequencing (GBS approach for high diversity species.

    Directory of Open Access Journals (Sweden)

    Robert J Elshire

    Full Text Available Advances in next generation technologies have driven the costs of DNA sequencing down to the point that genotyping-by-sequencing (GBS is now feasible for high diversity, large genome species. Here, we report a procedure for constructing GBS libraries based on reducing genome complexity with restriction enzymes (REs. This approach is simple, quick, extremely specific, highly reproducible, and may reach important regions of the genome that are inaccessible to sequence capture approaches. By using methylation-sensitive REs, repetitive regions of genomes can be avoided and lower copy regions targeted with two to three fold higher efficiency. This tremendously simplifies computationally challenging alignment problems in species with high levels of genetic diversity. The GBS procedure is demonstrated with maize (IBM and barley (Oregon Wolfe Barley recombinant inbred populations where roughly 200,000 and 25,000 sequence tags were mapped, respectively. An advantage in species like barley that lack a complete genome sequence is that a reference map need only be developed around the restriction sites, and this can be done in the process of sample genotyping. In such cases, the consensus of the read clusters across the sequence tagged sites becomes the reference. Alternatively, for kinship analyses in the absence of a reference genome, the sequence tags can simply be treated as dominant markers. Future application of GBS to breeding, conservation, and global species and population surveys may allow plant breeders to conduct genomic selection on a novel germplasm or species without first having to develop any prior molecular tools, or conservation biologists to determine population structure without prior knowledge of the genome or diversity in the species.

  11. A technique for rapid source apportionment applied to ambient organic aerosol measurements from a thermal desorption aerosol gas chromatograph (TAG

    Directory of Open Access Journals (Sweden)

    Y. Zhang

    2016-11-01

    Full Text Available We present a rapid method for apportioning the sources of atmospheric organic aerosol composition measured by gas chromatography–mass spectrometry methods. Here, we specifically apply this new analysis method to data acquired on a thermal desorption aerosol gas chromatograph (TAG system. Gas chromatograms are divided by retention time into evenly spaced bins, within which the mass spectra are summed. A previous chromatogram binning method was introduced for the purpose of chromatogram structure deconvolution (e.g., major compound classes (Zhang et al., 2014. Here we extend the method development for the specific purpose of determining aerosol samples' sources. Chromatogram bins are arranged into an input data matrix for positive matrix factorization (PMF, where the sample number is the row dimension and the mass-spectra-resolved eluting time intervals (bins are the column dimension. Then two-dimensional PMF can effectively do three-dimensional factorization on the three-dimensional TAG mass spectra data. The retention time shift of the chromatogram is corrected by applying the median values of the different peaks' shifts. Bin width affects chemical resolution but does not affect PMF retrieval of the sources' time variations for low-factor solutions. A bin width smaller than the maximum retention shift among all samples requires retention time shift correction. A six-factor PMF comparison among aerosol mass spectrometry (AMS, TAG binning, and conventional TAG compound integration methods shows that the TAG binning method performs similarly to the integration method. However, the new binning method incorporates the entirety of the data set and requires significantly less pre-processing of the data than conventional single compound identification and integration. In addition, while a fraction of the most oxygenated aerosol does not elute through an underivatized TAG analysis, the TAG binning method does have the ability to achieve molecular level

  12. System Design Description PFP Thermal Stabilization

    International Nuclear Information System (INIS)

    RISENMAY, H.R.

    2000-01-01

    The purpose of this document is to provide a system design description (SDD) and design basis for the Plutonium Finishing Plant (PFP) Thermal Stabilization project. The chief objective of the SDD is to document the Structures, Systems, and Components (SSCs) that establish and maintain the facility Safety Envelope necessary for normal safe operation of the facility; as identified in the FSAR, the OSRs, and Safety Assessment Documents (SADs). This safety equipment documentation should satisfy guidelines for the SDD given in WHC-SD-CP-TI-18 1, Criteria for Identification and Control of Equipment Necessary for Preservation of the Safety Envelope and Safe Operation of PFP. The basis for operational, alarm response, maintenance, and surveillance procedures are also identified and justified in this document. This document and its appendices address the following elements of the PFP Thermal Stabilization project: Functional and design requirements; Design description; Safety Envelope Analysis; Safety Equipment Class; and Operational, maintenance and surveillance procedures

  13. Lyapunov stability and thermal stability of partially relaxed fluids and plasmas

    International Nuclear Information System (INIS)

    Elsaesser, K.; Spiess, P.

    1996-01-01

    The relation between the Lyapunov stability of a Hamiltonian system and the thermal stability of a fluid whose temperature is controlled from outside is explored: The free energy as a functional of the correct variables (specific volume, local entropy, and some Clebsch potentials of the velocity) may serve as a Lyapunov functional, depending on the open-quote open-quote Casimirs close-quote close-quote as exchanged quantities. For a multi-species plasma one obtains a sufficient condition for stability: γ(v 2 /c 2 s )-1 s the sound speed. Some features of partially relaxed (T=const) cylindrical plasmas are also discussed. copyright 1996 American Institute of Physics

  14. Aging effects on vertical graphene nanosheets and their thermal stability

    Science.gov (United States)

    Ghosh, S.; Polaki, S. R.; Ajikumar, P. K.; Krishna, N. G.; Kamruddin, M.

    2018-03-01

    The present study investigates environmental aging effects and thermal stability of vertical graphene nanosheets (VGN). Self-organized VGN is synthesized by plasma enhanced chemical vapor deposition and exposed to ambient conditions over 6-month period to examine its aging behavior. A systematic inspection is carried out on morphology, chemical structure, wettability and electrical property by scanning electron microscopy, Raman spectroscopy, X-ray photoelectron spectroscopy, water contact angle and four-probe resistivity measurements at regular intervals, respectively. Detailed microscopic and spectroscopic analysis substantiated the retention of graphitic quality and surface chemistry of VGN over the test period. An unchanged sheet resistance and hydrophobicity reveals its electrical and wetting stability over the time, respectively. Thermogravimetric analysis ensures an excellent thermal stability of VGN up to 575 °C in ambient atmosphere. These findings of long-term morphological, structural, wetting, electrical and thermal stability of VGN validate their potential utilization for the next-generation device applications.

  15. Ballooning mode second stability region for sequences of tokamak equilibria

    International Nuclear Information System (INIS)

    Sugiyama, L.; Mark, J.W.K.

    A numerical study of several sequences of tokamak equilibria derived from two flux conserving sequences confirms the tendency of high n ideal MHD ballooning modes to stabilize for values of the plasma beta greater than a second critical beta, for sufficiently favorable equilibria. The major stabilizing effect of increasing the inverse rotational transform profile q(Psi) for equilibria with the same flux surface geometry is shown. The unstable region shifts toward larger shear d ln q/d ln γ and the width of the region measured in terms of the poloidal beta or a pressure gradient parameter, for fixed shear, decreases. The smaller aspect ratio sequences are more sensitive to changes in q and have less stringent limits on the attainable value of the plasma beta in the high beta stable region. Finally, the disconnected mode approximation is shown to provide a reasonable description of the second high beta stability boundary

  16. Characterization of genic microsatellite markers derived from expressed sequence tags in Pacific abalone ( Haliotis discus hannai)

    Science.gov (United States)

    Li, Qi; Shu, Jing; Zhao, Cui; Liu, Shikai; Kong, Lingfeng; Zheng, Xiaodong

    2010-01-01

    Simple sequence repeat (SSR) markers were developed from the expressed sequence tags (ESTs) of Pacific abalone ( Haliotis discus hannai). Repeat motifs were found in 4.95% of the ESTs at a frequency of one repeat every 10.04 kb of EST sequences, after redundancy elimination. Seventeen polymorphic EST-SSRs were developed. The number of alleles per locus varied from 2-17, with an average of 6.8 alleles per locus. The expected and observed heterozygosities ranged from 0.159 to 0.928 and from 0.132 to 0.922, respectively. Twelve of the 17 loci (70.6%) were successfully amplified in H. diversicolor. Seventeen loci segregated in three families, with three showing the presence of null alleles (17.6%). The adequate level of variability and low frequency of null alleles observed in H. discus hannai, together with the high rate of transportability across Haliotis species, make this set of EST-SSR markers an important tool for comparative mapping, marker-assisted selection, and evolutionary studies, not only in the Pacific abalone, but also in related species.

  17. Thermal stability of titanate nanotubes

    Czech Academy of Sciences Publication Activity Database

    Králová, Daniela; Kužel, R.; Kovářová, Jana; Dybal, Jiří; Šlouf, Miroslav

    2009-01-01

    Roč. 16, 2a (2009), s. 41-43 ISSN 1211-5894. [Struktura - Colloquium of Czech and Slovak Crystallographic Association. Hluboká nad Vltavou, 22.06.2009-25.06.2009] R&D Projects: GA ČR GA203/07/0717; GA AV ČR KAN200520704 Institutional research plan: CEZ:AV0Z40500505 Keywords : titanate nanotubes * thermal stability Subject RIV: CD - Macromolecular Chemistry

  18. Expressed sequence tag (EST) analysis of two subspecies of Metarhizium anisopliae reveals a plethora of secreted proteins with potential activity in insect hosts.

    Science.gov (United States)

    Freimoser, Florian M; Screen, Steven; Bagga, Savita; Hu, Gang; St Leger, Raymond J

    2003-01-01

    Expressed sequence tag (EST) libraries for Metarhizium anisopliae, the causative agent of green muscardine disease, were developed from the broad host-range pathogen Metarhizium anisopliae sf. anisopliae and the specific grasshopper pathogen, M. anisopliae sf. acridum. Approximately 1,700 5' end sequences from each subspecies were generated from cDNA libraries representing fungi grown under conditions that maximize secretion of cuticle-degrading enzymes. Both subspecies had ESTs for virtually all pathogenicity-related genes cloned to date from M. anisopliae, but many novel genes encoding potential virulence factors were also tagged. Enzymes with potential targets in the insect host included proteases, chitinases, phospholipases, lipases, esterases, phosphatases and enzymes producing toxic secondary metabolites. A diverse array of proteases composed 36 % of all M. anisopliae sf. anisopliae ESTs. Eighty percent of the ESTs that could be clustered into functional groups had significant matches (Ehistory of this clade.

  19. Phase Behavior, Thermal Stability and Rheological Properties of PPEK/PC Blends

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Phase behavior, thermal stability and rheological properties of the blends of poly(phthalazinone ether ketone) (PPEK)with bisphenol-A polycarbonate (PC) prepared by solution coprecipitation were studied using differential scanning calorimetry (DSC), Frourier-Transform IR spectroscopy (FT-IR), thermogravimetric analysis (TGA) and capillary rheometer. The DSC results indicated that PPEK/PC blends are almost immiscible in full compositions. FT-IR investigation showed that there were no apparent specific interactions between the constituent polymers. The blends keep excellent thermal stability and the addition of PC degrades the thermal stability of blends to some degree. The thermal degradation processes of the blends are much similar to that of PC. The studies on rheological properties of blends show that blending PPEK with PC is beneficial to reducing the melt viscosity and improving the appearance of PPEK.

  20. Engineering the ATLAS TAG Browser

    CERN Document Server

    Zhang, Q; The ATLAS collaboration

    2011-01-01

    ELSSI is a web-based event metadata (TAG) browser and event-level selection service for ATLAS. TAGs from all ATLAS physics and Monte Carlo data sets are routinely loaded into Oracle databases as an integral part of event processing. As data volumes increase, more and more sites are joining the distributed TAG data hosting topology. Meanwhile, TAG content and database schemata continue to evolve as new user requirements and additional sources of metadata emerge. All of this has posed many challenges to the development of ELSSI, which must support vast amounts of TAG data while source, content, geographic locations, and user query patterns may change over time. In this paper, we describe some of the challenges encountered in the process of developing ELSSI, and the software engineering strategies adopted to address those challenges. Approaches to management of access to data, browsing, data rendering, query building, query validation, execution, connection management, and communication with auxiliary services a...

  1. Engineering the ATLAS TAG Browser

    CERN Document Server

    Zhang, Q; The ATLAS collaboration

    2011-01-01

    ELSSI is a web-based event metadata (TAG) browser and event-level selection service for ATLAS. TAGs from all ATLAS physics and Monte Carlo data sets are routinely loaded into Oracle databases as an integral part of event processing. As data volumes increase, more and more sites are joining the distributed TAG data hosting topology[1]. Meanwhile, TAG content and database schemata continue to evolve as new user requirements and additional sources of metadata emerge. All of this has posed many challenges to the development of ELSSI, which must support vast amounts of TAG data while source, content, geographic locations, and user query patterns may change over time. In this paper, we describe some of the challenges encountered in the process of developing ELSSI, and the software engineering strategies adopted to address those challenges. Approaches to management of access to data, browsing, data rendering, query building, query validation, execution, connection management, and communication with auxiliary service...

  2. Pulsational stabilities of a star in thermal imbalance: comparison between the methods

    International Nuclear Information System (INIS)

    Vemury, S.K.

    1978-01-01

    The stability coefficients for quasi-adiabatic pulsations for a model in thermal imbalance are evaluated using the dynamical energy (DE) approach, the total (kinetic plus potential) energy (TE) approach, and the small amplitude (SA) approaches. From a comparison among the methods, it is found that there can exist two distinct stability coefficients under conditions of thermal imbalance as pointed out by Demaret. It is shown that both the TE approaches lead to one stability coefficient, while both the SA approaches lead to another coefficient. The coefficient obtained through the energy approaches is identified as the one which determines the stability of the velocity amplitudes.For a prenova model with a thin hydrogen-burning shell in thermal imbalance, several radial modes are found to be unstable both for radial displacements and for velocity amplitudes. However, a new kind of pulsational instability also appears, viz., while the radial displacements are unstable, the velocity amplitudes may be stabilized through the thermal imbalance terms

  3. Transient Thermal Stability of Polymer Nanocomposites

    Science.gov (United States)

    2012-08-01

    modified Montmorillonite, Nanocor masterbatch ) 1 wt % carbon black (Na,Ca)0.33(Al,Mg)2(Si4O10)(OH)2·nH2O Multiwalled Carbon Nanotubes (Nanocyl... masterbatch ) Twin screw extrusion (190C) Slow Heating Regime Thermogravimetric Analysis Nanospecies improve thermal stability as expected Laser

  4. Cationic oligopeptides with the repeating sequence L-Lysyl-L-alanyl-L-alanine: conformational and thermal stability stuydy using optical spectroscopic methods

    Czech Academy of Sciences Publication Activity Database

    Setnička, V.; Hlaváček, Jan; Urbanová, J.

    2009-01-01

    Roč. 15, č. 8 (2009), s. 533-539 ISSN 1075-2617 Institutional research plan: CEZ:AV0Z40550506 Keywords : cationic peptides * conformation * thermal stability * vibrational circular dichroism Subject RIV: CC - Organic Chemistry Impact factor: 1.807, year: 2009

  5. New insights into transcription fidelity: thermal stability of non-canonical structures in template DNA regulates transcriptional arrest, pause, and slippage.

    Science.gov (United States)

    Tateishi-Karimata, Hisae; Isono, Noburu; Sugimoto, Naoki

    2014-01-01

    The thermal stability and topology of non-canonical structures of G-quadruplexes and hairpins in template DNA were investigated, and the effect of non-canonical structures on transcription fidelity was evaluated quantitatively. We designed ten template DNAs: A linear sequence that does not have significant higher-order structure, three sequences that form hairpin structures, and six sequences that form G-quadruplex structures with different stabilities. Templates with non-canonical structures induced the production of an arrested, a slipped, and a full-length transcript, whereas the linear sequence produced only a full-length transcript. The efficiency of production for run-off transcripts (full-length and slipped transcripts) from templates that formed the non-canonical structures was lower than that from the linear. G-quadruplex structures were more effective inhibitors of full-length product formation than were hairpin structure even when the stability of the G-quadruplex in an aqueous solution was the same as that of the hairpin. We considered that intra-polymerase conditions may differentially affect the stability of non-canonical structures. The values of transcription efficiencies of run-off or arrest transcripts were correlated with stabilities of non-canonical structures in the intra-polymerase condition mimicked by 20 wt% polyethylene glycol (PEG). Transcriptional arrest was induced when the stability of the G-quadruplex structure (-ΔG°37) in the presence of 20 wt% PEG was more than 8.2 kcal mol(-1). Thus, values of stability in the presence of 20 wt% PEG are an important indicator of transcription perturbation. Our results further our understanding of the impact of template structure on the transcription process and may guide logical design of transcription-regulating drugs.

  6. 29 CFR 1926.752 - Site layout, site-specific erection plan and construction sequence.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 8 2010-07-01 2010-07-01 false Site layout, site-specific erection plan and construction... Steel Erection § 1926.752 Site layout, site-specific erection plan and construction sequence. (a... strength or sufficient strength to support the loads imposed during steel erection. (c) Site layout. The...

  7. Identification of candidates for cyclotide biosynthesis and cyclisation by expressed sequence tag analysis of Oldenlandia affinis

    Directory of Open Access Journals (Sweden)

    Suda Jan

    2010-02-01

    Full Text Available Abstract Background Cyclotides are a family of circular peptides that exhibit a range of biological activities, including anti-bacterial, cytotoxic, anti-HIV activities, and are proposed to function in plant defence. Their high stability has motivated their development as scaffolds for the stabilisation of peptide drugs. Oldenlandia affinis is a member of the Rubiaceae (coffee family from which 18 cyclotides have been sequenced to date, but the details of their processing from precursor proteins have only begun to be elucidated. To increase the speed at which genes involved in cyclotide biosynthesis and processing are being discovered, an expressed sequence tag (EST project was initiated to survey the transcript profile of O. affinis and to propose some future directions of research on in vivo protein cyclisation. Results Using flow cytometry the holoploid genome size (1C-value of O. affinis was estimated to be 4,210 - 4,284 Mbp, one of the largest genomes of the Rubiaceae family. High-quality ESTs were identified, 1,117 in total, from leaf cDNAs and assembled into 502 contigs, comprising 202 consensus sequences and 300 singletons. ESTs encoding the cyclotide precursors for kalata B1 (Oak1 and kalata B2 (Oak4 were among the 20 most abundant ESTs. In total, 31 ESTs encoded cyclotide precursors, representing a distinct commitment of 2.8% of the O. affinis transcriptome to cyclotide biosynthesis. The high expression levels of cyclotide precursor transcripts are consistent with the abundance of mature cyclic peptides in O. affinis. A new cyclotide precursor named Oak5 was isolated and represents the first cDNA for the bracelet class of cyclotides in O. affinis. Clones encoding enzymes potentially involved in processing cyclotides were also identified and include enzymes involved in oxidative folding and proteolytic processing. Conclusion The EST library generated in this study provides a valuable resource for the study of the cyclisation of plant

  8. Production and thermal stability of pure and Cr3+ -doped hydroxyapatite

    International Nuclear Information System (INIS)

    De Araujo, T S; De Souza, S O; De Sousa, E M B; Araujo, M S

    2010-01-01

    Hydroxyapatite (HAP) have been used as starting material for biomedical applications. The pure and Cr 3+ -doped hydroxyapatite were prepared by chemical precipitation reactions at 100, 500 e 800 0 C in order to investigate the thermal stability of these materials. The characterization of the thermal behavior of this phosphate, especially on the structural changes with heating, is very important for production of sunscreens The powders were characterized using chemical analysis: X-ray diffraction (XRD) and thermal analysis. The present study was successful in the preparation of pure hydroxyapatite and chromium substituted hydroxyapatites with good thermal stability and nanoparticles formation.

  9. Method for enhancing the thermal stability of ionic compounds

    DEFF Research Database (Denmark)

    2013-01-01

    This invention relates to a method for enhancing the thermal stability of ionic compounds including ionic liquids, by immobilization on porous solid support materials having a pore diameter of between about 20-200 AA, wherein the solid support does not have a pore size of 90 AA.......This invention relates to a method for enhancing the thermal stability of ionic compounds including ionic liquids, by immobilization on porous solid support materials having a pore diameter of between about 20-200 AA, wherein the solid support does not have a pore size of 90 AA....

  10. Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags.

    Directory of Open Access Journals (Sweden)

    Paul A Hohenlohe

    2010-02-01

    Full Text Available Next-generation sequencing technology provides novel opportunities for gathering genome-scale sequence data in natural populations, laying the empirical foundation for the evolving field of population genomics. Here we conducted a genome scan of nucleotide diversity and differentiation in natural populations of threespine stickleback (Gasterosteus aculeatus. We used Illumina-sequenced RAD tags to identify and type over 45,000 single nucleotide polymorphisms (SNPs in each of 100 individuals from two oceanic and three freshwater populations. Overall estimates of genetic diversity and differentiation among populations confirm the biogeographic hypothesis that large panmictic oceanic populations have repeatedly given rise to phenotypically divergent freshwater populations. Genomic regions exhibiting signatures of both balancing and divergent selection were remarkably consistent across multiple, independently derived populations, indicating that replicate parallel phenotypic evolution in stickleback may be occurring through extensive, parallel genetic evolution at a genome-wide scale. Some of these genomic regions co-localize with previously identified QTL for stickleback phenotypic variation identified using laboratory mapping crosses. In addition, we have identified several novel regions showing parallel differentiation across independent populations. Annotation of these regions revealed numerous genes that are candidates for stickleback phenotypic evolution and will form the basis of future genetic analyses in this and other organisms. This study represents the first high-density SNP-based genome scan of genetic diversity and differentiation for populations of threespine stickleback in the wild. These data illustrate the complementary nature of laboratory crosses and population genomic scans by confirming the adaptive significance of previously identified genomic regions, elucidating the particular evolutionary and demographic history of such

  11. Analysis of protein stability and ligand interactions by thermal shift assay.

    Science.gov (United States)

    Huynh, Kathy; Partch, Carrie L

    2015-02-02

    Purification of recombinant proteins for biochemical assays and structural studies is time-consuming and presents inherent difficulties that depend on the optimization of protein stability. The use of dyes to monitor thermal denaturation of proteins with sensitive fluorescence detection enables rapid and inexpensive determination of protein stability using real-time PCR instruments. By screening a wide range of solution conditions and additives in a 96-well format, the thermal shift assay easily identifies conditions that significantly enhance the stability of recombinant proteins. The same approach can be used as an initial low-cost screen to discover new protein-ligand interactions by capitalizing on increases in protein stability that typically occur upon ligand binding. This unit presents a methodological workflow for small-scale, high-throughput thermal denaturation of recombinant proteins in the presence of SYPRO Orange dye. Copyright © 2015 John Wiley & Sons, Inc.

  12. Can green solvents be alternatives for thermal stabilization of collagen?

    Science.gov (United States)

    Mehta, Ami; Rao, J Raghava; Fathima, Nishter Nishad

    2014-08-01

    "Go Green" campaign is gaining light for various industrial applications where water consumption needs to be reduced. To resolve this, industries have adopted usage of green, organic solvents, as an alternative to water. For leather making, tanning industry consumes gallons of water. Therefore, for adopting green solvents in leather making, it is necessary to evaluate its influence on type I collagen, the major protein present in the skin matrix. The thermal stability of collagen from rat tail tendon fiber (RTT) treated with seven green solvents namely, ethanol, ethyl lactate, ethyl acetate, propylene carbonate, propylene glycol, polyethylene glycol-200 and heptane was determined using differential scanning calorimetry (DSC). Crosslinking efficiency of basic chromium sulfate and wattle on RTT in green solvents was determined. DSC thermograms show increase in thermal stability of RTT collagen against heat with green solvents (>78°C) compared to water (63°C). In the presence of crosslinkers, RTT demonstrated thermal stability >100°C in some green solvents, resulting in increased intermolecular forces between collagen, solvent and crosslinkers. The significant improvement in thermal stability of collagen potentiates the capability of green solvents as an alternative for water. Copyright © 2014 Elsevier B.V. All rights reserved.

  13. An inexpensive and simple method for thermally stable immobilization of DNA on an unmodified glass surface: UV linking of poly(T)10-poly(C)10-tagged DNA probes

    DEFF Research Database (Denmark)

    Guðnason, Haukur; Dufva, Hans Martin; Bang, Dang Duong

    2008-01-01

    be linked by UV light irradiation onto a plain, unmodified glass surface. Probes immobilized onto unmodified glass microscope slides performed similarly to probes bound to commercial amino-silane-coated slides and had comparable detection limits. The TC-tagged probes linked to unmodified glass did not show...... any significant decrease in hybridization performance after a 20 min incubation in water at 100 degrees C prior to rehybridization, indicating a covalent bond between the TC tag and unmodified glass. The probes were used in thermal minisequencing cycling reactions. Furthermore, the TC tag improved...

  14. Jet Fuel Thermal Stability Investigations Using Ellipsometry

    Science.gov (United States)

    Nash, Leigh; Vasu, Subith S.; Klettlinger, Jennifer Lindsey

    2017-01-01

    Jet fuels are typically used for endothermic cooling in practical engines where their thermal stability is very important. In this work the thermal stability of Sasol IPK (a synthetic jet fuel) with varying levels of naphthalene has been studied on stainless steel substrates using spectroscopic ellipsometry in the temperature range 385-400 K. Ellipsometry is an optical technique that measures the changes in a light beam’s polarization and intensity after it reflects off of a thin film to determine the film’s thickness and optical properties. All of the tubes used were rated as thermally unstable by the color standard portion of the Jet Fuel Thermal Oxidation Test, and this was confirmed by the deposit thicknesses observed using ellipsometry. A new amorphous model on a stainless steel substrate was used to model the data and obtain the results. It was observed that, as would be expected, increasing the temperature of the tube increased the overall deposit amount for a constant concentration of naphthalene. The repeatability of these measurements was assessed using multiple trials of the same fuel at 385 K. Lastly, the effect of increasing the naphthalene concentration in the fuel at a constant temperature was found to increase the deposit thickness.In conclusion, ellipsometry was used to investigate the thermal stability of jet fuels on stainless steel substrate. The effects of increasing temperature and addition of naphthalene on stainless steel tubes with Sasol IPK fuel were investigated. It was found, as expected, that increasing temperature lead to an increase in deposit thickness. It wasAmerican Institute of Aeronautics and Astronautics6also found that increasing amounts of naphthalene increased the maximum deposit thickness. The repeatability of these measurements was investigated using multiple tests at the same conditions. The present work provides as a better quantitative tool compared to the widely used JFTOT technique. Future work will expand on the

  15. Comparative study of the conformational lock, dissociative thermal inactivation and stability of euphorbia latex and lentil seedling amine oxidases.

    Science.gov (United States)

    Amani, M; Moosavi-Movahedi, A A; Floris, G; Longu, S; Mura, A; Moosavi-Nejad, S Z; Saboury, A A; Ahmad, F

    2005-04-01

    The thermal stability of copper/quinone containing amine oxidases from Euphorbia characias latex (ELAO) and lentil seedlings (LSAO) was measured in 100 mM potassium phosphate buffer (pH 7.0) following changes in absorbance at 292 nm. ELAO was shown to be about 10 degrees C more stable than LSAO. The dissociative thermal inactivation of ELAO was studied using putrescine as substrate at different temperatures in the range 47-70 degrees C, and a "conformational lock" was developed using the theory pertaining to oligomeric enzyme. Moreover ELAO was shown to be more stable towards denaturants than LSAO, as confirmed by dodecyl trimethylammonium bromide denaturation curves. A comparison of the numbers of contact sites in inter-subunits of ELAO relative to LSAO led us to conclude that the higher stability of ELAO to temperature and towards denaturants was due to the presence of larger number of contact sites in the conformational lock of the enzyme. This study also gives a putative common mechanism for thermal inactivation of amine oxidases and explains the importance of C-terminal conserved amino acids residues in this class of enzymes.

  16. Thermal stability of tunneling spin polarization

    International Nuclear Information System (INIS)

    Kant, C.H.; Kohlhepp, J.T.; Paluskar, P.V.; Swagten, H.J.M.; Jonge, W.J.M. de

    2005-01-01

    We present a study of the thermal stability of tunneling spin polarization in Al/AlOx/ferromagnet junctions based on the spin-polarized tunneling technique, in which the Zeeman-split superconducting density of states in the Al electrode is used as a detector for the spin polarization. Thermal robustness of the polarization, which is of key importance for the performance of magnetic tunnel junction devices, is demonstrated for post-deposition anneal temperatures up to 500 o C with Co and Co 90 Fe 10 top electrodes, independent of the presence of an FeMn layer on top of the ferromagnet

  17. The Effect of Thermal Cycling Treatments on the Thermal Stability and Mechanical Properties of a Ti-Based Bulk Metallic Glass Composite

    Directory of Open Access Journals (Sweden)

    Fan Bu

    2016-11-01

    Full Text Available The effect of thermal cycling treatments on the thermal stability and mechanical properties of a Ti48Zr20Nb12Cu5Be15 bulk metallic glass composite (BMGC has been investigated. Results show that moderate thermal cycles in a temperature range of −196 °C (cryogenic temperature, CT to 25 °C (room temperature, RT or annealing time at CT has not induced obvious changes of thermal stability and then it decreases slightly over critical thermal parameters. In addition, the dendritic second phases with a bcc structure are homogeneously embedded in the amorphous matrix; no visible changes are detected, which shows structural stability. Excellent mechanical properties as high as 1599 MPa yield strength and 34% plastic strain are obtained, and the yield strength and elastic modulus also increase gradually. The effect on the stability is analyzed quantitatively by crystallization kinetics and plastic-flow models, and indicates that the reduction of structural relaxation enthalpy, which is related to the degradation of spatial heterogeneity, reduces thermal stability but does not imperatively deteriorate the plasticity.

  18. Thermal stability of carbon-encapsulated Fe-Nd-B nanoparticles

    International Nuclear Information System (INIS)

    Bystrzejewski, M.; Cudzilo, S.; Huczko, A.; Lange, H.

    2006-01-01

    Thermal stability of various magnetic nanomaterials is very essential, due to their prospective future applications. In this paper, thermal behaviour of the carbon-encapsulated Fe-Nd-B nanoparticles is studied. These nanostructures were produced by direct current arcing of carbon anodes filled with Nd 2 Fe 14 B material. The thermogravimetry and differential thermal analysis curves were recorded in an oxygen atmosphere. The thermal processes were monitored by X-ray diffraction to follow the changes in the phase composition. The investigated samples have been thermally stable up to 600 K

  19. Genome-wide identification of coding and non-coding conserved sequence tags in human and mouse genomes

    Directory of Open Access Journals (Sweden)

    Maggi Giorgio P

    2008-06-01

    Full Text Available Abstract Background The accurate detection of genes and the identification of functional regions is still an open issue in the annotation of genomic sequences. This problem affects new genomes but also those of very well studied organisms such as human and mouse where, despite the great efforts, the inventory of genes and regulatory regions is far from complete. Comparative genomics is an effective approach to address this problem. Unfortunately it is limited by the computational requirements needed to perform genome-wide comparisons and by the problem of discriminating between conserved coding and non-coding sequences. This discrimination is often based (thus dependent on the availability of annotated proteins. Results In this paper we present the results of a comprehensive comparison of human and mouse genomes performed with a new high throughput grid-based system which allows the rapid detection of conserved sequences and accurate assessment of their coding potential. By detecting clusters of coding conserved sequences the system is also suitable to accurately identify potential gene loci. Following this analysis we created a collection of human-mouse conserved sequence tags and carefully compared our results to reliable annotations in order to benchmark the reliability of our classifications. Strikingly we were able to detect several potential gene loci supported by EST sequences but not corresponding to as yet annotated genes. Conclusion Here we present a new system which allows comprehensive comparison of genomes to detect conserved coding and non-coding sequences and the identification of potential gene loci. Our system does not require the availability of any annotated sequence thus is suitable for the analysis of new or poorly annotated genomes.

  20. Analysis of expressed sequence tags of the cyclically parthenogenetic rotifer Brachionus plicatilis.

    Directory of Open Access Journals (Sweden)

    Koushirou Suga

    Full Text Available BACKGROUND: Rotifers are among the most common non-arthropod animals and are the most experimentally tractable members of the basal assemblage of metazoan phyla known as Gnathifera. The monogonont rotifer Brachionus plicatilis is a developing model system for ecotoxicology, aquatic ecology, cryptic speciation, and the evolution of sex, and is an important food source for finfish aquaculture. However, basic knowledge of the genome and transcriptome of any rotifer species has been lacking. METHODOLOGY/PRINCIPAL FINDINGS: We generated and partially sequenced a cDNA library from B. plicatilis and constructed a database of over 2300 expressed sequence tags corresponding to more than 450 transcripts. About 20% of the transcripts had no significant similarity to database sequences by BLAST; most of these contained open reading frames of significant length but few had recognized Pfam motifs. Sixteen transcripts accounted for 25% of the ESTs; four of these had no significant similarity to BLAST or Pfam databases. Putative up- and downstream untranslated regions are relatively short and AT rich. In contrast to bdelloid rotifers, there was no evidence of a conserved trans-spliced leader sequence among the transcripts and most genes were single-copy. CONCLUSIONS/SIGNIFICANCE: Despite the small size of this EST project it revealed several important features of the rotifer transcriptome and of individual monogonont genes. Because there is little genomic data for Gnathifera, the transcripts we found with no known function may represent genes that are species-, class-, phylum- or even superphylum-specific; the fact that some are among the most highly expressed indicates their importance. The absence of trans-spliced leader exons in this monogonont species contrasts with their abundance in bdelloid rotifers and indicates that the presence of this phenomenon can vary at the subphylum level. Our EST database provides a relatively large quantity of transcript

  1. Analysis of expressed sequence tags of the cyclically parthenogenetic rotifer Brachionus plicatilis.

    Science.gov (United States)

    Suga, Koushirou; Welch, David Mark; Tanaka, Yukari; Sakakura, Yoshitaka; Hagiwara, Atsushi

    2007-08-01

    Rotifers are among the most common non-arthropod animals and are the most experimentally tractable members of the basal assemblage of metazoan phyla known as Gnathifera. The monogonont rotifer Brachionus plicatilis is a developing model system for ecotoxicology, aquatic ecology, cryptic speciation, and the evolution of sex, and is an important food source for finfish aquaculture. However, basic knowledge of the genome and transcriptome of any rotifer species has been lacking. We generated and partially sequenced a cDNA library from B. plicatilis and constructed a database of over 2300 expressed sequence tags corresponding to more than 450 transcripts. About 20% of the transcripts had no significant similarity to database sequences by BLAST; most of these contained open reading frames of significant length but few had recognized Pfam motifs. Sixteen transcripts accounted for 25% of the ESTs; four of these had no significant similarity to BLAST or Pfam databases. Putative up- and downstream untranslated regions are relatively short and AT rich. In contrast to bdelloid rotifers, there was no evidence of a conserved trans-spliced leader sequence among the transcripts and most genes were single-copy. Despite the small size of this EST project it revealed several important features of the rotifer transcriptome and of individual monogonont genes. Because there is little genomic data for Gnathifera, the transcripts we found with no known function may represent genes that are species-, class-, phylum- or even superphylum-specific; the fact that some are among the most highly expressed indicates their importance. The absence of trans-spliced leader exons in this monogonont species contrasts with their abundance in bdelloid rotifers and indicates that the presence of this phenomenon can vary at the subphylum level. Our EST database provides a relatively large quantity of transcript-level data for B. plicatilis, and more generally of rotifers and other gnathiferan phyla, and

  2. Thermal interaction effect on nucleation site distribution in subcooled boiling

    International Nuclear Information System (INIS)

    Zou, Ling; Jones, Barclay

    2012-01-01

    An experimental work on subcooled boiling of refrigerant, R134a, to examine nucleation site distributions on both copper and stainless steel heating surfaces was performed. In order to obtain high fidelity active nucleation site density and distribution data, a high-speed digital camera was utilized to record bubble emission images from a view normal to heating surfaces. Statistical analyses on nucleation site data were done and their statistical distributions were obtained. Those experimentally observed nucleation site distributions were compared to the random spatial Poisson distribution. The comparisons showed that, rather than purely random, active nucleation site distributions on boiling surfaces are relatively more uniform. Experimental results also showed that on the copper heating surface, nucleation site distributions are slightly more uniform than on the stainless steel surface. This was concluded as the results of thermal interactions between nucleation sites with different solid thermal conductivities. A two dimensional thermal interaction model was then developed to quantitatively examine the thermal interactions between nucleation sites. The results give a reasonable explanation to the experimental observation on nucleation site distributions.

  3. A new tagging system for production of recombinant proteins in Drosophila S2 cells using the third domain of the urokinase receptor

    DEFF Research Database (Denmark)

    Gårdsvoll, Henrik; Hansen, Line V; Jørgensen, Thomas J D

    2007-01-01

    The use of protein fusion tag technology greatly facilitates detection, expression and purification of recombinant proteins, and the demands for new and more effective systems are therefore expanding. We have used a soluble truncated form of the third domain of the urokinase receptor...... as a convenient C-terminal fusion partner for various recombinant extracellular human proteins used in basic cancer research. The stability of this cystein-rich domain, which structure adopts a three-finger fold, provides an important asset for its applicability as a fusion tag for expression of recombinant...... chromatography procedure using the immobilized anti-uPAR monoclonal antibody R2. An optional enterokinase cleavage site is included between the various recombinant proteins and the linker region of the tag, which enables generation of highly pure preparations of tag-free recombinant proteins. Using this system...

  4. Lattice sites and stability of implanted Er in FZ and CZ Si

    CERN Document Server

    Wahl, U; Langouche, G; Vantomme, A

    1998-01-01

    We report on the lattice location of $^{167}$Er in Si measured by conversion electron emission channeling. In both FZ and CZ Si, a high fraction of Er (>65%) occupies near-tetrahedral interstitial (T) sites directly following 60 keV room temperature implantation at doses of 6 $\\times 10^{12}$ cm$^{-2}$. For higher doses, the as-implanted near-T fractions of Er visible by emission channeling are smaller, due to the beginning of amorphization. Following the recovery of implantation damage at 600°C, more than 70% of Er is found on near-T sites in both FZ and CZ Si. In FZ Si, Er exhibits a remarkable thermal stability and only prolonged annealing for several hours reduces the near-T fraction. On the other hand, annealing of CZ Si at 900°C for more than 10 minutes results in the majority of Er probes in sites of very low symmetry or disordered surroundings.

  5. Cell-free translational screening of an expression sequence tag library of Clonorchis sinensis for novel antigen discovery.

    Science.gov (United States)

    Kasi, Devi; Catherine, Christy; Lee, Seung-Won; Lee, Kyung-Ho; Kim, Yu Jung; Ro Lee, Myeong; Ju, Jung Won; Kim, Dong-Myung

    2017-05-01

    The rapidly evolving cloning and sequencing technologies have enabled understanding of genomic structure of parasite genomes, opening up new ways of combatting parasite-related diseases. To make the most of the exponentially accumulating genomic data, however, it is crucial to analyze the proteins encoded by these genomic sequences. In this study, we adopted an engineered cell-free protein synthesis system for large-scale expression screening of an expression sequence tag (EST) library of Clonorchis sinensis to identify potential antigens that can be used for diagnosis and treatment of clonorchiasis. To allow high-throughput expression and identification of individual genes comprising the library, a cell-free synthesis reaction was designed such that both the template DNA and the expressed proteins were co-immobilized on the same microbeads, leading to microbead-based linkage of the genotype and phenotype. This reaction configuration allowed streamlined expression, recovery, and analysis of proteins. This approach enabled us to identify 21 antigenic proteins. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:832-837, 2017. © 2017 American Institute of Chemical Engineers.

  6. Shape-stabilized phase change materials with high thermal conductivity based on paraffin/graphene oxide composite

    International Nuclear Information System (INIS)

    Mehrali, Mohammad; Latibari, Sara Tahan; Mehrali, Mehdi; Metselaar, Hendrik Simon Cornelis; Silakhori, Mahyar

    2013-01-01

    Highlights: ► The composite PCM was prepared with impregnation method. ► Shapes stabilized phase change material made with paraffin and GO composite. ► Determine effects of GO composite on shape stabilized PCM properties. ► The composite PCM has good thermal stability and form-stability. ► The composite PCM has much higher thermal conductivity than that of paraffin. - Abstract: This paper mainly focuses on the preparation, characterization, thermal properties and thermal stability and reliability of new form-stable composite phase change materials (PCMs) prepared by vacuum impregnation of paraffin within graphene oxide (GO) sheets. SEM and FT-IR techniques and TGA and DSC analysis are used for characterization of material and thermal properties. The composite PCM contained 48.3 wt.% of paraffin without leakage of melted PCM and therefore this composite found to be a form-stable composite PCM. SEM results indicate that the paraffin bounded into the pores of GO. FT-IR analysis showed there was no chemical reaction between paraffin and GO. Temperatures of melting and freezing and latent heats of the composite were 53.57 and 44.59 °C and 63.76 and 64.89 kJ/kg, respectively. Thermal cycling tests were done by 2500 melting/freezing cycling for verification of the form-stable composite PCM in terms of thermal reliability and chemical stability. Thermal conductivity of the composite PCM was highly improved from 0.305 to 0.985 (W/mk). As a result, the prepared paraffin/GO composite is appropriate PCM for thermal energy storage applications because of their acceptable thermal properties, good thermal reliability, chemical stability and thermal conductivities

  7. Case study of manufactured gas plant site remediations using thermal desorption

    Energy Technology Data Exchange (ETDEWEB)

    Vogel, R.G.; Hayes, T.; Slimon, K.F.; Unites, D. [Southern California Gas Company, Los Angeles, CA (United States)

    1995-12-31

    Southern California Gas Company (SoCal Gas) has recently remediated five of its former manufactured gas plant (MGP) sites using on-site and off-site thermal desorption. This technology has proven effective in the treatment of PAH-contaminated soils with widely variable concentrations. At two of the five sites, MGP-contaminated materials were excavated and thermally treated on site. At the other sites, MGP-contaminated materials were excavated and transported directly to an off-site thermal desorber. Much of the production was of oil-gas, giving lampblack contamination, but some coal tar was also present.

  8. Effect of carbon nanospheres on shape stabilization and thermal behavior of phase change materials for thermal energy storage

    International Nuclear Information System (INIS)

    Mehrali, Mohammad; Tahan Latibari, Sara; Mehrali, Mehdi; Mahlia, Teuku Meurah Indra; Cornelis Metselaar, Hendrik Simon

    2014-01-01

    Highlights: • Introducing novel form-stable PCM of stearic acid (SA)/carbon nanospheres (CNSs). • The highest stabilized SA content is 83 wt% in the SA/CNS composites. • Increasing thermal conductivity of composite phase change material with high amount of latent heat. - Abstract: Stearic acid (SA) is one of the main phase change materials (PCMs) for medium temperature thermal energy storage systems. In order to stabilize the shape and enhance the thermal conductivity of SA, the effects of adding carbon nanospheres (CNSs) as a carbon nanofiller were examined experimentally. The maximum mass fraction of SA retained in CNSs was found as 80 wt% without the leakage of SA in a melted state, even when it was heated over the melting point of SA. The dropping point test shows that there was clearly no liquid leakage through the phase change process at the operating temperature range of the composite PCMs. The thermal stability and thermal properties of composite PCMs were investigated with a thermogravimetric analyzer (TGA) and differential scanning calorimeter (DSC), respectively. The thermal conductivity of the SA/CNS composite was determined by the laser flash method. The thermal conductivity at 35 °C increased about 105% for the highest loading of CNS (50 wt%). The thermal cycling test proved that form-stable composite PCMs had good thermal reliability and chemical durability after 1000 cycles of melting and freezing, which is advantageous for latent heat thermal energy storage (LHTES)

  9. Thermal stability, swelling behavior and CO 2 absorption properties of Nanoscale Ionic Materials (NIMs)

    KAUST Repository

    Andrew Lin, Kun-Yi

    2014-11-11

    © The Royal Society of Chemistry 2015. Nanoscale Ionic Materials (NIMs) consist of a nanoscale core, a corona of charged brushes tethered on the surface of the core, and a canopy of the oppositely charged species linked to the corona. Unlike conventional polymeric nanocomposites, NIMs can display liquid-like behavior in the absence of solvents, have a negligible vapor pressure and exhibit unique solvation properties. These features enable NIMs to be a promising CO2 capture material. To optimize NIMs for CO2 capture, their structure-property relationships were examined by investigating the roles of the canopy and the core in their thermal stability, and thermally- and CO2-induced swelling behaviors. NIMs with different canopy sizes and core fractions were synthesized and their thermal stability as well as thermally- and CO2-induced swelling behaviors were determined using thermogravimetry, and ATR FT-IR and Raman spectroscopies. It was found that the ionic bonds between the canopy and the corona, as well as covalent bonds between the corona and the core significantly improved the thermal stability compared to pure polymer and polymer/nanofiller mixtures. A smaller canopy size and a larger core fraction led to a greater enhancement in thermal stability. This thermal stability enhancement was responsible for the long-term thermal stability of NIMs over 100 temperature swing cycles. Owing to their ordered structure, NIMs swelled less when heated or when they adsorbed CO2 compared to their corresponding polymers. This journal is

  10. Thermal stability, swelling behavior and CO 2 absorption properties of Nanoscale Ionic Materials (NIMs)

    KAUST Repository

    Andrew Lin, Kun-Yi; Park, Youngjune; Petit, Camille; Park, Ah-Hyung Alissa

    2014-01-01

    © The Royal Society of Chemistry 2015. Nanoscale Ionic Materials (NIMs) consist of a nanoscale core, a corona of charged brushes tethered on the surface of the core, and a canopy of the oppositely charged species linked to the corona. Unlike conventional polymeric nanocomposites, NIMs can display liquid-like behavior in the absence of solvents, have a negligible vapor pressure and exhibit unique solvation properties. These features enable NIMs to be a promising CO2 capture material. To optimize NIMs for CO2 capture, their structure-property relationships were examined by investigating the roles of the canopy and the core in their thermal stability, and thermally- and CO2-induced swelling behaviors. NIMs with different canopy sizes and core fractions were synthesized and their thermal stability as well as thermally- and CO2-induced swelling behaviors were determined using thermogravimetry, and ATR FT-IR and Raman spectroscopies. It was found that the ionic bonds between the canopy and the corona, as well as covalent bonds between the corona and the core significantly improved the thermal stability compared to pure polymer and polymer/nanofiller mixtures. A smaller canopy size and a larger core fraction led to a greater enhancement in thermal stability. This thermal stability enhancement was responsible for the long-term thermal stability of NIMs over 100 temperature swing cycles. Owing to their ordered structure, NIMs swelled less when heated or when they adsorbed CO2 compared to their corresponding polymers. This journal is

  11. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing.

    Directory of Open Access Journals (Sweden)

    Jonas Binladen

    2007-02-01

    Full Text Available The invention of the Genome Sequence 20 DNA Sequencing System (454 parallel sequencing platform has enabled the rapid and high-volume production of sequence data. Until now, however, individual emulsion PCR (emPCR reactions and subsequent sequencing runs have been unable to combine template DNA from multiple individuals, as homologous sequences cannot be subsequently assigned to their original sources.We use conventional PCR with 5'-nucleotide tagged primers to generate homologous DNA amplification products from multiple specimens, followed by sequencing through the high-throughput Genome Sequence 20 DNA Sequencing System (GS20, Roche/454 Life Sciences. Each DNA sequence is subsequently traced back to its individual source through 5'tag-analysis.We demonstrate that this new approach enables the assignment of virtually all the generated DNA sequences to the correct source once sequencing anomalies are accounted for (miss-assignment rate<0.4%. Therefore, the method enables accurate sequencing and assignment of homologous DNA sequences from multiple sources in single high-throughput GS20 run. We observe a bias in the distribution of the differently tagged primers that is dependent on the 5' nucleotide of the tag. In particular, primers 5' labelled with a cytosine are heavily overrepresented among the final sequences, while those 5' labelled with a thymine are strongly underrepresented. A weaker bias also exists with regards to the distribution of the sequences as sorted by the second nucleotide of the dinucleotide tags. As the results are based on a single GS20 run, the general applicability of the approach requires confirmation. However, our experiments demonstrate that 5'primer tagging is a useful method in which the sequencing power of the GS20 can be applied to PCR-based assays of multiple homologous PCR products. The new approach will be of value to a broad range of research areas, such as those of comparative genomics, complete mitochondrial

  12. An Expressed Sequence Tag Analysis of the Intertidal Brown Seaweeds Fucus serratus (L.) and F. vesiculosus (L.) (Heterokontophyta, Phaeophyceae) in Response to Abiotic Stressors

    NARCIS (Netherlands)

    Pearson, Gareth A.; Hoarau, Galice; Lago-Leston, Asuncion; Coyer, James A.; Kube, Michael; Reinhardt, Richard; Henckel, Kolja; Serrao, Ester T. A.; Corre, Erwan; Olsen, Jeanine L.

    In order to aid gene discovery and uncover genes responding to abiotic stressors in stress-tolerant brown algae of the genus Fucus, expressed sequence tags (ESTs) were studied in two species, Fucus serratus and Fucus vesiculosus. Clustering of over 12,000 ESTs from three libraries for heat

  13. Development, characterization and cross species amplification of polymorphic microsatellite markers from expressed sequence tags of turmeric (Curcuma longa L.).

    Science.gov (United States)

    Siju, S; Dhanya, K; Syamkumar, S; Sasikumar, B; Sheeja, T E; Bhat, A I; Parthasarathy, V A

    2010-02-01

    Expressed sequence tags (ESTs) from turmeric (Curcuma longa L.) were used for the screening of type and frequency of Class I (hypervariable) simple sequence repeats (SSRs). A total of 231 microsatellite repeats were detected from 12,593 EST sequences of turmeric after redundancy elimination. The average density of Class I SSRs accounts to one SSR per 17.96 kb of EST. Mononucleotides were the most abundant class of microsatellite repeat in turmeric ESTs followed by trinucleotides. A robust set of 17 polymorphic EST-SSRs were developed and used for evaluating 20 turmeric accessions. The number of alleles detected ranged from 3 to 8 per loci. The developed markers were also evaluated in 13 related species of C. longa confirming high rate (100%) of cross species transferability. The polymorphic microsatellite markers generated from this study could be used for genetic diversity analysis and resolving the taxonomic confusion prevailing in the genus.

  14. Thermal stability of radiation vulcanized EPDM rubber

    International Nuclear Information System (INIS)

    Abdel-Aziz, M.M.

    2005-01-01

    Thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC) have been used to study the thermal stability of gamma- ray vulcanized ethylene-propylene diene rubber (EPDM) stabilized with various types of antioxidants. The antioxidants used were penta erythrityl tetrakis(3,5- di-tert-butyl(-4-hydroxyphenyl)propionate (Irganox 1010), Irganox 1035, Irganox 1520 D, as primary antioxidants; Irganox B 561 and Irganox B 900, as synergistic blends; hindered amine light stabilizer (HALS), i.e. Tinuvin 622 LD; N-isopropyl-N-phenyl-p-phenylene diamine (IPPD) and Trimethyl quinoline (TMQ) and their mixtures. The measurements were carried out under atmospheric conditions. The effect of antioxidant type, selected concentration and mechanism of reaction were determined

  15. Relationship between mechanical characteristics and thermal shock stability of refractories

    International Nuclear Information System (INIS)

    Volkov-Husovic, T.; Raic, K.

    2003-01-01

    Thermal stability of the refractory material with the content of 60 % Al 2 O 3 was investigated. Water quench test (JUS.B.D8.319) was applied as experimental method for thermal stability testing. Damage of porous materials is commonly related to a modification of strength that is mostly a reduction. This is linked with characteristics related to pore space. Mechanical characteristics are considered such as compressive strength, dynamic modulus of elasticity and resistance parameters resulting from resonance frequency measurements, as well as ultrasonic velocity. (Original)

  16. Network structure and thermal stability study of high temperature seal glass

    Science.gov (United States)

    Lu, K.; Mahapatra, M. K.

    2008-10-01

    High temperature seal glass has stringent requirement on glass thermal stability, which is dictated by glass network structures. In this study, a SrO-La2O3-Al2O3-B2O3-SiO2 based glass system was studied using nuclear magnetic resonance, Raman spectroscopy, and x-ray diffraction for solid oxide cell application purpose. Glass structural unit neighboring environment and local ordering were evaluated. Glass network connectivity as well as silicon and boron glass former coordination were calculated for different B2O3:SiO2 ratios. Thermal stability of the borosilicate glasses was studied after thermal treatment at 850 °C. The study shows that high B2O3 content induces BO4 and SiO4 structural unit ordering, increases glass localized inhomogeneity, decreases glass network connectivity, and causes devitrification. Glass modifiers interact with either silicon- or boron-containing structural units and form different devitrified phases at different B2O3:SiO2 ratios. B2O3-free glass shows the best thermal stability among the studied compositions, remaining stable after thermal treatment for 200 h at 850 °C.

  17. Coenzyme- and His-tag-induced crystallization of octopine dehydrogenase

    International Nuclear Information System (INIS)

    Smits, Sander H. J.; Mueller, Andre; Grieshaber, Manfred K.; Schmitt, Lutz

    2008-01-01

    The crystal structure of octopine dehydrogenase revealed a specific role of the His 5 tag in inducing the crystal contacts required for successful crystallization. Over the last decade, protein purification has become more efficient and standardized through the introduction of affinity tags. The choice and position of the tag, however, can directly influence the process of protein crystallization. Octopine dehydrogenase (OcDH) without a His tag and tagged protein constructs such as OcDH-His 5 and OcDH-LEHis 6 have been investigated for their crystallizability. Only OcDH-His 5 yielded crystals; however, they were multiple. To improve crystal quality, the cofactor NADH was added, resulting in single crystals that were suitable for structure determination. As shown by the structure, the His 5 tag protrudes into the cleft between the NADH and l-arginine-binding domains and is mainly fixed in place by water molecules. The protein is thereby stabilized to such an extent that the formation of crystal contacts can proceed. Together with NADH, the His 5 tag obviously locks the enzyme into a specific conformation which induces crystal growth

  18. Structure-activity relationships between sterols and their thermal stability in oil matrix.

    Science.gov (United States)

    Hu, Yinzhou; Xu, Junli; Huang, Weisu; Zhao, Yajing; Li, Maiquan; Wang, Mengmeng; Zheng, Lufei; Lu, Baiyi

    2018-08-30

    Structure-activity relationships between 20 sterols and their thermal stabilities were studied in a model oil system. All sterol degradations were found to be consistent with a first-order kinetic model with determination of coefficient (R 2 ) higher than 0.9444. The number of double bonds in the sterol structure was negatively correlated with the thermal stability of sterol, whereas the length of the branch chain was positively correlated with the thermal stability of sterol. A quantitative structure-activity relationship (QSAR) model to predict thermal stability of sterol was developed by using partial least squares regression (PLSR) combined with genetic algorithm (GA). A regression model was built with R 2 of 0.806. Almost all sterol degradation constants can be predicted accurately with R 2 of cross-validation equals to 0.680. Four important variables were selected in optimal QSAR model and the selected variables were observed to be related with information indices, RDF descriptors, and 3D-MoRSE descriptors. Copyright © 2018 Elsevier Ltd. All rights reserved.

  19. Flexible all-carbon photovoltaics with improved thermal stability

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Chun; Ishihara, Hidetaka; Sodhi, Jaskiranjeet; Chen, Yen-Chang; Siordia, Andrew; Martini, Ashlie; Tung, Vincent C., E-mail: ctung@ucmerced.edu

    2015-04-15

    The structurally robust nature of nanocarbon allotropes, e.g., semiconducting single-walled carbon nanotubes (SWCNTs) and C{sub 60}s, makes them tantalizing candidates for thermally stable and mechanically flexible photovoltaic applications. However, C{sub 60}s rapidly dissociate away from the basal of SWCNTs under thermal stimuli as a result of weak intermolecular forces that “lock up” the binary assemblies. Here, we explore use of graphene nanoribbons (GNRs) as geometrically tailored protecting layers to suppress the unwanted dissociation of C{sub 60}s. The underlying mechanisms are explained using a combination of molecular dynamics simulations and transition state theory, revealing the temperature dependent disassociation of C{sub 60}s from the SWCNT basal plane. Our strategy provides fundamental guidelines for integrating all-carbon based nano-p/n junctions with optimized structural and thermal stability. External quantum efficiency and output current–voltage characteristics are used to experimentally quantify the effectiveness of GNR membranes under high temperature annealing. Further, the resulting C{sub 60}:SWCNT:GNR ternary composites display excellent mechanical stability, even after iterative bending tests. - Graphical abstract: The incorporation of solvent resistant, mechanically flexible and electrically addressable 2-D soft graphene nanoribbons facilitates the assembly of photoconductive carbon nano-p/n junctions for thermally stable and flexible photovoltaic cells.

  20. Flexible all-carbon photovoltaics with improved thermal stability

    International Nuclear Information System (INIS)

    Tang, Chun; Ishihara, Hidetaka; Sodhi, Jaskiranjeet; Chen, Yen-Chang; Siordia, Andrew; Martini, Ashlie; Tung, Vincent C.

    2015-01-01

    The structurally robust nature of nanocarbon allotropes, e.g., semiconducting single-walled carbon nanotubes (SWCNTs) and C 60 s, makes them tantalizing candidates for thermally stable and mechanically flexible photovoltaic applications. However, C 60 s rapidly dissociate away from the basal of SWCNTs under thermal stimuli as a result of weak intermolecular forces that “lock up” the binary assemblies. Here, we explore use of graphene nanoribbons (GNRs) as geometrically tailored protecting layers to suppress the unwanted dissociation of C 60 s. The underlying mechanisms are explained using a combination of molecular dynamics simulations and transition state theory, revealing the temperature dependent disassociation of C 60 s from the SWCNT basal plane. Our strategy provides fundamental guidelines for integrating all-carbon based nano-p/n junctions with optimized structural and thermal stability. External quantum efficiency and output current–voltage characteristics are used to experimentally quantify the effectiveness of GNR membranes under high temperature annealing. Further, the resulting C 60 :SWCNT:GNR ternary composites display excellent mechanical stability, even after iterative bending tests. - Graphical abstract: The incorporation of solvent resistant, mechanically flexible and electrically addressable 2-D soft graphene nanoribbons facilitates the assembly of photoconductive carbon nano-p/n junctions for thermally stable and flexible photovoltaic cells.

  1. Thermal stability and primary phase of Al-Ni(Cu)-La amorphous alloys

    International Nuclear Information System (INIS)

    Huang Zhenghua; Li Jinfu; Rao Qunli; Zhou Youhe

    2008-01-01

    Thermal stability and primary phase of Al 85+x Ni 9-x La 6 (x = 0-6) and Al 85 Ni 9-x Cu x La 6 (x = 0-9) amorphous alloys were investigated by X-ray diffraction and differential scanning calorimeter. It is revealed that replacing Ni in the Al 85 Ni 9 La 6 alloy by Cu decreases the thermal stability and makes the primary phase change from intermetallic compounds to single fcc-Al as the Cu content reaches and exceeds 4 at.%. When the Ni and La contents are fixed, replacing Al by Cu increases the thermal stability but also promotes the precipitation of single fcc-Al as the primary phase

  2. Thermal stability analysis and auxiliary power feedback control for the tokamak engineering test breeder (TETB-II)

    International Nuclear Information System (INIS)

    Sheng Guangzhao

    1993-01-01

    The thermal stability of TETB-II is analyzed using different methods, viz., POPCON, linear stability analysis and the time evolution calculation of plasma parameters. A thermal instability of the TETB-II is predicted. Auxiliary power feedback control for thermal stability appears feasible and efficient

  3. Expressed sequence tags related to nitrogen metabolism in maize inoculated with Azospirillum brasilense.

    Science.gov (United States)

    Pereira-Defilippi, L; Pereira, E M; Silva, F M; Moro, G V

    2017-05-31

    The relative quantitative real-time expression of two expressed sequence tags (ESTs) codifying for key enzymes in nitrogen metabolism in maize, nitrate reductase (ZmNR), and glutamine synthetase (ZmGln1-3) was performed for genotypes inoculated with Azospirillum brasilense. Two commercial single-cross hybrids (AG7098 and 2B707) and two experimental synthetic varieties (V2 and V4) were raised under controlled greenhouse conditions, in six treatment groups corresponding to different forms of inoculation and different levels of nitrogen application by top-dressing. The genotypes presented distinct responses to inoculation with A. brasilense. Increases in the expression of ZmNR were observed for the hybrids, while V4 only displayed a greater level of expression when the plants received nitrogenous fertilization by top-dressing and there was no inoculation. The expression of the ZmGln1-3EST was induced by A. brasilense in the hybrids and the variety V4. In contrast, the variety V2 did not respond to inoculation.

  4. Analysis of expressed sequence tags from the Ulva prolifera (Chlorophyta)

    Science.gov (United States)

    Niu, Jianfeng; Hu, Haiyan; Hu, Songnian; Wang, Guangce; Peng, Guang; Sun, Song

    2010-01-01

    In 2008, a green tide broke out before the sailing competition of the 29th Olympic Games in Qingdao. The causative species was determined to be Enteromorpha prolifera ( Ulva prolifera O. F. Müller), a familiar green macroalga along the coastline of China. Rapid accumulation of a large biomass of floating U. prolifera prompted research on different aspects of this species. In this study, we constructed a nonnormalized cDNA library from the thalli of U. prolifera and acquired 10 072 high-quality expressed sequence tags (ESTs). These ESTs were assembled into 3 519 nonredundant gene groups, including 1 446 clusters and 2 073 singletons. After annotation with the nr database, a large number of genes were found to be related with chloroplast and ribosomal protein, GO functional classification showed 1 418 ESTs participated in photosynthesis and 1 359 ESTs were responsible for the generation of precursor metabolites and energy. In addition, rather comprehensive carbon fixation pathways were found in U. prolifera using KEGG. Some stress-related and signal transduction-related genes were also found in this study. All the evidences displayed that U. prolifera had substance and energy foundation for the intense photosynthesis and the rapid proliferation. Phylogenetic analysis of cytochrome c oxidase subunit I revealed that this green-tide causative species is most closely affiliated to Pseudendoclonium akinetum (Ulvophyceae).

  5. Structure and Mechanical Properties of Al-Cu-Fe-X Alloys with Excellent Thermal Stability.

    Science.gov (United States)

    Školáková, Andrea; Novák, Pavel; Mejzlíková, Lucie; Průša, Filip; Salvetr, Pavel; Vojtěch, Dalibor

    2017-11-05

    In this work, the structure and mechanical properties of innovative Al-Cu-Fe based alloys were studied. We focused on preparation and characterization of rapidly solidified and hot extruded Al-Cu-Fe, Al-Cu-Fe-Ni and Al-Cu-Fe-Cr alloys. The content of transition metals affects mechanical properties and structure. For this reason, microstructure, phase composition, hardness and thermal stability have been investigated in this study. The results showed exceptional thermal stability of these alloys and very good values of mechanical properties. Alloying by chromium ensured the highest thermal stability, while nickel addition refined the structure of the consolidated alloy. High thermal stability of all tested alloys was described in context with the transformation of the quasicrystalline phases to other types of intermetallics.

  6. High thermal stability solution-processable narrow-band gap molecular semiconductors.

    Science.gov (United States)

    Liu, Xiaofeng; Hsu, Ben B Y; Sun, Yanming; Mai, Cheng-Kang; Heeger, Alan J; Bazan, Guillermo C

    2014-11-19

    A series of narrow-band gap conjugated molecules with specific fluorine substitution patterns has been synthesized in order to study the effect of fluorination on bulk thermal stability. As the number of fluorine substituents on the backbone increase, one finds more thermally robust bulk structures both under inert and ambient conditions as well as an increase in phase transition temperatures in the solid state. When integrated into field-effect transistor devices, the molecule with the highest degree of fluorination shows a hole mobility of 0.15 cm(2)/V·s and a device thermal stability of >300 °C. Generally, the enhancement in thermal robustness of bulk organization and device performance correlates with the level of C-H for C-F substitution. These findings are relevant for the design of molecular semiconductors that can be introduced into optoelectronic devices to be operated under a wide range of conditions.

  7. Tag-elese or The Language of Tags

    Directory of Open Access Journals (Sweden)

    Jan Simons

    2008-01-01

    Full Text Available The core "meme" of Web 2.0 from which almost all other memes radiated was: 'You control your own data' (O'Reilly, 2005, 3. Key instruments for this user control are tagging systems that allow users to freely assign keywords of their own choosing to Internet resources of their own making as well as to documents produced by others. Of course, freely chosen keywords tags do not necessarily follow prefixed taxonomies or classification systems. But going by the maxim that interaction creates similarity and similarity creates interaction, the idea - or hope - is, however, that the tagging practices of individual users will eventually converge into an emergent common vocabulary or folksonomy (Merholz, 2004; Shirky, 2005; Vander Wal, 2005b; Mika, 2007. It is far from clear, however, that free tagging systems will eventually yield controlled vocabularies, and there are many incentives for idiosyncratic, ambiguous, and inconsistent uses of tags. Left to themselves, free tagging systems seem to be too wild and too chaotic for any order to emerge. But are these free tagging systems really as "feral" as they seem to be, or do they only look uncontrolled because one has been looking for order in the wrong place? I have done a quick-and-dirty" analysis of Flickr's tag cloud. The concept was: if folksonomies encourage users to tap on their own vernacular, everyday natural language must somehow "guide" the tagging practices of users of tagging systems. Flickr's tag cloud has been choosen because it may teach us something about tagging systems and folksonomies, and not - or not primarily - because of what tags may tell us about pictures.

  8. Optimal control theory applied to fusion plasma thermal stabilization

    International Nuclear Information System (INIS)

    Sager, G.; Miley, G.; Maya, I.

    1985-01-01

    Many authors have investigated stability characteristics and performance of various burn control schemes. The work presented here represents the first application of optimal control theory to the problem of fusion plasma thermal stabilization. The objectives of this initial investigation were to develop analysis methods, demonstrate tractability, and present some preliminary results of optimal control theory in burn control research

  9. Cu-based shape memory alloys with enhanced thermal stability and mechanical properties

    International Nuclear Information System (INIS)

    Chung, C.Y.; Lam, C.W.H.

    1999-01-01

    Cu-based shape memory alloys were developed in the 1960s. They show excellent thermoelastic martensitic transformation. However the problems in mechanical properties and thermal instability have inhibited them from becoming promising engineering alloys. A new Cu-Zn-Al-Mn-Zr Cu-based shape memory alloy has been developed. With the addition of Mn and Zr, the martensitic transformation behaviour and the grain size ca be better controlled. The new alloys demonstrates good mechanical properties with ultimate tensile strenght and ductility, being 460 MPa and 9%, respectively. Experimental results revealed that the alloy has better thermal stability, i.e. martensite stabilisation is less serious. In ordinary Cu-Zn-Al alloys, martensite stabilisation usually occurs at room temperature. The new alloy shows better thermal stability even at elevated temperature (∝150 C, >A f =80 C). A limited small amount of martensite stabilisation was observed upon ageing of the direct quenched samples as well as the step quenched samples. This implies that the thermal stability of the new alloy is less dependent on the quenching procedure. Furthermore, such minor martensite stabilisation can be removed by subsequent suitable parent phase ageing. The new alloy is ideal for engineering applications because of its better thermal stability and better mechanical properties. (orig.)

  10. [Thermal stability of rhodopsins and opsins in warm- and cold-blooded vertebrates].

    Science.gov (United States)

    Berman, A L; Suvorov, S A; Parnova, R G; Gracheva, O A; Rychkova, M P

    1981-01-01

    Thermal stability of rhodopsins and opsins has been studied in endothermic (sheep, cattle, pig, rat) and ectothermic (frog) animals under two different conditions -- in the intact photoreceptor membranes (PM) and after substitution of the lipid surrounding of rhodopsins by molecules of a detergent Triton X-100. Lipid composition of PM in these animals was also studied, as well as the effect of proteases (pronase and papaine) upon thermal stability of rhodopsins in PM and in 1% Triton X-100 solutions. The thermal resistance of rhodopsins in PM was found to vary in the animals used to a great extent. The maximal differences in thermal stability of rhodopsins in ecto- and endothermic animals were due to the properties of photoreceptor protein itself, whereas in ectothermic animals they resulted mainly from differences in the lipid composition of PM. PM of endothermic animals differ from those of ectothermic ones by a lower content of polyenoic fatty acids and by a higher amount of phosphatidyl ethanolamine. The thermal stability of rhodopsins is not due to rhodopsin molecule as a whole, and depends mainly on its part which is directly bound to 11-cis retinal, located in hydrophobic region of PM and inaccessible to protease attack.

  11. Using TESS to predict transcription factor binding sites in DNA sequence.

    Science.gov (United States)

    Schug, Jonathan

    2008-03-01

    This unit describes how to use the Transcription Element Search System (TESS). This Web site predicts transcription factor binding sites (TFBS) in DNA sequence using two different kinds of models of sites, strings and positional weight matrices. The binding of transcription factors to DNA is a major part of the control of gene expression. Transcription factors exhibit sequence-specific binding; they form stronger bonds to some DNA sequences than to others. Identification of a good binding site in the promoter for a gene suggests the possibility that the corresponding factor may play a role in the regulation of that gene. However, the sequences transcription factors recognize are typically short and allow for some amount of mismatch. Because of this, binding sites for a factor can typically be found at random every few hundred to a thousand base pairs. TESS has features to help sort through and evaluate the significance of predicted sites.

  12. PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET sequence data

    Directory of Open Access Journals (Sweden)

    Wei Chia-Lin

    2006-08-01

    Full Text Available Abstract Background We recently developed the Paired End diTag (PET strategy for efficient characterization of mammalian transcriptomes and genomes. The paired end nature of short PET sequences derived from long DNA fragments raised a new set of bioinformatics challenges, including how to extract PETs from raw sequence reads, and correctly yet efficiently map PETs to reference genome sequences. To accommodate and streamline data analysis of the large volume PET sequences generated from each PET experiment, an automated PET data process pipeline is desirable. Results We designed an integrated computation program package, PET-Tool, to automatically process PET sequences and map them to the genome sequences. The Tool was implemented as a web-based application composed of four modules: the Extractor module for PET extraction; the Examiner module for analytic evaluation of PET sequence quality; the Mapper module for locating PET sequences in the genome sequences; and the ProjectManager module for data organization. The performance of PET-Tool was evaluated through the analyses of 2.7 million PET sequences. It was demonstrated that PET-Tool is accurate and efficient in extracting PET sequences and removing artifacts from large volume dataset. Using optimized mapping criteria, over 70% of quality PET sequences were mapped specifically to the genome sequences. With a 2.4 GHz LINUX machine, it takes approximately six hours to process one million PETs from extraction to mapping. Conclusion The speed, accuracy, and comprehensiveness have proved that PET-Tool is an important and useful component in PET experiments, and can be extended to accommodate other related analyses of paired-end sequences. The Tool also provides user-friendly functions for data quality check and system for multi-layer data management.

  13. Effect of thermal-treatment sequence on sound absorbing and mechanical properties of porous sound-absorbing/thermal-insulating composites

    Directory of Open Access Journals (Sweden)

    Huang Chen-Hung

    2016-01-01

    Full Text Available Due to recent rapid commercial and industrial development, mechanical equipment is supplemented massively in the factory and thus mechanical operation causes noise which distresses living at home. In livelihood, neighborhood, transportation equipment, jobsite construction noises impact on quality of life not only factory noise. This study aims to preparation technique and property evaluation of porous sound-absorbing/thermal-insulating composites. Hollow three-dimensional crimp PET fibers blended with low-melting PET fibers were fabricated into hollow PET/low-melting PET nonwoven after opening, blending, carding, lapping and needle-bonding process. Then, hollow PET/low-melting PET nonwovens were laminated into sound-absorbing/thermal-insulating composites by changing sequence of needle-bonding and thermal-treatment. The optimal thermal-treated sequence was found by tensile strength, tearing strength, sound-absorbing coefficient and thermal conductivity coefficient tests of porous composites.

  14. Telomeric expression sites are highly conserved in Trypanosoma brucei.

    Directory of Open Access Journals (Sweden)

    Christiane Hertz-Fowler

    Full Text Available Subtelomeric regions are often under-represented in genome sequences of eukaryotes. One of the best known examples of the use of telomere proximity for adaptive purposes are the bloodstream expression sites (BESs of the African trypanosome Trypanosoma brucei. To enhance our understanding of BES structure and function in host adaptation and immune evasion, the BES repertoire from the Lister 427 strain of T. brucei were independently tagged and sequenced. BESs are polymorphic in size and structure but reveal a surprisingly conserved architecture in the context of extensive recombination. Very small BESs do exist and many functioning BESs do not contain the full complement of expression site associated genes (ESAGs. The consequences of duplicated or missing ESAGs, including ESAG9, a newly named ESAG12, and additional variant surface glycoprotein genes (VSGs were evaluated by functional assays after BESs were tagged with a drug-resistance gene. Phylogenetic analysis of constituent ESAG families suggests that BESs are sequence mosaics and that extensive recombination has shaped the evolution of the BES repertoire. This work opens important perspectives in understanding the molecular mechanisms of antigenic variation, a widely used strategy for immune evasion in pathogens, and telomere biology.

  15. Enhancement of oxidative stability of the subtilisin nattokinase by site-directed mutagenesis expressed in Escherichia coli.

    Science.gov (United States)

    Weng, MeiZhi; Zheng, ZhongLiang; Bao, Wei; Cai, YongJun; Yin, Yan; Zou, GuoLin; Zou, GouLin

    2009-11-01

    Nattokinase (subtilisin NAT, NK) is a bacterial serine protease with strong fibrinolytic activity and it is a potent cardiovascular drug. In medical and commercial applications, however, it is susceptible to chemical oxidation, and subsequent inactivation or denaturation. Here we show that the oxidative stability of NK was substantially increased by optimizing the amino acid residues Thr(220) and Met(222), which were in the vicinity of the catalytic residue Ser(221) of the enzyme. Two nonoxidative amino acids (Ser and Ala) were introduced at these sites using site-directed mutagenesis. Active enzymes were successfully expressed in Escherichia coli with periplasmic secretion and enzymes were purified to homogeneity. The purified enzymes were analyzed with respect to oxidative stability, kinetic parameters, fibrinolytic activity and thermal stability. M222A mutant was found to have a greatly increased oxidative stability compared with wild-type enzyme and it was resistant to inactivation by more than 1 M H(2)O(2), whereas the wild-type enzyme was inactivated by 0.1 M H(2)O(2) (t(1/2) approximately 11.6 min). The other mutant (T220S) also showed an obvious increase in antioxidative ability. Molecular dynamic simulations on wild-type and T220S mutant proteins suggested that a hydrogen bond was formed between Ser(220) and Asn(155), and the spatial structure of Met(222) was changed compared with the wild-type. The present study demonstrates the feasibility of improving oxidative stability of NK by site-directed mutagenesis and shows successful protein engineering cases to improve stability of NK as a potent therapeutic agent.

  16. A genome-wide analysis of lentivector integration sites using targeted sequence capture and next generation sequencing technology.

    Science.gov (United States)

    Ustek, Duran; Sirma, Sema; Gumus, Ergun; Arikan, Muzaffer; Cakiris, Aris; Abaci, Neslihan; Mathew, Jaicy; Emrence, Zeliha; Azakli, Hulya; Cosan, Fulya; Cakar, Atilla; Parlak, Mahmut; Kursun, Olcay

    2012-10-01

    One application of next-generation sequencing (NGS) is the targeted resequencing of interested genes which has not been used in viral integration site analysis of gene therapy applications. Here, we combined targeted sequence capture array and next generation sequencing to address the whole genome profiling of viral integration sites. Human 293T and K562 cells were transduced with a HIV-1 derived vector. A custom made DNA probe sets targeted pLVTHM vector used to capture lentiviral vector/human genome junctions. The captured DNA was sequenced using GS FLX platform. Seven thousand four hundred and eighty four human genome sequences flanking the long terminal repeats (LTR) of pLVTHM fragment sequences matched with an identity of at least 98% and minimum 50 bp criteria in both cells. In total, 203 unique integration sites were identified. The integrations in both cell lines were totally distant from the CpG islands and from the transcription start sites and preferentially located in introns. A comparison between the two cell lines showed that the lentiviral-transduced DNA does not have the same preferred regions in the two different cell lines. Copyright © 2012 Elsevier B.V. All rights reserved.

  17. Structure and thermal stability of nanocrystalline materials

    Indian Academy of Sciences (India)

    In addition, study of the thermal stability of nanocrystalline materials against significant grain growth is both scientific and technological interest. A sharp increase in grain size (to micron levels) during consolidation of nanocrystalline powders to obtain fully dense materials may consequently result in the loss of some unique ...

  18. A Study of HTML Title Tag Creation Behavior of Academic Web Sites

    Science.gov (United States)

    Noruzi, Alireza

    2007-01-01

    The HTML title tag information should identify and describe exactly what a Web page contains. This paper analyzes the "Title element" and raises a significant question: "Why is the title tag important?" Search engines base search results and page rankings on certain criteria. Among the most important criteria is the presence of the search keywords…

  19. Air, aqueous and thermal stabilities of Ce3+ ions in cerium oxide nanoparticle layers with substrates

    KAUST Repository

    Naganuma, Tamaki

    2014-01-01

    Abundant oxygen vacancies coexisting with Ce3+ ions in fluorite cerium oxide nanoparticles (CNPs) have the potential to enhance catalytic ability, but the ratio of unstable Ce3+ ions in CNPs is typically low. Our recent work, however, demonstrated that the abundant Ce3+ ions created in cerium oxide nanoparticle layers (CNPLs) by Ar ion irradiation were stable in air at room temperature. Ce valence states in CNPs correlate with the catalytic ability that involves redox reactions between Ce3+ and Ce4+ ions in given application environments (e.g. high temperature in carbon monoxide gas conversion and immersion conditions in biomedical applications). To better understand the mechanism by which Ce3+ ions achieve stability in CNPLs, we examined (i) extra-long air-stability, (ii) thermal stability up to 500 °C, and (iii) aqueous stability of Ce 3+ ions in water, buffer solution and cell culture medium. It is noteworthy that air-stability of Ce3+ ions in CNPLs persisted for more than 1 year. Thermal stability results showed that oxidation of Ce 3+ to Ce4+ occurred at 350 °C in air. Highly concentrated Ce3+ ions in ultra-thin CNPLs slowly oxidized in water within 1 day, but stability was improved in the cell culture medium. Ce 3+ stability of CNPLs immersed in the medium was associated with phosphorus adsorption on the Ce3+ sites. This study also illuminates the potential interaction mechanisms of stable Ce3+ ions in CNPLs. These findings could be utilized to understand catalytic mechanisms of CNPs with abundant oxygen vacancies in their application environments. © The Royal Society of Chemistry 2014.

  20. Spin dynamics and thermal stability in L10 FePt

    Science.gov (United States)

    Chen, Tianran; Toomey, Wahida

    Increasing the data storage density of hard drives remains one of the continuing goals in magnetic recording technology. A critical challenge for increasing data density is the thermal stability of the written information, which drops rapidly as the bit size gets smaller. To maintain good thermal stability in small bits, one should consider materials with high anisotropy energy such as L10 FePt. High anisotropy energy nevertheless implies high coercivity, making it difficult to write information onto the disk. This issue can be overcome by a new technique called heat-assisted magnetic recording, where a laser is used to locally heat the recording medium to reduce its coercivity while retaining relatively good thermal stability. Many of the microscopic magnetic properties of L10 FePt, however, have not been theoretically well understood. In this poster, I will focus on a single L10 FePt grain, typically of a few nanometers. Specifically, I will discuss its critical temperature, size effect and, in particular, spin dynamics in the writing process, a key to the success of heat-assisted magnetic recording. WCU URF16.

  1. Structure and Mechanical Properties of Al-Cu-Fe-X Alloys with Excellent Thermal Stability

    Directory of Open Access Journals (Sweden)

    Andrea Školáková

    2017-11-01

    Full Text Available In this work, the structure and mechanical properties of innovative Al-Cu-Fe based alloys were studied. We focused on preparation and characterization of rapidly solidified and hot extruded Al-Cu-Fe, Al-Cu-Fe-Ni and Al-Cu-Fe-Cr alloys. The content of transition metals affects mechanical properties and structure. For this reason, microstructure, phase composition, hardness and thermal stability have been investigated in this study. The results showed exceptional thermal stability of these alloys and very good values of mechanical properties. Alloying by chromium ensured the highest thermal stability, while nickel addition refined the structure of the consolidated alloy. High thermal stability of all tested alloys was described in context with the transformation of the quasicrystalline phases to other types of intermetallics.

  2. Cyanine-based probe\\tag-peptide pair fluorescence protein imaging and fluorescence protein imaging methods

    Science.gov (United States)

    Mayer-Cumblidge, M. Uljana; Cao, Haishi

    2013-01-15

    A molecular probe comprises two arsenic atoms and at least one cyanine based moiety. A method of producing a molecular probe includes providing a molecule having a first formula, treating the molecule with HgOAc, and subsequently transmetallizing with AsCl.sub.3. The As is liganded to ethanedithiol to produce a probe having a second formula. A method of labeling a peptide includes providing a peptide comprising a tag sequence and contacting the peptide with a biarsenical molecular probe. A complex is formed comprising the tag sequence and the molecular probe. A method of studying a peptide includes providing a mixture containing a peptide comprising a peptide tag sequence, adding a biarsenical probe to the mixture, and monitoring the fluorescence of the mixture.

  3. Haplotypes of the TaGS5-A1 gene are associated with thousand-kernel weight in Chinese bread wheat

    Directory of Open Access Journals (Sweden)

    Wang Sha Sha

    2016-06-01

    Full Text Available In previous work, we cloned TaGS5 gene and found the association of TaGS5-A1 alleles with agronomic traits. In this study, the promoter sequence of the TaGS5-A1 gene was isolated from bread wheat. Sequencing results revealed that a G insertion was found in position -1925 bp of the TaGS5-A1 gene (Reference to ATG, which occurred in the Sp1 domain of the promoter sequence. Combined with previous single nucleotide polymorphism (SNP in the TaGS5-A1 exon sequence, four genotypes were formed at the TaGS5-A1 locus and were designated as TaGS5-A1a-a, TaGS5-A1a-b, TaGS5-A1b-a, and TaGS5-A1b-b, respectively. Analysis of the association of TaGS5-A1 alleles with agronomic traits indicated that cultivars with the TaGS5-A1a-b allele possessed significantly higher thousand-kernel weight (TKW and lower plant height than cultivars with the TaGS5-A1a-a allele, and cultivars with the TaGS5-A1b-b allele showed higher TKW than cultivars with the TaGS5-A1b-a allele. The differences of these traits between the TaGS5-A1a-a and TaGS5-A1a-b alleles were larger than those of the TaGS5-A1b-a and TaGS5-A1b-b alleles, suggesting that the -1925G insertion plays the more important role in TaGS5-A1a genotypes than in TaGS5-A1b genotypes. qRT-PCR indicated that TaGS5-A1b-b possessed the significantly highest expression level among four TaGS5-A1 haplotypes in mature seeds and further showed a significantly higher expression level than TaGS5-A1b-a at five different developmental stages of the seeds, suggesting that high expression of TaGS5-A1 was positively associated with high TKW in bread wheat. This study could provide a relatively superior genotype in view of TKW in wheat breeding programs and could also provide important information for dissection of the regulatory mechanism of the yield-related traits.

  4. On the impact of atmospheric thermal stability on the characteristics of nocturnal downslope flows

    Science.gov (United States)

    Ye, Z. J.; Garratt, J. R.; Segal, M.; Pielke, R. A.

    1990-04-01

    The impacts of background (or ambient) and local atmospheric thermal stabilities, and slope steepness, on nighttime thermally induced downslope flow in meso-β domains (i.e., 20 200 km horizontal extent) have been investigated using analytical and numerical model approaches. Good agreement between the analytical and numerical evaluations was found. It was concluded that: (i) as anticipated, the intensity of the downslope flow increases with increased slope steepness, although the depth of the downslope flow was found to be insensitive to slope steepness in the studied situations; (ii) the intensity of the downslope flow is generally independent of background atmospheric thermal stability; (iii) for given integrated nighttime cooling across the nocturnal boundary layer (NBL), Q s the local atmospheric thermal stability exerts a strong influence on downslope flow behavior: the downslope flow intensity increases when local atmospheric thermal stability increases; and (iv) the downslope flow intensity is proportional to Q s 1/2.

  5. Versatile Gene-Specific Sequence Tags for Arabidopsis Functional Genomics: Transcript Profiling and Reverse Genetics Applications

    Science.gov (United States)

    Hilson, Pierre; Allemeersch, Joke; Altmann, Thomas; Aubourg, Sébastien; Avon, Alexandra; Beynon, Jim; Bhalerao, Rishikesh P.; Bitton, Frédérique; Caboche, Michel; Cannoot, Bernard; Chardakov, Vasil; Cognet-Holliger, Cécile; Colot, Vincent; Crowe, Mark; Darimont, Caroline; Durinck, Steffen; Eickhoff, Holger; de Longevialle, Andéol Falcon; Farmer, Edward E.; Grant, Murray; Kuiper, Martin T.R.; Lehrach, Hans; Léon, Céline; Leyva, Antonio; Lundeberg, Joakim; Lurin, Claire; Moreau, Yves; Nietfeld, Wilfried; Paz-Ares, Javier; Reymond, Philippe; Rouzé, Pierre; Sandberg, Goran; Segura, Maria Dolores; Serizet, Carine; Tabrett, Alexandra; Taconnat, Ludivine; Thareau, Vincent; Van Hummelen, Paul; Vercruysse, Steven; Vuylsteke, Marnik; Weingartner, Magdalena; Weisbeek, Peter J.; Wirta, Valtteri; Wittink, Floyd R.A.; Zabeau, Marc; Small, Ian

    2004-01-01

    Microarray transcript profiling and RNA interference are two new technologies crucial for large-scale gene function studies in multicellular eukaryotes. Both rely on sequence-specific hybridization between complementary nucleic acid strands, inciting us to create a collection of gene-specific sequence tags (GSTs) representing at least 21,500 Arabidopsis genes and which are compatible with both approaches. The GSTs were carefully selected to ensure that each of them shared no significant similarity with any other region in the Arabidopsis genome. They were synthesized by PCR amplification from genomic DNA. Spotted microarrays fabricated from the GSTs show good dynamic range, specificity, and sensitivity in transcript profiling experiments. The GSTs have also been transferred to bacterial plasmid vectors via recombinational cloning protocols. These cloned GSTs constitute the ideal starting point for a variety of functional approaches, including reverse genetics. We have subcloned GSTs on a large scale into vectors designed for gene silencing in plant cells. We show that in planta expression of GST hairpin RNA results in the expected phenotypes in silenced Arabidopsis lines. These versatile GST resources provide novel and powerful tools for functional genomics. PMID:15489341

  6. Thermal stability and environmental compatibility of Inconel 617

    International Nuclear Information System (INIS)

    Kimball, O.F.

    1989-01-01

    The thermal stability and environmental compatibility of Inconel 617, a prime nuclear process heat steam reformer candidate alloy, are described in this paper. This commercially available wrought nickel-base alloy has excellent high-temperature strength but is subject to loss of toughness and ductility due to thermal instability. Work done to improve the thermal stability of this alloy is discussed. Room-temperature tensile and toughness data and microstructural information for Inconel 617 specimens exposed at elevated temperatures are presented. Preliminary data indicate that controlling the chemistry of Inconel 617 can provide a substantial improvement in thermal stability. Preliminary work to define the range of high-temperature gas-cooled reactor (HTGR) primary coolant compositions within which minimal deleterious gas/metal reactions occur with Inconel 617 is described. Within this gas chemistry range a stable surface oxide forms and only slight carburization occurs. In other gas chemistry ranges, rapid carburization or decarburization can occur. The gas corrosion experiments discussed are part of a series of relatively short-term exposures to HTGR helium in which the effects of different H 2 O concentrations (0.01 to 1.0 Pa) were determined as a function of the systematic variation of a second constituent (CO and CH 4 for this work) in the test gas. The composition of the basic HTGR helium was 40 Pa H 2 , 4 Pa CO, 0.02 Pa CO 2 , 2 Pa CH 4 in helium at 0.2 MPa. Two other CO levels (1 and 12 Pa) and one additional CH 4 level (0.63 Pa) were used in these experiments. Experimental exposure methods are discussed and the results of gas-metal interaction studies are presented. These results include carbon analyses and optical and scanning electron microscopy to determine the morphology and type of surface and subsurface microstructures. (author). 15 refs, 6 figs, 5 tabs

  7. Analysis of tag-position bias in MPSS technology

    Directory of Open Access Journals (Sweden)

    Rattray Magnus

    2006-04-01

    Full Text Available Abstract Background Massively Parallel Signature Sequencing (MPSS technology was recently developed as a high-throughput technology for measuring the concentration of mRNA transcripts in a sample. It has previously been observed that the position of the signature tag in a transcript (distance from 3' end can affect the measurement, but this effect has not been studied in detail. Results We quantify the effect of tag-position bias in Classic and Signature MPSS technology using published data from Arabidopsis, rice and human. We investigate the relationship between measured concentration and tag-position using nonlinear regression methods. The observed relationship is shown to be broadly consistent across different data sets. We find that there exist different and significant biases in both Classic and Signature MPSS data. For Classic MPSS data, genes with tag-position in the middle-range have highest measured abundance on average while genes with tag-position in the high-range, far from the 3' end, show a significant decrease. For Signature MPSS data, high-range tag-position genes tend to have a flatter relationship between tag-position and measured abundance. Thus, our results confirm that the Signature MPSS method fixes a substantial problem with the Classic MPSS method. For both Classic and Signature MPSS data there is a positive correlation between measured abundance and tag-position for low-range tag-position genes. Compared with the effects of mRNA length and number of exons, tag-position bias seems to be more significant in Arabadopsis. The tag-position bias is reflected both in the measured abundance of genes with a significant tag count and in the proportion of unexpressed genes identified. Conclusion Tag-position bias should be taken into consideration when measuring mRNA transcript abundance using MPSS technology, both in Classic and Signature MPSS methods.

  8. Gene discovery and transcript analyses in the corn smut pathogen Ustilago maydis: expressed sequence tag and genome sequence comparison

    Directory of Open Access Journals (Sweden)

    Saville Barry J

    2007-09-01

    Full Text Available Abstract Background Ustilago maydis is the basidiomycete fungus responsible for common smut of corn and is a model organism for the study of fungal phytopathogenesis. To aid in the annotation of the genome sequence of this organism, several expressed sequence tag (EST libraries were generated from a variety of U. maydis cell types. In addition to utility in the context of gene identification and structure annotation, the ESTs were analyzed to identify differentially abundant transcripts and to detect evidence of alternative splicing and anti-sense transcription. Results Four cDNA libraries were constructed using RNA isolated from U. maydis diploid teliospores (U. maydis strains 518 × 521 and haploid cells of strain 521 grown under nutrient rich, carbon starved, and nitrogen starved conditions. Using the genome sequence as a scaffold, the 15,901 ESTs were assembled into 6,101 contiguous expressed sequences (contigs; among these, 5,482 corresponded to predicted genes in the MUMDB (MIPS Ustilago maydis database, while 619 aligned to regions of the genome not yet designated as genes in MUMDB. A comparison of EST abundance identified numerous genes that may be regulated in a cell type or starvation-specific manner. The transcriptional response to nitrogen starvation was assessed using RT-qPCR. The results of this suggest that there may be cross-talk between the nitrogen and carbon signalling pathways in U. maydis. Bioinformatic analysis identified numerous examples of alternative splicing and anti-sense transcription. While intron retention was the predominant form of alternative splicing in U. maydis, other varieties were also evident (e.g. exon skipping. Selected instances of both alternative splicing and anti-sense transcription were independently confirmed using RT-PCR. Conclusion Through this work: 1 substantial sequence information has been provided for U. maydis genome annotation; 2 new genes were identified through the discovery of 619

  9. Thermal stability of α-amylase in aqueous cosolvent systems

    Indian Academy of Sciences (India)

    Prakash

    Department of Protein Chemistry and Technology, Central Food Technological Research ... Keywords. α-Amylase; cosolvents; preferential interaction parameters; thermal stability ...... simulations of trehalose as a 'dynamic reducer' for solvent.

  10. Thermal Stability of Li-Ion Cells

    International Nuclear Information System (INIS)

    ROTH, EMANUEL P.

    1999-01-01

    The thermal stability of Li-ion cells with intercalating carbon anodes and metal oxide cathodes was measured as a function of state of charge and temperature for two advanced cell chemistries. Cells of the 18650 design with Li(sub x)CoO(sub 2) cathodes (commercial SONY cells) and Li(sub x)Ni(sub 0.8)Co(sub 0.2)O(sub 2) cathodes were measured for thermal reactivity in the open circuit cell condition. Accelerating rate calorimetry (ARC) was used to measure cell thermal runaway as a function of state of charge (SOC). Microcalorimetry was used to measure the time dependence of heat generating side reactions also as a function of SOC. Components of cells were measured using differential scanning calorimetry (DSC) to study the thermal reactivity of the individual electrodes to determine the temperature regimes and conditions of the major thermal reactions. Thermal decomposition of the SEI layer at the anodes was identified as the initiating source for thermal runaway. The cells with Li(sub x)CoO(sub 2) cathodes showed greater sensitivity to SOC and higher accelerating heating rates than seen for the cells with Li(sub x)Ni(sub 0.8)Co(sub 0.2)O(sub 2)cathodes. Lower temperature reactions starting as low as 40 C were also observed that were SOC dependent but not accelerating. These reactions were also measured in the microcalorimeter and observed to decay over time with a power-law dependence and are believed to result in irreversible capacity loss in the cells

  11. Thermal treatment and non-thermal technologies for remediation of manufactured gas plant sites

    International Nuclear Information System (INIS)

    McGowan, T.F.; Greer, B.A.; Lawless, M.

    1996-01-01

    More than 1,500 manufactured gas plant (MGP) sites exist throughout the US. Many are contaminated with coal tar from coal-fueled gas works which produced town gas from the mid-1800s through the 1950s. Virtually all old US cities have such sites. Most are in downtown areas as they were installed for central distribution of manufactured gas. While a few sites are CERCLA/Superfund, most are not. However, the contaminants and methods used for remediation are similar to those used for Superfund clean-ups of coal tar contamination from wood-treating and coke oven facilities. Clean-up of sites is triggered by regulatory pressure, property transfers and re-development as well as releases to the environment--in particular, via groundwater migration. Due to utility de-regulation, site clean-ups may also be triggered by sale of a utility or of a specific utility site to other utilities. Utilities have used two approaches in dealing with their MGP sites. The first is do nothing and hope for the best. History suggests that, sooner or later, these sites become a bigger problem via a release, citizen lawsuit or regulatory/public service commission intervention. The second, far better approach is to define the problem now and make plans /for waste treatment or immobilization. This paper describes recent experience with a high capacity/low cost thermal desorption process for this waste and reviews non-thermal technology, such as bio-treatment, capping, recycling, and dig and haul. Cost data are provided for all technologies, and a case study for thermal treatment is also presented

  12. Thermal stability of butter oils produced from sheep’s non-pasteurized and pasteurized milk

    Directory of Open Access Journals (Sweden)

    FLAVIA POP

    Full Text Available The physical and chemical characteristics and thermal stability of butter oil produced from non-pasteurized and pasteurized sheep’s milk were studied. Thermal stability of samples was estimated by using the accelerated shelf-life testing method. Samples were stored at 50, 60 and 70oC in the dark and the reaction was monitored by measuring peroxide, thiobarbituric acid and free fatty acid values. The peroxide and thiobarbituric acid values increased as the temperature increased. The increase of acid values of the two samples was not significant. A slight increase in free fatty acid value showed that hydrolytic reactions were not responsible for the deterioration of butter oil samples in thermal stability studies. When compared, butter oil produced from pasteurized sheep’s milk has higher thermal stability than butter oil produced from non-pasteurized sheep’s milk. Although butter oil produced from non-pasteurized milk was not exposed to any heat treatment, the shelf-life of this product was lower than the shelf-life of butter oil produced from pasteurized sheep’s milk. Therefore, heat treatment for pasteurization did not affect the thermal stability of butter oil.

  13. Thermal stability of 4-substituted benzenediazonium tetrafluoroborates

    International Nuclear Information System (INIS)

    Bruner, V.Ya.

    1990-01-01

    Heating of tetraborates of 4-methyl-, 4-phenyl- and 4-dimethylaminobenzenediazonium at 95, 120 and 148 deg, correspondingly, causes their autocatalytic destruction, two moles of gas (nitrogen, boron fluoride) being liberated. The thermal stability of 4-substituted benzenediazonium tetrafluoroborates increases with the increase of the electron-donor activity of the substituent at benzene ring

  14. Myocardial tagging with steady state free precession techniques and semi-automatic postprocessing--impact on diagnostic value

    DEFF Research Database (Denmark)

    Johnson, Thorsten R C; Bayrhof, Nicole; Huber, Armin

    2007-01-01

    Our aim was to determine the diagnostic value of myocardial tagging sequences with regard to the evaluable share of the cardiac cycle. Thirty-three patients were examined at 1.5 T using tagging sequences with gradient-echo (GRE) readout, 18 patients at 1.5 T with steady-state free precession (SSF...

  15. Diversity analysis in Cannabis sativa based on large-scale development of expressed sequence tag-derived simple sequence repeat markers.

    Science.gov (United States)

    Gao, Chunsheng; Xin, Pengfei; Cheng, Chaohua; Tang, Qing; Chen, Ping; Wang, Changbiao; Zang, Gonggu; Zhao, Lining

    2014-01-01

    Cannabis sativa L. is an important economic plant for the production of food, fiber, oils, and intoxicants. However, lack of sufficient simple sequence repeat (SSR) markers has limited the development of cannabis genetic research. Here, large-scale development of expressed sequence tag simple sequence repeat (EST-SSR) markers was performed to obtain more informative genetic markers, and to assess genetic diversity in cannabis (Cannabis sativa L.). Based on the cannabis transcriptome, 4,577 SSRs were identified from 3,624 ESTs. From there, a total of 3,442 complementary primer pairs were designed as SSR markers. Among these markers, trinucleotide repeat motifs (50.99%) were the most abundant, followed by hexanucleotide (25.13%), dinucleotide (16.34%), tetranucloetide (3.8%), and pentanucleotide (3.74%) repeat motifs, respectively. The AAG/CTT trinucleotide repeat (17.96%) was the most abundant motif detected in the SSRs. One hundred and seventeen EST-SSR markers were randomly selected to evaluate primer quality in 24 cannabis varieties. Among these 117 markers, 108 (92.31%) were successfully amplified and 87 (74.36%) were polymorphic. Forty-five polymorphic primer pairs were selected to evaluate genetic diversity and relatedness among the 115 cannabis genotypes. The results showed that 115 varieties could be divided into 4 groups primarily based on geography: Northern China, Europe, Central China, and Southern China. Moreover, the coefficient of similarity when comparing cannabis from Northern China with the European group cannabis was higher than that when comparing with cannabis from the other two groups, owing to a similar climate. This study outlines the first large-scale development of SSR markers for cannabis. These data may serve as a foundation for the development of genetic linkage, quantitative trait loci mapping, and marker-assisted breeding of cannabis.

  16. Lignin-based carbon fibers: Carbon nanotube decoration and superior thermal stability

    KAUST Repository

    Xu, Xuezhu

    2014-08-23

    Lignin-based carbon fibers (CFs) decorated with carbon nanotubes (CNTs) were synthesized and their structure, thermal stability and wettability were systematically studied. The carbon fiber precursors were produced by electrospinning lignin/polyacrylonitrile solutions. CFs were obtained by pyrolyzing the precursors and CNTs were subsequently grown on the CFs to eventually achieve a CF–CNT hybrid structure. The processes of pyrolysis and CNT growth were conducted in a tube furnace using different conditions and the properties of the resultant products were studied and compared. The CF–CNT hybrid structure produced at 850 °C using a palladium catalyst showed the highest thermal stability, i.e., 98.3% residual weight at 950 °C. A mechanism for such superior thermal stability was postulated based on the results from X-ray diffraction, Raman spectroscopy, scanning and transmission electron microscopy, and electron energy loss spectroscopy analyses. The dense CNT decoration was found to increase the hydrophobicity of the CFs.

  17. Local order origin of thermal stability enhancement in amorphous Ag doping GeTe

    Energy Technology Data Exchange (ETDEWEB)

    Xu, L.; Li, Y.; Yu, N. N.; Zhong, Y. P.; Miao, X. S., E-mail: miaoxs@mail.hust.edu.cn [Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology (HUST), Wuhan 430074 (China); School of Optical and Electronic Information, Huazhong University of Science and Technology, Wuhan 430074 (China)

    2015-01-19

    We demonstrate the impacts of Ag doping on the local atomic structure of amorphous GeTe phase-change material. The variations of phonon vibrational modes, boding nature, and atomic structure are shown by Raman, X-ray photoelectron spectroscopy, and ab initio calculation. Combining the experiments and simulations, we observe that the number of Ge atoms in octahedral site decreases and that in tetrahedral site increases. This modification in local order of GeTe originating from the low valence element will affect the crystallization behavior of amorphous GeTe, which is verified by differential scanning calorimetry and transmission electron microscope results. This work not only gives the analysis on the structural change of GeTe with Ag dopants but also provides a method to enhance the thermal stability of amorphous phase-change materials for memory and brain-inspired computing applications.

  18. Hardness and thermal stability of cubic silicon nitride

    DEFF Research Database (Denmark)

    Jiang, Jianzhong; Kragh, Flemming; Frost, D. J.

    2001-01-01

    The hardness and thermal stability of cubic spinel silicon nitride (c-Si3N4), synthesized under high-pressure and high-temperature conditions, have been studied by microindentation measurements, and x-ray powder diffraction and scanning electron microscopy, respectively The phase at ambient...

  19. Interacting dark energy model and thermal stability

    Energy Technology Data Exchange (ETDEWEB)

    Bhandari, Pritikana; Haldar, Sourav; Chakraborty, Subenoy [Jadavpur University, Department of Mathematics, Kolkata, West Bengal (India)

    2017-12-15

    In the background of the homogeneous and isotropic FLRW model, the thermodynamics of the interacting DE fluid is investigated in the present work. By studying the thermodynamical parameters, namely the heat capacities and the compressibilities, both thermal and mechanical stability are discussed and the restrictions on the equation of state parameter of the dark fluid are analyzed. (orig.)

  20. Interacting dark energy model and thermal stability

    International Nuclear Information System (INIS)

    Bhandari, Pritikana; Haldar, Sourav; Chakraborty, Subenoy

    2017-01-01

    In the background of the homogeneous and isotropic FLRW model, the thermodynamics of the interacting DE fluid is investigated in the present work. By studying the thermodynamical parameters, namely the heat capacities and the compressibilities, both thermal and mechanical stability are discussed and the restrictions on the equation of state parameter of the dark fluid are analyzed. (orig.)

  1. Thermal stability of bubble domains in ferromagnetic discs

    Energy Technology Data Exchange (ETDEWEB)

    Hrkac, G [University of Sheffield, Engineering Materials, Mappin Street, Sheffield S1 3JD (United Kingdom) ; Bance, S [University of Sheffield, Engineering Materials, Mappin Street, Sheffield S1 3JD (United Kingdom) ; Goncharov, A [University of Sheffield, Engineering Materials, Mappin Street, Sheffield S1 3JD (United Kingdom) ; Schrefl, T [University of Sheffield, Engineering Materials, Mappin Street, Sheffield S1 3JD (United Kingdom) ; Suess, D [Vienna University of Technology, Wiedner Hauptstr. 8-10e, A-1040 Vienna (Austria)

    2007-05-07

    The transition and thermal stability of disc-shaped ferromagnetic particles at the temperature of T = 300 K with a uniaxial anisotropy along the symmetry axis from a bi-domain to a single domain state has been studied. The nudge elastic band method was used to map the energy landscape and to calculate the energy barrier between the transition states. For single FePt disc-shaped particles with perpendicular anisotropy three transition configurations have been found: single domain, stripe- and stable bubble domains at zero applied field. The single domain configuration along the positive anisotropy axis is reached by an annihilation process of the domain wall and the all-down state by a complex domain expansion process. Magnetization configurations in two interacting discs show an increase in thermal stability compared with single disc systems, which is attributed to the interacting magnetostatic energy between the two particles.

  2. Thermal stability of bubble domains in ferromagnetic discs

    International Nuclear Information System (INIS)

    Hrkac, G; Bance, S; Goncharov, A; Schrefl, T; Suess, D

    2007-01-01

    The transition and thermal stability of disc-shaped ferromagnetic particles at the temperature of T = 300 K with a uniaxial anisotropy along the symmetry axis from a bi-domain to a single domain state has been studied. The nudge elastic band method was used to map the energy landscape and to calculate the energy barrier between the transition states. For single FePt disc-shaped particles with perpendicular anisotropy three transition configurations have been found: single domain, stripe- and stable bubble domains at zero applied field. The single domain configuration along the positive anisotropy axis is reached by an annihilation process of the domain wall and the all-down state by a complex domain expansion process. Magnetization configurations in two interacting discs show an increase in thermal stability compared with single disc systems, which is attributed to the interacting magnetostatic energy between the two particles

  3. Generation and analysis of expressed sequence tags in the extreme large genomes Lilium and Tulipa

    Directory of Open Access Journals (Sweden)

    Shahin Arwa

    2012-11-01

    Full Text Available Abstract Background Bulbous flowers such as lily and tulip (Liliaceae family are monocot perennial herbs that are economically very important ornamental plants worldwide. However, there are hardly any genetic studies performed and genomic resources are lacking. To build genomic resources and develop tools to speed up the breeding in both crops, next generation sequencing was implemented. We sequenced and assembled transcriptomes of four lily and five tulip genotypes using 454 pyro-sequencing technology. Results Successfully, we developed the first set of 81,791 contigs with an average length of 514 bp for tulip, and enriched the very limited number of 3,329 available ESTs (Expressed Sequence Tags for lily with 52,172 contigs with an average length of 555 bp. The contigs together with singletons covered on average 37% of lily and 39% of tulip estimated transcriptome. Mining lily and tulip sequence data for SSRs (Simple Sequence Repeats showed that di-nucleotide repeats were twice more abundant in UTRs (UnTranslated Regions compared to coding regions, while tri-nucleotide repeats were equally spread over coding and UTR regions. Two sets of single nucleotide polymorphism (SNP markers suitable for high throughput genotyping were developed. In the first set, no SNPs flanking the target SNP (50 bp on either side were allowed. In the second set, one SNP in the flanking regions was allowed, which resulted in a 2 to 3 fold increase in SNP marker numbers compared with the first set. Orthologous groups between the two flower bulbs: lily and tulip (12,017 groups and among the three monocot species: lily, tulip, and rice (6,900 groups were determined using OrthoMCL. Orthologous groups were screened for common SNP markers and EST-SSRs to study synteny between lily and tulip, which resulted in 113 common SNP markers and 292 common EST-SSR. Lily and tulip contigs generated were annotated and described according to Gene Ontology terminology. Conclusions

  4. Generation and analysis of expressed sequence tags in the extreme large genomes Lilium and Tulipa.

    Science.gov (United States)

    Shahin, Arwa; van Kaauwen, Martijn; Esselink, Danny; Bargsten, Joachim W; van Tuyl, Jaap M; Visser, Richard G F; Arens, Paul

    2012-11-20

    Bulbous flowers such as lily and tulip (Liliaceae family) are monocot perennial herbs that are economically very important ornamental plants worldwide. However, there are hardly any genetic studies performed and genomic resources are lacking. To build genomic resources and develop tools to speed up the breeding in both crops, next generation sequencing was implemented. We sequenced and assembled transcriptomes of four lily and five tulip genotypes using 454 pyro-sequencing technology. Successfully, we developed the first set of 81,791 contigs with an average length of 514 bp for tulip, and enriched the very limited number of 3,329 available ESTs (Expressed Sequence Tags) for lily with 52,172 contigs with an average length of 555 bp. The contigs together with singletons covered on average 37% of lily and 39% of tulip estimated transcriptome. Mining lily and tulip sequence data for SSRs (Simple Sequence Repeats) showed that di-nucleotide repeats were twice more abundant in UTRs (UnTranslated Regions) compared to coding regions, while tri-nucleotide repeats were equally spread over coding and UTR regions. Two sets of single nucleotide polymorphism (SNP) markers suitable for high throughput genotyping were developed. In the first set, no SNPs flanking the target SNP (50 bp on either side) were allowed. In the second set, one SNP in the flanking regions was allowed, which resulted in a 2 to 3 fold increase in SNP marker numbers compared with the first set. Orthologous groups between the two flower bulbs: lily and tulip (12,017 groups) and among the three monocot species: lily, tulip, and rice (6,900 groups) were determined using OrthoMCL. Orthologous groups were screened for common SNP markers and EST-SSRs to study synteny between lily and tulip, which resulted in 113 common SNP markers and 292 common EST-SSR. Lily and tulip contigs generated were annotated and described according to Gene Ontology terminology. Two transcriptome sets were built that are valuable

  5. Study on the thermal-hydraulic stability of high burn up STEP III fuel in Japan

    International Nuclear Information System (INIS)

    Ishikawa, M.; Kitamura, H.; Toba, A.; Omoto, A.

    2004-01-01

    Japanese BWR utilities have performed a joint study of the Thermal Hydraulic Stability of High Burn up STEP III Fuel. In this study, the parametric dependency of thermal hydraulic stability threshold was obtained. It was confirmed through experiments that the STEP III Fuel has sufficient stability characteristics. (author)

  6. Improved determination of left ventricular volume with myocardial tagging

    International Nuclear Information System (INIS)

    Peshock, R.M.; Takai, H.; Baker, K.V.; Clarke, G.D.; McDonald, G.G.; Parkey, R.W.

    1991-01-01

    Cine MR imaging can be used to determine ventricular volume and ejection fraction. However, definition of the endocardial surface can be difficult, leading some investigators to suggest that black-blood studies are preferable. Grid tagging with use of spatial modulation of magnetization has been used to improve assessments of wall motion. The purpose of this paper, is to determine if grid tagging would also facilitate definition of the endocardial border for volume and ejection fraction calculations. Grid tagging based on spatial modulation of magnetization was implemented on a Toshiba 0.5-T MR imaging device. Standard RAO images were obtained in 10 normal volunteers with use of standard cine MR imaging sequences (33/22) with and without grid tagging. Images were analyzed to determine ventricular volume, cardiac output and wall motion. Images obtained without tagging generally showed good contrast at end diastole, but definition of the endocardial border was frequently more difficult in middle to late systole. Images with tagging provided significantly better definition of endocardial borders, particularly during systole

  7. Modifications to improve entrance slit thermal stability for grasshopper monochromators

    Science.gov (United States)

    Wallace, Daniel J.; Rogers, Gregory C.; Crossley, Sherry L.

    1994-08-01

    As new monochromators are designed for high-flux storage rings, computer modeling and thermal engineering can be done to process increased heat loads and achieve mechanical stability. Several older monochromators, such as the Mark 2 and Mark 5 Grasshopper monochromators, which were designed in 1974, have thermal instabilities in their entrance slit mechanisms. The Grasshoppers operating with narrow slits experience closure of the entrance slit from thermal expansion. In extreme cases, the thermal expansion of the precision components has caused permanent mechanical damage, leaving the slit uncalibrated and/or inoperable. For the Mark 2 and Mark 5 Grasshopper monochromators at the Synchrotron Radiation Center, the original 440 stainless steel entrance slit jaws were retrofitted with an Invar (low expansion Fe, Ni alloy) slit jaw. To transfer the heat from the critical components, two flexible heat straps of Cu were attached. These changes allow safe operation with a 10 μm entrance slit width where the previous limit was 30 μm. After an initial 2 min equilibration, the slit remains stable to 10%, with 100 mA of beam current. Additional improvements in slit thermal stability are planned for a third Grasshopper.

  8. Co-evaporation of fluoropolymer additives for improved thermal stability of organic semiconductors

    Science.gov (United States)

    Price, Jared S.; Wang, Baomin; Grede, Alex J.; Shen, Yufei; Giebink, Noel C.

    2017-08-01

    Reliability remains an ongoing challenge for organic light emitting diodes (OLEDs) as they expand in the marketplace. The ability to withstand operation and storage at elevated temperature is particularly important in this context, not only because of the inverse dependence of OLED lifetime on temperature, but also because high thermal stability is fundamentally important for high power/brightness operation as well as applications such as automotive lighting, where interior car temperatures often exceed the ambient by 50 °C or more. Here, we present a strategy to significantly increase the thermal stability of small molecule OLEDs by co-depositing an amorphous fluoropolymer, Teflon AF, to prevent catastrophic failure at elevated temperatures. Using this approach, we demonstrate that the thermal breakdown limit of common hole transport materials can be increased from typical temperatures of ˜100 °C to more than 200 °C while simultaneously improving their electrical transport properties. Similar thermal stability enhancements are demonstrated in simple bilayer OLEDs. These results point toward a general approach to engineer morphologically-stable organic electronic devices that are capable of operating or being stored in extreme thermal environments.

  9. High-level expression of soluble recombinant proteins in Escherichia coli using an HE-maltotriose-binding protein fusion tag.

    Science.gov (United States)

    Han, Yingqian; Guo, Wanying; Su, Bingqian; Guo, Yujie; Wang, Jiang; Chu, Beibei; Yang, Guoyu

    2018-02-01

    Recombinant proteins are commonly expressed in prokaryotic expression systems for large-scale production. The use of genetically engineered affinity and solubility enhancing fusion proteins has increased greatly in recent years, and there now exists a considerable repertoire of these that can be used to enhance the expression, stability, solubility, folding, and purification of their fusion partner. Here, a modified histidine tag (HE) used as an affinity tag was employed together with a truncated maltotriose-binding protein (MBP; consisting of residues 59-433) from Pyrococcus furiosus as a solubility enhancing tag accompanying a tobacco etch virus protease-recognition site for protein expression and purification in Escherichia coli. Various proteins tagged at the N-terminus with HE-MBP(Pyr) were expressed in E. coli BL21(DE3) cells to determine expression and solubility relative to those tagged with His6-MBP or His6-MBP(Pyr). Furthermore, four HE-MBP(Pyr)-fused proteins were purified by immobilized metal affinity chromatography to assess the affinity of HE with immobilized Ni 2+ . Our results showed that HE-MBP(Pyr) represents an attractive fusion protein allowing high levels of soluble expression and purification of recombinant protein in E. coli. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. Restriction site extension PCR: a novel method for high-throughput characterization of tagged DNA fragments and genome walking.

    Directory of Open Access Journals (Sweden)

    Jiabing Ji

    Full Text Available BACKGROUND: Insertion mutant isolation and characterization are extremely valuable for linking genes to physiological function. Once an insertion mutant phenotype is identified, the challenge is to isolate the responsible gene. Multiple strategies have been employed to isolate unknown genomic DNA that flanks mutagenic insertions, however, all these methods suffer from limitations due to inefficient ligation steps, inclusion of restriction sites within the target DNA, and non-specific product generation. These limitations become close to insurmountable when the goal is to identify insertion sites in a high throughput manner. METHODOLOGY/PRINCIPAL FINDINGS: We designed a novel strategy called Restriction Site Extension PCR (RSE-PCR to efficiently conduct large-scale isolation of unknown genomic DNA fragments linked to DNA insertions. The strategy is a modified adaptor-mediated PCR without ligation. An adapter, with complementarity to the 3' overhang of the endonuclease (KpnI, NsiI, PstI, or SacI restricted DNA fragments, extends the 3' end of the DNA fragments in the first cycle of the primary RSE-PCR. During subsequent PCR cycles and a second semi-nested PCR (secondary RSE-PCR, touchdown and two-step PCR are combined to increase the amplification specificity of target fragments. The efficiency and specificity was demonstrated in our characterization of 37 tex mutants of Arabidopsis. All the steps of RSE-PCR can be executed in a 96 well PCR plate. Finally, RSE-PCR serves as a successful alternative to Genome Walker as demonstrated by gene isolation from maize, a plant with a more complex genome than Arabidopsis. CONCLUSIONS/SIGNIFICANCE: RSE-PCR has high potential application in identifying tagged (T-DNA or transposon sequence or walking from known DNA toward unknown regions in large-genome plants, with likely application in other organisms as well.

  11. Organization and differential expression of the GACA/GATA tagged somatic and spermatozoal transcriptomes in Buffalo Bubalus bubalis

    Directory of Open Access Journals (Sweden)

    Srivastava Jyoti

    2008-03-01

    Full Text Available Abstract Background Simple sequence repeats (SSRs of GACA/GATA have been implicated with differentiation of sex-chromosomes and speciation. However, the organization of these repeats within genomes and transcriptomes, even in the best characterized organisms including human, remains unclear. The main objective of this study was to explore the buffalo transcriptome for its association with GACA/GATA repeats, and study the structural organization and differential expression of the GACA/GATA repeat tagged transcripts. Moreover, the distribution of GACA and GATA repeats in the prokaryotic and eukaryotic genomes was studied to highlight their significance in genome evolution. Results We explored several genomes and transcriptomes, and observed total absence of these repeats in the prokaryotes, with their gradual accumulation in higher eukaryotes. Further, employing novel microsatellite associated sequence amplification (MASA approach using varying length oligos based on GACA and GATA repeats; we identified and characterized 44 types of known and novel mRNA transcripts tagged with these repeats from different somatic tissues, gonads and spermatozoa of water buffalo Bubalus bubalis. GACA was found to be associated with higher number of transcripts compared to that with GATA. Exclusive presence of several GACA-tagged transcripts in a tissue or spermatozoa, and absence of the GATA-tagged ones in lung/heart highlights their tissue-specific significance. Of all the GACA/GATA tagged transcripts, ~30% demonstrated inter-tissue and/or tissue-spermatozoal sequence polymorphisms. Significantly, ~60% of the GACA-tagged and all the GATA-tagged transcripts showed highest or unique expression in the testis and/or spermatozoa. Moreover, ~75% GACA-tagged and all the GATA-tagged transcripts were found to be conserved across the species. Conclusion Present study is a pioneer attempt exploring GACA/GATA tagged transcriptome in any mammalian species highlighting their

  12. Thermal propagation and stability in superconducting films

    International Nuclear Information System (INIS)

    Gray, K.E.; Kampwirth, R.T.; Zasadzinski, J.F.; Ducharme, S.P.

    1983-01-01

    Thermal propagation and stable hot spots (normal domains) are studied in various high Tsub(c) superconducting films (Nb 3 Sn, Nb, NbN and Nb 3 Ge). A new energy balance is shown to give reasonable quantitative agreement of the dependence of the propagation velocity on the length of short normal domains. The steady state (zero velocity) measurements indicate the existence of two distinct situations for films on high thermal conductivity (sapphire) substrates. For low power per unit area the film and substrate have the same temperature, and the thermal properties of the substrate dominate. However, for higher power densities in short hot spots, the coupling is relatively weak and the thermal properties of the film alone are important. Here a connection is made between the critical current stability of superconducting films and a critical hot spot size for thermal propagation. As a result efficient heat removal is shown to dominate the stabilisation of superconducting films. The strong and weak coupling situations also lead to modifications of the models for propagation velocities on sapphire substrates. Self-healing of hot spots and other phenomena in superconducting film are explained. The potential use of the thermal propagation model in applications of superconductors, especially switches is discussed. (author)

  13. Thermal properties and stabilities of polymer thin films

    International Nuclear Information System (INIS)

    Kanaya, Toshiji; Kawashima, Kazuko; Inoue, Rintaro; Miyazaki, Tsukasa

    2009-01-01

    Recent extensive studies have revealed that polymer thin films showed very interesting but unusual thermal properties and stabilities. In the article we show that X-ray reflectivity and neutron reflectivity are very powerful tools to study the anomalous properties of polymer thin films. (author)

  14. Extreme temperature stability of thermally insulating graphene-mesoporous-silicon nanocomposite

    Science.gov (United States)

    Kolhatkar, Gitanjali; Boucherif, Abderraouf; Rahim Boucherif, Abderrahim; Dupuy, Arthur; Fréchette, Luc G.; Arès, Richard; Ruediger, Andreas

    2018-04-01

    We demonstrate the thermal stability and thermal insulation of graphene-mesoporous-silicon nanocomposites (GPSNC). By comparing the morphology of GPSNC carbonized at 650 °C as-formed to that after annealing, we show that this nanocomposite remains stable at temperatures as high as 1050 °C due to the presence of a few monolayers of graphene coating on the pore walls. This does not only make this material compatible with most thermal processes but also suggests applications in harsh high temperature environments. The thermal conductivity of GPSNCs carbonized at temperatures in the 500 °C-800 °C range is determined through Raman spectroscopy measurements. They indicate that the thermal conductivity of the composite is lower than that of silicon, with a value of 13 ± 1 W mK-1 at room temperature, and not affected by the thin graphene layer, suggesting a role of the high concentration of carbon related-defects as indicated by the high intensity of the D-band compared to G-band of the Raman spectra. This morphological stability at high temperature combined with a high thermal insulation make GPSNC a promising candidate for a broad range of applications including microelectromechanical systems and thermal effect microsystems such as flow sensors or IR detectors. Finally, at 120 °C, the thermal conductivity remains equal to that at room temperature, attesting to the potential of using our nanocomposite in devices that operate at high temperatures such as microreactors for distributed chemical conversion, solid oxide fuel cells, thermoelectric devices or thermal micromotors.

  15. Cyanine-based probe\\tag-peptide pair for fluorescence protein imaging and fluorescence protein imaging methods

    Science.gov (United States)

    Mayer-Cumblidge, M Uljana [Richland, WA; Cao, Haishi [Richland, WA

    2010-08-17

    A molecular probe comprises two arsenic atoms and at least one cyanine based moiety. A method of producing a molecular probe includes providing a molecule having a first formula, treating the molecule with HgOAc, and subsequently transmetallizing with AsCl.sub.3. The As is liganded to ethanedithiol to produce a probe having a second formula. A method of labeling a peptide includes providing a peptide comprising a tag sequence and contacting the peptide with a biarsenical molecular probe. A complex is formed comprising the tag sequence and the molecular probe. A method of studying a peptide includes providing a mixture containing a peptide comprising a peptide tag sequence, adding a biarsenical probe to the mixture, and monitoring the fluorescence of the mixture.

  16. Generation of expressed sequence tags for discovery of genes responsible for floral traits of Chrysanthemum morifolium by next-generation sequencing technology.

    Science.gov (United States)

    Sasaki, Katsutomo; Mitsuda, Nobutaka; Nashima, Kenji; Kishimoto, Kyutaro; Katayose, Yuichi; Kanamori, Hiroyuki; Ohmiya, Akemi

    2017-09-04

    Chrysanthemum morifolium is one of the most economically valuable ornamental plants worldwide. Chrysanthemum is an allohexaploid plant with a large genome that is commercially propagated by vegetative reproduction. New cultivars with different floral traits, such as color, morphology, and scent, have been generated mainly by classical cross-breeding and mutation breeding. However, only limited genetic resources and their genome information are available for the generation of new floral traits. To obtain useful information about molecular bases for floral traits of chrysanthemums, we read expressed sequence tags (ESTs) of chrysanthemums by high-throughput sequencing using the 454 pyrosequencing technology. We constructed normalized cDNA libraries, consisting of full-length, 3'-UTR, and 5'-UTR cDNAs derived from various tissues of chrysanthemums. These libraries produced a total number of 3,772,677 high-quality reads, which were assembled into 213,204 contigs. By comparing the data obtained with those of full genome-sequenced species, we confirmed that our chrysanthemum contig set contained the majority of all expressed genes, which was sufficient for further molecular analysis in chrysanthemums. We confirmed that our chrysanthemum EST set (contigs) contained a number of contigs that encoded transcription factors and enzymes involved in pigment and aroma compound metabolism that was comparable to that of other species. This information can serve as an informative resource for identifying genes involved in various biological processes in chrysanthemums. Moreover, the findings of our study will contribute to a better understanding of the floral characteristics of chrysanthemums including the myriad cultivars at the molecular level.

  17. Mechanical and thermal stability of graphene and graphene-based materials

    Science.gov (United States)

    Galashev, A. E.; Rakhmanova, O. R.

    2014-10-01

    Graphene has rapidly become one of the most popular materials for technological applications and a test material for new condensed matter ideas. This paper reviews the mechanical properties of graphene and effects related to them that have recently been discovered experimentally or predicted theoretically or by simulation. The topics discussed are of key importance for graphene's use in integrated electronics, thermal materials, and electromechanical devices and include the following: graphene transformation into other sp^2 hybridization forms; stability to stretching and compression; ion-beam-induced structural modifications; how defects and graphene edges affect the electronic properties and thermal stability of graphene and related composites.

  18. Phonon transmission and thermal conductance in one-dimensional system with on-site potential disorder

    International Nuclear Information System (INIS)

    Ma Songshan; Xu Hui; Deng Honggui; Yang Bingchu

    2011-01-01

    The role of on-site potential disorder on phonon transmission and thermal conductance of one-dimensional system is investigated. We found that the on-site potential disorder can lead to the localization of phonons, and has great effect on the phonon transmission and thermal conductance of the system. As on-site potential disorder W increases, the transmission coefficients decrease, and approach zero at the band edges. Corresponding, the thermal conductance decreases drastically, and the curves for thermal conductance exhibit a series of steps and plateaus. Meanwhile, when the on-site potential disorder W is strong enough, the thermal conductance decreases dramatically with the increase of system size N. We also found that the efficiency of reducing thermal conductance by increasing the on-site potential disorder strength is much better than that by increasing the on-site potential's amplitude. - Highlights: → We studied the effect of on-site potential disorder on thermal transport. → Increasing disorder will decrease thermal transport. → Increasing system size will also decrease its thermal conductance. → Increasing disorder is more efficient than other in reducing thermal conductance.

  19. Synthesis of Poly(cinnam-4'-yl methyl methacrylate) derivatives and their thermal stability as photoalignment layer

    International Nuclear Information System (INIS)

    Lee, Jong Woo; Kim, Hak Won; Kim, Hong Doo

    2001-01-01

    Photocyclizable poly(cinnam-4'-yl methyl methacrylate) derivatives bearing methoxy benzene (PMCMMA), anthracene (PACMMA), and coumarin (PCCMMMA) have been synthesized via Heck type reaction. Three different types of polymers are photoreactable using linearly polarized UV light and applicable as liquid crystal alignment layer. Anthracene and coumarin containing polymers (PACMMA, PCCMMA) have better thermal stability than PMCMMA. This observation may be attributed to the glass transition temperature elevation due to the bulky size and another photocrosslinking site provided by anthracene or coumarin group

  20. Tags Help Make Libraries Del.icio.us: Social Bookmarking and Tagging Boost Participation

    Science.gov (United States)

    Rethlefsen, Melissa L.

    2007-01-01

    Traditional library web products, whether online public access catalogs, library databases, or even library web sites, have long been rigidly controlled and difficult to use. Patrons regularly prefer Google's simple interface. Now social bookmarking and tagging tools help librarians bridge the gap between the library's need to offer authoritative,…

  1. In situ tagging technique for fishes provides insight into growth and movement of invasive lionfish.

    Science.gov (United States)

    Akins, John L; Morris, James A; Green, Stephanie J

    2014-10-01

    Information on fish movement and growth is primarily obtained through the marking and tracking of individuals with external tags, which are usually affixed to anesthetized individuals at the surface. However, the quantity and quality of data obtained by this method is often limited by small sample sizes owing to the time associated with the tagging process, high rates of tagging-related mortality, and displacement of tagged individuals from the initial capture location. To address these issues, we describe a technique for applying external streamer and dart tags in situ, which uses SCUBA divers to capture and tag individual fish on the sea floor without the use of anesthetic. We demonstrate this method for Indo-Pacific lionfish (Pterois volitans/P. miles), species which are particularly vulnerable to barotrauma when transported to and handled at the surface. To test our method, we tagged 161 individuals inhabiting 26 coral reef locations in the Bahamas over a period of 3 years. Our method resulted in no instances of barotrauma, reduced handling and recovery time, and minimal post-tagging release displacement compared with conventional ex situ tag application. Opportunistic resighting and recapture of tagged individuals reveals that lionfish exhibit highly variable site fidelity, movement patterns, and growth rates on invaded coral reef habitats. In total, 24% of lionfish were resighted between 29 and 188 days after tagging. Of these, 90% were located at the site of capture, while the remaining individuals were resighted between 200 m and 1.1 km from initial site of capture over 29 days later. In situ growth rates ranged between 0.1 and 0.6 mm/day. While individuals tagged with streamer tags posted slower growth rates with increasing size, as expected, there was no relationship between growth rate and fish size for individuals marked with dart tags, potentially because of large effects of tag presence on the activities of small bodied lionfish (i.e., lionfish

  2. Computational Identification of Protein Pupylation Sites by Using Profile-Based Composition of k-Spaced Amino Acid Pairs.

    Directory of Open Access Journals (Sweden)

    Md Mehedi Hasan

    Full Text Available Prokaryotic proteins are regulated by pupylation, a type of post-translational modification that contributes to cellular function in bacterial organisms. In pupylation process, the prokaryotic ubiquitin-like protein (Pup tagging is functionally analogous to ubiquitination in order to tag target proteins for proteasomal degradation. To date, several experimental methods have been developed to identify pupylated proteins and their pupylation sites, but these experimental methods are generally laborious and costly. Therefore, computational methods that can accurately predict potential pupylation sites based on protein sequence information are highly desirable. In this paper, a novel predictor termed as pbPUP has been developed for accurate prediction of pupylation sites. In particular, a sophisticated sequence encoding scheme [i.e. the profile-based composition of k-spaced amino acid pairs (pbCKSAAP] is used to represent the sequence patterns and evolutionary information of the sequence fragments surrounding pupylation sites. Then, a Support Vector Machine (SVM classifier is trained using the pbCKSAAP encoding scheme. The final pbPUP predictor achieves an AUC value of 0.849 in 10-fold cross-validation tests and outperforms other existing predictors on a comprehensive independent test dataset. The proposed method is anticipated to be a helpful computational resource for the prediction of pupylation sites. The web server and curated datasets in this study are freely available at http://protein.cau.edu.cn/pbPUP/.

  3. Characterization of expressed sequence tag-derived simple sequence repeat markers for Aspergillus flavus: emphasis on variability of isolates from the southern United States.

    Science.gov (United States)

    Wang, Xinwang; Wadl, Phillip A; Wood-Jones, Alicia; Windham, Gary; Trigiano, Robert N; Scruggs, Mary; Pilgrim, Candace; Baird, Richard

    2012-12-01

    Simple sequence repeat (SSR) markers were developed from Aspergillus flavus expressed sequence tag (EST) database to conduct an analysis of genetic relationships of Aspergillus isolates from numerous host species and geographical regions, but primarily from the United States. Twenty-nine primers were designed from 362 tri-nucleotide EST-SSR sequences. Eighteen polymorphic loci were used to genotype 96 Aspergillus species isolates. The number of alleles detected per locus ranged from 2 to 24 with a mean of 8.2 alleles. Haploid diversity ranged from 0.28 to 0.91. Genetic distance matrix was used to perform principal coordinates analysis (PCA) and to generate dendrograms using unweighted pair group method with arithmetic mean (UPGMA). Two principal coordinates explained more than 75 % of the total variation among the isolates. One clade was identified for A. flavus isolates (n = 87) with the other Aspergillus species (n = 7) using PCA, but five distinct clusters were present when the others taxa were excluded from the analysis. Six groups were noted when the EST-SSR data were compared using UPGMA. However, the latter PCA or UPGMA comparison resulted in no direct associations with host species, geographical region or aflatoxin production. Furthermore, there was no direct correlation to visible morphological features such as sclerotial types. The isolates from Mississippi Delta region, which contained the largest percentage of isolates, did not show any unusual clustering except for isolates K32, K55, and 199. Further studies of these three isolates are warranted to evaluate their pathogenicity, aflatoxin production potential, additional gene sequences (e.g., RPB2), and morphological comparisons.

  4. Analysis of expressed sequence tags from a NaHCO(3)-treated alkali-tolerant plant, Chloris virgata.

    Science.gov (United States)

    Nishiuchi, Shunsaku; Fujihara, Kazumasa; Liu, Shenkui; Takano, Tetsuo

    2010-04-01

    Chloris virgata Swartz (C. virgata) is a gramineous wild plant that can survive in saline-alkali areas in northeast China. To examine the tolerance mechanisms of C. virgata, we constructed a cDNA library from whole plants of C. virgata that had been treated with 100 mM NaHCO(3) for 24 h and sequenced 3168 randomly selected clones. Most (2590) of the expressed sequence tags (ESTs) showed significant similarity to sequences in the NCBI database. Of the 2590 genes, 1893 were unique. Gene Ontology (GO) Slim annotations were obtained for 1081 ESTs by BLAST2GO and it was found that 75 genes of them were annotated with GO terms "response to stress", "response to abiotic stimulus", and "response to biotic stimulus", indicating these genes were likely to function in tolerance mechanism of C. virgata. In a separate experiment, 24 genes that are known from previous studies to be associated with abiotic stress tolerance were further examined by real-time RT-PCR to see how their expressions were affected by NaHCO(3) stress. NaHCO(3) treatment up-regulated the expressions of pathogenesis-related gene (DC998527), Win1 precursor gene (DC998617), catalase gene (DC999385), ribosome inactivating protein 1 (DC999555), Na(+)/H(+) antiporter gene (DC998043), and two-component regulator gene (DC998236). Copyright 2010 Elsevier Masson SAS. All rights reserved.

  5. Expressed sequence tag analysis of functional genes associated with adventitious rooting in Liriodendron hybrids.

    Science.gov (United States)

    Zhong, Y D; Sun, X Y; Liu, E Y; Li, Y Q; Gao, Z; Yu, F X

    2016-06-24

    Liriodendron hybrids (Liriodendron chinense x L. tulipifera) are important landscaping and afforestation hardwood trees. To date, little genomic research on adventitious rooting has been reported in these hybrids, as well as in the genus Liriodendron. In the present study, we used adventitious roots to construct the first cDNA library for Liriodendron hybrids. A total of 5176 expressed sequence tags (ESTs) were generated and clustered into 2921 unigenes. Among these unigenes, 2547 had significant homology to the non-redundant protein database representing a wide variety of putative functions. Homologs of these genes regulated many aspects of adventitious rooting, including those for auxin signal transduction and root hair development. Results of quantitative real-time polymerase chain reaction showed that AUX1, IRE, and FB1 were highly expressed in adventitious roots and the expression of AUX1, ARF1, NAC1, RHD1, and IRE increased during the development of adventitious roots. Additionally, 181 simple sequence repeats were identified from 166 ESTs and more than 91.16% of these were dinucleotide and trinucleotide repeats. To the best of our knowledge, the present study reports the identification of the genes associated with adventitious rooting in the genus Liriodendron for the first time and provides a valuable resource for future genomic studies. Expression analysis of selected genes could allow us to identify regulatory genes that may be essential for adventitious rooting.

  6. Morphology, thermal, electrical and electrochemical stability of nano

    Indian Academy of Sciences (India)

    In the present work, an attempt has been made to develop nano aluminium oxide (Al2O3)-filled polyvinyl alcohol (PVA) composite gel electrolytes. Surface morphological studies, thermal behaviour, electrochemical stability and electrical characterization of these composite gel electrolytes have been performed. An increase ...

  7. Long-term stabilization considerations for decommissioned and reclaimed uranium sites

    International Nuclear Information System (INIS)

    Abt, S.R.; Nelson, J.D.; Johnson, T.L.

    1988-01-01

    The long-term stabilization of decommissioned uranium mill sites and of reclaimed uranium mill tailings sites encompass a broad spectrum of design capabilities. This paper presents a few of the quantitative methodologies recently developed or refined to evaluate physical factors (i.e. precipitation, fluvial geomorphology, stable slope, slope stabilization with riprap and riprap selection) that influence long-term stabilization of uranium mill and mill tailings sites. It is acknowledged that the degree of refinement of these methodologies are in their infancy and that extensive research and development are warranted to increase the level of assurance. However, these methodologies provide an initial guideline for evaluating long-term stabilization that has not been previously existed. The purpose of this paper is to present a review of currently available state-of-the-art engineering techniques and methodologies for the evaluation of reclamation plans designed to provide long-term stability against potential failure modes. In some cases, evaluative techniques have been developed for long-term stabilization where methodologies have not previously existed. Each methodology to be presented represents a starting point upon which additional research and/or development may be warranted

  8. Analysis of correlations between sites in models of protein sequences

    International Nuclear Information System (INIS)

    Giraud, B.G.; Lapedes, A.; Liu, L.C.

    1998-01-01

    A criterion based on conditional probabilities, related to the concept of algorithmic distance, is used to detect correlated mutations at noncontiguous sites on sequences. We apply this criterion to the problem of analyzing correlations between sites in protein sequences; however, the analysis applies generally to networks of interacting sites with discrete states at each site. Elementary models, where explicit results can be derived easily, are introduced. The number of states per site considered ranges from 2, illustrating the relation to familiar classical spin systems, to 20 states, suitable for representing amino acids. Numerical simulations show that the criterion remains valid even when the genetic history of the data samples (e.g., protein sequences), as represented by a phylogenetic tree, introduces nonindependence between samples. Statistical fluctuations due to finite sampling are also investigated and do not invalidate the criterion. A subsidiary result is found: The more homogeneous a population, the more easily its average properties can drift from the properties of its ancestor. copyright 1998 The American Physical Society

  9. QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects.

    Science.gov (United States)

    Meglécz, Emese; Costedoat, Caroline; Dubut, Vincent; Gilles, André; Malausa, Thibaut; Pech, Nicolas; Martin, Jean-François

    2010-02-01

    QDD is an open access program providing a user-friendly tool for microsatellite detection and primer design from large sets of DNA sequences. The program is designed to deal with all steps of treatment of raw sequences obtained from pyrosequencing of enriched DNA libraries, but it is also applicable to data obtained through other sequencing methods, using FASTA files as input. The following tasks are completed by QDD: tag sorting, adapter/vector removal, elimination of redundant sequences, detection of possible genomic multicopies (duplicated loci or transposable elements), stringent selection of target microsatellites and customizable primer design. It can treat up to one million sequences of a few hundred base pairs in the tag-sorting step, and up to 50,000 sequences in a single input file for the steps involving estimation of sequence similarity. QDD is freely available under the GPL licence for Windows and Linux from the following web site: http://www.univ-provence.fr/gsite/Local/egee/dir/meglecz/QDD.html. Supplementary data are available at Bioinformatics online.

  10. Synthesis of Ni-Zn ferrite nanoparticles in radiofrequency thermal plasma reactor and their use for purification of histidine-tagged proteins

    International Nuclear Information System (INIS)

    Feczko, Tivadar; Muskotal, Adel; Gal, Lorand; Szepvoelgyi, Janos; Sebestyen, Anett; Vonderviszt, Ferenc

    2008-01-01

    Superparamagnetic Ni-Zn ferrite nanoparticles were synthesized in radiofrequency thermal plasma reactor from aqueous solutions of Ni- and Zn-nitrates. The nanoparticles were studied for protein purification performance in both quantitative and qualitative terms. For comparison, experiments were also performed by Ni-charged affinity chromatography. It was proved that the Ni-Zn ferrite nanoparticles effectively purified histidine-tagged proteins with a maximum protein binding capacity of about 7% (w/w). Gel electrophoresis demonstrated better purification characteristics for magnetic nanoparticles than for affinity chromatography.

  11. Identification and characterization of 43 microsatellite markers derived from expressed sequence tags of the sea cucumber ( Apostichopus japonicus)

    Science.gov (United States)

    Jiang, Qun; Li, Qi; Yu, Hong; Kong, Lingfeng

    2011-06-01

    The sea cucumber Apostichopus japonicus is a commercially and ecologically important species in China. A total of 3056 potential unigenes were generated after assembling 7597 A. japonicus expressed sequence tags (ESTs) downloaded from Gen-Bank. Two hundred and fifty microsatellite-containing ESTs (8.18%) and 299 simple sequence repeats (SSRs) were detected. The average density of SSRs was 1 per 7.403 kb of EST after redundancy elimination. Di-nucleotide repeat motifs appeared to be the most abundant type with a percentage of 69.90%. Of the 126 primer pairs designed, 90 amplified the expected products and 43 showed polymorphism in 30 individuals tested. The number of alleles per locus ranged from 2 to 26 with an average of 7.0 alleles, and the observed and expected heterozygosities varied from 0.067 to 1.000 and from 0.066 to 0.959, respectively. These new EST-derived microsatellite markers would provide sufficient polymorphism for population genetic studies and genome mapping of this sea cucumber species.

  12. Thermal Stability of Woolly Erionite-K and Considerations about the Heat-Induced Behaviour of the Erionite Group

    Directory of Open Access Journals (Sweden)

    Paolo Ballirano

    2018-01-01

    Full Text Available The thermal behavior of a woolly erionite-K sample (Lander County, NV, USA, chemical formula (Ca2.03Na0.73K2.52Mg0.26[Al8.22Si27.78O71.80]·35.94H2O, was investigated in the 303–1173 K thermal range by in situ X-ray powder diffraction. Present data suggest a general thermally-induced volume contraction whose magnitude increases as S i S i + A l ratio becomes smaller. An inverse correlation between S i S i + A l ratio and Tdehydr is observed because higher S i S i + A l ratio values are associated to lower dehydration temperatures. A positive dependence exists between S i S i + A l ratio and Tbreak. A higher Si content results in a greater thermal stability, in agreement with the general trend observed in zeolites. On the contrary, no correlation has been found between Tbreak and weighted ionic potential (Z/rwt as suggested by reference data. Heating produces a general depletion of the Ca1, Ca2, Ca3, and K1 sites, which is counterbalanced by an increase of the K2 site scattering, even though the latter is not populated at RT. No “internal ion exchange” mechanism was apparently acting in the present sample differently from other erionite samples analysed in the past. At 303 K approximately 20 e− allocated at the OW H2O sites might be assigned to (extra-framework EF cations. Such fraction increases due to their migration from the extra-framework cation sites following the same mechanism reported in reference data.

  13. Theoretical bases on thermal stability of layered metallic systems

    International Nuclear Information System (INIS)

    Kadyrzhanov, K.K.; Rusakov, V.S.; Turkebaev, T.Eh.; Zhankadamova, A.M.; Ensebaeva, M.Z.

    2003-01-01

    The paper is dedicated to implementation of the theoretical bases for layered metallic systems thermal stabilization. The theory is based on the stabilization mechanism expense of the intermediate two-phase field formation. As parameters of calculated model are coefficients of mutual diffusion and inclusions sizes of generated phases in two-phase fields. The stabilization time dependence for beryllium-iron (Be (1.1 μm)-Fe(5.5 μm)) layered system from iron and beryllium diffusion coefficients, and inclusions sizes is shown as an example. Conclusion about possible mechanisms change at transition from microscopic consideration to the nano-crystal physics level is given

  14. Thermal site descriptive model. A strategy for the model development during site investigations - version 2

    International Nuclear Information System (INIS)

    Back, Paer-Erik; Sundberg, Jan

    2007-09-01

    This report presents a strategy for describing, predicting and visualising the thermal aspects of the site descriptive model. The strategy is an updated version of an earlier strategy applied in all SDM versions during the initial site investigation phase at the Forsmark and Oskarshamn areas. The previous methodology for thermal modelling did not take the spatial correlation fully into account during simulation. The result was that the variability of thermal conductivity in the rock mass was not sufficiently well described. Experience from earlier thermal SDMs indicated that development of the methodology was required in order describe the spatial distribution of thermal conductivity in the rock mass in a sufficiently reliable way, taking both variability within rock types and between rock types into account. A good description of the thermal conductivity distribution is especially important for the lower tail. This tail is important for the design of a repository because it affects the canister spacing. The presented approach is developed to be used for final SDM regarding thermal properties, primarily thermal conductivity. Specific objectives for the strategy of thermal stochastic modelling are: Description: statistical description of the thermal conductivity of a rock domain. Prediction: prediction of thermal conductivity in a specific rock volume. Visualisation: visualisation of the spatial distribution of thermal conductivity. The thermal site descriptive model should include the temperature distribution and thermal properties of the rock mass. The temperature is the result of the thermal processes in the repository area. Determination of thermal transport properties can be made using different methods, such as laboratory investigations, field measurements, modelling from mineralogical composition and distribution, modelling from density logging and modelling from temperature logging. The different types of data represent different scales, which has to be

  15. Thermal site descriptive model. A strategy for the model development during site investigations - version 2

    Energy Technology Data Exchange (ETDEWEB)

    Back, Paer-Erik; Sundberg, Jan [Geo Innova AB (Sweden)

    2007-09-15

    This report presents a strategy for describing, predicting and visualising the thermal aspects of the site descriptive model. The strategy is an updated version of an earlier strategy applied in all SDM versions during the initial site investigation phase at the Forsmark and Oskarshamn areas. The previous methodology for thermal modelling did not take the spatial correlation fully into account during simulation. The result was that the variability of thermal conductivity in the rock mass was not sufficiently well described. Experience from earlier thermal SDMs indicated that development of the methodology was required in order describe the spatial distribution of thermal conductivity in the rock mass in a sufficiently reliable way, taking both variability within rock types and between rock types into account. A good description of the thermal conductivity distribution is especially important for the lower tail. This tail is important for the design of a repository because it affects the canister spacing. The presented approach is developed to be used for final SDM regarding thermal properties, primarily thermal conductivity. Specific objectives for the strategy of thermal stochastic modelling are: Description: statistical description of the thermal conductivity of a rock domain. Prediction: prediction of thermal conductivity in a specific rock volume. Visualisation: visualisation of the spatial distribution of thermal conductivity. The thermal site descriptive model should include the temperature distribution and thermal properties of the rock mass. The temperature is the result of the thermal processes in the repository area. Determination of thermal transport properties can be made using different methods, such as laboratory investigations, field measurements, modelling from mineralogical composition and distribution, modelling from density logging and modelling from temperature logging. The different types of data represent different scales, which has to be

  16. Multiple tag labeling method for DNA sequencing

    Science.gov (United States)

    Mathies, R.A.; Huang, X.C.; Quesada, M.A.

    1995-07-25

    A DNA sequencing method is described which uses single lane or channel electrophoresis. Sequencing fragments are separated in the lane and detected using a laser-excited, confocal fluorescence scanner. Each set of DNA sequencing fragments is separated in the same lane and then distinguished using a binary coding scheme employing only two different fluorescent labels. Also described is a method of using radioisotope labels. 5 figs.

  17. Evaluation of visible implant elastomer tags in zebrafish (Danio rerio

    Directory of Open Access Journals (Sweden)

    Claudia Hohn

    2013-11-01

    The use of the visible implant elastomer (VIE tagging system in zebrafish (Danio rerio was examined. Two tag orientations (horizontal and vertical at the dorsal fin base were tested for tag retention, tag fragmentation and whether VIE tags affected growth and survival of juvenile zebrafish (1–4 month post hatch. Six tag locations (abdomen, anal fin base, caudal peduncle, dorsal fin base, pectoral fin base, isthmus and 5 tag colors (yellow, red, pink, orange, blue were evaluated for ease of VIE tag application and tag visibility in adult zebrafish. Long-term retention (1 year and multiple tagging sites (right and left of dorsal fin and pectoral fin base were examined in adult zebrafish. Lastly, survival of recombination activation gene 1−/− (rag1−/− zebrafish was evaluated after VIE tagging. The best tag location was the dorsal fin base, and the most visible tag color was pink. Growth rate of juvenile zebrafish was not affected by VIE tagging. Horizontal tagging is recommended in early stages of fish growth (1–2 months post hatch. VIE tags were retained for 1 year and tagging did not interfere with long-term growth and survival. There was no mortality associated with VIE tagging in rag1−/− zebrafish. The VIE tagging system is highly suitable for small-sized zebrafish. When familiar with the procedure, 120 adult zebrafish can be tagged in one hour. It does not increase mortality in adult zebrafish or interfere with growth in juvenile or adult zebrafish.

  18. Box–Behnken experimental design for investigation of stability and thermal conductivity of TiO2 nanofluids

    International Nuclear Information System (INIS)

    Lotfizadeh Dehkordi, Babak; Ghadimi, Azadeh; Metselaar, Henk S. C.

    2013-01-01

    The aim of this study is to investigate the effect of ultrasonication on the stability and thermal conductivity of TiO 2 water nanofluids. A UV–Vis spectrophotometer was employed to determine the relative stability of nanofluids. Response surface methodology based on the Box–Behnken design was implemented to investigate the influence of power of sonication (20–80 %), time of sonication (2–20 min), and volume concentration (0.1–1 vol%) of nanofluids as the independent variables. Second-order polynomial equations were established to predict the responses, thermal conductivity, and stability of nanofluids with the intervals of 1 week and 1 month. The significance of the models was tested by means of analysis of variance (ANOVA). The optimum stability and thermal conductivity of TiO 2 nanofluids with various sonication power and time at volume concentrations of 0.1, 0.55, and 1 % were studied. In addition, a correlation between the stability and thermal conductivity enhancement was derived in this study. The results revealed that, at low concentrations, nanofluids would become stable by low power and short period of sonication; however, no enhancement was observed in the thermal conductivity. Conversely, at high concentrations, stability and high thermal conductivity of nanofluids coincided at 1 vol%.

  19. Lignin-based carbon fibers: Carbon nanotube decoration and superior thermal stability

    KAUST Repository

    Xu, Xuezhu; Zhou, Jian; Jiang, Long; Lubineau, Gilles; Payne, Scott A.; Gutschmidt, David

    2014-01-01

    and the properties of the resultant products were studied and compared. The CF–CNT hybrid structure produced at 850 °C using a palladium catalyst showed the highest thermal stability, i.e., 98.3% residual weight at 950 °C. A mechanism for such superior thermal

  20. Thermal stability in a newly designed columnar-conical fluidized bed for combustion of rice husk

    Energy Technology Data Exchange (ETDEWEB)

    Rozainee, M.; Salema, A.A.; Ngo, S.P.; Chye, G.B. [Malaysian Technological Univ., Johor Bahru (Malaysia). Dept. of Chemical Engineering

    2006-07-01

    The effects of fluidizing and liquid propane gas (LPG) flow rates on thermal stability of a fluidized bed were examined. The aim of the study was to hybridize a columnar and conical fluidized bed (CCFB) in order to encourage the combustion of low-calorific fuels such as rice husks. Experiments were conducted to examine the thermal stability of the CCFB. Premixed primary air and liquid propane gas (LPG) was fed into the bed in order to verify its thermal stability. Temperature profiles of the combustor and bed were measured. The impact of the fluidizing velocity and LPG flow rate on the temperature profile was examined in order to analyze the influence of the fluidizing velocity and LPG rate on combustion rates. Results of the study showed that the combustion of the CCFB was sustained at a fluidizing velocity of 1.5 U{sub mf} and at an LPG flow rate of 8 liters per minute. Results of the study showed that fluidizing velocity played an important role on the thermal stability of the bed. It was concluded that the thermal stability of the combustor is sufficient for the CCFB. 13 refs., 2 tabs., 5 figs.

  1. Preparation and thermal stability of nickel nanowires via self ...

    Indian Academy of Sciences (India)

    Administrator

    Nickel nanowires; magnetic field; self-assembly; thermal stability. 1. Introduction ... vapour-phase techniques mainly include methods such as chemical ... 2.1 Materials and methods .... sum up, the colour change of NiO may be caused by the.

  2. Comparison of the movement and recapture of salmonid fishes tagged at two power plants

    International Nuclear Information System (INIS)

    Romberg, G.P.; Thommes, M.M.

    1974-01-01

    Fish tagging studies were conducted in the vicinity of Point Beach Nuclear Plant and Waukegan Power Plant to determine whether there were any seasonal or site specific differences in the residence behavior of salmonids at thermal discharges. Results showed that there were differences in the abundance and time of peak abundance of trout and salmon at the two power plant discharges. Certain species reacted differently to the two discharges probably as a result of maturity and water temperature. Salmonids did not appear to remain at either discharge for long periods. Direction of migration was affected by stocking location and water temperature

  3. Generation, analysis and functional annotation of expressed sequence tags from the ectoparasitic mite Psoroptes ovis

    Directory of Open Access Journals (Sweden)

    Kenyon Fiona

    2011-07-01

    Full Text Available Abstract Background Sheep scab is caused by Psoroptes ovis and is arguably the most important ectoparasitic disease affecting sheep in the UK. The disease is highly contagious and causes and considerable pruritis and irritation and is therefore a major welfare concern. Current methods of treatment are unsustainable and in order to elucidate novel methods of disease control a more comprehensive understanding of the parasite is required. To date, no full genomic DNA sequence or large scale transcript datasets are available and prior to this study only 484 P. ovis expressed sequence tags (ESTs were accessible in public databases. Results In order to further expand upon the transcriptomic coverage of P. ovis thus facilitating novel insights into the mite biology we undertook a larger scale EST approach, incorporating newly generated and previously described P. ovis transcript data and representing the largest collection of P. ovis ESTs to date. We sequenced 1,574 ESTs and assembled these along with 484 previously generated P. ovis ESTs, which resulted in the identification of 1,545 unique P. ovis sequences. BLASTX searches identified 961 ESTs with significant hits (E-value P. ovis ESTs. Gene Ontology (GO analysis allowed the functional annotation of 880 ESTs and included predictions of signal peptide and transmembrane domains; allowing the identification of potential P. ovis excreted/secreted factors, and mapping of metabolic pathways. Conclusions This dataset currently represents the largest collection of P. ovis ESTs, all of which are publicly available in the GenBank EST database (dbEST (accession numbers FR748230 - FR749648. Functional analysis of this dataset identified important homologues, including house dust mite allergens and tick salivary factors. These findings offer new insights into the underlying biology of P. ovis, facilitating further investigations into mite biology and the identification of novel methods of intervention.

  4. Thermal stability of α-amylase in aqueous cosolvent systems

    Indian Academy of Sciences (India)

    Prakash

    The activity and thermal stability of α-amylase were studied in the presence of different concentrations of ... 2.1 Materials ..... unfavourable free energy of transfer of amino acid side ..... folded protein with a hydrophobic dye: evidence that molten.

  5. Thermal stability of low dose Ga+ ion irradiated spin valves

    International Nuclear Information System (INIS)

    Qi Xianjin; Wang Yingang; Zhou Guanghong; Li Ziquan

    2009-01-01

    The thermal stability of low dose Ga + ion irradiated spin valves has been investigated and compared with that of the as-prepared ones. The dependences of exchange field, measured using vibrating sample magnetometer at room temperature, on magnetic field sweep rate and time spent at negative saturation of the pinned ferromagnetic layer, and training effect were explored. The training effect is observed on both the irradiated spin valves and the as-prepared ones. The magnetic field sweep rate dependence of the exchange bias field of the irradiated spin valves is nearly the same as that of the as-prepared ones. For the as-prepared structure thermal activation has been observed, which showed that holding the irradiated structure at negative saturation of the pinned ferromagnetic layer for up to 28 hours results in no change in the exchange field. The results indicate that the thermal stability of the ion irradiated spin valves is the same as or even better than the as-prepared ones.

  6. Comparative evaluation of thermal decomposition behavior and thermal stability of powdered ammonium nitrate under different atmosphere conditions.

    Science.gov (United States)

    Yang, Man; Chen, Xianfeng; Wang, Yujie; Yuan, Bihe; Niu, Yi; Zhang, Ying; Liao, Ruoyu; Zhang, Zumin

    2017-09-05

    In order to analyze the thermal decomposition characteristics of ammonium nitrate (AN), its thermal behavior and stability under different conditions are studied, including different atmospheres, heating rates and gas flow rates. The evolved decomposition gases of AN in air and nitrogen are analyzed with a quadrupole mass spectrometer. Thermal stability of AN at different heating rates and gas flow rates are studied by differential scanning calorimetry, thermogravimetric analysis, paired comparison method and safety parameter evaluation. Experimental results show that the major evolved decomposition gases in air are H 2 O, NH 3 , N 2 O, NO, NO 2 and HNO 3 , while in nitrogen, H 2 O, NH 3 , NO and HNO 3 are major components. Compared with nitrogen atmosphere, lower initial and end temperatures, higher heat flux and broader reaction temperature range are obtained in air. Meanwhile, higher air gas flow rate tends to achieve lower reaction temperature and to reduce thermal stability of AN. Self-accelerating decomposition temperature of AN in air is much lower than that in nitrogen. It is considered that thermostability of AN is influenced by atmosphere, heating rate and gas flow rate, thus changes of boundary conditions will influence its thermostability, which is helpful to its safe production, storage, transportation and utilization. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Illumina amplicon sequencing of 16S rRNA tag reveals bacterial community development in the rhizosphere of apple nurseries at a replant disease site and a new planting site.

    Directory of Open Access Journals (Sweden)

    Jian Sun

    Full Text Available We used a next-generation, Illumina-based sequencing approach to characterize the bacterial community development of apple rhizosphere soil in a replant site (RePlant and a new planting site (NewPlant in Beijing. Dwarfing apple nurseries of 'Fuji'/SH6/Pingyitiancha trees were planted in the spring of 2013. Before planting, soil from the apple rhizosphere of the replant site (ReSoil and from the new planting site (NewSoil was sampled for analysis on the Illumina MiSeq platform. In late September, the rhizosphere soil from both sites was resampled (RePlant and NewPlant. More than 16,000 valid reads were obtained for each replicate, and the community was composed of five dominant groups (Proteobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadetes and Actinobacteria. The bacterial diversity decreased after apple planting. Principal component analyses revealed that the rhizosphere samples were significantly different among treatments. Apple nursery planting showed a large impact on the soil bacterial community, and the community development was significantly different between the replanted and newly planted soils. Verrucomicrobia were less abundant in RePlant soil, while Pseudomonas and Lysobacter were increased in RePlant compared with ReSoil and NewPlant. Both RePlant and ReSoil showed relatively higher invertase and cellulase activities than NewPlant and NewSoil, but only NewPlant soil showed higher urease activity, and this soil also had the higher plant growth. Our experimental results suggest that planting apple nurseries has a significant impact on soil bacterial community development at both replant and new planting sites, and planting on new site resulted in significantly higher soil urease activity and a different bacterial community composition.

  8. Production for high thermal stability NdFeB magnets

    Energy Technology Data Exchange (ETDEWEB)

    Yu, L.Q. [College of Physics Science and Technology, China University of Petroleum (East China), Dongying 257061, Shandong Province (China)], E-mail: iyy2000@163.com; Zhang, J.; Hu, S.Q.; Han, Z.D. [College of Physics Science and Technology, China University of Petroleum (East China), Dongying 257061, Shandong Province (China); Yan, M. [State Key Lab of Silicon Materials, Zhejiang University, Hangzhou 310027 (China)

    2008-04-15

    To improve sintered NdFeB magnets' thermal stability and magnetic properties, combined addition of elements Cu and Gd was investigated. It was found that with Gd addition increase to 1.0%, the temperature coefficient {alpha} improved from -0.15 to -0.05%/deg. C (maximum working temperature 120 deg. C), but the remanence and the maximum energy product linearly decreased. With addition of Cu in Gd-containing magnets the intrinsic coercivity increased greatly, and the remanence increased also because of their density improvement, and optimum Cu content was achieved at 0.2%. Microstructure analysis showed that most of the Cu distributed at grain boundaries and led to clear and smooth morphologies. Magnets with high thermal stability {alpha}=-0.05%/deg. C and magnetic properties were obtained with addition of Gd=0.8% and Cu=0.2%.

  9. Preparation, structure and thermal stability of Cu/LDPE nanocomposites

    International Nuclear Information System (INIS)

    Xia Xianping; Cai Shuizhou; Xie Changsheng

    2006-01-01

    Copper/low-density-polyethylene (Cu/LDPE) nanocomposites have been prepared using a melt-blending technique in a single-screw extruder. Their structure and thermal characteristics are characterized by using X-ray diffraction (XRD), scanning electron microscopy (SEM), X-ray energy dispersive spectroscopy (EDS), differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA). The results of XRD, SEM and SEM-EDS Cu-mapping show that the nanocomposites are a hybrid of the polymer and the copper nanoparticles, and the copper nanoparticles aggregates were distributed uniformly in general. The results also show that the nanocomposites and the base resin, the pure LDPE, have a different crystalline structure and the same oriented characteristics owing to the presence of copper nanoparticles and the same cooling condition. The results of DSC show that the incorporation of copper nanoparticles can decrease the melting temperatures but increase the crystallization temperatures, and can lower the crystallinity degree of the matrix of the composites. The results of TGA show that the presence of copper nanoparticles can improve the thermal stability of the nanocomposites, a maximum increment of 18 deg. C is obtained comparing with the pure LDPE in this experiment. The results of TGA also show that the influence of the incorporation of the copper nanoparticles on the thermal stability of the Cu/LDPE nanocomposites is different from that of the non-metal nanoparticles on the polymer/non-metal nanocomposites and the copper microparticles on the Cu/LDPE microcomposites. The increase of the thermal stability of the Cu/LDPE nanocomposites will decrease when the content of the copper nanoparticles is more than 2 wt.%. The difference might be caused by the fact that the activity of the metal nanoparticles is much more higher than that of the non-metal nanoparticles, and the different size effect the different copper particles has

  10. Non-Thermal Treatment of Hanford Site Low-Level Mixed Waste

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-09-01

    DOE proposes to transport contact-handled LLMW from the Hanford Site to the Allied Technology Group (ATG) Mixed Waste Facility (MWF) in Richland, Washington, for non-thermal treatment and to return the treated waste to the Hanford Site for eventual land disposal. Over a 3-year period the waste would be staged to the ATG MWF, and treated waste would be returned to the Hanford Site. The ATG MWF would be located on an 18 hectare (ha) (45 acre [at]) ATG Site adjacent to ATG's licensed low-level waste processing facility at 2025 Battelle Boulevard. The ATG MWF is located approximately 0.8 kilometers (km) (0.5 miles [mi]) south of Horn Rapids Road and 1.6 km (1 mi) west of Stevens Drive. The property is located within the Horn Rapids triangle in northern Richland (Figure 2.1). The ATG MWF is to be located on the existing ATG Site, near the DOE Hanford Site, in an industrial area in the City of Richland. The effects of siting, construction, and overall operation of the MWF have been evaluated in a separate State Environmental Policy Act (SEPA) EIS (City of Richland 1998). The proposed action includes transporting the LLMW from the Hanford Site to the ATG Facility, non-thermal treatment of the LLMW at the ATG MWF, and transporting the waste from ATG back to the Hanford Site. Impacts fi-om waste treatment operations would be bounded by the ATG SEPA EIS, which included an evaluation of the impacts associated with operating the non-thermal portion of the MWF at maximum design capacity (8,500 metric tons per year) (City of Richland 1998). Up to 50 employees would be required for non-thermal treatment portion of the MWF. This includes 40 employees that would perform waste treatment operations and 10 support staff. Similar numbers were projected for the thermal treatment portion of the MWF (City of Richland 1998).

  11. Tag questions Tag questions

    Directory of Open Access Journals (Sweden)

    David Brazil

    2008-04-01

    Full Text Available The so-called 'tag' structures of English have received a lot of attention in language teaching programmes, attention that is not hard to justify when one considers the problems and anxiety they can occasion for many foreign learners. Most teachers one speaks to seem fairly willing to agree, however, that traditional treatments of the topic leave much to be desired. It happens, also, that, when considered collectively, the tags and some related phenomena have a special heoretical interest. For they constitute a field in which it seems essential to bring together insights that derive from the study of several aspects of linguistic organisation, aspects which in some recent work have been held to need distinctive kinds of descriptive category to handle. Traditional treatments have found it necessary to recognise different syntactic types (e.g. 'same polarity' and 'reversed polarity' tags and ifferent intonational treatments ("falling'and 'rising' tag; while the way the communicative significance of the various permutations is described normally requires reference to the expectations they signal regarding the immediately following behaviour of the other party (in the common phrase, 'What kind of answer they expect'. This last consideration places the matter squarely in the arena of recent work on the analysis of interactive discourse. The so-called 'tag' structures of English have received a lot of attention in language teaching programmes, attention that is not hard to justify when one considers the problems and anxiety they can occasion for many foreign learners. Most teachers one speaks to seem fairly willing to agree, however, that traditional treatments of the topic leave much to be desired. It happens, also, that, when considered collectively, the tags and some related phenomena have a special heoretical interest. For they constitute a field in which it seems essential to bring together insights that derive from the study of several aspects

  12. Thermal stability of biodiesel in supercritical methanol

    Energy Technology Data Exchange (ETDEWEB)

    Hiroaki Imahara; Eiji Minami; Shusaku Hari; Shiro Saka [Kyoto University, Kyoto (Japan). Department of Socio-Environmental Energy Science

    2008-01-15

    Non-catalytic biodiesel production technologies from oils/fats in plants and animals have been developed in our laboratory employing supercritical methanol. Due to conditions in high temperature and high pressure of the supercritical fluid, thermal stability of fatty acid methyl esters and actual biodiesel prepared from various plant oils was studied in supercritical methanol over a range of its condition between 270{sup o}C/17 MPa and 380{sup o}C/56 MPa. In addition, the effect of thermal degradation on cold flow properties was studied. As a result, it was found that all fatty acid methyl esters including poly-unsaturated ones were stable at 270{sup o}C/17 MPa, but at 350{sup o}C/43 MPa, they were partly decomposed to reduce the yield with isomerization from cis-type to trans-type. These behaviors were also observed for actual biodiesel prepared from linseed oil, safflower oil, which are high in poly-unsaturated fatty acids. Cold flow properties of actual biodiesel, however, remained almost unchanged after supercritical methanol exposure at 270{sup o}C/17 MPa and 350{sup o}C/43 MPa. For the latter condition, however, poly-unsaturated fatty acids were sacrificed to be decomposed and reduced in yield. From these results, it was clarified that reaction temperature in supercritical methanol process should be lower than 300{sup o}C, preferably 270{sup o}C with a supercritical pressure higher than 8.09 MPa, in terms of thermal stabilization for high-quality biodiesel production. 9 refs., 3 figs., 4 tabs.

  13. Tempting To Tag: An Experimental Comparison Of Four Tagging Input Mechanisms

    Directory of Open Access Journals (Sweden)

    Mark Melenhorst

    2010-01-01

    Full Text Available Tagging helps achieve improved indexing and recommendation of resources (e.g., videos or pictures in large data collections. In order to reap the benefits of tagging, people must be persuaded to label the resources they consume. This paper reports on a study in which four different tagging input mechanisms and their effect on users' motivation to tag were compared. The mechanisms consisted of a standard tag input box, a chatbot-like environment, a bookmarking mechanism, and a "tag and vote" game. The results of our experiment show that the use of the nonstandard tagging input mechanisms does not affect users' motivation to tag. In some instances tagging mechanisms were found to distract users from their primary task: consuming resources. Persuading people to tag might be accomplished more effectively by using other motivating tagging mechanisms (e.g., tagging games, or motivation could be created by explaining the usefulness of tagging.

  14. Physicochemical properties and thermal stability of quercetin hydrates in the solid state

    Energy Technology Data Exchange (ETDEWEB)

    Borghetti, G.S., E-mail: greicefarm@yahoo.com.br [Programa de Pos-Graduacao em Ciencias Farmaceuticas, Faculdade de Farmacia, Universidade Federal do Rio Grande do Sul, Av. Ipiranga 2752, CEP 90.610-000, Porto Alegre, RS (Brazil); Carini, J.P. [Programa de Pos-Graduacao em Ciencias Farmaceuticas, Faculdade de Farmacia, Universidade Federal do Rio Grande do Sul, Av. Ipiranga 2752, CEP 90.610-000, Porto Alegre, RS (Brazil); Honorato, S.B.; Ayala, A.P. [Departamento de Fisica, Universidade Federal do Ceara, Caixa Postal 6030, CEP 60.455-970, Fortaleza, CE (Brazil); Moreira, J.C.F. [Departamento de Bioquimica, Instituto de Ciencias Basicas da Saude, Universidade Federal do Rio Grande do Sul, Rua Ramiro Barcelos 2600, CEP 90035-003, Porto Alegre, RS (Brazil); Bassani, V.L. [Programa de Pos-Graduacao em Ciencias Farmaceuticas, Faculdade de Farmacia, Universidade Federal do Rio Grande do Sul, Av. Ipiranga 2752, CEP 90.610-000, Porto Alegre, RS (Brazil)

    2012-07-10

    Highlights: Black-Right-Pointing-Pointer Quercetin raw materials may present different degree of hydration. Black-Right-Pointing-Pointer Thermal stability of quercetin in the solid state depends on its degree of hydration. Black-Right-Pointing-Pointer Quercetin dehydrate is thermodynamically more stable than the other crystal forms. - Abstract: In the present work three samples of quercetin raw materials (QCTa, QCTb and QCTc), purchased from different Brazilian suppliers, were characterized employing scanning electron microscopy, Raman spectroscopy, simultaneous thermogravimetry and infrared spectroscopy, differential scanning calorimetry, and variable temperature-powder X-ray diffraction, in order to know their physicochemical properties, specially the thermal stability in solid state. The results demonstrated that the raw materials of quercetin analyzed present distinct crystalline structures, ascribed to the different degree of hydration of their crystal lattice. The thermal stability of these quercetin raw materials in the solid state was highly dependent on their degree of hydration, where QCTa (quercetin dihydrate) was thermodynamically more stable than the other two samples.

  15. Uncovering the role of the flexible C-terminal tail: A model study with Strep-tagged GFP.

    Science.gov (United States)

    Lassalle, Michael W; Kondou, Shinobu

    2016-06-01

    Recently, it has been recognized that, much like an electric current in an electric circuit, dynamic disruptions from flexible, unstructured regions distal to the active region are transferred through the contact network to the active site and influence protein stability and/or function. As transmembrane proteins frequently possess the β-barrel structure, studies of proteins with this topology are required. The unstructured lid segments of the β-barrel GFP protein are conserved and could play a role in the backbone stabilization required for chromophore function. A study of the disordered C-terminus and the function within the lid is necessary. In this study, we entirely truncated the flexible C-terminal tail and investigated the N-terminal Strep-tagged GFP by fluorescence spectroscopy, and the temperature- and GdnHCl-induced unfolding by circular dichroism. The introduction of the unstructured Strep-tag itself changed the unfolding pathway. Truncating the entire flexible tail did not decrease the fluorescence intensity to a large extent; however, the protein stability changed dramatically. The temperature for half-denaturation T 1/2 changed significantly from 79 °C for the wild-type to 72.8 °C for the mutant. Unfolding kinetics at different temperatures have been induced by 4 M GdnHCl, and the apparent Arrhenius activation energy decreased by 40% as compared to the wild-type.

  16. Uncovering the role of the flexible C-terminal tail: A model study with Strep-tagged GFP

    Directory of Open Access Journals (Sweden)

    Michael W. Lassalle

    2016-06-01

    Full Text Available Recently, it has been recognized that, much like an electric current in an electric circuit, dynamic disruptions from flexible, unstructured regions distal to the active region are transferred through the contact network to the active site and influence protein stability and/or function. As transmembrane proteins frequently possess the β-barrel structure, studies of proteins with this topology are required. The unstructured lid segments of the β-barrel GFP protein are conserved and could play a role in the backbone stabilization required for chromophore function. A study of the disordered C-terminus and the function within the lid is necessary. In this study, we entirely truncated the flexible C-terminal tail and investigated the N-terminal Strep-tagged GFP by fluorescence spectroscopy, and the temperature- and GdnHCl-induced unfolding by circular dichroism. The introduction of the unstructured Strep-tag itself changed the unfolding pathway. Truncating the entire flexible tail did not decrease the fluorescence intensity to a large extent; however, the protein stability changed dramatically. The temperature for half-denaturation T1/2 changed significantly from 79 °C for the wild-type to 72.8 °C for the mutant. Unfolding kinetics at different temperatures have been induced by 4 M GdnHCl, and the apparent Arrhenius activation energy decreased by 40% as compared to the wild-type.

  17. Probabilistic approaches for geotechnical site characterization and slope stability analysis

    CERN Document Server

    Cao, Zijun; Li, Dianqing

    2017-01-01

    This is the first book to revisit geotechnical site characterization from a probabilistic point of view and provide rational tools to probabilistically characterize geotechnical properties and underground stratigraphy using limited information obtained from a specific site. This book not only provides new probabilistic approaches for geotechnical site characterization and slope stability analysis, but also tackles the difficulties in practical implementation of these approaches. In addition, this book also develops efficient Monte Carlo simulation approaches for slope stability analysis and implements these approaches in a commonly available spreadsheet environment. These approaches and the software package are readily available to geotechnical practitioners and alleviate them from reliability computational algorithms. The readers will find useful information for a non-specialist to determine project-specific statistics of geotechnical properties and to perform probabilistic analysis of slope stability.

  18. The relationship between fatty acid compositions and thermal stability of extra virgin olive oils

    Directory of Open Access Journals (Sweden)

    Fayegh Moulodi

    2014-11-01

    Full Text Available Background: Fatty acids are one of the most important compounds in edible oils. Further, the stability of oils depends on the composition of fatty acids. So, this study was conducted to investigate the effect of fatty acid composition on the oxidative stability of extra virgin olive oils during the heating process. Methods: In total, eight samples of extra virgin olive oil were studied. To evaluate their thermal stability, the oils were heated at 120 ° C for 4 h and sampling was carried out in 2-hour intervals. Then, fatty acid composition, peroxide value, anisidine value and totox value were evaluated according to Iranian national standards. Results: Results showed a significantly direct correlation between Palmitoleic acid and Totox index in the second (r=0.786 and fourth hours (r=0.762, and between linoleic and Totox index in the second (r=0.643 and fourth hours (r=0.786. However, there was a significantly inverse relationship between oleic acid and Totox index in the fourth hour (r=-0.833. Conclusion: Result indicated that linoleic and Palmitoleic acids had a reducing effect on thermal stability of extra virgin olive oil after the second hour. But, Oleic acid caused a positive effect on thermal stability after the fourth hour. Thus, it is concluded that unsaturated fatty acids especially oleic acid affect the thermal stability at final hours.

  19. Thermal stability of detonation-produced micro and nanodiamonds

    Science.gov (United States)

    Efremov, V. P.; Zakatilova, E. I.; Maklashova, I. V.; Shevchenko, N. V.

    2018-01-01

    Detonation nanodiamonds are produced at utilization of high explosives. When an explosive blasts in a water environment, the detonation products contain microdiamonds, and in a gaseous medium, nanodiamonds. It is known that with decreasing size the influence of the surface energy of particles on their properties increases. Thus, it is interesting to compare the properties of detonation nano and microdiamonds. In this study, we have examined the thermal stability of diamond materials by synchronous thermal analysis. The experiments were performed at atmospheric pressure in argon flow for different heating rates in a range from room temperature to 1500 °C. Samples of initial and annealed micro and nanomaterials were studied using electron microscopy, x-ray and x-ray-fluorescence analysis. It was established that thermal and structural properties of micro and nanodiamonds differ substantially.

  20. TU-H-206-07: Assessment of Geometric Distortion in EPI with a SPAMM Tagged Acquisition

    Energy Technology Data Exchange (ETDEWEB)

    Hwang, K; Meier, J; Yung, J; Stafford, R [The University of Texas MD Anderson Cancer Center, Houston, TX (United States)

    2016-06-15

    Purpose: Echo planar imaging (EPI) is known to exhibit gross geometric distortion caused by multiple factors, including B0 inhomgeneity and transient eddy currents. However, diffusion weighted (DW) EPI has become indispensable for diagnosis and therapy assessment. We propose a methodology for quantifying distortion in EPI sequences that does not require the use of dedicated spatial accuracy phantoms, enabling flexibility in phantom design for QA of distortion effects in EPI protocols. Methods: The proposed methodology utilizes a saturation technique known as Spatial Modulation of Magnetization (SPAMM) that tags the imaging subject with saturated grid lines. Originally intended for tracking cardiac motion, these grids are applied to assess differences between diffusion weighting directions and b-values, or against a more geometrically robust sequence such as fast spin echo (FSE). The saturation preparation sequence consists of binomially weighted (e.g. 1-3-3-1) pulses interleaved with gradient blips along the frequency encode direction, followed by the same sequence with gradient blips in the phase encode direction. Three phantoms were assessed with these sequences: a spherical head-sized phantom, a large shimming phantom, and a modified PET ACR phantom that included compartments of water, air, oil, and Teflon. Each phantom was acquired with three sequences using parameters from a clinically appropriate protocol (22 cm head or 46 cm abdomen): a conventional DW-EPI sequence (3 DW directions), and both the DW-EPI and FSE sequences with tagging. Differences in grid locations were visualized with minimum intensity projection between images, and measured using intersecting locations on the grids. Results: Grid lines were clearly visualized on tagged images and enabled quantification of distortions. Maximum eddy current induced errors of 10.8 to 14.8 mm were observed in areas away from isocenter with DW gradients applied in various directions. Conclusion: SPAMM tagging

  1. Effect of Filler Concentration on Thermal Stability of Vinyl Copolymer Elastomer (VCE) Composites

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Dali [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Hubbard, Kevin Mark [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Devlin, David James [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Henderson, Kevin C. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Pacheco, Robin Montoya [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-03-06

    To study the thermal stability of vinyl copolymer elastomer (VCE) in its composite form, systematic TGA characterizations were conducted in both nonisothermal and isothermal modes. The effects of filler concentration on the aging behaviors of the VCE/filler composites were investigated under nitroplasticizer (NP) environment. FTIR characterization was used to probe the structural changes in the VCE polymer before and after the thermal treatments. This study suggests that the filler concentration significantly deteriorates the thermal stability of NP at a moderate temperature (< 70 °C). The degradation of NP, in turn, accelerates the aging process of the VCE polymer in its composite form.

  2. Top tagging with deep neural networks [Vidyo

    CERN Multimedia

    CERN. Geneva

    2017-01-01

    Recent literature on deep neural networks for top tagging has focussed on image based techniques or multivariate approaches using high level jet substructure variables. Here, we take a sequential approach to this task by using anordered sequence of energy deposits as training inputs. Unlike previous approaches, this strategy does not result in a loss of information during pixelization or the calculation of high level features. We also propose new preprocessing methods that do not alter key physical quantities such as jet mass. We compare the performance of this approach to standard tagging techniques and present results evaluating the robustness of the neural network to pileup.

  3. Adsorptive properties and thermal stability of carbon fibers modified by boron and phosphorus compounds

    International Nuclear Information System (INIS)

    Malygin, A.A.; Postnova, A.M.; Shevchenko, G.K.

    1996-01-01

    Sorptional characteristics as regards water vapors and thermal stability of carbon fibers modified by method of molecular superposition of borohydroxide groupings have been studied. Sorptional activity in the range of low and medium relative pressures of water vapors in modified samples increases several times, while thermal stability of carbon fiber increases, as well. 14 refs.; 1 fig.; 1 tab

  4. A wing expressed sequence tag resource for Bicyclus anynana butterflies, an evo-devo model

    Directory of Open Access Journals (Sweden)

    Gruber Jonathan D

    2006-05-01

    Full Text Available Abstract Background Butterfly wing color patterns are a key model for integrating evolutionary developmental biology and the study of adaptive morphological evolution. Yet, despite the biological, economical and educational value of butterflies they are still relatively under-represented in terms of available genomic resources. Here, we describe an Expression Sequence Tag (EST project for Bicyclus anynana that has identified the largest available collection to date of expressed genes for any butterfly. Results By targeting cDNAs from developing wings at the stages when pattern is specified, we biased gene discovery towards genes potentially involved in pattern formation. Assembly of 9,903 ESTs from a subtracted library allowed us to identify 4,251 genes of which 2,461 were annotated based on BLAST analyses against relevant gene collections. Gene prediction software identified 2,202 peptides, of which 215 longer than 100 amino acids had no homology to any known proteins and, thus, potentially represent novel or highly diverged butterfly genes. We combined gene and Single Nucleotide Polymorphism (SNP identification by constructing cDNA libraries from pools of outbred individuals, and by sequencing clones from the 3' end to maximize alignment depth. Alignments of multi-member contigs allowed us to identify over 14,000 putative SNPs, with 316 genes having at least one high confidence double-hit SNP. We furthermore identified 320 microsatellites in transcribed genes that can potentially be used as genetic markers. Conclusion Our project was designed to combine gene and sequence polymorphism discovery and has generated the largest gene collection available for any butterfly and many potential markers in expressed genes. These resources will be invaluable for exploring the potential of B. anynana in particular, and butterflies in general, as models in ecological, evolutionary, and developmental genetics.

  5. Thermal stability of Trichoderma reesei c30 cellulase and aspergillus niger; -glucosidase after ph and chemical modification

    Energy Technology Data Exchange (ETDEWEB)

    Woodward, J.; Whaley, K.S.; Zachry, G.S.; Wohlpart, D.L.

    1981-01-01

    Treatment of Trichoderma reesei C30 cellulase at pH 10.0 for 1 h at room temperature increased its pH and thermal stability. Chemical modification of the free epsilon-amino groups of cellulase at pH 10.0 resulted in no further increase in stability. Such chemical modification, however, decreased the thermal stability of the cellulose-cellulase complex. On the contrary, the chemical modification of Aspergillus niger glucosidase with glutaraldehyde at pH 8.0 increased the thermal stability of this enzyme.

  6. Stabilizing effect of epoxidized sunflower oil as a secondary stabilizer for Ca/Hg stabilized PVC

    Directory of Open Access Journals (Sweden)

    2008-01-01

    Full Text Available Unsaturated triglyceride oil sunflower was epoxidized and characterized by chemical and spectroscopic methods. Epoxidized sunflower oil (ESO was used as an organic thermal co-stabilizer for rigid poly(vinyl chloride (PVC in the presence of tricalcium dicitrate (Ca3(C6H5O72 and mercury (II acetate (Hg(CH3COO2. The thermo-oxidative degradation of PVC was studied in the presence of these ternary stabilizer systems at 170, 180, 190 and 200°C in N2 atmosphere. The effects of metal carboxylate combination Ca/Hg in the absence and in the presence of epoxidized sunflower oil on static heat treatment of PVC have been studied. The formation of polyene sequences was investigated by UV-visible and FT-IR spectroscopy and by comparing viscosity data obtained in the presence and in the absence of the additives. It was found that the additives retard the rate of degradation and reduce the extent of polymer chain scission associated with the thermal degradation of poly(vinyl chloride. Synergistic effects were found when stabilizer was blended in 50:50 weight ratios with either. It was found that ESO exerted a stabilizing effect on the degradation of PVC. The activation energy for degraded PVC in absence of stabilizers was 38.6 kJ•mol–1 and in the presence of Ca/Hg and Ca/Hg/ESO were 53.3 and 64.7 kJ•mol–1 respectively. In order of compare the efficiency of the epoxidized sunflower oil with these metal soap stabilizers, thermal stabilities were evaluated on the basis of evolved hydrogen chloride determined by conductometry technique and degree of discoloration are discussed.

  7. Strength and thermal stability of fiber reinforced plastic composites ...

    African Journals Online (AJOL)

    Therefore, the strength properties and thermal stability of plastic composites reinforced with rattan fibers were investigated in this work. Particles of rattan species (Eremospatha macrocarpa (EM) and Laccosperma secundiflorum (LS)) were blended with High-Density Polyethylene (HDPE) to produce fiber reinforced plastic ...

  8. Analyses of expressed sequence tags from the maize foliar pathogen Cercospora zeae-maydis identity novel genes expressed during vegetative infectious, and repoductive growth

    OpenAIRE

    Bluhm, B.H.; Lindquist, E.; Kema, G.H.J.; Goodwin, S.B.; Dunkle, L.D.

    2008-01-01

    The ascomycete fungus Cercospora zeae-maydis is an aggressive foliar pathogen of maize that causes substantial losses annually throughout the Western Hemisphere. Despite its impact on maize production, little is known about the regulation of pathogenesis in C. zeae-maydis at the molecular level. The objectives of this study were to generate a collection of expressed sequence tags (ESTs) from C. zeae-maydis and evaluate their expression during vegetative, infectious, and reproductive growth. R...

  9. Analyses of expressed sequence tags from the maize foliar pathogen Cercospora zeae-maydis identify novel genes expressed during vegetative, infectious, and reproductive growth

    OpenAIRE

    Bluhm, Burton H; Dhillon, Braham; Lindquist, Erika A; Kema, Gert HJ; Goodwin, Stephen B; Dunkle, Larry D

    2008-01-01

    Abstract Background The ascomycete fungus Cercospora zeae-maydis is an aggressive foliar pathogen of maize that causes substantial losses annually throughout the Western Hemisphere. Despite its impact on maize production, little is known about the regulation of pathogenesis in C. zeae-maydis at the molecular level. The objectives of this study were to generate a collection of expressed sequence tags (ESTs) from C. zeae-maydis and evaluate their expression during vegetative, infectious, and re...

  10. Enhanced thermal stability of RuO2/polyimide interface for flexible device applications

    Science.gov (United States)

    Music, Denis; Schmidt, Paul; Chang, Keke

    2017-09-01

    We have studied the thermal stability of RuO2/polyimide (Kapton) interface using experimental and theoretical methods. Based on calorimetric and spectroscopic analyses, this inorganic-organic system does not exhibit any enthalpic peaks as well as all bonds in RuO2 and Kapton are preserved up to 500 °C. In addition, large-scale density functional theory based molecular dynamics, carried out in the same temperature range, validates the electronic structure and points out that numerous Ru-C and a few Ru-O covalent/ionic bonds form across the RuO2/Kapton interface. This indicates strong adhesion, but there is no evidence of Kapton degradation upon thermal excitation. Furthermore, RuO2 does not exhibit any interfacial bonds with N and H in Kapton, providing additional evidence for the thermal stability notion. It is suggested that the RuO2/Kapton interface is stable due to aromatic architecture of Kapton. This enhanced thermal stability renders Kapton an appropriate polymeric substrate for RuO2 containing systems in various applications, especially for flexible microelectronic and energy devices.

  11. 1-, 2-, and 4-Ethynylpyrenes in the Structure of Twisted Intercalating Nucleic Acids: Structure, Thermal Stability, and Fluorescence Relationship

    DEFF Research Database (Denmark)

    Filichev, Vyacheslav V; Astakhova, Irina V.; Malakhov, Andrei D.

    2008-01-01

    to ortho in homopyrimidine TINAs. Thus, for para-TINAs the bulge insertion of an intercalator led to high thermal stability of Hoogsteen-type parallel triplexes and duplexes, whereas Watson-Cricktype duplexes were destabilized. In the case of ortho-TINA, both Hoogsteen and Watson-Crick-type complexes were......A postsynthetic, on-column Sonogashira reaction was applied on DNA molecules modified by 2- or 4-iodophenylmethylglycerol in the middle of the sequence, to give the corresponding ortho- and para-twisted intercalating nucleic acids (TINA) with 1-, 2-, and 4-ethynylpyrene residues. The convenient...

  12. Thermo-mechanical actuator-based miniature tagging module for localization in capsule endoscopy

    Science.gov (United States)

    Chandrappan, Jayakrishnan; Ruiqi, Lim; Su, Nandar; Yen Yi, Germaine Hoe; Vaidyanathan, Kripesh

    2011-04-01

    Capsule endoscopy is a frontline medical diagnostic tool for the gastro intestinal tract disorders. During diagnosis, efficient localization techniques are essential to specify a pathological area that may require further diagnosis or treatment. This paper presents the development of a miniature tagging module that relies on a novel concept to label the region of interest and has the potential to integrate with a capsule endoscope. The tagging module is a compact thermo-mechanical actuator loaded with a biocompatible micro tag. A low power microheater attached to the module serves as the thermal igniter for the mechanical actuator. At optimum temperature, the actuator releases the micro tag instantly and penetrates the mucosa layer of a GI tract, region of interest. Ex vivo animal trials are conducted to verify the feasibility of the tagging module concept. X-ray imaging is used to detect the location of the micro tag embedded in the GI tract wall. The method is successful, and radiopaque micro tags can provide valuable pre-operative position information on the infected area to facilitate further clinical procedures.

  13. The use of external electronic tags on fish: an evaluation of tag retention and tagging effects

    DEFF Research Database (Denmark)

    Jepsen, Niels; Thorstad, Eva B.; Havn, Torgeir

    2015-01-01

    External tagging of fish with electronic tags has been used for decades for a wide range of marine and freshwater species. In the early years of fish telemetry research, it was the most commonly used attachment method, but later internal implants became preferred. Recently, the number of telemetry...... unsuitable for surgical implantation, or when using tags with sensors recording the external environment. The most commonly reported problems with external tags are tissue damage, premature tag loss, and decreased swimming capacity, but the effects are highly context dependent and species specific. Reduced......, but particularly there are few studies on predation risk, social interactions, and studies distinguishing capture and handling effects from tagging effects. For PSATs, especially those that are large relative to fish size, there are particular problems with a high proportion of premature tag losses, reduced...

  14. Thermal and mechanical stability of retained austenite in aluminum-containing multiphase TRIP steels

    CERN Document Server

    Zwaag, S; Kruijver, S O; Sietsma, J

    2002-01-01

    Stability of retained austenite is the key issue to understand transformation-induced plasticity (TRIP) effect. In this work, both thermal stability and mechanical stability are investigated by thermo-magnetic as well as in situ conventional X-ray diffraction and micro synchrotron radiation diffraction measurements. The thermal stability in a 0.20C-1.52Mn-0.25Si-0.96Al (wt%) TRIP steel is studied in the temperature range between 5 and 300 K under a constant magnetic field of 5T. It is found that almost all austenite transforms thermally to martensite upon cooling to 5K and M sub s and M sub f temperatures are analyzed to be 355 and 115 K. Transformation kinetics on the fraction versus temperature relation are well described by a model based on thermodynamics. From the in situ conventional X-ray and synchrotron diffraction measurements in a 0.17C-1.46Mn-0.26Si-1.81Al (wt%) steel, the volume fraction of retained austenite is found to decrease as the strain increases according to Ludwigson and Berger relation. T...

  15. Analysis and functional annotation of expressed sequence tags (ESTs from multiple tissues of oil palm (Elaeis guineensis Jacq.

    Directory of Open Access Journals (Sweden)

    Lee Weng-Wah

    2007-10-01

    Full Text Available Abstract Background Oil palm is the second largest source of edible oil which contributes to approximately 20% of the world's production of oils and fats. In order to understand the molecular biology involved in in vitro propagation, flowering, efficient utilization of nitrogen sources and root diseases, we have initiated an expressed sequence tag (EST analysis on oil palm. Results In this study, six cDNA libraries from oil palm zygotic embryos, suspension cells, shoot apical meristems, young flowers, mature flowers and roots, were constructed. We have generated a total of 14537 expressed sequence tags (ESTs from these libraries, from which 6464 tentative unique contigs (TUCs and 2129 singletons were obtained. Approximately 6008 of these tentative unique genes (TUGs have significant matches to the non-redundant protein database, from which 2361 were assigned to one or more Gene Ontology categories. Predominant transcripts and differentially expressed genes were identified in multiple oil palm tissues. Homologues of genes involved in many aspects of flower development were also identified among the EST collection, such as CONSTANS-like, AGAMOUS-like (AGL2, AGL20, LFY-like, SQUAMOSA, SQUAMOSA binding protein (SBP etc. Majority of them are the first representatives in oil palm, providing opportunities to explore the cause of epigenetic homeotic flowering abnormality in oil palm, given the importance of flowering in fruit production. The transcript levels of two flowering-related genes, EgSBP and EgSEP were analysed in the flower tissues of various developmental stages. Gene homologues for enzymes involved in oil biosynthesis, utilization of nitrogen sources, and scavenging of oxygen radicals, were also uncovered among the oil palm ESTs. Conclusion The EST sequences generated will allow comparative genomic studies between oil palm and other monocotyledonous and dicotyledonous plants, development of gene-targeted markers for the reference genetic map

  16. Box-Behnken experimental design for investigation of stability and thermal conductivity of TiO{sub 2} nanofluids

    Energy Technology Data Exchange (ETDEWEB)

    Lotfizadeh Dehkordi, Babak, E-mail: babakld@siswa.um.edu.my; Ghadimi, Azadeh; Metselaar, Henk S. C., E-mail: h.metselaar@um.edu.my [University of Malaya, Department of Mechanical Engineering, Faculty of Engineering (Malaysia)

    2013-01-15

    The aim of this study is to investigate the effect of ultrasonication on the stability and thermal conductivity of TiO{sub 2} water nanofluids. A UV-Vis spectrophotometer was employed to determine the relative stability of nanofluids. Response surface methodology based on the Box-Behnken design was implemented to investigate the influence of power of sonication (20-80 %), time of sonication (2-20 min), and volume concentration (0.1-1 vol%) of nanofluids as the independent variables. Second-order polynomial equations were established to predict the responses, thermal conductivity, and stability of nanofluids with the intervals of 1 week and 1 month. The significance of the models was tested by means of analysis of variance (ANOVA). The optimum stability and thermal conductivity of TiO{sub 2} nanofluids with various sonication power and time at volume concentrations of 0.1, 0.55, and 1 % were studied. In addition, a correlation between the stability and thermal conductivity enhancement was derived in this study. The results revealed that, at low concentrations, nanofluids would become stable by low power and short period of sonication; however, no enhancement was observed in the thermal conductivity. Conversely, at high concentrations, stability and high thermal conductivity of nanofluids coincided at 1 vol%.

  17. Thermal stability of atom configurations around Er atoms doped in InP by OMVPE

    International Nuclear Information System (INIS)

    Ofuchi, Hironori; Ito, Takashi; Kawamoto, Takeshi; Tabuchi, Masao; Fujiwara, Yasufumi; Takeda, Yoshikazu

    1999-01-01

    It has been found that there is a threshold growth temperature between 550 deg C and 580 deg C for the change of local structure around Er atoms in InP doped Er atoms grown by organometallic vapor phase epitaxy (OMVPE). To understand whether the structure change is induced at the growing surface or during the growth as an in situ annealing, the thermal stability of the local structures around the Er atoms doped in InP by the OMVPE at 530 deg C has been investigated by the extended X-ray absorption fine structure (EXAFS). The EXAFS analysis revealed that the local structure around the Er atoms, which existed substitutionally on In sites in the InP lattice, was stable against the post-growth annealing even for 1 h at 650 deg C. Therefore, it is concluded that the local structures are formed on the growth front, and not in the volume of InP by thermal annealing during or after the growth. (author)

  18. Thermal stability of liquid antioxidative extracts from pomegranate peel

    Science.gov (United States)

    This research was carried out to assess the potential of using the natural antioxidants in pomegranate peel extracts as replacement for synthetic antioxidants. As a result the thermal stability of pomegranate peel extract products during sterilization and storage, and its effect on industrial, color...

  19. Population structure of pigs determined by single nucleotide polymorphisms observed in assembled expressed sequence tags.

    Science.gov (United States)

    Matsumoto, Toshimi; Okumura, Naohiko; Uenishi, Hirohide; Hayashi, Takeshi; Hamasima, Noriyuki; Awata, Takashi

    2012-01-01

    We have collected more than 190000 porcine expressed sequence tags (ESTs) from full-length complementary DNA (cDNA) libraries and identified more than 2800 single nucleotide polymorphisms (SNPs). In this study, we tentatively chose 222 SNPs observed in assembled ESTs to study pigs of different breeds; 104 were selected by comparing the cDNA sequences of a Meishan pig and samples of three-way cross pigs (Landrace, Large White, and Duroc: LWD), and 118 were selected from LWD samples. To evaluate the genetic variation between the chosen SNPs from pig breeds, we determined the genotypes for 192 pig samples (11 pig groups) from our DNA reference panel with matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Of the 222 reference SNPs, 186 were successfully genotyped. A neighbor-joining tree showed that the pig groups were classified into two large clusters, namely, Euro-American and East Asian pig populations. F-statistics and the analysis of molecular variance of Euro-American pig groups revealed that approximately 25% of the genetic variations occurred because of intergroup differences. As the F(IS) values were less than the F(ST) values(,) the clustering, based on the Bayesian inference, implied that there was strong genetic differentiation among pig groups and less divergence within the groups in our samples. © 2011 The Authors. Animal Science Journal © 2011 Japanese Society of Animal Science.

  20. Thermal stability and modeling of lithium ion batteries

    Science.gov (United States)

    Botte, Gerardine Gabriela

    2000-10-01

    First-principles mathematical models were developed to examine the effect of the lithium-lithium ion interactions inside the anode particles on the performance of a lithium foil cell. Two different models were developed: the chemical potential model (CPM) that includes the lithium-lithium ion interactions inside the anode particles and the diffusion model (DIM) that does not include the interactions. Significant differences in the thermal and electrochemical performance of the cell were observed between the two approaches. The temperature of the cell predicted by the DFM is higher than the one predicted by the CPM at a given capacity. The discharge time of the cell predicted by the DFM is shorter than the one predicted by the CPM. The results indicate that the cell needs to be modeled using the CPM approach especially at high discharge rates. An evaluation of the numerical techniques, control volume formulation (CVF) and finite difference method (FDM), used for the models was performed. It is shown that the truncation error is the same for both methods when the boundary conditions are of the Dirichlet type, the system of equations are linear and represented in Cartesian coordinates. A new technique to analyze the accuracy of the methods is presented. The only disadvantage of the FDM is that it failed to conserve mass for a small number of nodes when both boundary conditions include a derivative term whereas the CVF did conserve mass for these cases. However, for a large number of nodes the FDM provides mass conservation. It is important to note that the CVF has only (DeltaX) order of accuracy for a Neumann type boundary condition whereas the FDM has (DeltaX) 2 order. The second topic of this dissertation presents a study of the thermal stability of LiPF6 EC:EMC electrolyte for lithium ion batteries. A differential scanning calorimeter (DSC) was used to perform the study of the electrolyte. For first time, the effect of different variables on its thermal stability

  1. Directed supramolecular surface assembly of SNAP-tag fusion proteins

    NARCIS (Netherlands)

    Uhlenheuer, D.A.; Wasserberg, D.; Haase, C.; Nguyen, H.; Schenkel, J.H.; Huskens, J.; Ravoo, B.J.; Jonkheijm, P.; Brunsveld, L.

    2012-01-01

    Supramolecular assembly of proteins on surfaces and vesicles was investigated by site-selective incorporation of a supramolecular guest element on proteins. Fluorescent proteins were site-selectively labeled with bisadamantane by SNAP-tag technology. The assembly of the bisadamantane functionalized

  2. Directed Supramolecular Surface Assembly of SNAP-tag Fusion Proteins

    NARCIS (Netherlands)

    Uhlenheuer, D.A.; Wasserberg, D.; Haase, C.; Nguyen, Hoang D.; Schenkel, J.H.; Huskens, Jurriaan; Ravoo, B.J.; Jonkheijm, Pascal; Brunsveld, Luc

    2012-01-01

    Supramolecular assembly of proteins on surfaces and vesicles was investigated by site-selective incorporation of a supramolecular guest element on proteins. Fluorescent proteins were site-selectively labeled with bisadamantane by SNAP-tag technology. The assembly of the bisadamantane functionalized

  3. High-quality Thermodynamic Data on the Stability Changes of Proteins Upon Single-site Mutations

    Energy Technology Data Exchange (ETDEWEB)

    Pucci, Fabrizio, E-mail: fapucci@ulb.ac.be; Bourgeas, Raphaël, E-mail: rbourgeas@ulb.ac.be; Rooman, Marianne, E-mail: mrooman@ulb.ac.be [Department of BioModeling, BioInformatics and BioProcesses, Université Libre de Bruxelles, CP 165/61, Roosevelt Avenue 50, 1050 Brussels, Belgium and Interuniversity Institute of Bioinformatics in Brussels, CP 263, Triumph Bld, 1050 Brussels (Belgium)

    2016-06-15

    We have set up and manually curated a dataset containing experimental information on the impact of amino acid substitutions in a protein on its thermal stability. It consists of a repository of experimentally measured melting temperatures (T{sub m}) and their changes upon point mutations (ΔT{sub m}) for proteins having a well-resolved x-ray structure. This high-quality dataset is designed for being used for the training or benchmarking of in silico thermal stability prediction methods. It also reports other experimentally measured thermodynamic quantities when available, i.e., the folding enthalpy (ΔH) and heat capacity (ΔC{sub P}) of the wild type proteins and their changes upon mutations (ΔΔH and ΔΔC{sub P}), as well as the change in folding free energy (ΔΔG) at a reference temperature. These data are analyzed in view of improving our insights into the correlation between thermal and thermodynamic stabilities, the asymmetry between the number of stabilizing and destabilizing mutations, and the difference in stabilization potential of thermostable versus mesostable proteins.

  4. Billfish Tagging

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The SWFSC's constituent-based Billfish Tagging Program began in 1963 and since that time has provided conventional spaghetti type tags and tagging supplies to...

  5. APPLICABILITY ANALYSIS OF THE PHASE CORRELATION ALGORITHM FOR STABILIZATION OF VIDEO FRAMES SEQUENCES FOR CAPILLARY BLOOD FLOW

    Directory of Open Access Journals (Sweden)

    K. A. Karimov

    2016-05-01

    Full Text Available Videocapillaroscopy is a convenient and non-invasive method of blood flow parameters recovery in the capillaries. Capillaries position can vary at recorded video sequences due to the registration features of capillary blood flow. Stabilization algorithm of video capillary blood flow based on phase correlation is proposed and researched. This algorithm is compared to the known algorithms of video frames stabilization with full-frame superposition and with key points. Programs, based on discussed algorithms, are compared under processing the experimentally recorded video sequences of human capillaries and under processing of computer-simulated sequences of video frames with the specified offset. The full-frame superposition algorithm provides high quality of stabilization; however, the program based on this algorithm requires significant computational resources. Software implementation of the algorithm based on the detection of the key points is characterized by good performance, but provides low quality of stabilization for video sequences capillary blood flow. Algorithm based on phase correlation method provides high quality of stabilization and program realization of this algorithm requires minimal computational resources. It is shown that the phase correlation algorithm is the most useful for stabilization of video sequences for capillaries blood flow. Obtained findings can be used in the software for biomedical diagnostics.

  6. Endoprotease profiling with double-tagged peptide substrates: a new diagnostic approach in oncology.

    Science.gov (United States)

    Peccerella, Teresa; Lukan, Nadine; Hofheinz, Ralf; Schadendorf, Dirk; Kostrezewa, Markus; Neumaier, Michael; Findeisen, Peter

    2010-02-01

    The measurement of disease-related proteolytic activity in complex biological matrices like serum is of emerging interest to improve the diagnosis of malignant diseases. We developed a mass spectrometry (MS)-based functional proteomic profiling approach that tracks degradation of artificial endoprotease substrates in serum specimens. The synthetic reporter peptides that are cleaved by tumor-associated endopeptidases were systematically optimized with regard to flanking affinity tags, linkers, and stabilizing elements. Serum specimens were incubated with reporter peptides under standardized conditions and the peptides subsequently extracted with affinity chromatography before MS. In a pilot study an optimized reporter peptide with the cleavage motif WKPYDAADL was added to serum specimens from colorectal tumor patients (n = 50) and healthy controls (n = 50). This reporter peptide comprised a known cleavage site for the cysteine-endopeptidase "cancer procoagulant." Serial affinity chromatography using biotin- and 6xHis tags was superior to the single affinity enrichment using only 6xHis tags. Furthermore, protease-resistant stop elements ensured signal accumulation after prolonged incubation. In contrast, signals from reporter peptides without stop elements vanished completely after prolonged incubation owing to their total degradation. Reporter-peptide spiking showed good reproducibility, and the difference in proteolytic activity between serum specimens from cancer patients and controls was highly significant (P < 0.001). The introduction of a few structural key elements (affinity tags, linkers, d-amino acids) into synthetic reporter peptides increases the diagnostic sensitivity for MS-based protease profiling of serum specimens. This new approach might lead to functional MS-based protease profiling for improved disease classification.

  7. Thermal Degradation Mechanism of a Thermostable Polyester Stabilized with an Open-Cage Oligomeric Silsesquioxane

    Directory of Open Access Journals (Sweden)

    Yolanda Bautista

    2017-12-01

    Full Text Available A polyester composite was prepared through the polymerization of an unsaturated ester resin with styrene and an open-cage oligomeric silsesquioxane with methacrylate groups. The effect of the open-cage oligomeric silsesquioxane on the thermal stability of the thermostable polyester was studied using both thermogravimetric analysis and differential thermal analysis. The results showed that the methacryl oligomeric silsesquioxane improved the thermal stability of the polyester. The decomposition mechanism of the polyester/oligomer silsesquioxane composite was proposed by Fourier transform infrared spectroscopy (FTIR analysis of the volatiles.

  8. Engineered disulfide bonds increase active-site local stability and reduce catalytic activity of a cold-adapted alkaline phosphatase.

    Science.gov (United States)

    Asgeirsson, Bjarni; Adalbjörnsson, Björn Vidar; Gylfason, Gudjón Andri

    2007-06-01

    Alkaline phosphatase is an extracellular enzyme that is membrane-bound in eukaryotes but resides in the periplasmic space of bacteria. It normally carries four cysteine residues that form two disulfide bonds, for instance in the APs of Escherichia coli and vertebrates. An AP variant from a Vibrio sp. has only one cysteine residue. This cysteine is second next to the nucleophilic serine in the active site. We have individually modified seven residues to cysteine that are on two loops predicted to be within a 5 A radius. Four of them formed a disulfide bond to the endogenous cysteine. Thermal stability was monitored by circular dichroism and activity measurements. Global stability was similar to the wild-type enzyme. However, a significant increase in heat-stability was observed for the disulfide-containing variants using activity as a measure, together with a large reduction in catalytic rates (k(cat)) and a general decrease in Km values. The results suggest that a high degree of mobility near the active site and in the helix carrying the endogenous cysteine is essential for full catalytic efficiency in the cold-adapted AP.

  9. Thermal stability and structural characteristics of PTHF–Mmt organophile nanocomposite

    Directory of Open Access Journals (Sweden)

    Youcef Hattab

    2015-05-01

    The objective of this study is to use organophilized montmorillonites in the presence of monomer tetrahydrofuran to obtain polytétrahydrofuran montmorillonites (PTHF–Mmt of composites by polymerization in situ. The organophilisation of the Mmt is formed by active cationic surface. The obtained results show an increase in the distance inside the reticular in the diffractograms of X-rays (DRX and the appearance of absorption bands of the characteristics of polytétrahydrofuran on the spectra of infrared spectroscopy (IR, which indicate pre-polymerization of tetrahydrofuran in the galleries of clay and, therefore, the obtaining of a nanocomposite. We have also studied the thermal stability of the samples by differential analysis calorimetric (DSC analysis, and we can conclude that the nanocomposites are stabilized thermally by the presence of clay in the matrix.

  10. Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags

    DEFF Research Database (Denmark)

    de Souza, S J; Camargo, A A; Briones, M R

    2000-01-01

    Transcribed sequences in the human genome can be identified with confidence only by alignment with sequences derived from cDNAs synthesized from naturally occurring mRNAs. We constructed a set of 250,000 cDNAs that represent partial expressed gene sequences and that are biased toward the central ...

  11. Thermal stability of poly(3-hydroxybutyrate)/vegetable fiber composites

    Science.gov (United States)

    Cipriano, Pâmela Bento; de Sá, Mayelli Dantas; Andrade, André L. Simões; de Carvalho, Laura Hecker; Canedo, Eduardo Luis

    2015-05-01

    The present work deals with the thermal stability during and after processing of composites of poly(3-hydroxybutyrate) (PHB) - a fully biodegradable semi-crystalline thermoplastic obtained from renewable resources through low-impact biotechnological process, biocompatible and non-toxic - and vegetable fiber from the fruit (coconut) of babassu palm tree. PHB/babassu composites with 0, 5, 10 and 20% w/w load were prepared in a laboratory internal mixer. Two fractions of the mesocarp of babassu with different particle sizes were compounded with PHB and test specimens molded by compression. The effect of loading level and processing conditions on torque, temperature and mechanical energy dissipation were studied using a new engineering model. It was found that PHB degrades during processing at temperatures slightly above the melting point. To minimize thermal degradation stabilizer and chain extender additives were incorporated, with mixed results. These findings were confirmed by the dependence of the melt flow rate on the processing temperature.

  12. Thermal Stabilization of Enzymes Immobilized within Carbon Paste Electrodes.

    Science.gov (United States)

    Wang, J; Liu, J; Cepra, G

    1997-08-01

    In this note we report on the remarkable thermal stabilization of enzymes immobilized in carbon paste electrodes. Amperometric biosensors are shown for the first time to withstand a prolonged high-temperature (>50 °C) stress. Nearly full activity of glucose oxidase is retained over periods of up to 4 months of thermal stress at 60-80 °C. Dramatic improvements in the thermostability are observed for polyphenol oxidase, lactate oxidase, alcohol oxidase, horseradish peroxidase, and amino acid oxidase. Such resistance to heat-induced denaturation is attributed to the conformational rigidity of these biocatalysts within the highly hydrophobic (mineral oil or silicone grease) pasting liquid. While no chemical stabilizer is needed for attaining such protective action, it appears that low humidity (i.e., low water content) is essential for minimizing the protein mobility. Besides their implications for electrochemical biosensors, such observations should lead to a new generation of thermoresistant enzyme reactors based on nonpolar semisolid supports.

  13. On site DNA barcoding by nanopore sequencing.

    Directory of Open Access Journals (Sweden)

    Michele Menegon

    Full Text Available Biodiversity research is becoming increasingly dependent on genomics, which allows the unprecedented digitization and understanding of the planet's biological heritage. The use of genetic markers i.e. DNA barcoding, has proved to be a powerful tool in species identification. However, full exploitation of this approach is hampered by the high sequencing costs and the absence of equipped facilities in biodiversity-rich countries. In the present work, we developed a portable sequencing laboratory based on the portable DNA sequencer from Oxford Nanopore Technologies, the MinION. Complementary laboratory equipment and reagents were selected to be used in remote and tough environmental conditions. The performance of the MinION sequencer and the portable laboratory was tested for DNA barcoding in a mimicking tropical environment, as well as in a remote rainforest of Tanzania lacking electricity. Despite the relatively high sequencing error-rate of the MinION, the development of a suitable pipeline for data analysis allowed the accurate identification of different species of vertebrates including amphibians, reptiles and mammals. In situ sequencing of a wild frog allowed us to rapidly identify the species captured, thus confirming that effective DNA barcoding in the field is possible. These results open new perspectives for real-time-on-site DNA sequencing thus potentially increasing opportunities for the understanding of biodiversity in areas lacking conventional laboratory facilities.

  14. Thermal cycling behaviour and thermal stability of uranium-molybdenum alloys of low molybdenum content

    International Nuclear Information System (INIS)

    Decours, J.; Fabrique, B.; Peault, O.

    1963-01-01

    We have studied the behaviour during thermal cycling of as-cast U-Mo alloys whose molybdenum content varies from 0.5 to 3 per cent; results are given concerning grain stability during extended heat treatments and the effect of treatments combining protracted heating with thermal cycling. The thermal cycling treatments were carried out at 550, 575, 600 and 625 deg C for 1000 cycles; the protracted heating experiments were done at 550, 575, 600 and 625 deg C for 2000 hours (4000 hrs at 625 deg C). The 0.5 per cent alloy resists much better to the thermal cycling than does the non-alloyed uranium. This resistance is, however, much lower than that of alloys containing over l per cent, even at 550 deg C it improves after a heat treatment for grain-refining. Alloys of over 1.1 per cent have a very good resistance to a cycling treatment even at 625 deg C, and this behaviour improves with increasing concentrations up to 3 per cent. An increase in the temperature up to the γ-phase has few disadvantages provided that it is followed by rapid cooling (50 to 100 deg C/min). The α grain is fine, the γ-phase is of the modular form, and the behaviour during a thermal cycling treatment is satisfactory. If this cooling is slow (15 deg /hr) the α-grain is coarse and cycling treatment behaviour is identical to that of the 0.5 per cent alloy. The protracted heat treatments showed that the α-grain exhibits satisfactory stability after 2000 hours at 575, 600 and 625 deg C, and after 4000 hours at 625 deg C. A heat cycling treatment carried out after these tests affects only very little the behaviour of these alloys during cycling. (authors) [fr

  15. Sub-wavelength plasmonic readout for direct linear analysis of optically tagged DNA

    Science.gov (United States)

    Varsanik, Jonathan; Teynor, William; LeBlanc, John; Clark, Heather; Krogmeier, Jeffrey; Yang, Tian; Crozier, Kenneth; Bernstein, Jonathan

    2010-02-01

    This work describes the development and fabrication of a novel nanofluidic flow-through sensing chip that utilizes a plasmonic resonator to excite fluorescent tags with sub-wavelength resolution. We cover the design of the microfluidic chip and simulation of the plasmonic resonator using Finite Difference Time Domain (FDTD) software. The fabrication methods are presented, with testing procedures and preliminary results. This research is aimed at improving the resolution limits of the Direct Linear Analysis (DLA) technique developed by US Genomics [1]. In DLA, intercalating dyes which tag a specific 8 base-pair sequence are inserted in a DNA sample. This sample is pumped though a nano-fluidic channel, where it is stretched into a linear geometry and interrogated with light which excites the fluorescent tags. The resulting sequence of optical pulses produces a characteristic "fingerprint" of the sample which uniquely identifies any sample of DNA. Plasmonic confinement of light to a 100 nm wide metallic nano-stripe enables resolution of a higher tag density compared to free space optics. Prototype devices have been fabricated and are being tested with fluorophore solutions and tagged DNA. Preliminary results show evanescent coupling to the plasmonic resonator is occurring with 0.1 micron resolution, however light scattering limits the S/N of the detector. Two methods to reduce scattered light are presented: index matching and curved waveguides.

  16. Metal ion-specific thermal stability of bacterial S-Layers

    Energy Technology Data Exchange (ETDEWEB)

    Drobot, Bjoern; Raff, Johannes [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). Div. Biogeochemistry; Fahmy, Karim [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). Div. Biophysics

    2016-07-01

    Many bacteria are covered by a surface layer (S-layer), i.e., a para-crystalline two-dimensional array of proteins which control cell shape, act as molecular sieves and have potential applications as radionuclide-binding material for bioremediation of polluted areas. Knowledge and control of the metal-dependent stability of the purified proteins is required for their technical application. Here, we have explored by differential scanning calorimetry the thermal stability of the S-layer protein slp-B53 from Lysinibacillus sphaericus, a Gram-positive bacterium isolated from a uranium mining waste pile [1].

  17. On thermal stability of cyanocomplexes of some transition metals

    International Nuclear Information System (INIS)

    Sergeeva, A.N.; Pavlenko, L.I.; Dovgej, V.V.; Zubritskaya, D.I.; Tkachenko, Zh.I.

    1981-01-01

    The experimental data on the study of thermal stability of the coordination cyanides of the composition M'sub(x)[M''(CN)sub(y)]xnHsub(2)O, where M'=K; M''=V(2,3), Mo(2,4), Re(3,5), Ru(2); x=3,4; y=6-8; n=1-3, are generalized and systematized. Three main stages of decomposition of cyanocomlexes, proceeding in argon medium at 20-900 deg, are established. Hexacyanocomplexes of Re(3), Mo(2), Ru(2), V(2) according to their increasing thermal stability can be arranged in the series: K 3 [Re(CN) 6 ] 4 [Mo(CN) 6 ] 4 [Ru(CN) 6 ] 4 [V(CN) 6 ], from which it follows that cyanocomplexes of d-metals of periods 6 and 5 are less thermally stable than similar complexes of d-metal of period 4. The decomposition of cyanides of the type M(CN) 2 in the case of ruthenium ends with the formation of free metal at 470-670 deg, for rhenium - with the formation of free metal and rhenium nitride ReN 2 at 680-700 deg, for molybdenum - molybdenum carbide Mo 2 C at > 670 deg, for vanadium - vanadium carbide VC at 705 deg [ru

  18. Discovery and mapping of a new expressed sequence tag-single nucleotide polymorphism and simple sequence repeat panel for large-scale genetic studies and breeding of Theobroma cacao L.

    Science.gov (United States)

    Allegre, Mathilde; Argout, Xavier; Boccara, Michel; Fouet, Olivier; Roguet, Yolande; Bérard, Aurélie; Thévenin, Jean Marc; Chauveau, Aurélie; Rivallan, Ronan; Clement, Didier; Courtois, Brigitte; Gramacho, Karina; Boland-Augé, Anne; Tahi, Mathias; Umaharan, Pathmanathan; Brunel, Dominique; Lanaud, Claire

    2012-01-01

    Theobroma cacao is an economically important tree of several tropical countries. Its genetic improvement is essential to provide protection against major diseases and improve chocolate quality. We discovered and mapped new expressed sequence tag-single nucleotide polymorphism (EST-SNP) and simple sequence repeat (SSR) markers and constructed a high-density genetic map. By screening 149 650 ESTs, 5246 SNPs were detected in silico, of which 1536 corresponded to genes with a putative function, while 851 had a clear polymorphic pattern across a collection of genetic resources. In addition, 409 new SSR markers were detected on the Criollo genome. Lastly, 681 new EST-SNPs and 163 new SSRs were added to the pre-existing 418 co-dominant markers to construct a large consensus genetic map. This high-density map and the set of new genetic markers identified in this study are a milestone in cocoa genomics and for marker-assisted breeding. The data are available at http://tropgenedb.cirad.fr. PMID:22210604

  19. Extracting Tag Hierarchies

    Science.gov (United States)

    Tibély, Gergely; Pollner, Péter; Vicsek, Tamás; Palla, Gergely

    2013-01-01

    Tagging items with descriptive annotations or keywords is a very natural way to compress and highlight information about the properties of the given entity. Over the years several methods have been proposed for extracting a hierarchy between the tags for systems with a "flat", egalitarian organization of the tags, which is very common when the tags correspond to free words given by numerous independent people. Here we present a complete framework for automated tag hierarchy extraction based on tag occurrence statistics. Along with proposing new algorithms, we are also introducing different quality measures enabling the detailed comparison of competing approaches from different aspects. Furthermore, we set up a synthetic, computer generated benchmark providing a versatile tool for testing, with a couple of tunable parameters capable of generating a wide range of test beds. Beside the computer generated input we also use real data in our studies, including a biological example with a pre-defined hierarchy between the tags. The encouraging similarity between the pre-defined and reconstructed hierarchy, as well as the seemingly meaningful hierarchies obtained for other real systems indicate that tag hierarchy extraction is a very promising direction for further research with a great potential for practical applications. Tags have become very prevalent nowadays in various online platforms ranging from blogs through scientific publications to protein databases. Furthermore, tagging systems dedicated for voluntary tagging of photos, films, books, etc. with free words are also becoming popular. The emerging large collections of tags associated with different objects are often referred to as folksonomies, highlighting their collaborative origin and the “flat” organization of the tags opposed to traditional hierarchical categorization. Adding a tag hierarchy corresponding to a given folksonomy can very effectively help narrowing or broadening the scope of search

  20. Extracting tag hierarchies.

    Directory of Open Access Journals (Sweden)

    Gergely Tibély

    Full Text Available Tagging items with descriptive annotations or keywords is a very natural way to compress and highlight information about the properties of the given entity. Over the years several methods have been proposed for extracting a hierarchy between the tags for systems with a "flat", egalitarian organization of the tags, which is very common when the tags correspond to free words given by numerous independent people. Here we present a complete framework for automated tag hierarchy extraction based on tag occurrence statistics. Along with proposing new algorithms, we are also introducing different quality measures enabling the detailed comparison of competing approaches from different aspects. Furthermore, we set up a synthetic, computer generated benchmark providing a versatile tool for testing, with a couple of tunable parameters capable of generating a wide range of test beds. Beside the computer generated input we also use real data in our studies, including a biological example with a pre-defined hierarchy between the tags. The encouraging similarity between the pre-defined and reconstructed hierarchy, as well as the seemingly meaningful hierarchies obtained for other real systems indicate that tag hierarchy extraction is a very promising direction for further research with a great potential for practical applications. Tags have become very prevalent nowadays in various online platforms ranging from blogs through scientific publications to protein databases. Furthermore, tagging systems dedicated for voluntary tagging of photos, films, books, etc. with free words are also becoming popular. The emerging large collections of tags associated with different objects are often referred to as folksonomies, highlighting their collaborative origin and the "flat" organization of the tags opposed to traditional hierarchical categorization. Adding a tag hierarchy corresponding to a given folksonomy can very effectively help narrowing or broadening the scope of

  1. Extracting tag hierarchies.

    Science.gov (United States)

    Tibély, Gergely; Pollner, Péter; Vicsek, Tamás; Palla, Gergely

    2013-01-01

    Tagging items with descriptive annotations or keywords is a very natural way to compress and highlight information about the properties of the given entity. Over the years several methods have been proposed for extracting a hierarchy between the tags for systems with a "flat", egalitarian organization of the tags, which is very common when the tags correspond to free words given by numerous independent people. Here we present a complete framework for automated tag hierarchy extraction based on tag occurrence statistics. Along with proposing new algorithms, we are also introducing different quality measures enabling the detailed comparison of competing approaches from different aspects. Furthermore, we set up a synthetic, computer generated benchmark providing a versatile tool for testing, with a couple of tunable parameters capable of generating a wide range of test beds. Beside the computer generated input we also use real data in our studies, including a biological example with a pre-defined hierarchy between the tags. The encouraging similarity between the pre-defined and reconstructed hierarchy, as well as the seemingly meaningful hierarchies obtained for other real systems indicate that tag hierarchy extraction is a very promising direction for further research with a great potential for practical applications. Tags have become very prevalent nowadays in various online platforms ranging from blogs through scientific publications to protein databases. Furthermore, tagging systems dedicated for voluntary tagging of photos, films, books, etc. with free words are also becoming popular. The emerging large collections of tags associated with different objects are often referred to as folksonomies, highlighting their collaborative origin and the "flat" organization of the tags opposed to traditional hierarchical categorization. Adding a tag hierarchy corresponding to a given folksonomy can very effectively help narrowing or broadening the scope of search. Moreover

  2. Thermal stability and thermal conductivity of phosphorene in phosphorene/graphene van der Waals heterostructures.

    Science.gov (United States)

    Pei, Qing-Xiang; Zhang, Xiaoliang; Ding, Zhiwei; Zhang, Ying-Yan; Zhang, Yong-Wei

    2017-07-14

    Phosphorene, a new two-dimensional (2D) semiconducting material, has attracted tremendous attention recently. However, its structural instability under ambient conditions poses a great challenge to its practical applications. A possible solution for this problem is to encapsulate phosphorene with more stable 2D materials, such as graphene, forming van der Waals heterostructures. In this study, using molecular dynamics simulations, we show that the thermal stability of phosphorene in phosphorene/graphene heterostructures can be enhanced significantly. By sandwiching phosphorene between two graphene sheets, its thermally stable temperature is increased by 150 K. We further study the thermal transport properties of phosphorene and find surprisingly that the in-plane thermal conductivity of phosphorene in phosphorene/graphene heterostructures is much higher than that of the free-standing one, with a net increase of 20-60%. This surprising increase in thermal conductivity arises from the increase in phonon group velocity and the extremely strong phonon coupling between phosphorene and the graphene substrate. Our findings have an important meaning for the practical applications of phosphorene in nanodevices.

  3. Improved thermal stability and wettability behavior of thermoplastic polyurethane / barium metaborate composites

    International Nuclear Information System (INIS)

    Baştürka, Emre; Madakbaş, Seyfullah; Kahraman, Memet Vezir

    2016-01-01

    In this paper, it was targeted to the enhance thermal stability and wettability behavior of thermoplastic polyurethane (TPU) by adding barium metaborate. TPU-Barium metaborate composites were prepared by adding various proportions of barium metaborate to TPU. The chemical structures of the composites were characterised by fourier transform infrared spectroscopy (FTIR) and X-ray diffraction (XRD) analysis. All prepared composites have extremely high Tg and thermal stability as determined from DSC and TGA analysis. All composite materials have the Tg ranging from 15 to 35 °C. The surface morphologies of the composites were investigated by a scanning electron microscopy. Mechanical properties of the samples were characterized with stress-strain test. Hydrophobicity of the samples was determined by the contact angle measurements. The obtained results proved that thermal, hydrophobic and mechanical properties were improved. (author)

  4. Improved thermal stability and wettability behavior of thermoplastic polyurethane / barium metaborate composites

    Energy Technology Data Exchange (ETDEWEB)

    Baştürka, Emre; Madakbaş, Seyfullah; Kahraman, Memet Vezir, E-mail: smadakbas@marmara.edu.tr [Department of Chemistry, Marmara University, Istanbul (Turkey)

    2016-03-15

    In this paper, it was targeted to the enhance thermal stability and wettability behavior of thermoplastic polyurethane (TPU) by adding barium metaborate. TPU-Barium metaborate composites were prepared by adding various proportions of barium metaborate to TPU. The chemical structures of the composites were characterised by fourier transform infrared spectroscopy (FTIR) and X-ray diffraction (XRD) analysis. All prepared composites have extremely high Tg and thermal stability as determined from DSC and TGA analysis. All composite materials have the Tg ranging from 15 to 35 °C. The surface morphologies of the composites were investigated by a scanning electron microscopy. Mechanical properties of the samples were characterized with stress-strain test. Hydrophobicity of the samples was determined by the contact angle measurements. The obtained results proved that thermal, hydrophobic and mechanical properties were improved. (author)

  5. Improving the Mechanical Performance and Thermal Stability of a PVA-Clay Nanocomposite by Electron Beam Irradiation

    Science.gov (United States)

    Shokuhi Rad, A.; Ebrahimi, D.

    2017-07-01

    The effects of electron beam irradiation and presence of clay on the mechanical properties and thermal stability of montmorillonite clay-modified polyvinyl alcohol nanocomposites were studied. By using the X-ray diffraction (XRD) and transmission electron microscopy (TEM), the microstructure of the nanocomposites was investigated. The results obtained from TEM and XRD tests showed that montmorillonite clay nanoparticles were located in the polyvinyl alcohol phase. The XRD analysis confirmed the formation of an exfoliated structure in nanocomposites samples. Increasing the amount of clay to 20 wt.% increased the tensile strength and modulus of the nanocomposite. Irradiation up to an absorbed dose of 100 kGy increased its mechanical properties and thermal stability, but at higher irradiation levels, the mechanical strength and thermal stability declined. The sample with 20 wt.% of the nanofiller, exposed to 100 kGy, showed the highest mechanical strength and thermal stability.

  6. Stability of recursive out-of-sequence measurement filters: an open problem

    Science.gov (United States)

    Chen, Lingji; Moshtagh, Nima; Mehra, Raman K.

    2011-06-01

    In many applications where communication delays are present, measurements with earlier time stamps can arrive out-of-sequence, i.e., after state estimates have been obtained for the current time instant. To incorporate such an Out-Of-Sequence Measurement (OOSM), many algorithms have been proposed in the literature to obtain or approximate the optimal estimate that would have been obtained if the OOSM had arrived in-sequence. When OOSM occurs repeatedly, approximate estimations as a result of incorporating one OOSM have to serve as the basis for incorporating yet another OOSM. The question of whether the "approximation of approximation" is well behaved, i.e., whether approximation errors accumulate in a recursive setting, has not been adequately addressed in the literature. This paper draws attention to the stability question of recursive OOSM processing filters, formulates the problem in a specific setting, and presents some simulation results that suggest that such filters are indeed well-behaved. Our hope is that more research will be conducted in the future to rigorously establish stability properties of these filters.

  7. Polyethylene Glycol Based Graphene Aerogel Confined Phase Change Materials with High Thermal Stability.

    Science.gov (United States)

    Fu, Yang; Xiong, Weilai; Wang, Jianying; Li, Jinghua; Mei, Tao; Wang, Xianbao

    2018-05-01

    Polyethylene glycol (PEG) based graphene aerogel (GA) confined shaped-stabilized phase change materials (PCMs) are simply prepared by a one-step hydrothermal method. Three-dimensional GA inserted by PEG molecule chains, as a supporting material, obtained by reducing graphene oxide sheets, is used to keep their stabilized shape during a phase change process. The volume of GA is obviously expended after adding PEG, and only 9.8 wt% of GA make the composite achieve high energy efficiency without leakage during their phase change because of hydrogen bonding widely existing in the GA/PEG composites (GA-PCMs). The heat storage energy of GA-PCMs is 164.9 J/g, which is 90.2% of the phase change enthalpy of pure PEG. In addition, this composite inherits the natural thermal properties of graphene and thus shows enhanced thermal conductivity compared with pure PEG. This novel study provides an efficient way to fabricate shape-stabilized PCMs with a high content of PEG for thermal energy storage.

  8. Thermal stabilities of various rubber vulcanization cured by sulfur, peroxide and gamma radiation

    International Nuclear Information System (INIS)

    Basfar, A.A.; Shamshad Ahmed; Abdel Aziz, M.M.

    1999-01-01

    Sulfur and peroxide-cured rubber vulcanizates of NR and EPDM were obtained by blending the elastomers with fillers, antioxidants and appropriate accelerators, followed by vulcanization at 150 - 160 degree C. Blends of the same elastomers with appropriate co-agents and additives were also cured by gamma radiation at 150 and 200 kGy. A comparison of the thermal stabilities of these vulcanizates prepared by different curing techniques has been made by thermogravimetric analysis (TGA), assessed on the basis of comparison of DTG peak maxima, temperature for loss of 50% mass and actual thermal curves. The comparison reveals that the sulfur-cured vulcanizates are less thermally stable than their peroxide-cured counterparts. This may be attributed to the presence of a stronger C-C bond in case of peroxide-cured vulcanizates compared to weaker C-S sub x-C bond in case of sulfur-cured vulcanizates. However, compared to peroxide-cured vulcanizates, radiation-cured formulations demonstrated much improved thermal stability. This may originate from the existence of more uniformly distributed crosslinks and the enhanced rate of crosslink formation in the radiation process as compared to peroxide curing. In all the formulations whether sulfur, peroxide or radiation-cured, the natural rubber vulcanizates were found to be thermally much inferior to the synthetic contender, EPDM. Influence of variation of the amount of co-agent and other additives on the thermal stabilities of formulations of radiation cured NR and EPDM vulcanizates was also investigated

  9. Thermal-hydraulics stability of natural circulation BWR under startup. Flashing effects

    International Nuclear Information System (INIS)

    Hu, Rui; Kazimi, Mujid S.

    2009-01-01

    To help achieve the necessary natural circulation flow, a fairly long chimney is installed in a boiling natural circulation reactor like the ESBWR. In such systems, thermal-hydraulic stability during low pressure start-up should be examined while considering the flashing induced by the pressure drop in the channel and the chimney due to gravity head. In this work, a BWR stability analysis code in the frequency domain, named FISTAB (Flashing-Induced STability Analysis for BWR), was developed to address the issue of flashing-induced instability. A thermal-hydraulics non-homogeneous equilibrium model (NHEM) based on a drift flux formulation along with a lumped fuel dynamics model is incorporated in the work. The vapor generation rate is derived from the mixture energy conservation equation while considering the effect of flashing. The functionality of the FISTAB code was confirmed by comparison to experimental results from SIRIUS-N facility at CRIEPI, Japan. Both stationary and perturbation results agree well with the experimental results. (author)

  10. Preparation, characterization, and thermal stability of B2O3-ZrO2

    Directory of Open Access Journals (Sweden)

    Theresia Debora Simbolon

    2017-04-01

    Full Text Available Synthesis of the borate-based compound with ZrOCl2 to form B2O3-ZrO2 has been conducted. The compound was characterized by FT-IR spectrophotometer, X-ray diffraction, acidity and thermal stability test. The results showed that the FT-IR main vibration spectrum of B2O3-ZrO2 compound has appeared at wave number 401.2 cm-1 for Zr-O bonding vibration, 617.2 cm-1 for B-O-B bonding vibration and 910.4 cm-1 for B-O bonding vibration. The XRD diffraction pattern shows B2O3-ZrO2 compound has an amorphous structure. The FT-IR spectrum after saturated with ammonia and potentiometric titration indicates that the compound of B2O3-ZrO2 has acidic properties with a strong level of acidity. Thermal stability test shows that the B2O3-ZrO2 compounds have high stability on temperature with increasing crystallinity after the compound was heated at 700 °C. Keywords: B2O3-ZrO2, impregnation, thermal stability.

  11. Comparative Performance of Acoustic-tagged and PIT-tagged Juvenile Salmonids

    Energy Technology Data Exchange (ETDEWEB)

    Hockersmith, Eric E.; Brown, Richard S.; Liedtke, Theresa L.

    2008-02-01

    Numerous research tools and technologies are currently being used to evaluate fish passage and survival to determine the impacts of the Federal Columbia River Power System (FCRPS) on endangered and threatened juvenile salmonids, including PIT tags, balloon tags, hydroacoustic evaluations, radio telemetry, and acoustic telemetry. Each has advantages and disadvantages, but options are restricted in some situations because of limited capabilities of a specific technology, lack of detection capability downstream, or availability of adequate numbers of fish. However, there remains concern about the comparative effects of the tag or the tagging procedure on fish performance. The recently developed Juvenile Salmonid Acoustic Telemetry System (JSATS) acoustic transmitter is the smallest active acoustic tag currently available. The goal of this study was to determine whether fish tagged with the JSATS acoustic-telemetry tag can provide unbiased estimates of passage behavior and survival within the performance life of the tag. We conducted both field and laboratory studies to assess tag effects. For the field evaluation we released a total of 996 acoustic-tagged fish in conjunction with 21,026 PIT-tagged fish into the tailrace of Lower Granite Dam on 6 and 13 May. Travel times between release and downstream dams were not significantly different for the majority of the reaches between acoustic-tagged and PIT-tagged fish. In addition to the field evaluation, a series of laboratory experiments were conducted to determine if growth and survival of juvenile Chinook salmon surgically implanted with acoustic transmitters is different than untagged or PIT tagged juvenile Chinook salmon. Only yearling fish with integrated and non-integrated transmitters experienced mortalities, and these were low (<4.5%). Mortality among sub-yearling control and PIT-tag treatments ranged up to 7.7% while integrated and non-integrated treatments had slightly higher rates (up to 8.3% and 7

  12. Folding and activity of hybrid sequence, disulfide-stabilized peptides

    Energy Technology Data Exchange (ETDEWEB)

    Pease, J.H.B.; Storrs, R.W.; Wemmer, D.E. (Univ. of California, Berkeley (USA))

    1990-08-01

    Peptides have been synthesized that have hybrid sequences, partially derived from the bee venom peptide apamin and partially from the S peptide of ribonuclease A. The hybrid peptides were demonstrated by NMR spectroscopy to fold, forming the same disulfides and basic three-dimensional structure as native apamin, containing a {beta}-turn and an {alpha}-helix. These hybrids were active in complementing S protein, reactivating nuclease activity. In addition, the hybrid peptide was effective in inducing antibodies that cross-react with the RNase, without conjugation to a carrier protein. The stability of the folded structure of this peptide suggests that it should be possible to elicit antibodies that will react not only with a specific sequence, but also with a specific secondary structure. Hybrid sequence peptides also provide opportunities to study separately nucleation and propagation steps in formation of secondary structure. The authors show that in S peptide the {alpha}-helix does not end abruptly but rather terminates gradually over four or five residues. In general, these hybrid sequence peptides, which fold predictably because of disulfide bond formation, can provide opportunities for examining structure - function relationships for many biologically active sequences.

  13. Folding and activity of hybrid sequence, disulfide-stabilized peptides

    International Nuclear Information System (INIS)

    Pease, J.H.B.; Storrs, R.W.; Wemmer, D.E.

    1990-01-01

    Peptides have been synthesized that have hybrid sequences, partially derived from the bee venom peptide apamin and partially from the S peptide of ribonuclease A. The hybrid peptides were demonstrated by NMR spectroscopy to fold, forming the same disulfides and basic three-dimensional structure as native apamin, containing a β-turn and an α-helix. These hybrids were active in complementing S protein, reactivating nuclease activity. In addition, the hybrid peptide was effective in inducing antibodies that cross-react with the RNase, without conjugation to a carrier protein. The stability of the folded structure of this peptide suggests that it should be possible to elicit antibodies that will react not only with a specific sequence, but also with a specific secondary structure. Hybrid sequence peptides also provide opportunities to study separately nucleation and propagation steps in formation of secondary structure. The authors show that in S peptide the α-helix does not end abruptly but rather terminates gradually over four or five residues. In general, these hybrid sequence peptides, which fold predictably because of disulfide bond formation, can provide opportunities for examining structure - function relationships for many biologically active sequences

  14. The temperature dependence of thermooptical properties of magnetooptical TAG ceramics doped with silicon and titanium

    Science.gov (United States)

    Starobor, Aleksey; Palashov, Oleg

    2018-04-01

    Thermal effects in terbium aluminum garnet (TAG) ceramics (thermal lens and thermally induced depolarization) doped with silicon and titanium were investigated in temperature range of 79-293K. Samples with low dopant concentrations shows decreasing of negative thermal effects with cooling to 79 K. However for most part of samples thermal depolarization starts increasing after initial decreasing with cooling. Apparently it is connected with defects in media. Best sample (0.4 at% of Si) as pure TAG shows monotonous decreasing of thermally induced depolarization and 3.5 times Verdet constant increasing with cooling to 79 K, that leads to 1.8-times advantage over common magnetooptical media - terbium gallium garnet. It allows to provide an isolation of 30 dB at a radiation power of more than 6 kW as estimated. However, the procedure for creating ceramics samples obviously needs improvement because of the large scatter in the quality of the samples.

  15. Tagging the European eel Anguilla anguilla (L.) with coded wire tags

    DEFF Research Database (Denmark)

    Thomassen, S.; Pedersen, Michael Ingemann; Holdensgaard, G.

    2000-01-01

    The coded wire tag (CWT) system was examined as a possible tool for tagging European eels (Anguilla anguilla). Two size groups of eels (3.8 and 10.2 g) were tagged with CWTs in the dorsal musculature, Tag loss 28 days after tagging was 3.1% for the small and 0.7% for the large groups of eels...

  16. Thermal Shock Resistance of Stabilized Zirconia/Metal Coat on Polymer Matrix Composites by Thermal Spraying Process

    Science.gov (United States)

    Zhu, Ling; Huang, Wenzhi; Cheng, Haifeng; Cao, Xueqiang

    2014-12-01

    Stabilized zirconia/metal coating systems were deposited on the polymer matrix composites by a combined thermal spray process. Effects of the thicknesses of metal layers and ceramic layer on thermal shock resistance of the coating systems were investigated. According to the results of thermal shock lifetime, the coating system consisting of 20 μm Zn and 125 μm 8YSZ exhibited the best thermal shock resistance. Based on microstructure evolution, failure modes and failure mechanism of the coating systems were proposed. The main failure modes were the formation of vertical cracks and delamination in the outlayer of substrate, and the appearance of coating spallation. The residual stress, thermal stress and oxidation of substrate near the substrate/metal layer interface were responsible for coating failure, while the oxidation of substrate near the substrate/coating interface was the dominant one.

  17. Site-specific tagging proteins with a rigid, small and stable transition metal chelator, 8-hydroxyquinoline, for paramagnetic NMR analysis

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Yin; Huang, Feng [Nankai University, State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) (China); Huber, Thomas [Australian National University, Research School of Chemistry (Australia); Su, Xun-Cheng, E-mail: xunchengsu@nankai.edu.cn [Nankai University, State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) (China)

    2016-02-15

    Design of a paramagnetic metal binding motif in a protein is a valuable way for understanding the function, dynamics and interactions of a protein by paramagnetic NMR spectroscopy. Several strategies have been proposed to site-specifically tag proteins with paramagnetic lanthanide ions. Here we report a simple approach of engineering a transition metal binding motif via site-specific labelling of a protein with 2-vinyl-8-hydroxyquinoline (2V-8HQ). The protein-2V-8HQ adduct forms a stable complex with transition metal ions, Mn(II), Co(II), Ni(II), Cu(II) and Zn(II). The paramagnetic effects generated by these transition metal ions were evaluated by NMR spectroscopy. We show that 2V-8HQ is a rigid and stable transition metal binding tag. The coordination of the metal ion can be assisted by protein sidechains. More importantly, tunable paramagnetic tensors are simply obtained in an α-helix that possesses solvent exposed residues in positions i and i + 3, where i is the residue to be mutated to cysteine, i + 3 is Gln or Glu or i − 4 is His. The coordination of a sidechain carboxylate/amide or imidazole to cobalt(II) results in different structural geometries, leading to different paramagnetic tensors as shown by experimental data.

  18. Phenols and aromatic amines as thermal stabilizers in polyolefin processing

    Czech Academy of Sciences Publication Activity Database

    Pospíšil, Jan; Habicher, W. D.; Al-Malaika, S.; Zweifel, H.; Nešpůrek, Stanislav

    2001-01-01

    Roč. 176, - (2001), s. 55-63 ISSN 1022-1360. [International Conference on Polymer Modification, Degradation and Stabilization /1./. Palermo , 03.09.2000-07.09.2000] R&D Projects: GA AV ČR IAA1050901; GA MŠk ME 184; GA MŠk ME 372; GA AV ČR KSK4050111 Institutional research plan: CEZ:AV0Z4050913 Keywords : thermal stabilizers * phenols * aromatic amines Subject RIV: CD - Macromolecular Chemistry Impact factor: 0.634, year: 2001

  19. PET Imaging Stability Measurements During Simultaneous Pulsing of Aggressive MR Sequences on the SIGNA PET/MR System.

    Science.gov (United States)

    Deller, Timothy W; Khalighi, Mohammad Mehdi; Jansen, Floris P; Glover, Gary H

    2018-01-01

    The recent introduction of simultaneous whole-body PET/MR scanners has enabled new research taking advantage of the complementary information obtainable with PET and MRI. One such application is kinetic modeling, which requires high levels of PET quantitative stability. To accomplish the required PET stability levels, the PET subsystem must be sufficiently isolated from the effects of MR activity. Performance measurements have previously been published, demonstrating sufficient PET stability in the presence of MR pulsing for typical clinical use; however, PET stability during radiofrequency (RF)-intensive and gradient-intensive sequences has not previously been evaluated for a clinical whole-body scanner. In this work, PET stability of the GE SIGNA PET/MR was examined during simultaneous scanning of aggressive MR pulse sequences. Methods: PET performance tests were acquired with MR idle and during simultaneous MR pulsing. Recent system improvements mitigating RF interference and gain variation were used. A fast recovery fast spin echo MR sequence was selected for high RF power, and an echo planar imaging sequence was selected for its high heat-inducing gradients. Measurements were performed to determine PET stability under varying MR conditions using the following metrics: sensitivity, scatter fraction, contrast recovery, uniformity, count rate performance, and image quantitation. A final PET quantitative stability assessment for simultaneous PET scanning during functional MRI studies was performed with a spiral in-and-out gradient echo sequence. Results: Quantitation stability of a 68 Ge flood phantom was demonstrated within 0.34%. Normalized sensitivity was stable during simultaneous scanning within 0.3%. Scatter fraction measured with a 68 Ge line source in the scatter phantom was stable within the range of 40.4%-40.6%. Contrast recovery and uniformity were comparable for PET images acquired simultaneously with multiple MR conditions. Peak noise equivalent count

  20. Tempting to Tag : An Experimental Comparison of Four Tagging Input Mechanisms

    OpenAIRE

    Melenhorst, Mark; van Velsen, Lex

    2010-01-01

    Tagging helps achieve improved indexing and recommendation of resources (e.g., videos or pictures) in large data collections. In order to reap the benefits of tagging, people must be persuaded to label the resources they consume. This paper reports on a study in which four different tagging input mechanisms and their effect on users' motivation to tag were compared. The mechanisms consisted of a standard tag input box, a chatbot-like environment, a bookmarking mechanism, and a "tag and v...

  1. Low-Temperature Bainite: A Thermal Stability Study

    Science.gov (United States)

    Santajuana, Miguel A.; Rementeria, Rosalia; Kuntz, Matthias; Jimenez, Jose A.; Caballero, Francisca G.; Garcia-Mateo, Carlos

    2018-06-01

    The thermal stability of nanobainitic structures obtained by heat treating two different high-carbon high-silicon steels at temperatures between 200 °C and 600 °C has been investigated by means of three complementary techniques, i.e., field emission gun-scanning electron microscopy, X-ray diffraction, and high-resolution dilatometry. Three main stages have been established, each of them characterized by a distinctive microstructure. Furthermore, the nanocrystalline structure generated by the bainite reaction confers the steel with an extraordinary tempering resistance.

  2. Impact of impurity content on the sintering resistance and phase stability of dysprosia- and yttria-stabilized zirconia thermal barrier coatings

    Czech Academy of Sciences Publication Activity Database

    Curry, N.; Janikowski, W.; Pala, Zdeněk; Vilémová, Monika; Markocsan, N.

    2014-01-01

    Roč. 23, 1-2 (2014), s. 160-169 ISSN 1059-9630. [International Thermal Spray Conference (ITSC2013). Busan, 13.05.2013-15.05.2013] Institutional support: RVO:61389021 Keywords : atmospheric plasma spray (APS) * thermal and phase stability of coatings * thermal barrier coatings (TBCs) * thermal conductivity * zirconia Subject RIV: JH - Ceramics, Fire-Resistant Materials and Glass Impact factor: 1.344, year: 2014 http://link.springer.com/article/10.1007%2Fs11666-013-0014-9/fulltext.html

  3. Bounds of thermal stability of infinite cylindrical structures with non-uniform internal heat generation

    International Nuclear Information System (INIS)

    Gadalla, M.A.

    1992-01-01

    This paper presents an overview analyses of the thermal instability or thermal viability of infinite cylindrical structures with non-linear and non-uniform internal heat generation. The structure may be subjected to different and combined boundary conditions. An analytical solution is obtained for the generalized problem in spite of the non-linearity and the non-homogeneity of the source term. Four case studies with different boundary conditions are presented. The analyses show that the critical parameter for thermal stability may be though of as an altitude of surface below which the cylindrical structure will be thermally stable and performance worthy. The results also show that the bounds of thermal stability of a cylindrical structure system (solid or hollow) is eminently determined by the boundary conditions to which the system is subjected and can significantly alter the life-span of the structure

  4. Design of a Humidity Sensor Tag for Passive Wireless Applications.

    Science.gov (United States)

    Wu, Xiang; Deng, Fangming; Hao, Yong; Fu, Zhihui; Zhang, Lihua

    2015-10-07

    This paper presents a wireless humidity sensor tag for low-cost and low-power applications. The proposed humidity sensor tag, based on radio frequency identification (RFID) technology, was fabricated in a standard 0.18 μm complementary metal oxide semiconductor (CMOS) process. The top metal layer was deposited to form the interdigitated electrodes, which were then filled with polyimide as the humidity sensing layer. A two-stage rectifier adopts a dynamic bias-voltage generator to boost the effective gate-source voltage of the switches in differential-drive architecture, resulting in a flat power conversion efficiency curve. The capacitive sensor interface, based on phase-locked loop (PLL) theory, employs a simple architecture and can work with 0.5 V supply voltage. The measurement results show that humidity sensor tag achieves excellent linearity, hysteresis and stability performance. The total power-dissipation of the sensor tag is 2.5 μW, resulting in a maximum operating distance of 23 m under 4 W of radiation power of the RFID reader.

  5. Effect of stacking sequence and surface treatment on the thermal conductivity of multilayered hybrid nano-composites

    Science.gov (United States)

    Papanicolaou, G. C.; Pappa, E. J.; Portan, D. V.; Kotrotsos, A.; Kollia, E.

    2018-02-01

    The aim of the present investigation was to study the effect of both the stacking sequence and surface treatment on the thermal conductivity of multilayered hybrid nano-composites. Four types of multilayered hybrid nanocomposites were manufactured and tested: Nitinol- CNTs (carbon nanotubes)- Acrylic resin; Nitinol- Acrylic resin- CNTs; Surface treated Nitinol- CNTs- Acrylic resin and Surface treated Nitinol- Acrylic resin- CNTs. Surface treatment of Nitinol plies was realized by means of the electrochemical anodization. Surface topography of the anodized nitinol sheets was investigated through Scanning Electron Microscopy (SEM). It was found that the overall thermal response of the manufactured multilayered nano-composites was greatly influenced by both the anodization and the stacking sequence. A theoretical model for the prediction of the overall thermal conductivity has been developed considering the nature of the different layers, their stacking sequence as well as the interfacial thermal resistance. Thermal conductivity and Differential Scanning Calorimetry (DSC) measurements were conducted, to verify the predicted by the model overall thermal conductivities. In all cases, a good agreement between theoretical predictions and experimental results was found.

  6. Assessment of social values in thermal plant siting

    International Nuclear Information System (INIS)

    Anon.

    1976-01-01

    The objective of the project is to develop a method for combining social values with techno-economic data for better decision making in thermal nuclear power plant siting. Quantified technical impact data which is socially weighted will allow for the optimal choice of site/design alternatives. In this phase, a study of community leadership in energy/environment issues was conducted in a town familiar with a (nuclear) thermal power plant. Secondly, a linear composite analysis of the measurement problems associated with combining diverse scales of impacts was completed. Third, a revision of the social values instrument used in a previous phase of the study was initiated. Finally, liaison activities with utilities were undertaken. Quantification of three of the technical impact factors is currently underway

  7. The First Molecular Identification of an Olive Collection Applying Standard Simple Sequence Repeats and Novel Expressed Sequence Tag Markers.

    Science.gov (United States)

    Mousavi, Soraya; Mariotti, Roberto; Regni, Luca; Nasini, Luigi; Bufacchi, Marina; Pandolfi, Saverio; Baldoni, Luciana; Proietti, Primo

    2017-01-01

    Germplasm collections of tree crop species represent fundamental tools for conservation of diversity and key steps for its characterization and evaluation. For the olive tree, several collections were created all over the world, but only few of them have been fully characterized and molecularly identified. The olive collection of Perugia University (UNIPG), established in the years' 60, represents one of the first attempts to gather and safeguard olive diversity, keeping together cultivars from different countries. In the present study, a set of 370 olive trees previously uncharacterized was screened with 10 standard simple sequence repeats (SSRs) and nine new EST-SSR markers, to correctly and thoroughly identify all genotypes, verify their representativeness of the entire cultivated olive variation, and validate the effectiveness of new markers in comparison to standard genotyping tools. The SSR analysis revealed the presence of 59 genotypes, corresponding to 72 well known cultivars, 13 of them resulting exclusively present in this collection. The new EST-SSRs have shown values of diversity parameters quite similar to those of best standard SSRs. When compared to hundreds of Mediterranean cultivars, the UNIPG olive accessions were splitted into the three main populations (East, Center and West Mediterranean), confirming that the collection has a good representativeness of the entire olive variability. Furthermore, Bayesian analysis, performed on the 59 genotypes of the collection by the use of both sets of markers, have demonstrated their splitting into four clusters, with a well balanced membership obtained by EST respect to standard SSRs. The new OLEST ( Olea expressed sequence tags) SSR markers resulted as effective as the best standard markers. The information obtained from this study represents a high valuable tool for ex situ conservation and management of olive genetic resources, useful to build a common database from worldwide olive cultivar collections

  8. Thermal Stability of Frozen Volatiles in the North Polar Region of Mercury

    Science.gov (United States)

    Paige, David A.; Siegler, Matthew A.; Harmon, John K.; Smith, David E.; Zuber, Maria T.; Neumann, Gregory A.; Solomon, Sean C.

    2012-01-01

    Earth-based radar observations have revealed the presence on Mercury of anomalously bright, depolarizing features that appear to be localized in the permanently shadowed regions of high-latitude impact craters [1]. Observations of similar radar signatures over a range of radar wavelengths implies that they correspond to deposits that are highly transparent at radar wavelengths and extend to depths of several meters below the surface [1]. Thermal models using idealized crater topographic profiles have predicted the thermal stability of surface and subsurface water ice at these same latitudes [2]. One of the major goals of the MESSENGER mission is to characterize the nature of radar-bright craters and presumed associated frozen volatile deposits at the poles of Mercury through complementary orbital observations by a suite of instruments [3]. Here we report on an examination of the thermal stability of water ice and other frozen volatiles in the north polar region of Mercury using topographic profiles obtained by the Mercury Laser Altimeter (MLA) instrument [4] in conjunction with a three-dimensional ray-tracing thermal model previously used to study the thermal environment of polar craters on the Moon [5].

  9. Thermal conductivity of cement stabilized earth bricks reinforced with date palm fiber

    Science.gov (United States)

    Berrehail, Tahar; Zemmouri, Noureddine; Agoudjil, Boudjemaa

    2018-05-01

    Recently, some cheap materials are available and adaptable to climate seem to meet current requirements. This paper investigates the thermal and mechanical properties of cement stabilized earth bricks(CSEB) reinforced with date palm fibers (DPF). The main goal is to develop and expand the field of use of these materials in the construction sector, and investigate the possibility of new bio composite as renewable, insulating building material with low cost, made of earth and reinforced with palm wood waste. In this study, a particular interest is brought to the thermal and mechanical characteristics, which constitute a decisive character for the choice of a building material. A series of earthen samples stabilized at 5% and reinforced with DPF of various fiber weight fractions, (5%, 10%), were manufactured and compacted applying two levels compacting, (5MPa and 10MPa). Compressive strength and thermal conductivity were experimentally studied; heating capacity and diffusivity were indirectly calculated. It was found that the fibrous reinforcement proved thermal conductivity and compressive strength. it also enhanced thermal performances. Thus, the results found allow us to investigate hygrothermal behaviour and its impact on occupants comfort.

  10. Dual Mode Fluorophore-Doped Nickel Nitrilotriacetic Acid-Modified Silica Nanoparticles Combine Histidine-Tagged Protein Purification with Site-Specific Fluorophore Labeling

    OpenAIRE

    Kim, Sung Hoon; Jeyakumar, M.; Katzenellenbogen, John A.

    2007-01-01

    We present the first example of a fluorophore-doped nickel chelate surface- modified silica nanoparticle that functions in a dual mode, combining histidine-tagged protein purification with site-specific fluorophore labeling. Tetramethylrhodamine (TMR)-doped silica nanoparticles, estimated to contain 700–900 TMRs per ca. 23-nm particle, were surface modified with nitrilotriacetic acid (NTA), producing TMR-SiO2-NTA-Ni+2. Silica-embedded TMR retains very high quantum yield, is resistant to quenc...

  11. Investigation for thermal stability of U3Si2 and protection methods

    International Nuclear Information System (INIS)

    Zhang Huiying; Sun Jichang; Sun Rongxian

    1994-08-01

    The thermal stability of U 3 Si 2 in Ar, N 2 and air, and the interaction between U 3 Si 2 and Al, Zr have been investigated by thermal analysis method. According to the results of thermal analysis, protection measures for various procedures have been improved. From the practice, it shows that the protection measures can ensure the safety of production and raise the product quality as well as reduce the cost effectively

  12. Enhancement of thermal stability of silver(I) acetylacetonate by platinum(II) acetylacetonate

    Czech Academy of Sciences Publication Activity Database

    Křenek, T.; Kovářík, T.; Pola, M.; Jakubec, Ivo; Bezdička, Petr; Bastl, Zdeněk; Pokorná, Dana; Urbanová, Markéta; Galíková, Anna; Pola, Josef

    2013-01-01

    Roč. 554, FEB (2013), s. 1-7 ISSN 0040-6031 Institutional support: RVO:61388980 ; RVO:61388955 ; RVO:67985858 Keywords : thermal gravimetric analysis * differential scanning calorimetry * silver(I) acetylacetonate * platinum(II) acetylacetonate * enhancement of thermal stability Subject RIV: CA - Inorganic Chemistry; CF - Physical ; Theoretical Chemistry (UFCH-W) Impact factor: 2.105, year: 2013

  13. Cormorant predation on PIT-tagged lake fish

    DEFF Research Database (Denmark)

    Skov, Christian; Jepsen, Niels; Baktoft, Henrik

    2014-01-01

    The present study use data from recovered PIT (Passive Integrated Transponder) tags to explore species-and size-specific annual predation rates by cormorants on three common lacustrine fishes (size range 120-367 mm) in a European lake; roach (Rutilus rutilus), common bream (Abramis brama) and perch...... (Perca fluviatilis). In addition, we quantify the level of age/size truncation that cormorant predation could introduce in a population of perch, an important fish for recreational angling as well as for trophic interactions and ecosystem function in European lakes. Based on three years of PIT tagging...... of fish in Lake Viborg and subsequent recoveries of PIT tags from nearby cormorant roosting and breeding sites, we show that cormorants are major predators of roach, bream and perch within the size groups we investigated and for all species larger individuals had higher predation rates. Perch appear...

  14. Web 2.0 OLAP: From Data Cubes to Tag Clouds

    Science.gov (United States)

    Aouiche, Kamel; Lemire, Daniel; Godin, Robert

    Increasingly, business projects are ephemeral. New Business Intelligence tools must support ad-lib data sources and quick perusal. Meanwhile, tag clouds are a popular community-driven visualization technique. Hence, we investigate tag-cloud views with support for OLAP operations such as roll-ups, slices, dices, clustering, and drill-downs. As a case study, we implemented an application where users can upload data and immediately navigate through its ad hoc dimensions. To support social networking, views can be easily shared and embedded in other Web sites. Algorithmically, our tag-cloud views are approximate range top-k queries over spontaneous data cubes. We present experimental evidence that iceberg cuboids provide adequate online approximations. We benchmark several browser-oblivious tag-cloud layout optimizations.

  15. Thermal stability of homo- and copolymers of vinyl fluoride

    International Nuclear Information System (INIS)

    Raucher, D.; Levy, M.

    1979-01-01

    The thermal stability of poly(vinyl fluoride)(PVF) was studied by thermal gravimetry and mass spectrometry (TGA and TGA-MS). In low-molecular-weight polymers a two-step decomposition pattern was observed. It consisted of the dehydrofluorination to a polyene chain followed by decomposition of the resulting polyene at higher temperatures. Copolymers of vinyl fluoride-vinyl acetate (VF-VAc) and vinyl fluoride-vinyl chloride (VF-VCl) showed a simultaneous evolution of hydrofluoric acid and acetic acid and hydrofluoric acid and hydrochloric acid, respectively. This suggests that after the elimination of the weakest link a spontaneous elimination of neighboring HF molecules takes place

  16. Ionic conductivity and thermal stability of magnetron-sputtered nanocrystalline yttria-stabilized zirconia

    DEFF Research Database (Denmark)

    Sillassen, M.; Eklund, P.; Sridharan, M.

    2009-01-01

    Thermally stable, stoichiometric, cubic yttria-stabilized zirconia (YSZ) thin-film electrolytes have been synthesized by reactive pulsed dc magnetron sputtering from a Zr–Y (80/20 at. %) alloy target. Films deposited at floating potential had a texture. Single-line profile analysis of the 111 x.......5% at bias voltages of −175 and −200 V with additional incorporation of argon. The films were thermally stable; very limited grain coarsening was observed up to an annealing temperature of 800 °C. Temperature-dependent impedance spectroscopy analysis of the YSZ films with Ag electrodes showed that the in......-plane ionic conductivity was within one order of magnitude higher in films deposited with substrate bias corresponding to a decrease in grain size compared to films deposited at floating potential. This suggests that there is a significant contribution to the ionic conductivity from grain boundaries...

  17. Effect of thermal protectants on the stability of bovine milk immunoglobulin G

    Energy Technology Data Exchange (ETDEWEB)

    Chen, C. C. [National Taiwan University, Taipei, Taiwan (China); Chang, H. M.

    1998-09-15

    pH stability, thermal stability, and the effect of homogenization and ultrasonic treatment on the stability of bovine milk immunoglobulin G (IgG) in model systems was studied. Separated IgG (0.02 mg/mL) was found to be unstable and susceptible to denaturation when incubated at pH 4 or 10 or thermally treated at temperature 75 degrees C. IgG in the colostrum, on the other hand, was found to be much more stable than in whey or in PBS when thermally treated at temperatures in the range of 75-100 degrees C. The residual IgC content reduced more sharply with increasing heating times, and almost no IgG content was detected when IgG in PBS (0.15 M NaCl/0.01 M phosphate buffer, pH 7.0) was heated at 95 degrees C for 15 s, whereas the corresponding residual IgG contents in whey and colostrum were found to be 42 and 59%, respectively. For IgG in PBS heated at 95 degrees C for 15 s, addition of 5% fructose or maltose displayed most remarkable protection effects by raising the residual IgG content to 31%, followed by sucrose, lactose, glucose, and galactose. However, extravagant addition ( 30%) to IgG in PBS led to a decline in residual IgG content. Addition of 0.4% glutamic acid and 2% glycine to IgG in PBS heated at 95 degrees C for 15 s also remarkably improved the residual IgG content by 13.5 and 26.7%, respectively. Glycerol and sugar alcohol, such as sorbitol, stabilized IgG during the thermal treatment.

  18. Effect of thermal protectants on the stability of bovine milk immunoglobulin G

    International Nuclear Information System (INIS)

    Chen, C.C.; Chang, H.M.

    1998-01-01

    pH stability, thermal stability, and the effect of homogenization and ultrasonic treatment on the stability of bovine milk immunoglobulin G (IgG) in model systems was studied. Separated IgG (0.02 mg/mL) was found to be unstable and susceptible to denaturation when incubated at pH 4 or 10 or thermally treated at temperature 75 degrees C. IgG in the colostrum, on the other hand, was found to be much more stable than in whey or in PBS when thermally treated at temperatures in the range of 75-100 degrees C. The residual IgC content reduced more sharply with increasing heating times, and almost no IgG content was detected when IgG in PBS (0.15 M NaCl/0.01 M phosphate buffer, pH 7.0) was heated at 95 degrees C for 15 s, whereas the corresponding residual IgG contents in whey and colostrum were found to be 42 and 59%, respectively. For IgG in PBS heated at 95 degrees C for 15 s, addition of 5% fructose or maltose displayed most remarkable protection effects by raising the residual IgG content to 31%, followed by sucrose, lactose, glucose, and galactose. However, extravagant addition ( 30%) to IgG in PBS led to a decline in residual IgG content. Addition of 0.4% glutamic acid and 2% glycine to IgG in PBS heated at 95 degrees C for 15 s also remarkably improved the residual IgG content by 13.5 and 26.7%, respectively. Glycerol and sugar alcohol, such as sorbitol, stabilized IgG during the thermal treatment

  19. 40 CFR 35.4045 - What requirements must my group meet as a TAG recipient?

    Science.gov (United States)

    2010-07-01

    ... for the purpose of participating in decision making at the Superfund site for which we provide a TAG... 40 Protection of Environment 1 2010-07-01 2010-07-01 false What requirements must my group meet as... Responsibilities As A Tag Recipient § 35.4045 What requirements must my group meet as a TAG recipient? Your group...

  20. Thermal stability and high temperature polymorphism of topochemically-prepared Dion–Jacobson triple-layered perovskites

    Energy Technology Data Exchange (ETDEWEB)

    Guertin, Stephen L.; Josepha, Elisha A.; Montasserasadi, Dariush; Wiley, John B., E-mail: jwiley@uno.edu

    2015-10-25

    The thermal stability of six Dion–Jacobson-related triple layered perovskites, ACa{sub 2}Nb{sub 3}O{sub 10} (A = H, NH{sub 4}, Li, Na, K, CuCl), was explored to 1000 °C. Each compound was produced topochemically by low-temperature (<500 °C) ion exchange from RbCa{sub 2}Nb{sub 3}O{sub 10}. The thermal behavior of the series was examined by variable temperature X-ray powder diffraction experiments in tandem with thermogravimetric analysis and differential scanning calorimetry. Five of the species were found to be low temperature/metastable phases, decomposing below 900 °C, where the stability of the series decreased with decreasing interlayer cation size. The compounds, A = Li, Na, K, exhibited high temperature polymorphism, with a completely reversible transition evident for KCa{sub 2}Nb{sub 3}O{sub 10}. - Highlights: • Thermal stability of topochemically prepared triple-layered perovskites studied. • Clear correlation seen between stability and identity of interlayer cation. • Several in ACa{sub 2}Nb{sub 3}O{sub 10} series (A = Li, Na, K) exhibit high temperature polymorphism.

  1. Thermal stability study of crystalline and novel spray-dried amorphous nilotinib hydrochloride.

    Science.gov (United States)

    Herbrink, Maikel; Vromans, Herman; Schellens, Jan; Beijnen, Jos; Nuijen, Bastiaan

    2018-01-30

    The thermal characteristics and the thermal degradation of crystalline and amorphous nilotinib hydrochloride (NH) were studied. The spray drying technique was successfully utilized for the amorphization of NH and was evaluated by spectroscopic techniques and differential scanning calorimetry (DSC). The ethanolic spray drying process yielded amorphous NH with a glass transition temperature (T g ) of 147°C. Thermal characterization of the amorphous phase was performed by heat capacity measurements using modulated DSC (mDSC). Thermal degradation was studied by thermogravimetric analysis (TGA). The derived thermodynamic properties of the amorphous NH indicate fragile behaviour and a low crystallization tendency. NH was found to be molecularly stable up to 193°C. After which, the thermal degradation displayed two phases. The values of the thermal degradation parameters were estimated using the Ozawa-Flynn-Wall and Friedman non-isothermal, model-free, isoconversional methods The results indicate the two phases to be single-step reactions. The examination of the physical stability of amorphous NH during storage and at elevated temperatures showed stability at 180°C for at least 5h and at 20-25°C/60% RH for at least 6 months. During these periods, no crystallization was observed. This study is the first to report the thermal characteristics of NH. Additionally, it is also the first to describe the full thermal analysis of a spray-dried amorphous drug. The thermal data may be used in the projection of future production processes and storage conditions of amorphous NH. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites.

    Science.gov (United States)

    Sharpe, Richard M; Koepke, Tyson; Harper, Artemus; Grimes, John; Galli, Marco; Satoh-Cruz, Mio; Kalyanaraman, Ananth; Evans, Katherine; Kramer, David; Dhingra, Amit

    2016-01-01

    High-throughput sequencing continues to produce an immense volume of information that is processed and assembled into mature sequence data. Data analysis tools are urgently needed that leverage the embedded DNA sequence polymorphisms and consequent changes to restriction sites or sequence motifs in a high-throughput manner to enable biological experimentation. CisSERS was developed as a standalone open source tool to analyze sequence datasets and provide biologists with individual or comparative genome organization information in terms of presence and frequency of patterns or motifs such as restriction enzymes. Predicted agarose gel visualization of the custom analyses results was also integrated to enhance the usefulness of the software. CisSERS offers several novel functionalities, such as handling of large and multiple datasets in parallel, multiple restriction enzyme site detection and custom motif detection features, which are seamlessly integrated with real time agarose gel visualization. Using a simple fasta-formatted file as input, CisSERS utilizes the REBASE enzyme database. Results from CisSERS enable the user to make decisions for designing genotyping by sequencing experiments, reduced representation sequencing, 3'UTR sequencing, and cleaved amplified polymorphic sequence (CAPS) molecular markers for large sample sets. CisSERS is a java based graphical user interface built around a perl backbone. Several of the applications of CisSERS including CAPS molecular marker development were successfully validated using wet-lab experimentation. Here, we present the tool CisSERS and results from in-silico and corresponding wet-lab analyses demonstrating that CisSERS is a technology platform solution that facilitates efficient data utilization in genomics and genetics studies.

  3. Influence of nano-AlN particles on thermal conductivity, thermal stability and cure behavior of cycloaliphatic epoxy/trimethacrylate system

    Directory of Open Access Journals (Sweden)

    2011-02-01

    Full Text Available We have prepared a series of nano-sized aluminium nitride (nano-AlN/cycloaliphatic epoxy/trimethacrylate (TMPTMA systems and investigated their morphology, thermal conductivity, thermal stability and curing behavior. Experimental results show that the thermal conductivity of composites increases with the nano-AlN filler content, the maximum value is up to 0.47 W/(m.K. Incorporation of a small amount of the nano-AlN filler into the epoxy/TMPTMA system improves the thermal stability. For instance, the thermal degradation temperature at 5% weight loss of nano-AlN/epoxy/TMPTMA system with only 1 wt% nano-AlN was improved by ~8ºC over the neat epoxy/TMPTMA system. The effect of nano-AlN particles on the cure behavior of epoxy/TMPTMA systems was studied by dynamic differential scanning calorimetry. The results showed that the addition of silane treated nano-AlN particles does not change the curing reaction mechanism and silane treated nano-AlN particles could bring positive effect on the processing of composite since it needs shorter pre-cure time and lower pre-temperature, meanwhile the increase of glass transition temperature of the nanocomposite improves the heat resistance.

  4. Organic transistors with high thermal stability for medical applications.

    Science.gov (United States)

    Kuribara, Kazunori; Wang, He; Uchiyama, Naoya; Fukuda, Kenjiro; Yokota, Tomoyuki; Zschieschang, Ute; Jaye, Cherno; Fischer, Daniel; Klauk, Hagen; Yamamoto, Tatsuya; Takimiya, Kazuo; Ikeda, Masaaki; Kuwabara, Hirokazu; Sekitani, Tsuyoshi; Loo, Yueh-Lin; Someya, Takao

    2012-03-06

    The excellent mechanical flexibility of organic electronic devices is expected to open up a range of new application opportunities in electronics, such as flexible displays, robotic sensors, and biological and medical electronic applications. However, one of the major remaining issues for organic devices is their instability, especially their thermal instability, because low melting temperatures and large thermal expansion coefficients of organic materials cause thermal degradation. Here we demonstrate the fabrication of flexible thin-film transistors with excellent thermal stability and their viability for biomedical sterilization processes. The organic thin-film transistors comprise a high-mobility organic semiconductor, dinaphtho[2,3-b:2',3'-f]thieno[3,2-b]thiophene, and thin gate dielectrics comprising a 2-nm-thick self-assembled monolayer and a 4-nm-thick aluminium oxide layer. The transistors exhibit a mobility of 1.2 cm(2) V(-1)s(-1) within a 2 V operation and are stable even after exposure to conditions typically used for medical sterilization.

  5. Ontologies and tag-statistics

    Science.gov (United States)

    Tibély, Gergely; Pollner, Péter; Vicsek, Tamás; Palla, Gergely

    2012-05-01

    Due to the increasing popularity of collaborative tagging systems, the research on tagged networks, hypergraphs, ontologies, folksonomies and other related concepts is becoming an important interdisciplinary area with great potential and relevance for practical applications. In most collaborative tagging systems the tagging by the users is completely ‘flat’, while in some cases they are allowed to define a shallow hierarchy for their own tags. However, usually no overall hierarchical organization of the tags is given, and one of the interesting challenges of this area is to provide an algorithm generating the ontology of the tags from the available data. In contrast, there are also other types of tagged networks available for research, where the tags are already organized into a directed acyclic graph (DAG), encapsulating the ‘is a sub-category of’ type of hierarchy between each other. In this paper, we study how this DAG affects the statistical distribution of tags on the nodes marked by the tags in various real networks. The motivation for this research was the fact that understanding the tagging based on a known hierarchy can help in revealing the hidden hierarchy of tags in collaborative tagging systems. We analyse the relation between the tag-frequency and the position of the tag in the DAG in two large sub-networks of the English Wikipedia and a protein-protein interaction network. We also study the tag co-occurrence statistics by introducing a two-dimensional (2D) tag-distance distribution preserving both the difference in the levels and the absolute distance in the DAG for the co-occurring pairs of tags. Our most interesting finding is that the local relevance of tags in the DAG (i.e. their rank or significance as characterized by, e.g., the length of the branches starting from them) is much more important than their global distance from the root. Furthermore, we also introduce a simple tagging model based on random walks on the DAG, capable of

  6. Ontologies and tag-statistics

    International Nuclear Information System (INIS)

    Tibély, Gergely; Vicsek, Tamás; Pollner, Péter; Palla, Gergely

    2012-01-01

    Due to the increasing popularity of collaborative tagging systems, the research on tagged networks, hypergraphs, ontologies, folksonomies and other related concepts is becoming an important interdisciplinary area with great potential and relevance for practical applications. In most collaborative tagging systems the tagging by the users is completely ‘flat’, while in some cases they are allowed to define a shallow hierarchy for their own tags. However, usually no overall hierarchical organization of the tags is given, and one of the interesting challenges of this area is to provide an algorithm generating the ontology of the tags from the available data. In contrast, there are also other types of tagged networks available for research, where the tags are already organized into a directed acyclic graph (DAG), encapsulating the ‘is a sub-category of’ type of hierarchy between each other. In this paper, we study how this DAG affects the statistical distribution of tags on the nodes marked by the tags in various real networks. The motivation for this research was the fact that understanding the tagging based on a known hierarchy can help in revealing the hidden hierarchy of tags in collaborative tagging systems. We analyse the relation between the tag-frequency and the position of the tag in the DAG in two large sub-networks of the English Wikipedia and a protein-protein interaction network. We also study the tag co-occurrence statistics by introducing a two-dimensional (2D) tag-distance distribution preserving both the difference in the levels and the absolute distance in the DAG for the co-occurring pairs of tags. Our most interesting finding is that the local relevance of tags in the DAG (i.e. their rank or significance as characterized by, e.g., the length of the branches starting from them) is much more important than their global distance from the root. Furthermore, we also introduce a simple tagging model based on random walks on the DAG, capable of

  7. Passive wireless tags for tongue controlled assistive technology interfaces

    Science.gov (United States)

    Rakibet, Osman O.; Horne, Robert J.; Kelly, Stephen W.

    2016-01-01

    Tongue control with low profile, passive mouth tags is demonstrated as a human–device interface by communicating values of tongue-tag separation over a wireless link. Confusion matrices are provided to demonstrate user accuracy in targeting by tongue position. Accuracy is found to increase dramatically after short training sequences with errors falling close to 1% in magnitude with zero missed targets. The rate at which users are able to learn accurate targeting with high accuracy indicates that this is an intuitive device to operate. The significance of the work is that innovative very unobtrusive, wireless tags can be used to provide intuitive human–computer interfaces based on low cost and disposable mouth mounted technology. With the development of an appropriate reading system, control of assistive devices such as computer mice or wheelchairs could be possible for tetraplegics and others who retain fine motor control capability of their tongues. The tags contain no battery and are intended to fit directly on the hard palate, detecting tongue position in the mouth with no need for tongue piercings. PMID:27222736

  8. Recent advances in thermal analysis and stability evaluation of insensitive plastic bonded explosives (PBXs)

    International Nuclear Information System (INIS)

    Yan, Qi-Long; Zeman, Svatopluk; Elbeih, Ahmed

    2012-01-01

    Highlights: ► We summarize currently used insensitive polymer based explosives and their ingredients. ► We examine the calculation methods that are suitable for kinetic evaluation of polymer based explosives. ► The calculation method for thermal stability parameters of polymer based explosives are summarized, which mainly include shelf life, explosion delay, critical temperature, thermostability threshold, 500 day cookoff temperature and approximate time to explosion. ► The polymer bases could greatly affect the thermal properties of PBXs, including their thermal stability, kinetic parameters and thermodynamic properties. ► PBXs, containing some innovative energetic fillers such as CL-20, NTO, Fox-12 and BCHMX, are only at design stage, which need more research work in the future. - Abstract: In this paper, several fundamental investigations published over the past decades with regard to the thermal analysis of polymer-based explosives (PBXs) have been briefly reviewed. A number of explosive fillers and polymer bases that were used as their main ingredients of PBXs are summarized herein. In addition, the calculation methods for their decomposition kinetics and thermal stability parameters are also introduced in detail. It was concluded that only PBXs based on HMX, RDX and TATB have been widely investigated, and that some other PBXs containing innovative fillers, such as CL-20, TNAZ, NTO and BCHMX are at the design stage. The isoconversional methods and model fitting procedures are usually used to analyze the discrete thermolysis processes of PBXs. In addition, their thermal stability parameters such as shelf life, explosion delay, critical temperature, thermostability threshold, 500-day cookoff temperature and approximate time to explosion could be calculated easily from the kinetic data.

  9. Attachment Site Cysteine Thiol pKa Is a Key Driver for Site-Dependent Stability of THIOMAB Antibody-Drug Conjugates.

    Science.gov (United States)

    Vollmar, Breanna S; Wei, Binqing; Ohri, Rachana; Zhou, Jianhui; He, Jintang; Yu, Shang-Fan; Leipold, Douglas; Cosino, Ely; Yee, Sharon; Fourie-O'Donohue, Aimee; Li, Guangmin; Phillips, Gail L; Kozak, Katherine R; Kamath, Amrita; Xu, Keyang; Lee, Genee; Lazar, Greg A; Erickson, Hans K

    2017-10-18

    The incorporation of cysteines into antibodies by mutagenesis allows for the direct conjugation of small molecules to specific sites on the antibody via disulfide bonds. The stability of the disulfide bond linkage between the small molecule and the antibody is highly dependent on the location of the engineered cysteine in either the heavy chain (HC) or the light chain (LC) of the antibody. Here, we explore the basis for this site-dependent stability. We evaluated the in vivo efficacy and pharmacokinetics of five different cysteine mutants of trastuzumab conjugated to a pyrrolobenzodiazepine (PBD) via disulfide bonds. A significant correlation was observed between disulfide stability and efficacy for the conjugates. We hypothesized that the observed site-dependent stability of the disulfide-linked conjugates could be due to differences in the attachment site cysteine thiol pK a . We measured the cysteine thiol pK a using isothermal titration calorimetry (ITC) and found that the variants with the highest thiol pK a (LC K149C and HC A140C) were found to yield the conjugates with the greatest in vivo stability. Guided by homology modeling, we identified several mutations adjacent to LC K149C that reduced the cysteine thiol pK a and, thus, decreased the in vivo stability of the disulfide-linked PBD conjugated to LC K149C. We also present results suggesting that the high thiol pK a of LC K149C is responsible for the sustained circulation stability of LC K149C TDCs utilizing a maleimide-based linker. Taken together, our results provide evidence that the site-dependent stability of cys-engineered antibody-drug conjugates may be explained by interactions between the engineered cysteine and the local protein environment that serves to modulate the side-chain thiol pK a . The influence of cysteine thiol pK a on stability and efficacy offers a new parameter for the optimization of ADCs that utilize cysteine engineering.

  10. The influence of oxygen contamination on the thermal stability and hardness of nanocrystalline Ni–W alloys

    Energy Technology Data Exchange (ETDEWEB)

    Marvel, Christopher J., E-mail: cjm312@lehigh.edu [Department of Materials Science and Engineering, Lehigh University, Bethlehem, PA 18015 (United States); Yin, Denise [Department of Materials Science and Engineering, Lehigh University, Bethlehem, PA 18015 (United States); Cantwell, Patrick R. [Department of Mechanical Engineering, Rose-Hulman Institute of Technology, Terre Haute, IN 47803 (United States); Harmer, Martin P. [Department of Materials Science and Engineering, Lehigh University, Bethlehem, PA 18015 (United States)

    2016-05-10

    Nanocrystalline Ni–W alloys are reported in the literature to be stabilized against high temperature grain growth by W-segregation at the grain boundaries. However, alternative thermal stability mechanisms have been insufficiently investigated, especially in the presence of impurities. This study explored the influence of oxygen impurities on the thermal stability and mechanical properties of electrodeposited Ni-23 at% W with aberration-corrected scanning transmission electron microscopy (STEM) and nanoindentation hardness testing. The primary finding of this study was that nanoscale oxides were of sufficient size and volume fraction to inhibit grain growth. The oxide particles were predominantly located on grain boundaries and triple points, which strongly suggests that a particle drag mechanism was active during annealing. In addition, W-segregation was observed at the oxide/Ni(W) interfaces rather than the presumed Ni(W) grain boundaries, further supporting the argument that alternative mechanisms are responsible for thermal stability in these alloys. Lastly, alloys with nanoscale oxides exhibited a higher hardness compared to similar alloys without oxides, suggesting that the particles are widely advantageous. Overall, this work demonstrates that impurity oxide particles can limit grain growth, and alternative mechanisms may be responsible for Ni–W thermal stability.

  11. Effects of thermal treatment on mineralogy and heavy metal behavior in iron oxide stabilized air pollution control residues

    DEFF Research Database (Denmark)

    Sørensen, Mette Abildgaard; Bender-Koch, C.; Starckpoole, M. M.

    2000-01-01

    Stabilization of air pollution control residues by coprecipitation with ferrous iron and subsequent thermal treatment (at 600 and 900 °C) has been examined as a means to reduce heavy metal leaching and to improve product stability. Changes in mineralogy and metal binding were analyzed using various...... analytical and environmental techniques. Ferrihydrite was formed initially but transformed upon thermal treatment to more stable and crystalline iron oxides (maghemite and hematite). For some metals leaching studies showed more substantial binding after thermal treatment, while other metals either....... Thermal treatment of the stabilized residues produced structures with an inherently better iron oxide stability. However, the concentration of metals in the leachate generally increased as a consequence of the decreased solubility of metals in the more stable iron oxide structure....

  12. Thermal Stability and Proton Conductivity of Rare Earth Orthophosphate Hydrates

    DEFF Research Database (Denmark)

    Anfimova, Tatiana; Li, Qingfeng; Jensen, Jens Oluf

    2014-01-01

    as the rhabdophane structure is preserved. The bound hydrate water is accommodated in the rhabdophane structure and is stable at temperatures of up to 650 oC. The thermal stability of the hydrate water and the phosphate structure are of significance for the proton conductivity. The LaPO4·0.6H2O and NdPO4•0.5H2O......Hydrated orthophosphate powders of three rare earth metals, lanthanum, neodymium and gadolinium, were prepared and studied as potential proton conducting materials for intermediate temperature electrochemical applications. The phosphates undergo a transformation from the rhabdophane structure...... to the monazite structure upon dehydration. The thermal stability of the hydrate is studied and found to contain water of two types, physically adsorbed and structurally bound hydrate water. The adsorbed water is correlated to the specific surface area and can be reversibly recovered when dehydrated as long...

  13. Ionoluminscence of partially-stabilized zirconia for thermal barrier coatings

    International Nuclear Information System (INIS)

    Rebollo, N.R.; Ruvalcaba-Sil, J.L.; Miranda, J.

    2007-01-01

    Ionoluminescence is explored as an alternative technique to study the high temperature phase stability of zirconia-based oxides. The evolution of an initially metastable single tetragonal phase towards de-stabilization is investigated for three single-doped zirconia compositions with Y, Yb and Gd. The differences in de-stabilization paths are identified using X-ray diffraction and ionoluminescence; elemental analysis is also performed using particle-induced X-ray emission. X-ray diffraction studies reveal a different scenario for each of the compositions selected; the differences are strongly influenced by the thermodynamic driving forces associated to the fluorite-to-tetragonal displacive transformation. Ionoluminescence studies indicate a significant increment on the signal intensity for de-stabilized samples, relative to previous annealing stages. There are also more subtle differences in the luminescent response from the samples at intermediate annealing stages also related to phase changes. This study provides a basis to characterize phase evolution in single-doped zirconia compositions for thermal insulation applications using luminescence

  14. Thermal stability of DNA quadruplex-duplex hybrids.

    Science.gov (United States)

    Lim, Kah Wai; Khong, Zi Jian; Phan, Anh Tuân

    2014-01-14

    DNA has the capacity to adopt several distinct structural forms, such as duplex and quadruplex helices, which have been implicated in cellular processes and shown to exhibit important functional properties. Quadruplex-duplex hybrids, generated from the juxtaposition of these two structural elements, could find applications in therapeutics and nanotechnology. Here we used NMR and CD spectroscopy to investigate the thermal stability of two classes of quadruplex-duplex hybrids comprising fundamentally distinct modes of duplex and quadruplex connectivity: Construct I involves the coaxial orientation of the duplex and quadruplex helices with continual base stacking across the two components; Construct II involves the orthogonal orientation of the duplex and quadruplex helices with no base stacking between the two components. We have found that for both constructs, the stability of the quadruplex generally increases with the length of the stem-loop incorporated, with respect to quadruplexes comprising nonstructured loops of the same length, which showed a continuous drop in stability with increasing loop length. The stability of these complexes, particularly Construct I, can be substantially influenced by the base-pair steps proximal to the quadruplex-duplex junction. Bulges at the junction are largely detrimental to the adoption of the desired G-quadruplex topology for Construct I but not for Construct II. These findings should facilitate future design and prediction of quadruplex-duplex hybrids.

  15. Structure and Mechanical Properties of Al-Cu-Fe-X Alloys with Excellent Thermal Stability

    OpenAIRE

    Školáková, Andrea; Novák, Pavel; Mejzlíková, Lucie; Průša, Filip; Salvetr, Pavel; Vojtěch, Dalibor

    2017-01-01

    In this work, the structure and mechanical properties of innovative Al-Cu-Fe based alloys were studied. We focused on preparation and characterization of rapidly solidified and hot extruded Al-Cu-Fe, Al-Cu-Fe-Ni and Al-Cu-Fe-Cr alloys. The content of transition metals affects mechanical properties and structure. For this reason, microstructure, phase composition, hardness and thermal stability have been investigated in this study. The results showed exceptional thermal stability of these allo...

  16. Preparation of shape-stabilized co-crystallized poly (ethylene glycol) composites as thermal energy storage materials

    International Nuclear Information System (INIS)

    Qian, Yong; Wei, Ping; Jiang, Pingkai; Li, Zhi; Yan, Yonggang; Ji, Kejian; Deng, Weihua

    2013-01-01

    Highlights: • Shape-stabilized PEG composites were prepared by sol–gel process. • The increased energy storage ability of composite was from cocrystallization effect. • Diammonium phosphate improved flame retardancy properties of PEG composite. • PEG composites had potential to be used as thermal energy storage materials. - Abstract: Shape-stabilized co-crystallized poly (ethylene glycol) (PEG) composites were prepared by sol–gel process. Tetraethoxysilane was utilized as supporting matrix precursor. The crystallization property as well as thermal energy storage properties of PEG was influenced by silica network. The combination of PEG 2k and PEG 10k with suitable ratio (3:1 by weight) led to synergistically increased fusion enthalpy attributed to cocrystallization effect. Furthermore, halogen-free flame retarded PEG composites were obtained using diammonium phosphate as flame retardant. With suitable composition, the latent heat value of flame retarded PEG composite was 96.7 kJ/kg accompanied with good thermal stability and improved flame retardancy properties. Fourier transform infrared spectrum (FT-IR), X-ray diffraction (XRD), polarized optical microscope (POM) and scanning electron microscope (SEM) were used to characterize the structure of PEG composites. Thermal stability properties of PEG composites were investigated by thermogravimetric analyzer (TGA). Char residue obtained from muffle furnace of PEG composites was analyzed by SEM and FT-IR. Flame retardancy properties of PEG composites were estimated by pyrolysis combustion flow calorimeter. Results showed that it was potential for shape-stabilized halogen-free flame retarded PEG composite to be applied in thermal energy storage field

  17. Structural properties, deformation behavior and thermal stability of martensitic Ti-Nb alloys

    Energy Technology Data Exchange (ETDEWEB)

    Boenisch, Matthias

    2016-06-10

    . Also, experimental evidence indicates a deformation-induced martensite to austenite (α'' → β) conversion. The influence of Nb content on the thermal stability and on the occurrence of decomposition reactions in martensitic Ti-Nb alloys is examined by isochronal differential scanning calorimetry, dilatometry and in-situ synchrotron X-ray diffraction complemented by transmission electron microscopy. The thermal decomposition and transformation behavior exhibits various phase transformation sequences during heating into the β-phase field in dependence of composition. Eventually, the transformation temperatures, interval, hysteresis and heat of the β <-> α'' martensitic transformation are investigated in relation to the Nb content. The results obtained in this study are useful for the development and optimization of β-stabilized Ti-based alloys for structural, Ni-free shape memory and/or superelastic, as well as for biomedical applications.

  18. Synthesis of Zirconium-Containing Polyhedral Oligometallasilsesquioxane as an Efficient Thermal Stabilizer for Silicone Rubber

    Directory of Open Access Journals (Sweden)

    Jiedong Qiu

    2018-05-01

    Full Text Available Free radicals play a negative role during the thermal degradation of silicone rubber (SR. Quenching free radicals is proposed to be an efficient way to improve the thermal-oxidative stability of SR. In this work, a novel zirconium-containing polyhedral oligometallasilsesquioxane (Zr-POSS with free-radical quenching capability was synthesized and characterized. The incorporation of Zr-POSS effectively improved the thermal-oxidative stability of SR. The T5 (temperature at 5% weight loss of SR/Zr-POSS significantly increased by 31.7 °C when compared to the unmodified SR. Notably, after aging 12 h at 280 °C, SR/Zr-POSS was still retaining about 65%, 60%, 75%, and 100% of the tensile strength, tear strength, elongation at break, and hardness before aging, respectively, while the mechanical properties of the unmodified SR were significantly decreased. The possible mechanism of Zr-POSS for improving the thermal-oxidative stability of SR was intensively studied and it was revealed that the POSS structure could act as a limiting point to suppress the random scission reaction of backbone. Furthermore, Zr could quench the free radicals by its empty orbital and transformation of valence states. Therefore, it effectively suppressed the thermal-oxidative degradation and crosslinking reaction of the side chains.

  19. Evidence of Alternative Cystatin C Signal Sequence Cleavage Which Is Influenced by the A25T Polymorphism.

    Directory of Open Access Journals (Sweden)

    Annie Nguyen

    Full Text Available Cystatin C (Cys C is a small, potent, cysteine protease inhibitor. An Ala25Thr (A25T polymorphism in Cys C has been associated with both macular degeneration and late-onset Alzheimer's disease. Previously, studies have suggested that this polymorphism may compromise the secretion of Cys C. Interestingly, we found that untagged A25T, A25T tagged C-terminally with FLAG, or A25T FLAG followed by green fluorescent protein (GFP, were all secreted as efficiently from immortalized human cells as their wild-type (WT counterparts (e.g., 112%, 100%, and 88% of WT levels from HEK-293T cells, respectively. Supporting these observations, WT and A25T Cys C variants also showed similar intracellular steady state levels. Furthermore, A25T Cys C did not activate the unfolded protein response and followed the same canonical endoplasmic reticulum (ER-Golgi trafficking pathway as WT Cys C. WT Cys C has been shown to undergo signal sequence cleavage between residues Gly26 and Ser27. While the A25T polymorphism did not affect Cys C secretion, we hypothesized that it may alter where the Cys C signal sequence is preferentially cleaved. Under normal conditions, WT and A25T Cys C have the same signal sequence cleavage site after Gly26 (referred to as 'site 2' cleavage. However, in particular circumstances when the residues around site 2 are modified (such as by the presence of an N-terminal FLAG tag immediately after Gly26, or by a Gly26Lys (G26K mutation, A25T has a significantly higher likelihood than WT Cys C of alternative signal sequence cleavage after Ala20 ('site 1' or even earlier in the Cys C sequence. Overall, our results indicate that the A25T polymorphism does not cause a significant reduction in Cys C secretion, but instead predisposes the protein to be cleaved at an alternative signal sequence cleavage site if site 2 is hindered. Additional N-terminal amino acids resulting from alternative signal sequence cleavage may, in turn, affect the protease

  20. Thermal stability of intermediate band behavior in Ti implanted Si

    Energy Technology Data Exchange (ETDEWEB)

    Olea, J.; Pastor, D.; Martil, I.; Gonzalez-Diaz, G. [Dpto. De Fisica Aplicada III (Electricidad y Electronica), Facultad de Ciencias Fisicas, Universidad Complutense de Madrid, E-28040 Madrid (Spain)

    2010-11-15

    Ti implantation in Si with very high doses has been performed. Subsequent Pulsed Laser Melting (PLM) annealing produces good crystalline lattice with electrical transport properties that are well explained by the Intermediate Band (IB) theory. Thermal stability of this new material is analyzed by means of isochronal annealing in thermodynamic equilibrium conditions at increasing temperature. A progressive deactivation of the IB behavior is shown during thermal annealing, and structural and electrical measurements are reported in order to find out the origin of this result. (author)

  1. Chemical and thermal stability of core-shelled magnetite nanoparticles and solid silica

    Science.gov (United States)

    Cendrowski, Krzysztof; Sikora, Pawel; Zielinska, Beata; Horszczaruk, Elzbieta; Mijowska, Ewa

    2017-06-01

    Pristine nanoparticles of magnetite were coated by solid silica shell forming core/shell structure. 20 nm thick silica coating significantly enhanced the chemical and thermal stability of the iron oxide. Chemical and thermal stability of this structure has been compared to the magnetite coated by mesoporous shell and pristine magnetite nanoparticles. It is assumed that six-membered silica rings in a solid silica shell limit the rate of oxygen diffusion during thermal treatment in air and prevent the access of HCl molecules to the core during chemical etching. Therefore, the core/shell structure with a solid shell requires a longer time to induce the oxidation of iron oxide to a higher oxidation state and, basically, even strong concentrated acid such as HCl is not able to dissolve it totally in one month. This leads to the desired performance of the material in potential applications such as catalysis and environmental protection.

  2. The influence of polyol type on cell geometry and the thermal stability of polyurethane foams

    Directory of Open Access Journals (Sweden)

    Prendžov Slobodan J.

    2006-01-01

    Full Text Available The aim of this study was to examine the influence of substituting defined amounts of polyol Voranol 3322 by polyol Voranol CP 1055 on the cell geometry and thermal stability of the synthesized flexible polyurethane foams. The influence of the amount of antipyrene on the cell geometry and their thermal stability was also investigated. The following components were used in the synthesis of the polyurethanes: a mixture of two polyols (Voranol 3322 with the hydroxyl number 47 mg KOH/g, mean molecular mass 3400 and Voranol CP 1055 with the hydroxyl number 156 mg KOH/g, mean molecular mass 1000, toluene discarnate as the isocyanate component, a combination of an organic-metallic compound and a tertiary amine as catalysts, surfactant and water as the coreactant. The thermal stability was determined by thermogravimetric analysis (in a nitrogen atmosphere. The cell geometry was analyzed by optical microscopy. Examination of the cell geometry revealed different cell shapes. The form factor as an indicator of cell deviation from spherical shape increased (more round forms were observed with increasing amount of Voranol CP 1055. The TG examination showed that specimens with 6 and 8 g of Voranol 3322 substituted by Voranol CP 1055 completely degraded at 350 °C, while foams with 10 and 12 g of Voranol 3322 substituted by Voranol CP 1055 displayed lower mass loss at higher temperatures and had residual masses of 46 % and 43 % at 600°C respectively. The addition of antipyrene in an amount of 1% (based on the amount of polyol contributed to improved thermal stability, no visible color change of the specimen tested at 210°C for 40 minutes, and to rounder cell forms. Considering the obtained results it can be concluded that an increase in the amount of Voranol CP 1055 yielded more spherically shaped cells and better thermal stability of the synthesized flexible polyurethane foams. The addition of antipyrene improves the thermal stability and the cell geometry.

  3. Thermal stability of Trichoderma reesei C30 cellulase and Aspergillus niger. beta. -glucosidase after pH and chemical modification

    Energy Technology Data Exchange (ETDEWEB)

    Woodward, J.; Whaley, K.S.; Zachry, G.S.; Wohlpart, D.L.

    1981-01-01

    Treatment of Trichoderma reesei C30 cellulase at pH 10.0 for 1 h at room temperature increased its pH and thermal stability. Chemical modification of the free epsilon-amino groups of cellulase at pH 10.0 resulted in no further increase in stability. Such chemical modification, however, decreased the thermal stability of the cellulose-cellulase complex. On the contrary, the chemical modification of Aspergillus niger ..beta..-glucosidase with glutaraldehyde at pH 8.0 increased the thermal stability of this enzyme.

  4. Preparation, characterization, and thermal stability of β-cyclodextrin/soybean lecithin inclusion complex.

    Science.gov (United States)

    Wang, Xinge; Luo, Zhigang; Xiao, Zhigang

    2014-01-30

    β-Cyclodextrin (β-CD), which is widely used to increase the stability, solubility, and bioavailability of guests, can form host-guest inclusion complexes with a wide variety of organic molecules. In this study the β-CD/soybean lecithin inclusion complex was prepared. The effect of reaction parameters such as reaction temperature, reaction time and the molar ratio of β-CD/soybean lecithin on inclusion ratio were studied. The inclusion ratio of the product prepared under the optimal conditions of β-CD/soybean lecithin molar ratio 2:1, reaction temperature 60°C reaction time 2h was 40.2%. The results of UV-vis, DSC, XRD and FT-IR spectrum indicated the formation of inclusion complex. The thermal stability experiment indicated that the thermal stability of soybean lecithin in inclusion complex was significantly improved compared with free soybean lecithin. Copyright © 2013 Elsevier Ltd. All rights reserved.

  5. Examination of lignocellulosic fibers for chemical, thermal, and separations properties: Addressing thermo-chemical stability issues

    Science.gov (United States)

    Johnson, Carter David

    Natural fiber-plastic composites incorporate thermoplastic resins with fibrous plant-based materials, sometimes referred to as biomass. Pine wood mill waste has been the traditional source of natural fibrous feedstock. In anticipation of a waste wood shortage other fibrous biomass materials are being investigated as potential supplements or replacements. Perennial grasses, agricultural wastes, and woody biomass are among the potential source materials. As these feedstocks share the basic chemical building blocks; cellulose, hemicellulose, and lignin, they are collectively called lignocellulosics. Initial investigation of a number of lignocellulosic materials, applied to fiber-plastic composite processing and material testing, resulted in varied results, particularly response to processing conditions. Less thermally stable lignocellulosic filler materials were physically changed in observable ways: darkened color and odor. The effect of biomass materials' chemical composition on thermal stability was investigated an experiment involving determination of the chemical composition of seven lignocellulosics: corn hull, corn stover, fescue, pine, soy hull, soy stover, and switchgrass. These materials were also evaluated for thermal stability by thermogravimetric analysis. The results of these determinations indicated that both chemical composition and pretreatment of lignocellulosic materials can have an effect on their thermal stability. A second study was performed to investigate what effect different pretreatment systems have on hybrid poplar, pine, and switchgrass. These materials were treated with hot water, ethanol, and a 2:1 benzene/ethanol mixture for extraction times of: 1, 3, 6, 12, and 24 hours. This factorial experiment demonstrated that both extraction time and medium have an effect on the weight percent of extractives removed from all three material types. The extracted materials generated in the above study were then subjected to an evaluation of thermal

  6. Thermal stabilities of electromechanical properties in cobalt-modified strontium bismuth titanate (SrBi{sub 4}Ti{sub 4}O{sub 15})

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Qian; Cao, Zhao-Peng; Wang, Chun-Ming, E-mail: wangcm@sdu.edu.cn; Fu, Qing-Wei; Yin, De-Fu; Tian, Hu-He

    2016-07-25

    Bismuth layer-structured ferroelectric (BLSF) strontium bismuth titanate (SrBi{sub 4}Ti{sub 4}O{sub 15}, SBT) ceramic oxides with B-site cobalt substitutions have been synthesized using conventional solid–state reaction. The dielectric, piezoelectric, and ferroelectric properties of cobalt-modified SBT are investigated in detail. The results indicate that cobalt is very effective in promoting the piezoelectric performance of SBT. The SBT modified with 3 mol% Co{sup 3+} (SBT-3Co) exhibits the optimized piezoelectric properties, with a piezoelectric constant d{sub 33} of 28 pC/N, which is the highest value among the modified SBT-based piezoelectric ceramics ever reported. The temperature-dependent electrical impedance, resonance frequencies, and electromechanical coupling factors (k{sub p} and k{sub t}) reveal that the cobalt-modified SBT ceramics have good thermal stabilities of electromechanical properties up to 300 °C. These results demonstrate that the cobalt-modified SBT ceramics are promising materials for high temperature piezoelectric sensors applications. - Graphical abstract: The manuscript deals with the thermal stabilities of piezoelectric properties of cobalt-modified SrBi{sub 4}Ti{sub 4}O{sub 15} (SBT) ceramics. The 3 mol% Co{sup 3+} modified SBT (SBT-3Co) ceramics exhibit a piezoelectric constant d{sub 33} of 28 pC/N and a Curie temperature T{sub c} of 528 °C. The SBT-3Co ceramics have good thermal stabilities of electromechanical properties up to 300 °C. - Highlights: • A high level of piezoelectric performance (d{sub 33}∼28 pC/N)is obtained. • High Curie temperature (T{sub c}∼528 °C) is acquired for the optimal composition. • The SBT-3Co exhibits good thermal stabilities of electromechanical properties. • The Co-modified SrBi{sub 4}Ti{sub 4}O{sub 15} is promising as high temperature piezoelectric material.

  7. Polyacrolein/mesoporous silica nanocomposite: Synthesis, thermal stability and covalent lipase immobilization

    Energy Technology Data Exchange (ETDEWEB)

    Motevalizadeh, Seyed Farshad; Khoobi, Mehdi; Shabanian, Meisam [Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences, Tehran 14176 (Iran, Islamic Republic of); Asadgol, Zahra; Faramarzi, Mohammad Ali [Department of Pharmaceutical Biotechnology, Faculty of Pharmacy and Biotechnology Research Center, Tehran University of Medical Sciences, P.O. Box 14155-6451, Tehran 14176 (Iran, Islamic Republic of); Shafiee, Abbas, E-mail: ashafiee@ams.ac.ir [Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences, Tehran 14176 (Iran, Islamic Republic of); Center of Excellence in Biothermodynamics, University of Tehran, Tehran (Iran, Islamic Republic of)

    2013-12-16

    In this work, new polyacrolein/MCM-41 nanocomposites with good phase mixing behavior were prepared through an emulsion polymerization technique. Mesoporous silica was synthesized by in situ assembly of tetraethyl orthosilicate (TEOS) and cetyl trimethyl ammonium bromide (CTAB). The structure and properties of polyacrolein containing nanosized MCM-41 particle (5 and 10 wt%), were investigated by Fourier transform infrared spectroscopy (FTIR), X-ray diffraction, Dynamic light scattering (DLS), scanning electron microscopy (SEM), transmission electron microscopy (TEM), N{sub 2} adsorption techniques, and thermogravimetric (TGA) analyses. The SEM images from the final powder have revealed good dispersion of the MCM-41 nanoparticles throughout polymeric matrix with no distinct voids between two phases. The results indicated that the thermal properties of the nanocomposite were enhanced by addition of MCM-41. Thermomyces lanuginosa lipase (TLL) was used as a model biocatalyst and successfully immobilized with polyacrolein and the nanocomposite via covalent bonds with the aldehyde groups. The activity between free enzyme, polyacrolein, and MCM-41 nanocomposite (10 wt%)-immobilized TLL was compared. The immobilized lipase with the nanocomposite shows better operational stability such as pH tolerance, thermal and storage stability. In addition, the immobilized lipase with the nanocomposite can be easily recovered and retained at 74% of its initial activity after 15 time reuses. - Graphical abstract: The influence of incorporation of mesoporous MCM-41 nanoparticle with polyacrolein on the thermal properties and enzyme immobilization was investigated. - Highlights: • Polyacrolein/MCM-41 nanocomposites were prepared by emulsion polymerization method. • Thermal stability and char residues in nanocomposites were improved. • Nanocomposites significant effects on immobilization of lipase.

  8. Thermal and chemical stabilities of some synthesized inorganic ion exchange materials

    International Nuclear Information System (INIS)

    EI-Naggar, I.M.; Abou-Mesalam, M.M.; El-Shorbagy, M.M.; Shady, S.A.

    2006-01-01

    Chromium and cerium titanate as inorganic ion exchange materials were synthesized by the reaction of potassium chromate or ammonium eerie nitrate with titanium tetrachloride with molar ratio equal unity. The crystal system of both chromium and cerium titanates were determined and set to be monoclinic and orthorhombic system's, respectively. The chemical composition of both chromium and cerium titanates was determined by X-ray fluorescence technique and based on the data obtained with other different techniques. A molecular formula for chromium and cerium titanates as Cr 2 Ti 12 O 27 . 13H 2 O and Ce 2 Ti 3 O 10 . 7.46H 2 O, respectively, was proposed. Thermal stabilities of both ion exchangers were investigated at different heating temperatures. Also the stability of chromium and cerium titanates for chemical attack was studied in different media. The data obtained showed high thermal and chemical stabilities of chromium and cerium titanate ion exchangers compared with the same group of ion exchange materials. The ion exchange capacities of chromium and cerium titanates at different heating temperature were also investigated

  9. Thermal and chemical stabilities of some synthesized inorganic ion exchange materials

    International Nuclear Information System (INIS)

    El-Naggar, I.M.; Abou-Mesalam, M. M.; El-Shorbagy, M.M.; Shady, S.A.

    2005-01-01

    Chromium and cerium titanate as inorganic ion exchange materials were synthesized by the reaction of potassium chromate or ammonium ceric nitrate with titanium tetrachloride with molar ratio equal unity. The crystal system of both chromium and cerium titanates were determined and set to be monoclinic and orthorhombic systems, respectively. The chemical composition of both chromium and cerium titanates were determined by X-ray fluorescence technique and based on the data obtained with other different techniques. We can proposed molecular formula for chromium and cerium titanates as Cr 2 Ti 1 2O27. 13H 2 O and Ce 2 ThO10. 7.46 H 2 O, respectively. Thermal stability of both ion exchangers was investigated at different heating temperatures. Also the stability of chromium and cerium titanates for chemical attack was studied in different media. The data obtained showed high thermal and chemical stabilities of chromium and cerium titanate ion exchangers compared to the same group of ion exchange materials. The ion exchange capacities of chromium and cerium titanates at different heating temperature were investigated

  10. Thermal Stability and Reactivity of Cathode Materials for Li-Ion Batteries.

    Science.gov (United States)

    Huang, Yiqing; Lin, Yuh-Chieh; Jenkins, David M; Chernova, Natasha A; Chung, Youngmin; Radhakrishnan, Balachandran; Chu, Iek-Heng; Fang, Jin; Wang, Qi; Omenya, Fredrick; Ong, Shyue Ping; Whittingham, M Stanley

    2016-03-23

    The thermal stability of electrochemically delithiated Li0.1Ni0.8Co0.15Al0.05O2 (NCA), FePO4 (FP), Mn0.8Fe0.2PO4 (MFP), hydrothermally synthesized VOPO4, LiVOPO4, and electrochemically lithiated Li2VOPO4 is investigated by differential scanning calorimetry (DSC) and thermogravimetric analysis, coupled with mass spectrometry (TGA-MS). The thermal stability of the delithiated materials is found to be in the order of NCA cathode is indeed predicted to be marginally less stable than FP but significantly more stable than NCA in the absence of electrolyte. An analysis of the reaction equilibria between VOPO4 and EC using a multicomponent phase diagram approach yields products and reaction enthalpies that are highly consistent with the experiment results.

  11. CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites.

    Directory of Open Access Journals (Sweden)

    Richard M Sharpe

    Full Text Available High-throughput sequencing continues to produce an immense volume of information that is processed and assembled into mature sequence data. Data analysis tools are urgently needed that leverage the embedded DNA sequence polymorphisms and consequent changes to restriction sites or sequence motifs in a high-throughput manner to enable biological experimentation. CisSERS was developed as a standalone open source tool to analyze sequence datasets and provide biologists with individual or comparative genome organization information in terms of presence and frequency of patterns or motifs such as restriction enzymes. Predicted agarose gel visualization of the custom analyses results was also integrated to enhance the usefulness of the software. CisSERS offers several novel functionalities, such as handling of large and multiple datasets in parallel, multiple restriction enzyme site detection and custom motif detection features, which are seamlessly integrated with real time agarose gel visualization. Using a simple fasta-formatted file as input, CisSERS utilizes the REBASE enzyme database. Results from CisSERS enable the user to make decisions for designing genotyping by sequencing experiments, reduced representation sequencing, 3'UTR sequencing, and cleaved amplified polymorphic sequence (CAPS molecular markers for large sample sets. CisSERS is a java based graphical user interface built around a perl backbone. Several of the applications of CisSERS including CAPS molecular marker development were successfully validated using wet-lab experimentation. Here, we present the tool CisSERS and results from in-silico and corresponding wet-lab analyses demonstrating that CisSERS is a technology platform solution that facilitates efficient data utilization in genomics and genetics studies.

  12. Approximation properties of haplotype tagging

    Directory of Open Access Journals (Sweden)

    Dreiseitl Stephan

    2006-01-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs are locations at which the genomic sequences of population members differ. Since these differences are known to follow patterns, disease association studies are facilitated by identifying SNPs that allow the unique identification of such patterns. This process, known as haplotype tagging, is formulated as a combinatorial optimization problem and analyzed in terms of complexity and approximation properties. Results It is shown that the tagging problem is NP-hard but approximable within 1 + ln((n2 - n/2 for n haplotypes but not approximable within (1 - ε ln(n/2 for any ε > 0 unless NP ⊂ DTIME(nlog log n. A simple, very easily implementable algorithm that exhibits the above upper bound on solution quality is presented. This algorithm has running time O((2m - p + 1 ≤ O(m(n2 - n/2 where p ≤ min(n, m for n haplotypes of size m. As we show that the approximation bound is asymptotically tight, the algorithm presented is optimal with respect to this asymptotic bound. Conclusion The haplotype tagging problem is hard, but approachable with a fast, practical, and surprisingly simple algorithm that cannot be significantly improved upon on a single processor machine. Hence, significant improvement in computatational efforts expended can only be expected if the computational effort is distributed and done in parallel.

  13. Using high thermal stability flexible thin film thermoelectric generator at moderate temperature

    Science.gov (United States)

    Zheng, Zhuang-Hao; Luo, Jing-Ting; Chen, Tian-Bao; Zhang, Xiang-Hua; Liang, Guang-Xing; Fan, Ping

    2018-04-01

    Flexible thin film thermoelectric devices are extensively used in the microscale industry for powering wearable electronics. In this study, comprehensive optimization was conducted in materials and connection design for fabricating a high thermal stability flexible thin film thermoelectric generator. First, the thin films in the generator, including the electrodes, were prepared by magnetron sputtering deposition. The "NiCu-Cu-NiCu" multilayer electrode structure was applied to ensure the thermal stability of the device used at moderate temperature in an air atmosphere. A design with metal layer bonding and series accordant connection was then employed. The maximum efficiency of a single PN thermocouple generator is >11%, and the output power loss of the generator is <10% after integration.

  14. Study on thermal stability and chemical structure of polyamide blended with small amount of Cu

    International Nuclear Information System (INIS)

    Arai, Tsuyoshi; Ueno, Tomonaga; Kajiya, Takafumi; Ishikawa, Tomoyuki; Takeda, Kunihiko

    2007-01-01

    The thermal stability and the chemical structure of Polyamide 66 (PA66) blended with a small amount of copper have been studied. The thermal degradation of the blend with 35 ppm or more of copper was restrained and no strong influence of the concentration of copper was observed. The molecular weight of PA66 decreased by the thermal aging process but the amount of decrease of the blend was smaller than that of the non-blend. The water uptake of the blend increased. The chemical structure, which was observed by IR and NMR, changed slightly by blending with copper after aging at higher temperatures. Multiple items influenced the thermal stability of PA66 blended with a small amount of copper instead of just one. Namely, the main chain of PA66 is cut by heat and the degree of the cut is restrained by the copper. The diffusion time of copper atoms that disperse uniformly in the PA66 matrix is short enough to cover the individual amide groups and the effect enlarges the entire configuration of the PA66 chain to enhance the thermal stability. (author)

  15. Thermal stability study for candidate stainless steels of GEN IV reactors

    International Nuclear Information System (INIS)

    Simeg Veternikova, J.; Degmova, J.; Pekarcikova, M.; Simko, F.; Petriska, M.; Skarba, M.; Mikula, P.; Pupala, M.

    2016-01-01

    Highlights: • Thermal resistance of advanced stainless steels were observed at 1000 °C. • GEN IV candidate steels were confronted to classic AISI steels. • ODS AISI 316 has weaker thermal resistance than classic AISI steel. • Ferritic ODS steels and NF 709 has better thermal resistance than AISI steels. - Abstract: Candidate stainless steels for GEN IV reactors were investigated in term of thermal and corrosion stability at high temperatures. New austenitic steel (NF 709), austenitic ODS steel (ODS 316) and two ferritic ODS steels (MA 956 and MA 957) were exposed to around 1000 °C in inert argon atmosphere at pressure of ∼8 MPa. The steels were further studied in a light of vacancy defects presence by positron annihilation spectroscopy and their thermal resistance was confronted to classic AISI steels. The thermal strain supported a creation of oxide layers observed by scanning electron microscopy (SEM).

  16. Thermal stability study for candidate stainless steels of GEN IV reactors

    Energy Technology Data Exchange (ETDEWEB)

    Simeg Veternikova, J., E-mail: jana.veternikova@stuba.sk [Institute of Nuclear and Physical Engineering, Faculty of Electrical and Information Technology, Slovak University of Technology, Ilkovicova 3, 812 19 Bratislava (Slovakia); Degmova, J. [Institute of Nuclear and Physical Engineering, Faculty of Electrical and Information Technology, Slovak University of Technology, Ilkovicova 3, 812 19 Bratislava (Slovakia); Pekarcikova, M. [Institute of Materials Science, Faculty of Materials Science and Technology, Slovak University of Technology, Paulinska 16, 917 24 Trnava (Slovakia); Simko, F. [Department of Molten Salts, Institute of Inorganic Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, 845 36 Bratislava (Slovakia); Petriska, M. [Institute of Nuclear and Physical Engineering, Faculty of Electrical and Information Technology, Slovak University of Technology, Ilkovicova 3, 812 19 Bratislava (Slovakia); Skarba, M. [Slovak University of Technology, Vazovova 5, 812 43 Bratislava (Slovakia); Mikula, P. [Institute of Nuclear and Physical Engineering, Faculty of Electrical and Information Technology, Slovak University of Technology, Ilkovicova 3, 812 19 Bratislava (Slovakia); Pupala, M. [Department of Molten Salts, Institute of Inorganic Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, 845 36 Bratislava (Slovakia)

    2016-11-30

    Highlights: • Thermal resistance of advanced stainless steels were observed at 1000 °C. • GEN IV candidate steels were confronted to classic AISI steels. • ODS AISI 316 has weaker thermal resistance than classic AISI steel. • Ferritic ODS steels and NF 709 has better thermal resistance than AISI steels. - Abstract: Candidate stainless steels for GEN IV reactors were investigated in term of thermal and corrosion stability at high temperatures. New austenitic steel (NF 709), austenitic ODS steel (ODS 316) and two ferritic ODS steels (MA 956 and MA 957) were exposed to around 1000 °C in inert argon atmosphere at pressure of ∼8 MPa. The steels were further studied in a light of vacancy defects presence by positron annihilation spectroscopy and their thermal resistance was confronted to classic AISI steels. The thermal strain supported a creation of oxide layers observed by scanning electron microscopy (SEM).

  17. Sequence Capture versus Restriction Site Associated DNA Sequencing for Shallow Systematics.

    Science.gov (United States)

    Harvey, Michael G; Smith, Brian Tilston; Glenn, Travis C; Faircloth, Brant C; Brumfield, Robb T

    2016-09-01

    Sequence capture and restriction site associated DNA sequencing (RAD-Seq) are two genomic enrichment strategies for applying next-generation sequencing technologies to systematics studies. At shallow timescales, such as within species, RAD-Seq has been widely adopted among researchers, although there has been little discussion of the potential limitations and benefits of RAD-Seq and sequence capture. We discuss a series of issues that may impact the utility of sequence capture and RAD-Seq data for shallow systematics in non-model species. We review prior studies that used both methods, and investigate differences between the methods by re-analyzing existing RAD-Seq and sequence capture data sets from a Neotropical bird (Xenops minutus). We suggest that the strengths of RAD-Seq data sets for shallow systematics are the wide dispersion of markers across the genome, the relative ease and cost of laboratory work, the deep coverage and read overlap at recovered loci, and the high overall information that results. Sequence capture's benefits include flexibility and repeatability in the genomic regions targeted, success using low-quality samples, more straightforward read orthology assessment, and higher per-locus information content. The utility of a method in systematics, however, rests not only on its performance within a study, but on the comparability of data sets and inferences with those of prior work. In RAD-Seq data sets, comparability is compromised by low overlap of orthologous markers across species and the sensitivity of genetic diversity in a data set to an interaction between the level of natural heterozygosity in the samples examined and the parameters used for orthology assessment. In contrast, sequence capture of conserved genomic regions permits interrogation of the same loci across divergent species, which is preferable for maintaining comparability among data sets and studies for the purpose of drawing general conclusions about the impact of

  18. Stabilization and isolation of low-level liquid waste disposal sites

    International Nuclear Information System (INIS)

    Phillips, S.J.; Gilbert, T.W.

    1987-01-01

    Rockwell Hanford Operations is developing and testing equipment for stabilization and isolation of low-level radioactive liquid waste disposal sites. Stabilization and isolation are accomplished by a dynamic consolidation and particulate grout injection system. System equipment components include: a mobile grout plant for transport, mixing, and pumping of particulate grout; a vibratory hammer/extractor for consolidation of waste, backfill, and for emplacement of the injector; dynamic consolidation/injector probe for introducing grout into fill material; and an open-void surface injector that uses surface or subsurface mechanical or pneumatic packers and displacement gas filtration for introducing grout into disposal structure access piping. Treatment of a liquid-waste disposal site yields a physically stable, cementitious monolith. Additional testing and modification of this equipment for other applications to liquid waste disposal sites is in progress

  19. The effect of copper, MDA, and accelerated aging on jet fuel thermal stability as measured by the gravimetric JFTOT

    Energy Technology Data Exchange (ETDEWEB)

    Pande, S.G. [Geo-Centers, Inc., Ft. Washington, MD (United States); Hardy, D.R. [Navy Technology Center for Safety and Survivability, Washington, DC (United States)

    1995-05-01

    Thermally unstable jet fuels pose operational problems. In order to adequately identify such fuels, factors that realistically impact on thermal stability were examined. Evaluation was based on a quantitative method of measuring thermal stability, viz., NRL`s recently developed gravimetric JFTOT. This method gives a quantitative measurement of both the strip deposit and filterables formed. The pertinent factors examined, included the individual and interactive effects of: soluble copper, MDA (metal deactivator), and aging. The latter was accelerated to simulate field conditions of approximately six months aging at ambient temperature and pressure. The results indicate that the individual and interactive effects of copper, MDA, and accelerated aging appear to be fuel dependent. Based on the results, the three test fuels examined (one JP-8 and two JP-5s) were categorized as exhibiting very good, typical, and poor thermal stabilities, respectively. For both the very good and poor thermal stability fuels, the effect of copper in conjunction with accelerated aging did not significantly increase the total thermal deposits of the neat fuels. In contrast, for the typical thermal stability fuel, the combined effects of copper and accelerated aging, did. Furthermore, the addition of MDA prior to aging of the copper-doped, typical stability fuel significantly counteracted the adverse effect of copper and aging. A similar beneficial effect of MDA was not observed for the poor stability fuel. These results focus on the compositional differences among fuels and the need to elucidate these differences (physical and chemical) for a better understanding and prediction of their performance.

  20. Degradation mechanism and thermal stability of urea nitrate below the melting point

    International Nuclear Information System (INIS)

    Desilets, Sylvain; Brousseau, Patrick; Chamberland, Daniel; Singh, Shanti; Feng, Hongtu; Turcotte, Richard; Anderson, John

    2011-01-01

    Highlights: → Decomposition mechanism of urea nitrate. → Spectral characterization of the decomposition mechanism. → Thermal stability of urea nitrate at 50, 70 and 100 o C. → Chemical balance of decomposed products released. - Abstract: Aging and degradation of urea nitrate below the melting point, at 100 o C, was studied by using thermal analysis and spectroscopic methods including IR, Raman, 1 H and 13 C NMR techniques. It was found that urea nitrate was completely degraded after 72 h at 100 o C into a mixture of solids (69%) and released gaseous species (31%). The degradation mechanism below the melting point was clearly identified. The remaining solid mixture was composed of ammonium nitrate, urea and biuret while unreacted residual nitric and isocyanic acids as well as traces of ammonia were released as gaseous species at 100 o C. The thermal stability of urea nitrate, under extreme storage conditions (50 o C), was also examined by isothermal nano-calorimetry.

  1. Sets of RNA repeated tags and hybridization-sensitive fluorescent probes for distinct images of RNA in a living cell.

    Directory of Open Access Journals (Sweden)

    Takeshi Kubota

    Full Text Available BACKGROUND: Imaging the behavior of RNA in a living cell is a powerful means for understanding RNA functions and acquiring spatiotemporal information in a single cell. For more distinct RNA imaging in a living cell, a more effective chemical method to fluorescently label RNA is now required. In addition, development of the technology labeling with different colors for different RNA would make it easier to analyze plural RNA strands expressing in a cell. METHODOLOGY/PRINCIPAL FINDINGS: Tag technology for RNA imaging in a living cell has been developed based on the unique chemical functions of exciton-controlled hybridization-sensitive oligonucleotide (ECHO probes. Repetitions of selected 18-nucleotide RNA tags were incorporated into the mRNA 3'-UTR. Pairs with complementary ECHO probes exhibited hybridization-sensitive fluorescence emission for the mRNA expressed in a living cell. The mRNA in a nucleus was detected clearly as fluorescent puncta, and the images of the expression of two mRNAs were obtained independently and simultaneously with two orthogonal tag-probe pairs. CONCLUSIONS/SIGNIFICANCE: A compact and repeated label has been developed for RNA imaging in a living cell, based on the photochemistry of ECHO probes. The pairs of an 18-nt RNA tag and the complementary ECHO probes are highly thermostable, sequence-specifically emissive, and orthogonal to each other. The nucleotide length necessary for one tag sequence is much shorter compared with conventional tag technologies, resulting in easy preparation of the tag sequences with a larger number of repeats for more distinct RNA imaging.

  2. Three-Dimensional Protein Fold Determination from Backbone Amide Pseudocontact Shifts Generated by Lanthanide Tags at Multiple Sites

    KAUST Repository

    Yagi, Hiromasa

    2013-06-01

    Site-specific attachment of paramagnetic lanthanide ions to a protein generates pseudocontact shifts (PCS) in the nuclear magnetic resonance (NMR) spectra of the protein that are easily measured as changes in chemical shifts. By labeling the protein with lanthanide tags at four different sites, PCSs are observed for most amide protons and accurate information is obtained about their coordinates in three-dimensional space. The approach is demonstrated with the chaperone ERp29, for which large differences have been reported between X-ray and NMR structures of the C-terminal domain, ERp29-C. The results unambiguously show that the structure of rat ERp29-C in solution is similar to the crystal structure of human ERp29-C. PCSs of backbone amides were the only structural restraints required. Because these can be measured for more dilute protein solutions than other NMR restraints, the approach greatly widens the range of proteins amenable to structural studies in solution. © 2013 Elsevier Ltd. All rights reserved.

  3. Hypergraph topological quantities for tagged social networks

    Science.gov (United States)

    Zlatić, Vinko; Ghoshal, Gourab; Caldarelli, Guido

    2009-09-01

    Recent years have witnessed the emergence of a new class of social networks, which require us to move beyond previously employed representations of complex graph structures. A notable example is that of the folksonomy, an online process where users collaboratively employ tags to resources to impart structure to an otherwise undifferentiated database. In a recent paper, we proposed a mathematical model that represents these structures as tripartite hypergraphs and defined basic topological quantities of interest. In this paper, we extend our model by defining additional quantities such as edge distributions, vertex similarity and correlations as well as clustering. We then empirically measure these quantities on two real life folksonomies, the popular online photo sharing site Flickr and the bookmarking site CiteULike. We find that these systems share similar qualitative features with the majority of complex networks that have been previously studied. We propose that the quantities and methodology described here can be used as a standard tool in measuring the structure of tagged networks.

  4. HEURISTIC METHODS FOR TEST SEQUENCING IN TELECOMMUNICATION SATELLITES

    OpenAIRE

    Boche-Sauvan , Ludivine; Cabon , Bertrand; Huguet , Marie-José; Hébrard , Emmanuel

    2014-01-01

    Colloque avec actes et comité de lecture. internationale.; International audience; The increasing complexity in telecommunication satellite payload design demands new test sequencing approaches to face the induced increase of validation complexity. In such a sequencing problem, each test requires specific payload equipment states at a dedicated temperature range. The industrial objectives are both to reduce the total time of tests and to keep the thermal stability of the payload. For solving ...

  5. In vivo tumor angiogenesis imaging with site-specific labeled 99mTc-HYNIC-VEGF

    International Nuclear Information System (INIS)

    Blankenberg, Francis G.; Backer, Marina V.; Patel, Vimalkumar; Backer, Joseph M.; Levashova, Zoia

    2006-01-01

    We recently developed a cysteine-containing peptide tag (C-tag) that allows for site-specific modification of C-tag-containing fusion proteins with a bifunctional chelator, HYNIC (hydrazine nicotinamide)-maleimide. We then constructed and expressed C-tagged vascular endothelial growth factor (VEGF) and labeled it with HYNIC. We wished to test 99m Tc-HYNIC-C-tagged VEGF ( 99m Tc-HYNIC-VEGF) for the imaging of tumor vasculature before and after antiangiogenic (low continuous dosing, metronomic) and tumoricidal (high-dose) cyclophosphamide treatment. HYNIC-maleimide was reacted with the two thiol groups of C-tagged VEGF without any effect on biologic activity in vitro. 99m Tc-HYNIC-VEGF was prepared using tin/tricine as an exchange reagent, and injected via the tail vein (200-300 μCi, 1-2 μg protein) followed by microSPECT imaging 1 h later. Sequencing analysis of HYNIC-containing peptides obtained after digestion confirmed the site-specific labeling of the two accessible thiol groups of C-tagged VEGF. Tumor vascularity was easily visualized with 99m Tc/VEGF in Balb/c mice with 4T1 murine mammary carcinoma 10 days after implantation into the left axillary fat pad in controls (12.3±5.0 tumor/bkg, n=27) along with its decrease following treatment with high (150 mg/kg q.o.d. x 4; 1.14±0.48 tumor/bkg, n=9) or low (25 mg/kg q.d. x 7; 1.03±0.18 tumor/bkg, n=9) dose cyclophosphamide. Binding specificity was confirmed by observing a 75% decrease in tumor uptake of 99m Tc/biotin-inactivated VEGF, as compared with 99m Tc-HYNIC-VEGF. 99m Tc can be loaded onto C-tagged VEGF in a site-specific fashion without reducing its bioactivity. 99m Tc-HYNIC-VEGF can be rapidly prepared for the imaging of tumor vasculature and its response to different types of chemotherapy. (orig.)

  6. Enhanced coercivity thermal stability realized in Nd–Fe–B thin films diffusion-processed by Nd–Co alloys

    Energy Technology Data Exchange (ETDEWEB)

    Zhong, Hui; Fu, Yanqing [Key laboratory of electromagnetic processing of materials (EPM), Ministry of Education, Northeastern University, Shenyang 110819 (China); Department of Physics and Chemistry of Materials, School of Materials Science and Engineering, Northeastern University, Shenyang 110819 (China); Li, Guojian; Liu, Tie [Key laboratory of electromagnetic processing of materials (EPM), Ministry of Education, Northeastern University, Shenyang 110819 (China); Cui, Weibin, E-mail: cuiweibin@epm.neu.edu.cn [Key laboratory of electromagnetic processing of materials (EPM), Ministry of Education, Northeastern University, Shenyang 110819 (China); Department of Physics and Chemistry of Materials, School of Materials Science and Engineering, Northeastern University, Shenyang 110819 (China); Liu, Wei; Zhang, Zhidong [Shenyang National Laboratory for Materials Science, Institute of Metal Research (IMR), Chinese Academy of Sciences (CAS), Shenyang 110016 (China); Wang, Qiang, E-mail: wangq@mail.neu.edu.cn [Key laboratory of electromagnetic processing of materials (EPM), Ministry of Education, Northeastern University, Shenyang 110819 (China)

    2017-03-15

    A proposed Nd{sub 2}Fe{sub 14}B-core/Nd{sub 2}(Fe, Co){sub 14}B-shell microstructure was realized by diffusion-processing textured Nd{sub 14}Fe{sub 77}B{sub 9} single-layer film with Nd{sub 100−x}Co{sub x} (x=10, 20 and 40) alloys to improve the coercivity thermal stability. The ambient coercivity was increased from around 1 T in single-layer film to nearly 2 T in diffusion-processed films, which was due to the Nd-rich grain boundaries as seen from transmission electron microscopy (TEM) images. The coercivity thermal stability was improved by the core/shell microstructure because Nd-rich grain boundaries provided the high ambient coercivity and Co-rich shell provided the improved coercivity stability. - Highlights: • Core–shell microstructure proposed for enhancing the coercivity thermal stability. • Coercivity enhanced to nearly 2 T by diffusion-processing with Nd–Co alloy. • Good squareness and highly textured microstructure obtained. • Nd-rich phases observed by TEM after diffusion process. • Coercivity thermal stability improved with minor Co addition in grain boundary regions.

  7. The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags

    DEFF Research Database (Denmark)

    Brentani, Helena; Caballero, Otávia L; Camargo, Anamaria A

    2003-01-01

    expressed sequence tags (ESTs) from human tumors and their corresponding normal tissues in the public databases. The data currently define approximately 23,500 genes, of which only approximately 1,250 are still represented only by ESTs. Examination of the EST coverage of known cancer-related (CR) genes...... reveals that ESTs, indicating that the representation of genes associated with commonly studied tumors is high. The careful recording of the origin of all ESTs we have produced has enabled detailed definition of where the genes they represent are expressed in the human body....... More than 100,000 ESTs are available for seven tissues, indicating a surprising variability of gene usage that has led to the discovery of a significant number of genes with restricted expression, and that may thus be therapeutically useful. The ESTs also reveal novel nonsynonymous germline variants...

  8. Thermal stability and filterability of jet fuels containing PDR additives in small-scale tests and realistic rig simulations

    Energy Technology Data Exchange (ETDEWEB)

    Bauldreay, J.M.; Clark, R.H.; Heins, R.J. [Shell Research, Ltd., Chester (United Kingdom)

    1995-05-01

    Specification, small-scale and realistic fuel simulation tests have addressed concerns about the impact of pipeline drag reducer (PDR) flow modifying additives on jet fuel handling and performance. A typical PDR additive tended to block filters which were similar to those used in the specification Jet Fuel Thermal Oxidation Tester (JFTOT) and other thermal stability test apparatus. Blockages reduced flow rates and PDR concentrations downstream of the filters. Consequently two PDR additives (A&B) were tested in JFTOT apparatus without the usual in-line pre-filters as part of a Ministry of Defense (MoD) co-ordinated Round Robin exercise. Some fuel/PDR additive combinations caused decreases in JFTOT breakpoints. Effects were additive- (type, concentration and degree of shear) and fuel-dependent; most failures were caused by filter blockages and not by a failing lacquer rating. In further work at Thornton, the thermal stability characteristics of similar fuel/additive combinations have been examined in non-specification tests. In Flask Oxidation Tests, PDR additives caused no significant increase in the liquid phase oxidation rates of the fuels. Additives were tested in the Single Tube Heat Transfer Rig (STHTR) which duplicates many of the conditions of a heat exchanger element in an engine`s fuel supply system. B produced an average two-fold decrease in thermal stability in a Merox fuel; A had no significant effect. In hydrotreated fuel, B reduced the thermal stability up to five-fold. A had little effect below 205{degrees}C, while at higher temperatures there may have been a marginal improvement in thermal stability. Again, certain jet fuel/PDR combinations were seen to reduce thermal stability.

  9. Thermal and electrochemical stability of tungsten carbide catalyst supports

    Energy Technology Data Exchange (ETDEWEB)

    Chhina, H. [Ballard Power Systems, 9000 Glenlyon Parkway, Burnaby, BC (Canada); Department of Materials Engineering, University of British Columbia, Vancouver, BC (Canada); Campbell, S. [Ballard Power Systems, 9000 Glenlyon Parkway, Burnaby, BC (Canada); Kesler, O. [Department of Mechanical Engineering, University of British Columbia, Vancouver, BC (Canada)

    2007-02-10

    The thermal and electrochemical stability of tungsten carbide (WC), with and without a catalyst dispersed on it, have been investigated to evaluate the potential suitability of the material as an oxidation-resistant catalyst support. Standard techniques currently used to disperse Pt on carbon could not be used to disperse Pt on WC, so an alternative method was developed and used to disperse Pt on both commercially available WC and on carbon for comparison of stability. Electrochemical testing was performed by applying oxidation cycles between +0.6 V and +1.8 V to the support-catalyst material combinations and monitoring the activity of the supported catalyst over 100 oxidation cycles. Comparisons of activity change with cumulative oxidation cycles were made between C and WC supports with comparable loadings of catalyst by weight, solid volume, and powder volume. WC was found to be more thermally and electrochemically stable than currently used carbon support material Vulcan XC-72R. However, further optimization of the particle sizes and dispersion of Pt/WC catalyst/support materials and of comparison standards between new candidate materials and existing carbon-based supports are required. (author)

  10. Soil stabilization mat for lunar launch/landing site

    Science.gov (United States)

    Acord, Amy L.; Cohenour, Mark W.; Ephraim, Daniel; Gochoel, Dennis; Roberts, Jefferson G.

    1990-01-01

    Facilities which are capable of handling frequent arrivals and departures of spaceships between Earth and a lunar colony are necessary. The facility must be able to provide these services with minimal interruption of operational activity within the colony. The major concerns associated with the space traffic are the dust and rock particles that will be kicked up by the rocket exhaust. As a result of the reduced gravitation of the Moon, these particles scatter over large horizontal distances. This flying debris will not only seriously interrupt the routine operations of the colony, but could cause damage to the equipment and facilities surrounding the launch site. An approach to overcome this problem is presented. A proposed design for a lunar take-off/landing mat is presented. This proposal goes beyond dealing with the usual problems of heat and load resistances associated with take-off and landing, by solving the problem of soil stabilization at the site. Through adequate stabilization, the problem of flying debris is eliminated.

  11. Thermal Stability of Nanocrystalline Copper for Potential Use in Printed Wiring Board Applications

    Science.gov (United States)

    Woo, Patrick Kai Fai

    Copper is a widely used conductor in the manufacture of printed wiring boards (PWB). The trends in miniaturization of electronic devices create increasing challenges to all electronic industries. In particular PWB manufacturers face great challenges because the increasing demands in greater performance and device miniaturization pose enormous difficulties in manufacturing and product reliability. Nanocrystalline and ultra-fine grain copper can potentially offer increased reliability and functionality of the PWB due to the increases in strength and achievable wiring density by reduction in grain size. The first part of this thesis is concerned with the synthesis and characterization of nanocrystalline and ultra-fine grain-sized copper for potential applications in the PWB industry. Nanocrystalline copper with different amounts of sulfur impurities (25-230ppm) and grain sizes (31-49nm) were produced and their hardness, electrical resistivity and etchability were determined. To study the thermal stability of nanocrystalline copper, differential scanning calorimetry and isothermal heat treatments combined with electron microscopy techniques for microstructural analysis were used. Differential scanning calorimetry was chosen to continuously monitor the grain growth process in the temperature range from 40?C to 400?C. During isothermal annealing experiments samples were annealed at 23?C, 100?C and 300?C to study various potential thermal issues for these materials in PWB applications such as the long-term room temperature thermal stability as well as for temperature excursions above the operation temperature and peak temperature exposure during the PWB manufacturing process. From all annealing experiments the various grain growth events and the overall stability of these materials were analyzed in terms of driving and dragging forces. Experimental evidence is presented which shows that the overall thermal stability, grain boundary character and texture evolution of

  12. Decision Tree Algorithm-Generated Single-Nucleotide Polymorphism Barcodes of rbcL Genes for 38 Brassicaceae Species Tagging.

    Science.gov (United States)

    Yang, Cheng-Hong; Wu, Kuo-Chuan; Chuang, Li-Yeh; Chang, Hsueh-Wei

    2018-01-01

    DNA barcode sequences are accumulating in large data sets. A barcode is generally a sequence larger than 1000 base pairs and generates a computational burden. Although the DNA barcode was originally envisioned as straightforward species tags, the identification usage of barcode sequences is rarely emphasized currently. Single-nucleotide polymorphism (SNP) association studies provide us an idea that the SNPs may be the ideal target of feature selection to discriminate between different species. We hypothesize that SNP-based barcodes may be more effective than the full length of DNA barcode sequences for species discrimination. To address this issue, we tested a r ibulose diphosphate carboxylase ( rbcL ) S NP b arcoding (RSB) strategy using a decision tree algorithm. After alignment and trimming, 31 SNPs were discovered in the rbcL sequences from 38 Brassicaceae plant species. In the decision tree construction, these SNPs were computed to set up the decision rule to assign the sequences into 2 groups level by level. After algorithm processing, 37 nodes and 31 loci were required for discriminating 38 species. Finally, the sequence tags consisting of 31 rbcL SNP barcodes were identified for discriminating 38 Brassicaceae species based on the decision tree-selected SNP pattern using RSB method. Taken together, this study provides the rational that the SNP aspect of DNA barcode for rbcL gene is a useful and effective sequence for tagging 38 Brassicaceae species.

  13. Testing of Method for Assessing of Room Thermal Stability

    Directory of Open Access Journals (Sweden)

    Charvátová Hana

    2017-01-01

    Full Text Available The paper presents the interim results of our research on the developing methodological procedure which could be used for assessment of a thermal stability of buildings with regards to its thermal accumulative parameters. The principle of testing is based on a combination of computer simulation of cooled room model developed in COMSOL Multiphysics software and on theoretical calculations with respect to compliance with valid European and Czech technical standards used in building industry and architecture under conditions obtained by real measurement for the room to be tested. The presented example shows the effect of the heataccumulation properties of the outside wall insulation materials on the course of the cooling room for winter conditions.

  14. Synthesis, characterization and thermal stability of solid solutions Zr (Y, Fe, MoO2

    Directory of Open Access Journals (Sweden)

    Felipe Legorreta-García

    2015-05-01

    Full Text Available The synthesis of Fe3+, Mo4+ and Y3+ fully stabilized zirconia by the nitrate/urea combustion route and thermal stability in air was investigated. The solid solution obtained was characterized by X ray diffraction (XRD, scanning electron microscopy (SEM and used the BET method for determining specific surface. The ceramic powders obtained were calcined at 1473 K in air atmosphere in order to determine their thermal stability. The scanning electron microscopy (SEM results showed a homogeneous grain surface, measuring several tens of micrometers across. The crystallographic study revealed that by this method it was successfully achieved zirconia doped with Fe3+, Mo4+ and Y3+ ions in the zirconia tetragonal monophase, even after calcinations.

  15. Biotin-tagged proteins: Reagents for efficient ELISA-based serodiagnosis and phage display-based affinity selection.

    Science.gov (United States)

    Verma, Vaishali; Kaur, Charanpreet; Grover, Payal; Gupta, Amita; Chaudhary, Vijay K

    2018-01-01

    The high-affinity interaction between biotin and streptavidin has opened avenues for using recombinant proteins with site-specific biotinylation to achieve efficient and directional immobilization. The site-specific biotinylation of proteins carrying a 15 amino acid long Biotin Acceptor Peptide tag (BAP; also known as AviTag) is effected on a specific lysine either by co-expressing the E. coli BirA enzyme in vivo or by using purified recombinant E. coli BirA enzyme in the presence of ATP and biotin in vitro. In this paper, we have designed a T7 promoter-lac operator-based expression vector for rapid and efficient cloning, and high-level cytosolic expression of proteins carrying a C-terminal BAP tag in E. coli with TEV protease cleavable N-terminal deca-histidine tag, useful for initial purification. Furthermore, a robust three-step purification pipeline integrated with well-optimized protocols for TEV protease-based H10 tag removal, and recombinant BirA enzyme-based site-specific in vitro biotinylation is described to obtain highly pure biotinylated proteins. Most importantly, the paper demonstrates superior sensitivities in indirect ELISA with directional and efficient immobilization of biotin-tagged proteins on streptavidin-coated surfaces in comparison to passive immobilization. The use of biotin-tagged proteins through specific immobilization also allows more efficient selection of binders from a phage-displayed naïve antibody library. In addition, for both these applications, specific immobilization requires much less amount of protein as compared to passive immobilization and can be easily multiplexed. The simplified strategy described here for the production of highly pure biotin-tagged proteins will find use in numerous applications, including those, which may require immobilization of multiple proteins simultaneously on a solid surface.

  16. Explanation of L→H mode transition based on gradient stabilization of edge thermal fluctuations

    International Nuclear Information System (INIS)

    Stacey, W.M.

    1996-01-01

    A linear analysis of thermal fluctuations, using a fluid model which treats the large radial gradient related phenomena in the plasma edge, leads to a constraint on the temperature and density gradients for stabilization of edge temperature fluctuations. A temperature gradient, or conductive edge heat flux, threshold is identified. It is proposed that the L→H transition takes place when the conductive heat flux to the edge produces a sufficiently large edge temperature gradient to stabilize the edge thermal fluctuations. The consequences following from this mechanism for the L→H transition are in accord with observed phenomena associated with the L→H transition and with the observed parameter dependences of the power threshold. First, a constraint is established on the edge temperature and density gradients that are sufficient for the stability of edge temperature fluctuations. A slab approximation for the thin plasma edge and a fluid model connected to account for the large radial gradients present in the plasma edge are used. Equilibrium solutions are characterized by the value of the density and of its gradient L n -1 double-bond - n -1 , etc. Temperature fluctuations expanded about the equilibrium value are then used in the energy balance equation summed over plasma ions, electrons and impurities to obtain, after linearization, an expression for the growth rate ω of edge localized thermal fluctuations. Thermal stability of the equilibrium solution requires ω ≤ 0, which establishes a constraint that must be satisfied by L n -1 and L T -1 . The limiting value of the constraint (ω = 0) leads to an expression for the minimum value of that is sufficient for thermal stability, for a given value of L T -1. It is found that there is a minimum value of the temperature gradient, (L T -1 ) min that is necessary for a stable solution to exist for any value of L n -1

  17. An SSVEP-actuated brain computer interface using phase-tagged flickering sequences: a cursor system.

    Science.gov (United States)

    Lee, Po-Lei; Sie, Jyun-Jie; Liu, Yu-Ju; Wu, Chi-Hsun; Lee, Ming-Huan; Shu, Chih-Hung; Li, Po-Hung; Sun, Chia-Wei; Shyu, Kuo-Kai

    2010-07-01

    This study presents a new steady-state visual evoked potential (SSVEP)-based brain computer interface (BCI). SSVEPs, induced by phase-tagged flashes in eight light emitting diodes (LEDs), were used to control four cursor movements (up, right, down, and left) and four button functions (on, off, right-, and left-clicks) on a screen menu. EEG signals were measured by one EEG electrode placed at Oz position, referring to the international EEG 10-20 system. Since SSVEPs are time-locked and phase-locked to the onsets of SSVEP flashes, EEG signals were bandpass-filtered and segmented into epochs, and then averaged across a number of epochs to sharpen the recorded SSVEPs. Phase lags between the measured SSVEPs and a reference SSVEP were measured, and targets were recognized based on these phase lags. The current design used eight LEDs to flicker at 31.25 Hz with 45 degrees phase margin between any two adjacent SSVEP flickers. The SSVEP responses were filtered within 29.25-33.25 Hz and then averaged over 60 epochs. Owing to the utilization of high-frequency flickers, the induced SSVEPs were away from low-frequency noises, 60 Hz electricity noise, and eye movement artifacts. As a consequence, we achieved a simple architecture that did not require eye movement monitoring or other artifact detection and removal. The high-frequency design also achieved a flicker fusion effect for better visualization. Seven subjects were recruited in this study to sequentially input a command sequence, consisting of a sequence of eight cursor functions, repeated three times. The accuracy and information transfer rate (mean +/- SD) over the seven subjects were 93.14 +/- 5.73% and 28.29 +/- 12.19 bits/min, respectively. The proposed system can provide a reliable channel for severely disabled patients to communicate with external environments.

  18. Flavonoid Biosynthesis Genes Putatively Identified in the Aromatic Plant Polygonum minus via Expressed Sequences Tag (EST Analysis

    Directory of Open Access Journals (Sweden)

    Zamri Zainal

    2012-02-01

    Full Text Available P. minus is an aromatic plant, the leaf of which is widely used as a food additive and in the perfume industry. The leaf also accumulates secondary metabolites that act as active ingredients such as flavonoid. Due to limited genomic and transcriptomic data, the biosynthetic pathway of flavonoids is currently unclear. Identification of candidate genes involved in the flavonoid biosynthetic pathway will significantly contribute to understanding the biosynthesis of active compounds. We have constructed a standard cDNA library from P. minus leaves, and two normalized full-length enriched cDNA libraries were constructed from stem and root organs in order to create a gene resource for the biosynthesis of secondary metabolites, especially flavonoid biosynthesis. Thus, large‑scale sequencing of P. minus cDNA libraries identified 4196 expressed sequences tags (ESTs which were deposited in dbEST in the National Center of Biotechnology Information (NCBI. From the three constructed cDNA libraries, 11 ESTs encoding seven genes were mapped to the flavonoid biosynthetic pathway. Finally, three flavonoid biosynthetic pathway-related ESTs chalcone synthase, CHS (JG745304, flavonol synthase, FLS (JG705819 and leucoanthocyanidin dioxygenase, LDOX (JG745247 were selected for further examination by quantitative RT-PCR (qRT-PCR in different P. minus organs. Expression was detected in leaf, stem and root. Gene expression studies have been initiated in order to better understand the underlying physiological processes.

  19. PIT Tagging Anurans

    Science.gov (United States)

    McCreary, Brome

    2008-01-01

    The following video demonstrates a procedure to insert a passive integrated transponder (PIT) tag under the skin of an anuran (frog or toad) for research and monitoring purposes. Typically, a 12.5 mm tag (0.5 in.) is used to uniquely identify individual anurans as smal as 40 mm (1.6 in.) in length from snout to vent. Smaller tags are also available and allow smaller anurans to be tagged. The procedure does not differ for other sizes of tages or other sizes of anurans. Anyone using this procedure should ensure that the tag is small enough to fit easily behind the sacral hump of the anuran, as shown in this video.

  20. Magnetic properties and thermal stability of MnBi/NdFeB hybrid bonded magnets

    International Nuclear Information System (INIS)

    Cao, S.; Yue, M.; Yang, Y. X.; Zhang, D. T.; Liu, W. Q.; Zhang, J. X.; Guo, Z. H.; Li, W.

    2011-01-01

    Magnetic properties and thermal stability were investigated for the MnBi/NdFeB (MnBi = 0, 20, 40, 60, 80, and 100 wt.%) bonded hybrid magnets prepared by spark plasma sintering (SPS) technique. Effect of MnBi content on the magnetic properties of the hybrid magnets was studied. With increasing MnBi content, the coercivity of the MnBi/NdFeB hybrid magnets increases rapidly, while the remanence and maximum energy product drops simultaneously. Thermal stability measurement on MnBi magnet, NdFeB magnet, and the hybrid magnet with 20 wt.% MnBi indicates that both the NdFeB magnet and the MnBi/NdFeB hybrid magnet have a negative temperature coefficient of coercivity, while the MnBi magnet has a positive one. The (BH) max of the MnBi/NdFeB magnet (MnBi = 20 wt.%) is 5.71 MGOe at 423 K, which is much higher than 3.67 MGOe of the NdFeB magnet, indicating a remarkable improvement of thermal stability.

  1. Autoxidation of jet fuels: Implications for modeling and thermal stability

    Energy Technology Data Exchange (ETDEWEB)

    Heneghan, S.P. [Univ. of Dayton Research Institute, OH (United States); Chin, L.P. [Systems Research Laboratories, Inc., Dayton, OH (United States)

    1995-05-01

    The study and modeling of jet fuel thermal deposition is dependent on an understanding of and ability to model the oxidation chemistry. Global modeling of jet fuel oxidation is complicated by several facts. First, liquid jet fuels are hard to heat rapidly and fuels may begin to oxidize during the heat-up phase. Non-isothermal conditions can be accounted for but the evaluation of temperature versus time is difficult. Second, the jet fuels are a mixture of many compounds that may oxidize at different rates. Third, jet fuel oxidation may be autoaccelerating through the decomposition of the oxidation products. Attempts to model the deposition of jet fuels in two different flowing systems showed the inadequacy of a simple two-parameter global Arrhenius oxidation rate constant. Discarding previous assumptions about the form of the global rate constants results in a four parameter model (which accounts for autoacceleration). This paper discusses the source of the rate constant form and the meaning of each parameter. One of these parameters is associated with the pre-exponential of the autoxidation chain length. This value is expected to vary inversely to thermal stability. We calculate the parameters for two different fuels and discuss the implication to thermal and oxidative stability of the fuels. Finally, we discuss the effect of non-Arrhenius behavior on current modeling of deposition efforts.

  2. Cutaneous skin tag

    Science.gov (United States)

    Skin tag; Acrochordon; Fibroepithelial polyp ... have diabetes. They are thought to occur from skin rubbing against skin. ... The tag sticks out of the skin and may have a short, narrow stalk connecting it to the surface of the skin. Some skin tags are as long as ...

  3. Toward Improved Lifetimes of Organic Solar Cells under Thermal Stress: Substrate-Dependent Morphological Stability of PCDTBT:PCBM Films and Devices.

    Science.gov (United States)

    Li, Zhe; Ho Chiu, Kar; Shahid Ashraf, Raja; Fearn, Sarah; Dattani, Rajeev; Cheng Wong, Him; Tan, Ching-Hong; Wu, Jiaying; Cabral, João T; Durrant, James R

    2015-10-15

    Morphological stability is a key requirement for outdoor operation of organic solar cells. We demonstrate that morphological stability and lifetime of polymer/fullerene based solar cells under thermal stress depend strongly on the substrate interface on which the active layer is deposited. In particular, we find that the stability of benchmark PCDTBT/PCBM solar cells under modest thermal stress is substantially increased in inverted solar cells employing a ZnO substrate compared to conventional devices employing a PSS substrate. This improved stability is observed to correlate with PCBM nucleation at the 50 nm scale, which is shown to be strongly influenced by different substrate interfaces. Employing this approach, we demonstrate remarkable thermal stability for inverted PCDTBT:PC70BM devices on ZnO substrates, with negligible (humidity exposure as widely reported previously, can also demonstrate enhanced morphological stability. As such we show that the choice of suitable substrate interfaces may be a key factor in achieving prolonged lifetimes for organic solar cells under thermal stress conditions.

  4. Conformational stabilization of the membrane embedded targeting domain of the lysosomal peptide transporter TAPL for solution NMR

    Energy Technology Data Exchange (ETDEWEB)

    Tumulka, Franz [Goethe-University Frankfurt, Institute of Biochemistry, Biocenter (Germany); Roos, Christian; Loehr, Frank [Goethe-University Frankfurt, Institute of Biophysical Chemistry, Biocenter (Germany); Bock, Christoph [Goethe-University Frankfurt, Institute of Biochemistry, Biocenter (Germany); Bernhard, Frank; Doetsch, Volker [Goethe-University Frankfurt, Institute of Biophysical Chemistry, Biocenter (Germany); Abele, Rupert, E-mail: abele@em.uni-frankfurt.de [Goethe-University Frankfurt, Institute of Biochemistry, Biocenter (Germany)

    2013-10-15

    The ATP binding cassette transporter TAPL translocates cytosolic peptides into the lumen of lysosomes driven by the hydrolysis of ATP. Functionally, this transporter can be divided into coreTAPL, comprising the transport function, and an additional N-terminal transmembrane domain called TMD0, which is essential for lysosomal targeting and mediates the interaction with the lysosomal associated membrane proteins LAMP-1 and LAMP-2. To elucidate the structure of this unique domain, we developed protocols for the production of high quantities of cell-free expressed TMD0 by screening different N-terminal expression tags. Independently of the amino acid sequence, high expression was detected for AU-rich sequences in the first seven codons, decreasing the free energy of RNA secondary structure formation at translation initiation. Furthermore, avoiding NGG codons in the region of translation initiation demonstrated a positive effect on expression. For NMR studies, conditions were optimized for high solubilization efficiency, long-term stability, and high quality spectra. A most critical step was the careful exchange of the detergent used for solubilization by the detergent dihexanoylphosphatidylcholine. Several constructs of different size were tested in order to stabilize the fold of TMD0 as well as to reduce the conformation exchange. NMR spectra with sufficient resolution and homogeneity were finally obtained with a TMD0 derivative only modified by a C-terminal His{sub 10}-tag and containing a codon optimized AT-rich sequence.

  5. Fabrication, thermal properties and thermal stabilities of microencapsulated n-alkane with poly(lauryl methacrylate) as shell

    International Nuclear Information System (INIS)

    Qiu, Xiaolin; Lu, Lixin; Wang, Ju; Tang, Guoyi; Song, Guolin

    2015-01-01

    Highlights: • Microencapsulation of octadecane and paraffin by crosslinked poly(lauryl methacrylate). • Octadecane microcapsules have a melting enthalpy of about 118 J g −1 . • Weight loss temperatures of the microcapsules were increased by 67 °C and 28 °C. • Phase change enthalpies decreased by around 10 wt% after 500 thermal cycles. • Foams with microcapsules can be applied for passive temperature control. - Abstract: Microencapsulation of n-octadecane or paraffin with poly(lauryl methacrylate) (PLMA) shell was performed by a suspension-like polymerization. The polymer shell was crosslinked by pentaerythritol tetraacrylate (PETRA). The surface morphologies of microcapsules were investigated by scanning electron microscopy (SEM). Phase change properties, thermal reliabilities and thermal stabilities of microcapsules were determined by differential scanning calorimetry (DSC) and thermal gravimetric analysis (TGA). The n-octadecane microcapsule exhibits higher melting enthalpy (118.0 J g −1 ) and crystallization enthalpy (108.3 J g −1 ) compared with the paraffin microcapsule. The thermal resistant temperatures were enhanced by more than 25 °C when n-alkanes were microencapsulated by PLMA. The PCM contents of microcapsules decreased by less than 4 wt% and 6 wt% after 500 and 1000 thermal cycles, respectively. Heat-up experiments indicated that microcapsule-treated foams exhibited upgraded thermal regulation capacities. Consequently, microencapsulated n-octadecane or paraffin with PLMA as shell possesses good potentials for heat storage and thermal regulation.

  6. Preliminary hazards analysis of thermal scrap stabilization system. Revision 1

    International Nuclear Information System (INIS)

    Lewis, W.S.

    1994-01-01

    This preliminary analysis examined the HA-21I glovebox and its supporting systems for potential process hazards. Upon further analysis, the thermal stabilization system has been installed in gloveboxes HC-21A and HC-21C. The use of HC-21C and HC-21A simplified the initial safety analysis. In addition, these gloveboxes were cleaner and required less modification for operation than glovebox HA-21I. While this document refers to glovebox HA-21I for the hazards analysis performed, glovebox HC-21C is sufficiently similar that the following analysis is also valid for HC-21C. This hazards analysis document is being re-released as revision 1 to include the updated flowsheet document (Appendix C) and the updated design basis (Appendix D). The revised Process Flow Schematic has also been included (Appendix E). This Current revision incorporates the recommendations provided from the original hazards analysis as well. The System Design Description (SDD) has also been appended (Appendix H) to document the bases for Safety Classification of thermal stabilization equipment

  7. Pressure effects on the thermal stability of silicon carbide fibers

    Science.gov (United States)

    Jaskowiak, Martha H.; Dicarlo, James A.

    1989-01-01

    Commercially available polymer derived SiC fibers were treated at temperatures from 1000 to 2200 C in vacuum and argon gas pressure of 1 and 1360 atm. Effects of gas pressure on the thermal stability of the fibers were determined through property comparison between the pressure treated fibers and vacuum treated fibers. Investigation of the thermal stability included studies of the fiber microstructure, weight loss, grain growth, and tensile strength. The 1360 atm argon gas treatment was found to shift the onset of fiber weight loss from 1200 to above 1500 C. Grain growth and tensile strength degradation were correlated with weight loss and were thus also inhibited by high pressure treatments. Additional heat treatment in 1 atm argon of the fibers initially treated at 1360 atm argon caused further weight loss and tensile strength degradation, thus indicating that high pressure inert gas conditions would be effective only in delaying fiber strength degradation. However, if the high gas pressure could be maintained throughout composite fabrication, then the composites could be processed at higher temperatures.