WorldWideScience

Sample records for squid rna editing

  1. REDIdb: the RNA editing database.

    Science.gov (United States)

    Picardi, Ernesto; Regina, Teresa Maria Rosaria; Brennicke, Axel; Quagliariello, Carla

    2007-01-01

    The RNA Editing Database (REDIdb) is an interactive, web-based database created and designed with the aim to allocate RNA editing events such as substitutions, insertions and deletions occurring in a wide range of organisms. The database contains both fully and partially sequenced DNA molecules for which editing information is available either by experimental inspection (in vitro) or by computational detection (in silico). Each record of REDIdb is organized in a specific flat-file containing a description of the main characteristics of the entry, a feature table with the editing events and related details and a sequence zone with both the genomic sequence and the corresponding edited transcript. REDIdb is a relational database in which the browsing and identification of editing sites has been simplified by means of two facilities to either graphically display genomic or cDNA sequences or to show the corresponding alignment. In both cases, all editing sites are highlighted in colour and their relative positions are detailed by mousing over. New editing positions can be directly submitted to REDIdb after a user-specific registration to obtain authorized secure access. This first version of REDIdb database stores 9964 editing events and can be freely queried at http://biologia.unical.it/py_script/search.html.

  2. RNA Editing in Plant Mitochondria

    Science.gov (United States)

    Hiesel, Rudolf; Wissinger, Bernd; Schuster, Wolfgang; Brennicke, Axel

    1989-12-01

    Comparative sequence analysis of genomic and complementary DNA clones from several mitochondrial genes in the higher plant Oenothera revealed nucleotide sequence divergences between the genomic and the messenger RNA-derived sequences. These sequence alterations could be most easily explained by specific post-transcriptional nucleotide modifications. Most of the nucleotide exchanges in coding regions lead to altered codons in the mRNA that specify amino acids better conserved in evolution than those encoded by the genomic DNA. Several instances show that the genomic arginine codon CGG is edited in the mRNA to the tryptophan codon TGG in amino acid positions that are highly conserved as tryptophan in the homologous proteins of other species. This editing suggests that the standard genetic code is used in plant mitochondria and resolves the frequent coincidence of CGG codons and tryptophan in different plant species. The apparently frequent and non-species-specific equivalency of CGG and TGG codons in particular suggests that RNA editing is a common feature of all higher plant mitochondria.

  3. Statistical Physics Approaches to RNA Editing

    Science.gov (United States)

    Bundschuh, Ralf

    2012-02-01

    The central dogma of molecular Biology states that DNA is transcribed base by base into RNA which is in turn translated into proteins. However, some organisms edit their RNA before translation by inserting, deleting, or substituting individual or short stretches of bases. In many instances the mechanisms by which an organism recognizes the positions at which to edit or by which it performs the actual editing are unknown. One model system that stands out by its very high rate of on average one out of 25 bases being edited are the Myxomycetes, a class of slime molds. In this talk we will show how the computational methods and concepts from statistical Physics can be used to analyze DNA and protein sequence data to predict editing sites in these slime molds and to guide experiments that identified previously unknown types of editing as well as the complete set of editing events in the slime mold Physarum polycephalum.

  4. ADAR RNA editing below the backbone.

    Science.gov (United States)

    Keegan, Liam; Khan, Anzer; Vukic, Dragana; O'Connell, Mary

    2017-09-01

    ADAR RNA editing enzymes ( a denosine d e a minases acting on R NA) that convert adenosine bases to inosines were first identified biochemically 30 years ago. Since then, studies on ADARs in genetic model organisms, and evolutionary comparisons between them, continue to reveal a surprising range of pleiotropic biological effects of ADARs. This review focuses on Drosophila melanogaster , which has a single Adar gene encoding a homolog of vertebrate ADAR2 that site-specifically edits hundreds of transcripts to change individual codons in ion channel subunits and membrane and cytoskeletal proteins. Drosophila ADAR is involved in the control of neuronal excitability and neurodegeneration and, intriguingly, in the control of neuronal plasticity and sleep. Drosophila ADAR also interacts strongly with RNA interference, a key antiviral defense mechanism in invertebrates. Recent crystal structures of human ADAR2 deaminase domain-RNA complexes help to interpret available information on Drosophila ADAR isoforms and on the evolution of ADARs from tRNA deaminase ADAT proteins. ADAR RNA editing is a paradigm for the now rapidly expanding range of RNA modifications in mRNAs and ncRNAs. Even with recent progress, much remains to be understood about these groundbreaking ADAR RNA modification systems. © 2017 Keegan et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  5. The art of editing RNA structural alignments

    DEFF Research Database (Denmark)

    Andersen, Ebbe Sloth

    2014-01-01

    Manual editing of RNA structural alignments may be considered more art than science, since it still requires an expert biologist to take multiple levels of information into account and be slightly creative when constructing high-quality alignments. Even though the task is rather tedious, it is re......Manual editing of RNA structural alignments may be considered more art than science, since it still requires an expert biologist to take multiple levels of information into account and be slightly creative when constructing high-quality alignments. Even though the task is rather tedious...

  6. RNA Editing and Drug Discovery for Cancer Therapy

    Directory of Open Access Journals (Sweden)

    Wei-Hsuan Huang

    2013-01-01

    Full Text Available RNA editing is vital to provide the RNA and protein complexity to regulate the gene expression. Correct RNA editing maintains the cell function and organism development. Imbalance of the RNA editing machinery may lead to diseases and cancers. Recently, RNA editing has been recognized as a target for drug discovery although few studies targeting RNA editing for disease and cancer therapy were reported in the field of natural products. Therefore, RNA editing may be a potential target for therapeutic natural products. In this review, we provide a literature overview of the biological functions of RNA editing on gene expression, diseases, cancers, and drugs. The bioinformatics resources of RNA editing were also summarized.

  7. ExpEdit: a webserver to explore human RNA editing in RNA-Seq experiments.

    Science.gov (United States)

    Picardi, Ernesto; D'Antonio, Mattia; Carrabino, Danilo; Castrignanò, Tiziana; Pesole, Graziano

    2011-05-01

    ExpEdit is a web application for assessing RNA editing in human at known or user-specified sites supported by transcript data obtained by RNA-Seq experiments. Mapping data (in SAM/BAM format) or directly sequence reads [in FASTQ/short read archive (SRA) format] can be provided as input to carry out a comparative analysis against a large collection of known editing sites collected in DARNED database as well as other user-provided potentially edited positions. Results are shown as dynamic tables containing University of California, Santa Cruz (UCSC) links for a quick examination of the genomic context. ExpEdit is freely available on the web at http://www.caspur.it/ExpEdit/.

  8. Mediated Plastid RNA Editing in Plant Immunity

    Science.gov (United States)

    García-Andrade, Javier; Ramírez, Vicente; López, Ana; Vera, Pablo

    2013-01-01

    Plant regulatory circuits coordinating nuclear and plastid gene expression have evolved in response to external stimuli. RNA editing is one of such control mechanisms. We determined the Arabidopsis nuclear-encoded homeodomain-containing protein OCP3 is incorporated into the chloroplast, and contributes to control over the extent of ndhB transcript editing. ndhB encodes the B subunit of the chloroplast NADH dehydrogenase-like complex (NDH) involved in cyclic electron flow (CEF) around photosystem I. In ocp3 mutant strains, ndhB editing efficiency decays, CEF is impaired and disease resistance to fungal pathogens substantially enhanced, a process recapitulated in plants defective in editing plastid RNAs encoding NDH complex subunits due to mutations in previously described nuclear-encoded pentatricopeptide-related proteins (i.e. CRR21, CRR2). Furthermore, we observed that following a pathogenic challenge, wild type plants respond with editing inhibition of ndhB transcript. In parallel, rapid destabilization of the plastidial NDH complex is also observed in the plant following perception of a pathogenic cue. Therefore, NDH complex activity and plant immunity appear as interlinked processes. PMID:24204264

  9. Genetic mapping uncovers cis-regulatory landscape of RNA editing.

    Science.gov (United States)

    Ramaswami, Gokul; Deng, Patricia; Zhang, Rui; Anna Carbone, Mary; Mackay, Trudy F C; Li, Jin Billy

    2015-09-16

    Adenosine-to-inosine (A-to-I) RNA editing, catalysed by ADAR enzymes conserved in metazoans, plays an important role in neurological functions. Although the fine-tuning mechanism provided by A-to-I RNA editing is important, the underlying rules governing ADAR substrate recognition are not well understood. We apply a quantitative trait loci (QTL) mapping approach to identify genetic variants associated with variability in RNA editing. With very accurate measurement of RNA editing levels at 789 sites in 131 Drosophila melanogaster strains, here we identify 545 editing QTLs (edQTLs) associated with differences in RNA editing. We demonstrate that many edQTLs can act through changes in the local secondary structure for edited dsRNAs. Furthermore, we find that edQTLs located outside of the edited dsRNA duplex are enriched in secondary structure, suggesting that distal dsRNA structure beyond the editing site duplex affects RNA editing efficiency. Our work will facilitate the understanding of the cis-regulatory code of RNA editing.

  10. Ebola virus RNA editing depends on the primary editing site sequence and an upstream secondary structure.

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    Masfique Mehedi

    Full Text Available Ebolavirus (EBOV, the causative agent of a severe hemorrhagic fever and a biosafety level 4 pathogen, increases its genome coding capacity by producing multiple transcripts encoding for structural and nonstructural glycoproteins from a single gene. This is achieved through RNA editing, during which non-template adenosine residues are incorporated into the EBOV mRNAs at an editing site encoding for 7 adenosine residues. However, the mechanism of EBOV RNA editing is currently not understood. In this study, we report for the first time that minigenomes containing the glycoprotein gene editing site can undergo RNA editing, thereby eliminating the requirement for a biosafety level 4 laboratory to study EBOV RNA editing. Using a newly developed dual-reporter minigenome, we have characterized the mechanism of EBOV RNA editing, and have identified cis-acting sequences that are required for editing, located between 9 nt upstream and 9 nt downstream of the editing site. Moreover, we show that a secondary structure in the upstream cis-acting sequence plays an important role in RNA editing. EBOV RNA editing is glycoprotein gene-specific, as a stretch encoding for 7 adenosine residues located in the viral polymerase gene did not serve as an editing site, most likely due to an absence of the necessary cis-acting sequences. Finally, the EBOV protein VP30 was identified as a trans-acting factor for RNA editing, constituting a novel function for this protein. Overall, our results provide novel insights into the RNA editing mechanism of EBOV, further understanding of which might result in novel intervention strategies against this viral pathogen.

  11. Ebola virus RNA editing depends on the primary editing site sequence and an upstream secondary structure.

    Science.gov (United States)

    Mehedi, Masfique; Hoenen, Thomas; Robertson, Shelly; Ricklefs, Stacy; Dolan, Michael A; Taylor, Travis; Falzarano, Darryl; Ebihara, Hideki; Porcella, Stephen F; Feldmann, Heinz

    2013-01-01

    Ebolavirus (EBOV), the causative agent of a severe hemorrhagic fever and a biosafety level 4 pathogen, increases its genome coding capacity by producing multiple transcripts encoding for structural and nonstructural glycoproteins from a single gene. This is achieved through RNA editing, during which non-template adenosine residues are incorporated into the EBOV mRNAs at an editing site encoding for 7 adenosine residues. However, the mechanism of EBOV RNA editing is currently not understood. In this study, we report for the first time that minigenomes containing the glycoprotein gene editing site can undergo RNA editing, thereby eliminating the requirement for a biosafety level 4 laboratory to study EBOV RNA editing. Using a newly developed dual-reporter minigenome, we have characterized the mechanism of EBOV RNA editing, and have identified cis-acting sequences that are required for editing, located between 9 nt upstream and 9 nt downstream of the editing site. Moreover, we show that a secondary structure in the upstream cis-acting sequence plays an important role in RNA editing. EBOV RNA editing is glycoprotein gene-specific, as a stretch encoding for 7 adenosine residues located in the viral polymerase gene did not serve as an editing site, most likely due to an absence of the necessary cis-acting sequences. Finally, the EBOV protein VP30 was identified as a trans-acting factor for RNA editing, constituting a novel function for this protein. Overall, our results provide novel insights into the RNA editing mechanism of EBOV, further understanding of which might result in novel intervention strategies against this viral pathogen.

  12. Re-editing the paradigm of Cytidine (C) to Uridine (U) RNA editing.

    Science.gov (United States)

    Fossat, Nicolas; Tam, Patrick P L

    2014-01-01

    Cytidine (C) to Uridine (U) RNA editing is a post-trancriptional modification that until recently was known to only affect Apolipoprotein b (Apob) RNA and minimally require 2 components of the C to U editosome, the deaminase APOBEC1 and the RNA-binding protein A1CF. Our latest work has identified a novel RNA-binding protein, RBM47, as a core component of the editosome, which can substitute A1CF for the editing of ApoB mRNA. In addition, new RNA species that are subjected to C to U editing have been identified. Here, we highlight these recent discoveries and discuss how they change our view of the composition of the C to U editing machinery and expand our knowledge of the functional attributes of C to U RNA editing.

  13. Regulation of Na+/K+ ATPase transport velocity by RNA editing.

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    Claudia Colina

    2010-11-01

    Full Text Available Because firing properties and metabolic rates vary widely, neurons require different transport rates from their Na(+/K(+ pumps in order to maintain ion homeostasis. In this study we show that Na(+/K(+ pump activity is tightly regulated by a novel process, RNA editing. Three codons within the squid Na(+/K(+ ATPase gene can be recoded at the RNA level, and the efficiency of conversion for each varies dramatically, and independently, between tissues. At one site, a highly conserved isoleucine in the seventh transmembrane span can be converted to a valine, a change that shifts the pump's intrinsic voltage dependence. Mechanistically, the removal of a single methyl group specifically targets the process of Na(+ release to the extracellular solution, causing a higher turnover rate at the resting membrane potential.

  14. Deletions in cox2 mRNA result in loss of splicing and RNA editing and gain of novel RNA editing sites.

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    Stefanie Grüttner

    Full Text Available As previously demonstrated, the maize cox2 RNA is fully edited in cauliflower mitochondria. Use of constructs with a deleted cox2 intron, however, led to a loss of RNA editing at almost all editing sites, with only a few sites still partially edited. Likewise, one deletion in exon 1 and three in exon 2 abolish RNA editing at all cox2 sites analyzed. Furthermore, intron splicing is abolished using these deletions. Mutation of a cytosine residue, which is normally edited and localized directly adjacent to the intron, to thymidine did not result in restoration of splicing, indicating that the loss of splicing was not due to loss of RNA editing. One deletion in exon 2 did not lead to loss of splicing. Instead, most editing sites were found to be edited, only three were not edited. Unexpectedly, we observed additional RNA editing events at new sites. Thus it appears that deletions in the cox2 RNA sequence can have a strong effect on RNA processing, leading to loss of splicing, loss of editing at all sites, or even to a gain of new editing sites. As these effects are not limited to the vicinity of the respective deletions, but appear to be widespread or even affect all editing sites, they may not be explained by the loss of PPR binding sites. Instead, it appears that several parts of the cox2 transcript are required for proper RNA processing. This indicates the roles of the RNA sequence and structural elements in the recognition of the editing sites.

  15. REDIdb: an upgraded bioinformatics resource for organellar RNA editing sites.

    Science.gov (United States)

    Picardi, Ernesto; Regina, Teresa M R; Verbitskiy, Daniil; Brennicke, Axel; Quagliariello, Carla

    2011-03-01

    RNA editing is a post-transcriptional molecular process whereby the information in a genetic message is modified from that in the corresponding DNA template by means of nucleotide substitutions, insertions and/or deletions. It occurs mostly in organelles by clade-specific diverse and unrelated biochemical mechanisms. RNA editing events have been annotated in primary databases as GenBank and at more sophisticated level in the specialized databases REDIdb, dbRES and EdRNA. At present, REDIdb is the only freely available database that focuses on the organellar RNA editing process and annotates each editing modification in its biological context. Here we present an updated and upgraded release of REDIdb with a web-interface refurbished with graphical and computational facilities that improve RNA editing investigations. Details of the REDIdb features and novelties are illustrated and compared to other RNA editing databases. REDIdb is freely queried at http://biologia.unical.it/py_script/REDIdb/. Copyright © 2010 Elsevier B.V. and Mitochondria Research Society. All rights reserved.

  16. Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome

    DEFF Research Database (Denmark)

    Peng, Zhiyu; Cheng, Yanbing; Tan, Bertrand Chin-Ming

    2012-01-01

    a computational pipeline that carefully controls for false positives while calling RNA editing events from genome and whole-transcriptome data of the same individual. We identified 22,688 RNA editing events in noncoding genes and introns, untranslated regions and coding sequences of protein-coding genes. Most......RNA editing is a post-transcriptional event that recodes hereditary information. Here we describe a comprehensive profile of the RNA editome of a male Han Chinese individual based on analysis of ∼767 million sequencing reads from poly(A)(+), poly(A)(-) and small RNA samples. We developed...... changes (∼93%) converted A to I(G), consistent with known editing mechanisms based on adenosine deaminase acting on RNA (ADAR). We also found evidence of other types of nucleotide changes; however, these were validated at lower rates. We found 44 editing sites in microRNAs (miRNAs), suggesting a potential...

  17. C to U RNA editing mediated by APOBEC1 requires RNA-binding protein RBM47.

    Science.gov (United States)

    Fossat, Nicolas; Tourle, Karin; Radziewic, Tania; Barratt, Kristen; Liebhold, Doreen; Studdert, Joshua B; Power, Melinda; Jones, Vanessa; Loebel, David A F; Tam, Patrick P L

    2014-08-01

    Cytidine (C) to Uridine (U) RNA editing is a post-transcriptional modification that is accomplished by the deaminase APOBEC1 and its partnership with the RNA-binding protein A1CF. We identify and characterise here a novel RNA-binding protein, RBM47, that interacts with APOBEC1 and A1CF and is expressed in tissues where C to U RNA editing occurs. RBM47 can substitute for A1CF and is necessary and sufficient for APOBEC1-mediated editing in vitro. Editing is further impaired in Rbm47-deficient mutant mice. These findings suggest that RBM47 and APOBEC1 constitute the basic machinery for C to U RNA editing. © 2014 The Authors.

  18. REDItools: high-throughput RNA editing detection made easy.

    Science.gov (United States)

    Picardi, Ernesto; Pesole, Graziano

    2013-07-15

    The reliable detection of RNA editing sites from massive sequencing data remains challenging and, although several methodologies have been proposed, no computational tools have been released to date. Here, we introduce REDItools a suite of python scripts to perform high-throughput investigation of RNA editing using next-generation sequencing data. REDItools are in python programming language and freely available at http://code.google.com/p/reditools/. ernesto.picardi@uniba.it or graziano.pesole@uniba.it Supplementary data are available at Bioinformatics online.

  19. Evolutionary analysis reveals regulatory and functional landscape of coding and non-coding RNA editing.

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    Zhang, Rui; Deng, Patricia; Jacobson, Dionna; Li, Jin Billy

    2017-02-01

    Adenosine-to-inosine RNA editing diversifies the transcriptome and promotes functional diversity, particularly in the brain. A plethora of editing sites has been recently identified; however, how they are selected and regulated and which are functionally important are largely unknown. Here we show the cis-regulation and stepwise selection of RNA editing during Drosophila evolution and pinpoint a large number of functional editing sites. We found that the establishment of editing and variation in editing levels across Drosophila species are largely explained and predicted by cis-regulatory elements. Furthermore, editing events that arose early in the species tree tend to be more highly edited in clusters and enriched in slowly-evolved neuronal genes, thus suggesting that the main role of RNA editing is for fine-tuning neurological functions. While nonsynonymous editing events have been long recognized as playing a functional role, in addition to nonsynonymous editing sites, a large fraction of 3'UTR editing sites is evolutionarily constrained, highly edited, and thus likely functional. We find that these 3'UTR editing events can alter mRNA stability and affect miRNA binding and thus highlight the functional roles of noncoding RNA editing. Our work, through evolutionary analyses of RNA editing in Drosophila, uncovers novel insights of RNA editing regulation as well as its functions in both coding and non-coding regions.

  20. Genetic Determinants of RNA Editing Levels of ADAR Targets in Drosophila melanogaster

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    Yerbol Z. Kurmangaliyev

    2016-02-01

    Full Text Available RNA editing usually affects only a fraction of expressed transcripts and there is a vast amount of variation in editing levels of ADAR (adenosine deaminase, RNA-specific targets. Here we explore natural genetic variation affecting editing levels of particular sites in 81 natural strains of Drosophila melanogaster. The analysis of associations between editing levels and single-nucleotide polymorphisms allows us to map putative cis-regulatory regions affecting editing of 16 A-to-I editing sites (cis-RNA editing quantitative trait loci or cis-edQTLs, P < 10−8. The observed changes in editing levels are validated by independent molecular technique. All identified regulatory variants are located in close proximity of modulated editing sites. Moreover, colocalized editing sites are often regulated by same loci. Similar to expression and splicing QTL studies, the characterization of edQTLs will greatly expand our understanding of cis-regulatory evolution of gene expression.

  1. Abundant off-target edits from site-directed RNA editing can be reduced by nuclear localization of the editing enzyme.

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    Vallecillo-Viejo, Isabel C; Liscovitch-Brauer, Noa; Montiel-Gonzalez, Maria Fernanda; Eisenberg, Eli; Rosenthal, Joshua J C

    2018-01-02

    Site-directed RNA editing (SDRE) is a general strategy for making targeted base changes in RNA molecules. Although the approach is relatively new, several groups, including our own, have been working on its development. The basic strategy has been to couple the catalytic domain of an adenosine (A) to inosine (I) RNA editing enzyme to a guide RNA that is used for targeting. Although highly efficient on-target editing has been reported, off-target events have not been rigorously quantified. In this report we target premature termination codons (PTCs) in messages encoding both a fluorescent reporter protein and the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) protein transiently transfected into human epithelial cells. We demonstrate that while on-target editing is efficient, off-target editing is extensive, both within the targeted message and across the entire transcriptome of the transfected cells. By redirecting the editing enzymes from the cytoplasm to the nucleus, off-target editing is reduced without compromising the on-target editing efficiency. The addition of the E488Q mutation to the editing enzymes, a common strategy for increasing on-target editing efficiency, causes a tremendous increase in off-target editing. These results underscore the need to reduce promiscuity in current approaches to SDRE.

  2. Integrity of the core mitochondrial RNA-binding complex 1/nis vital for trypanosome RNA editing

    Czech Academy of Sciences Publication Activity Database

    Huang, Zhenqiu; Faktorová, Drahomíra; Křížová, A.; Kafková, L.; Read, L. K.; Lukeš, Julius; Hashimi, Hassan

    2015-01-01

    Roč. 21, č. 12 (2015), s. 2088-2102 ISSN 1355-8382 R&D Projects: GA ČR GA15-21974S EU Projects: European Commission(XE) 289007 Institutional support: RVO:60077344 Keywords : RNA editing * mitochondrion * trypanosome Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.344, year: 2015

  3. RNA editing in Drosophila melanogaster: new targets and functionalconsequences

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    Stapleton, Mark; Carlson, Joseph W.; Celniker, Susan E.

    2006-09-05

    Adenosine deaminases that act on RNA (ADARs) catalyze the site-specific conversion of adenosine to inosine in primary mRNA transcripts. These re-coding events affect coding potential, splice-sites, and stability of mature mRNAs. ADAR is an essential gene and studies in mouse, C. elegans, and Drosophila suggest its primary function is to modify adult behavior by altering signaling components in the nervous system. By comparing the sequence of isogenic cDNAs to genomic DNA, we have identified and experimentally verified 27 new targets of Drosophila ADAR. Our analyses lead us to identify new classes of genes whose transcripts are targets of ADAR including components of the actin cytoskeleton, and genes involved in ion homeostasis and signal transduction. Our results indicate that editing in Drosophila increases the diversity of the proteome, and does so in a manner that has direct functional consequences on protein function.

  4. Regulation of Gene Expression by DNA Methylation and RNA Editing in Animals

    DEFF Research Database (Denmark)

    Li, Qiye

    , there has been growing interest in exploring the modifications occurring at the RNA level, which can impact the fate and function of mRNA. One fascinating type of such modifications is RNA editing, which alters specific nucleotides in transcribed RNA and thus can produce transcripts that are not encoded...... (Heterocephalus glaber), a eusocial mammal living in cooperative colonies. Finally, I introduce a software package that I developed that is specifically designed for the genome-wide identification of RNA-editing sites in animals, with the ultimate aim of promoting the evolutionary and functional study of RNA...... editing in different species....

  5. AZIN1 RNA editing confers cancer stemness and enhances oncogenic potential in colorectal cancer.

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    Shigeyasu, Kunitoshi; Okugawa, Yoshinaga; Toden, Shusuke; Miyoshi, Jinsei; Toiyama, Yuji; Nagasaka, Takeshi; Takahashi, Naoki; Kusunoki, Masato; Takayama, Tetsuji; Yamada, Yasuhide; Fujiwara, Toshiyoshi; Chen, Leilei; Goel, Ajay

    2018-06-21

    Adenosine-to-inosine (A-to-I) RNA editing, a process mediated by adenosine deaminases that act on the RNA (ADAR) gene family, is a recently discovered epigenetic modification dysregulated in human cancers. However, the clinical significance and the functional role of RNA editing in colorectal cancer (CRC) remain unclear. We have systematically and comprehensively investigated the significance of the expression status of ADAR1 and of the RNA editing levels of antizyme inhibitor 1 (AZIN1), one of the most frequently edited genes in cancers, in 392 colorectal tissues from multiple independent CRC patient cohorts. Both ADAR1 expression and AZIN1 RNA editing levels were significantly elevated in CRC tissues when compared with corresponding normal mucosa. High levels of AZIN1 RNA editing emerged as a prognostic factor for overall survival and disease-free survival and were an independent risk factor for lymph node and distant metastasis. Furthermore, elevated AZIN1 editing identified high-risk stage II CRC patients. Mechanistically, edited AZIN1 enhances stemness and appears to drive the metastatic processes. We have demonstrated that edited AZIN1 functions as an oncogene and a potential therapeutic target in CRC. Moreover, AZIN1 RNA editing status could be used as a clinically relevant prognostic indicator in CRC patients.

  6. Canonical A-to-I and C-to-U RNA editing is enriched at 3'UTRs and microRNA target sites in multiple mouse tissues.

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    Tongjun Gu

    Full Text Available RNA editing is a process that modifies RNA nucleotides and changes the efficiency and fidelity of the central dogma. Enzymes that catalyze RNA editing are required for life, and defects in RNA editing are associated with many diseases. Recent advances in sequencing have enabled the genome-wide identification of RNA editing sites in mammalian transcriptomes. Here, we demonstrate that canonical RNA editing (A-to-I and C-to-U occurs in liver, white adipose, and bone tissues of the laboratory mouse, and we show that apparent non-canonical editing (all other possible base substitutions is an artifact of current high-throughput sequencing technology. Further, we report that high-confidence canonical RNA editing sites can cause non-synonymous amino acid changes and are significantly enriched in 3' UTRs, specifically at microRNA target sites, suggesting both regulatory and functional consequences for RNA editing.

  7. RNA Editing During Sexual Development Occurs in Distantly Related Filamentous Ascomycetes.

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    Teichert, Ines; Dahlmann, Tim A; Kück, Ulrich; Nowrousian, Minou

    2017-04-01

    RNA editing is a post-transcriptional process that modifies RNA molecules leading to transcript sequences that differ from their template DNA. A-to-I editing was found to be widely distributed in nuclear transcripts of metazoa, but was detected in fungi only recently in a study of the filamentous ascomycete Fusarium graminearum that revealed extensive A-to-I editing of mRNAs in sexual structures (fruiting bodies). Here, we searched for putative RNA editing events in RNA-seq data from Sordaria macrospora and Pyronema confluens, two distantly related filamentous ascomycetes, and in data from the Taphrinomycete Schizosaccharomyces pombe. Like F. graminearum, S. macrospora is a member of the Sordariomycetes, whereas P. confluens belongs to the early-diverging group of Pezizomycetes. We found extensive A-to-I editing in RNA-seq data from sexual mycelium from both filamentous ascomycetes, but not in vegetative structures. A-to-I editing was not detected in different stages of meiosis of S. pombe. A comparison of A-to-I editing in S. macrospora with F. graminearum and P. confluens, respectively, revealed little conservation of individual editing sites. An analysis of RNA-seq data from two sterile developmental mutants of S. macrospora showed that A-to-I editing is strongly reduced in these strains. Sequencing of cDNA fragments containing more than one editing site from P. confluens showed that at the beginning of sexual development, transcripts were incompletely edited or unedited, whereas in later stages transcripts were more extensively edited. Taken together, these data suggest that A-to-I RNA editing is an evolutionary conserved feature during fruiting body development in filamentous ascomycetes. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  8. TbRGG2 facilitates kinetoplastid RNA editing initiation and progression past intrinsic pause sites.

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    Ammerman, Michelle L; Presnyak, Vladimir; Fisk, John C; Foda, Bardees M; Read, Laurie K

    2010-11-01

    TbRGG2 is an essential kinetoplastid RNA editing accessory factor that acts specifically on pan-edited RNAs. To understand the mechanism of TbRGG2 action, we undertook an in-depth analysis of edited RNA populations in TbRGG2 knockdown cells and an in vitro examination of the biochemical activities of the protein. We demonstrate that TbRGG2 down-regulation more severely impacts editing at the 5' ends of pan-edited RNAs than at their 3' ends. The initiation of editing is reduced to some extent in TbRGG2 knockdown cells. In addition, TbRGG2 plays a post-initiation role as editing becomes stalled in TbRGG2-depleted cells, resulting in an overall decrease in the 3' to 5' progression of editing. Detailed analyses of edited RNAs from wild-type and TbRGG2-depleted cells reveal that TbRGG2 facilitates progression of editing past intrinsic pause sites that often correspond to the 3' ends of cognate guide RNAs (gRNAs). In addition, noncanonically edited junction regions are either absent or significantly shortened in TbRGG2-depleted cells, consistent with impaired gRNA transitions. Sequence analysis further suggests that TbRGG2 facilitates complete utilization of certain gRNAs. In vitro RNA annealing and in vivo RNA unwinding assays demonstrate that TbRGG2 can modulate RNA-RNA interactions. Collectively, these data are consistent with a model in which TbRGG2 facilitates initiation and 3' to 5' progression of editing through its ability to affect gRNA utilization, both during the transition between specific gRNAs and during usage of certain gRNAs.

  9. Accurate identification of RNA editing sites from primitive sequence with deep neural networks.

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    Ouyang, Zhangyi; Liu, Feng; Zhao, Chenghui; Ren, Chao; An, Gaole; Mei, Chuan; Bo, Xiaochen; Shu, Wenjie

    2018-04-16

    RNA editing is a post-transcriptional RNA sequence alteration. Current methods have identified editing sites and facilitated research but require sufficient genomic annotations and prior-knowledge-based filtering steps, resulting in a cumbersome, time-consuming identification process. Moreover, these methods have limited generalizability and applicability in species with insufficient genomic annotations or in conditions of limited prior knowledge. We developed DeepRed, a deep learning-based method that identifies RNA editing from primitive RNA sequences without prior-knowledge-based filtering steps or genomic annotations. DeepRed achieved 98.1% and 97.9% area under the curve (AUC) in training and test sets, respectively. We further validated DeepRed using experimentally verified U87 cell RNA-seq data, achieving 97.9% positive predictive value (PPV). We demonstrated that DeepRed offers better prediction accuracy and computational efficiency than current methods with large-scale, mass RNA-seq data. We used DeepRed to assess the impact of multiple factors on editing identification with RNA-seq data from the Association of Biomolecular Resource Facilities and Sequencing Quality Control projects. We explored developmental RNA editing pattern changes during human early embryogenesis and evolutionary patterns in Drosophila species and the primate lineage using DeepRed. Our work illustrates DeepRed's state-of-the-art performance; it may decipher the hidden principles behind RNA editing, making editing detection convenient and effective.

  10. An RNA editing/dsRNA binding-independent gene regulatory mechanism of ADARs and its clinical implication in cancer.

    Science.gov (United States)

    Qi, Lihua; Song, Yangyang; Chan, Tim Hon Man; Yang, Henry; Lin, Chi Ho; Tay, Daryl Jin Tai; Hong, HuiQi; Tang, Sze Jing; Tan, Kar Tong; Huang, Xi Xiao; Lin, Jaymie Siqi; Ng, Vanessa Hui En; Maury, Julien Jean Pierre; Tenen, Daniel G; Chen, Leilei

    2017-10-13

    Adenosine-to-inosine (A-to-I) RNA editing, catalyzed by Adenosine DeAminases acting on double-stranded RNA(dsRNA) (ADAR), occurs predominantly in the 3' untranslated regions (3'UTRs) of spliced mRNA. Here we uncover an unanticipated link between ADARs (ADAR1 and ADAR2) and the expression of target genes undergoing extensive 3'UTR editing. Using METTL7A (Methyltransferase Like 7A), a novel tumor suppressor gene with multiple editing sites at its 3'UTR, we demonstrate that its expression could be repressed by ADARs beyond their RNA editing and double-stranded RNA (dsRNA) binding functions. ADARs interact with Dicer to augment the processing of pre-miR-27a to mature miR-27a. Consequently, mature miR-27a targets the METTL7A 3'UTR to repress its expression level. In sum, our study unveils that the extensive 3'UTR editing of METTL7A is merely a footprint of ADAR binding, and there are a subset of target genes that are equivalently regulated by ADAR1 and ADAR2 through their non-canonical RNA editing and dsRNA binding-independent functions, albeit maybe less common. The functional significance of ADARs is much more diverse than previously appreciated and this gene regulatory function of ADARs is most likely to be of high biological importance beyond the best-studied editing function. This non-editing side of ADARs opens another door to target cancer. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  11. Regulatory factors governing adenosine-to-inosine (A-to-I) RNA editing.

    Science.gov (United States)

    Hong, HuiQi; Lin, Jaymie Siqi; Chen, Leilei

    2015-03-31

    Adenosine-to-inosine (A-to-I) RNA editing, the most prevalent mode of transcript modification in higher eukaryotes, is catalysed by the adenosine deaminases acting on RNA (ADARs). A-to-I editing imposes an additional layer of gene regulation as it dictates various aspects of RNA metabolism, including RNA folding, processing, localization and degradation. Furthermore, editing events in exonic regions contribute to proteome diversity as translational machinery decodes inosine as guanosine. Although it has been demonstrated that dysregulated A-to-I editing contributes to various diseases, the precise regulatory mechanisms governing this critical cellular process have yet to be fully elucidated. However, integration of previous studies revealed that regulation of A-to-I editing is multifaceted, weaving an intricate network of auto- and transregulations, including the involvement of virus-originated factors like adenovirus-associated RNA. Taken together, it is apparent that tipping of any regulatory components will have profound effects on A-to-I editing, which in turn contributes to both normal and aberrant physiological conditions. A complete understanding of this intricate regulatory network may ultimately be translated into new therapeutic strategies against diseases driven by perturbed RNA editing events. Herein, we review the current state of knowledge on the regulatory mechanisms governing A-to-I editing and propose the role of other co-factors that may be involved in this complex regulatory process.

  12. Predicting RNA hyper-editing with a novel tool when unambiguous alignment is impossible.

    Science.gov (United States)

    McKerrow, Wilson H; Savva, Yiannis A; Rezaei, Ali; Reenan, Robert A; Lawrence, Charles E

    2017-07-10

    Repetitive elements are now known to have relevant cellular functions, including self-complementary sequences that form double stranded (ds) RNA. There are numerous pathways that determine the fate of endogenous dsRNA, and misregulation of endogenous dsRNA is a driver of autoimmune disease, particularly in the brain. Unfortunately, the alignment of high-throughput, short-read sequences to repeat elements poses a dilemma: Such sequences may align equally well to multiple genomic locations. In order to differentiate repeat elements, current alignment methods depend on sequence variation in the reference genome. Reads are discarded when no such variations are present. However, RNA hyper-editing, a possible fate for dsRNA, introduces enough variation to distinguish between repeats that are otherwise identical. To take advantage of this variation, we developed a new algorithm, RepProfile, that simultaneously aligns reads and predicts novel variations. RepProfile accurately aligns hyper-edited reads that other methods discard. In particular we predict hyper-editing of Drosophila melanogaster repeat elements in vivo at levels previously described only in vitro, and provide validation by Sanger sequencing sixty-two individual cloned sequences. We find that hyper-editing is concentrated in genes involved in cell-cell communication at the synapse, including some that are associated with neurodegeneration. We also find that hyper-editing tends to occur in short runs. Previous studies of RNA hyper-editing discarded ambiguously aligned reads, ignoring hyper-editing in long, perfect dsRNA - the perfect substrate for hyper-editing. We provide a method that simulation and Sanger validation show accurately predicts such RNA editing, yielding a superior picture of hyper-editing.

  13. Genetic Determinants of RNA Editing Levels of ADAR Targets in Drosophila melanogaster.

    Science.gov (United States)

    Kurmangaliyev, Yerbol Z; Ali, Sammi; Nuzhdin, Sergey V

    2015-12-12

    RNA editing usually affects only a fraction of expressed transcripts and there is a vast amount of variation in editing levels of ADAR (adenosine deaminase, RNA-specific) targets. Here we explore natural genetic variation affecting editing levels of particular sites in 81 natural strains of Drosophila melanogaster. The analysis of associations between editing levels and single-nucleotide polymorphisms allows us to map putative cis-regulatory regions affecting editing of 16 A-to-I editing sites (cis-RNA editing quantitative trait loci or cis-edQTLs, P < 10(-8)). The observed changes in editing levels are validated by independent molecular technique. All identified regulatory variants are located in close proximity of modulated editing sites. Moreover, colocalized editing sites are often regulated by same loci. Similar to expression and splicing QTL studies, the characterization of edQTLs will greatly expand our understanding of cis-regulatory evolution of gene expression. Copyright © 2016 Kurmangaliyev et al.

  14. Condition-specific RNA editing in the coral symbiont Symbiodinium microadriaticum

    KAUST Repository

    Liew, Yi Jin

    2017-03-01

    RNA editing is a rare post-transcriptional event that provides cells with an additional level of gene expression regulation. It has been implicated in various processes including adaptation, viral defence and RNA interference; however, its potential role as a mechanism in acclimatization has just recently been recognised. Here, we show that RNA editing occurs in 1.6% of all nuclear-encoded genes of Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals. All base-substitution edit types were present, and statistically significant motifs were associated with three edit types. Strikingly, a subset of genes exhibited condition-specific editing patterns in response to different stressors that resulted in significant increases of non-synonymous changes. We posit that this previously unrecognised mechanism extends this organism’s capability to respond to stress beyond what is encoded by the genome. This in turn may provide further acclimatization capacity to these organisms, and by extension, their coral hosts.

  15. Condition-specific RNA editing in the coral symbiont Symbiodinium microadriaticum

    KAUST Repository

    Liew, Yi Jin; Li, Yong; Baumgarten, Sebastian; Voolstra, Christian R.; Aranda, Manuel

    2017-01-01

    RNA editing is a rare post-transcriptional event that provides cells with an additional level of gene expression regulation. It has been implicated in various processes including adaptation, viral defence and RNA interference; however, its potential role as a mechanism in acclimatization has just recently been recognised. Here, we show that RNA editing occurs in 1.6% of all nuclear-encoded genes of Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals. All base-substitution edit types were present, and statistically significant motifs were associated with three edit types. Strikingly, a subset of genes exhibited condition-specific editing patterns in response to different stressors that resulted in significant increases of non-synonymous changes. We posit that this previously unrecognised mechanism extends this organism’s capability to respond to stress beyond what is encoded by the genome. This in turn may provide further acclimatization capacity to these organisms, and by extension, their coral hosts.

  16. Genome-Independent Identification of RNA Editing by Mutual Information (GIREMI) | Informatics Technology for Cancer Research (ITCR)

    Science.gov (United States)

    Identification of single-nucleotide variants in RNA-seq data. Current version focuses on detection of RNA editing sites without requiring genome sequence data. New version is under development to separately identify RNA editing sites and genetic variants using RNA-seq data alone.

  17. Editing of HIV-1 RNA by the double-stranded RNA deaminase ADAR1 stimulates viral infection

    Science.gov (United States)

    Doria, Margherita; Neri, Francesca; Gallo, Angela; Farace, Maria Giulia; Michienzi, Alessandro

    2009-01-01

    Adenosine deaminases that act on dsRNA (ADARs) are enzymes that target double-stranded regions of RNA converting adenosines into inosines (A-to-I editing) thus contributing to genome complexity and fine regulation of gene expression. It has been described that a member of the ADAR family, ADAR1, can target viruses and affect their replication process. Here we report evidence showing that ADAR1 stimulates human immuno deficiency virus type 1 (HIV-1) replication by using both editing-dependent and editing-independent mechanisms. We show that over-expression of ADAR1 in HIV-1 producer cells increases viral protein accumulation in an editing-independent manner. Moreover, HIV-1 virions generated in the presence of over-expressed ADAR1 but not an editing-inactive ADAR1 mutant are released more efficiently and display enhanced infectivity, as demonstrated by challenge assays performed with T cell lines and primary CD4+ T lymphocytes. Finally, we report that ADAR1 associates with HIV-1 RNAs and edits adenosines in the 5′ untranslated region (UTR) and the Rev and Tat coding sequence. Overall these results suggest that HIV-1 has evolved mechanisms to take advantage of specific RNA editing activity of the host cell and disclose a stimulatory function of ADAR1 in the spread of HIV-1. PMID:19651874

  18. REDIdb 3.0: A Comprehensive Collection of RNA Editing Events in Plant Organellar Genomes.

    Science.gov (United States)

    Lo Giudice, Claudio; Pesole, Graziano; Picardi, Ernesto

    2018-01-01

    RNA editing is an important epigenetic mechanism by which genome-encoded transcripts are modified by substitutions, insertions and/or deletions. It was first discovered in kinetoplastid protozoa followed by its reporting in a wide range of organisms. In plants, RNA editing occurs mostly by cytidine (C) to uridine (U) conversion in translated regions of organelle mRNAs and tends to modify affected codons restoring evolutionary conserved aminoacid residues. RNA editing has also been described in non-protein coding regions such as group II introns and structural RNAs. Despite its impact on organellar transcriptome and proteome complexity, current primary databases still do not provide a specific field for RNA editing events. To overcome these limitations, we developed REDIdb a specialized database for RNA editing modifications in plant organelles. Hereafter we describe its third release containing more than 26,000 events in a completely novel web interface to accommodate RNA editing in its genomics, biological and evolutionary context through whole genome maps and multiple sequence alignments. REDIdb is freely available at http://srv00.recas.ba.infn.it/redidb/index.html.

  19. REDIdb 3.0: A Comprehensive Collection of RNA Editing Events in Plant Organellar Genomes

    Directory of Open Access Journals (Sweden)

    Claudio Lo Giudice

    2018-04-01

    Full Text Available RNA editing is an important epigenetic mechanism by which genome-encoded transcripts are modified by substitutions, insertions and/or deletions. It was first discovered in kinetoplastid protozoa followed by its reporting in a wide range of organisms. In plants, RNA editing occurs mostly by cytidine (C to uridine (U conversion in translated regions of organelle mRNAs and tends to modify affected codons restoring evolutionary conserved aminoacid residues. RNA editing has also been described in non-protein coding regions such as group II introns and structural RNAs. Despite its impact on organellar transcriptome and proteome complexity, current primary databases still do not provide a specific field for RNA editing events. To overcome these limitations, we developed REDIdb a specialized database for RNA editing modifications in plant organelles. Hereafter we describe its third release containing more than 26,000 events in a completely novel web interface to accommodate RNA editing in its genomics, biological and evolutionary context through whole genome maps and multiple sequence alignments. REDIdb is freely available at http://srv00.recas.ba.infn.it/redidb/index.html

  20. RNA editing in kinetoplastid parasites: what to do with U

    NARCIS (Netherlands)

    Sloof, P.; Benne, R.

    1997-01-01

    The editing of the mitochondrial RNAs of kinetoplastid protozoa is a bizarre form of transcript maturation that involves insertion and deletion of uridylate residues. Editing leads to the formation of translational initiation and termination codons, the correction of gene-encoded reading frame

  1. A genome-wide map of hyper-edited RNA reveals numerous new sites

    Science.gov (United States)

    Porath, Hagit T.; Carmi, Shai; Levanon, Erez Y.

    2014-01-01

    Adenosine-to-inosine editing is one of the most frequent post-transcriptional modifications, manifested as A-to-G mismatches when comparing RNA sequences with their source DNA. Recently, a number of RNA-seq data sets have been screened for the presence of A-to-G editing, and hundreds of thousands of editing sites identified. Here we show that existing screens missed the majority of sites by ignoring reads with excessive (‘hyper’) editing that do not easily align to the genome. We show that careful alignment and examination of the unmapped reads in RNA-seq studies reveal numerous new sites, usually many more than originally discovered, and in precisely those regions that are most heavily edited. Specifically, we discover 327,096 new editing sites in the heavily studied Illumina Human BodyMap data and more than double the number of detected sites in several published screens. We also identify thousands of new sites in mouse, rat, opossum and fly. Our results establish that hyper-editing events account for the majority of editing sites. PMID:25158696

  2. Regulation of gene expression in neuronal tissue by RNA interference and editing

    DEFF Research Database (Denmark)

    Venø, Morten Trillingsgaard

    No tissue in the mammalian organism is more complex than the brain. This complexity is in part the result of precise timing and interplay of a large number mechanisms modulating gene expression post-transcriptionally. Fine-tuning mechanisms such as A-to-I editing of RNA transcripts and regulation...... mediated by microRNAs are crucial for the correct function of the mammalian brain. We are addressing A-to-I editing and regulation by microRNAs with spatio-temporal resolution in the embryonic porcine brain by Solexa sequencing of microRNAs and 454 sequencing of edited neuronal messenger RNAs, resulting...... in detailed data of both of these fine-tuning mechanisms in the embryonic development of the pig. Editing levels of transcripts examined are generally seen to increase through development, in agreement with editing of specific microRNA also examined in the Solexa sequencing study. Three studies examining...

  3. RNA editing is induced by type I interferon in esophageal squamous cell carcinoma.

    Science.gov (United States)

    Zhang, Jinyao; Chen, Zhaoli; Tang, Zefang; Huang, Jianbing; Hu, Xueda; He, Jie

    2017-07-01

    In recent years, abnormal RNA editing has been shown to play an important role in the development of esophageal squamous cell carcinoma, as such abnormal editing is catalyzed by ADAR (adenosine deaminases acting on RNA). However, the regulatory mechanism of ADAR1 in esophageal squamous cell carcinomas remains largely unknown. In this study, we investigated ADAR1 expression and its association with RNA editing in esophageal squamous cell carcinomas. RNA sequencing applied to esophageal squamous cell carcinoma clinical samples showed that ADAR1 expression was correlated with the expression of STAT1, STAT2, and IRF9. In vitro experiments showed that the abundance of ADAR1 protein was associated with the induced activation of the JAK/STAT pathway by type I interferon. RNA sequencing results showed that treatment with type I interferon caused an increase in the number and degree of RNA editing in esophageal squamous cell carcinoma cell lines. In conclusion, the activation of the JAK/STAT pathway is a regulatory mechanism of ADAR1 expression and causes abnormal RNA editing profile in esophageal squamous cell carcinoma. This mechanism may serve as a new target for esophageal squamous cell carcinoma therapy.

  4. A distant cis acting intronic element induces site-selective RNA editing

    DEFF Research Database (Denmark)

    Daniel, Chammiran; Venø, Morten Trillingsgaard; Ekdahl, Ylva

    2012-01-01

    Transcripts have been found to be site selectively edited from adenosine-to-inosine (A-to-I) in the mammalian brain, mostly in genes involved in neurotransmission. While A-to-I editing occurs at double-stranded structures, other structural requirements are largely unknown. We have investigated...... shown to be important for A-to-I editing. We demonstrate that the element also can induce editing in related but normally not edited RNA sequences. In human, thousands of genes are edited in duplexes formed by inverted repeats in non-coding regions. It is likely that numerous such duplexes can induce...... the requirements for editing at the I/M site in the Gabra-3 transcript of the GABA(A) receptor. We identify an evolutionarily conserved intronic duplex, 150 nt downstream of the exonic hairpin where the I/M site resides, which is required for its editing. This is the first time a distant RNA structure has been...

  5. How the SQUID was born

    International Nuclear Information System (INIS)

    Silver, Arnold H

    2006-01-01

    I was asked to speak about the discovery and invention of the SQUID at the International Superconducting Electronics Conference (ISEC) 2005 banquet. This narrative is based on my personal recollections of the sequence of events and the motivations. I have edited the text and added figures for clarity. Although it is an old story, it may contain some useful lessons

  6. How the SQUID was born

    Energy Technology Data Exchange (ETDEWEB)

    Silver, Arnold H [Northrop Grumman Space Technology, One Space Park, Redondo Beach, CA 90278 (United States)

    2006-05-15

    I was asked to speak about the discovery and invention of the SQUID at the International Superconducting Electronics Conference (ISEC) 2005 banquet. This narrative is based on my personal recollections of the sequence of events and the motivations. I have edited the text and added figures for clarity. Although it is an old story, it may contain some useful lessons.

  7. Proofreading in vivo: Editing of homocysteine by methionyl-tRNA synthetase in Escherichia coli

    International Nuclear Information System (INIS)

    Jakubowski, H.

    1990-01-01

    Previous in vitro studies have established a pre-transfer proofreading mechanism for editing of homocysteine by bacterial methionyl-, isoleucyl-, and valyl-tRNA synthetases. The unusual feature of the editing is the formation of a distinct compound, homocysteine thiolactone. Now, two-dimensional TLC analysis of 35S-labeled amino acids extracted from cultures of the bacterium Escherichia coli reveals that the thiolactone is also synthesized in vivo. In E. coli, the thiolactone is made from homocysteine in a reaction catalyzed by methionyl-tRNA synthetase. One molecule of homocysteine is edited as thiolactone per 109 molecules of methionine incorporated into protein in vivo. These results not only directly demonstrate that the adenylate proofreading pathway for rejection of misactivated homocysteine operates in vivo in E. coli but, in general, establish the importance of error-editing mechanisms in living cells

  8. Inherited variants affecting RNA editing may contribute to ovarian cancer susceptibility

    DEFF Research Database (Denmark)

    Permuth, Jennifer B; Reid, Brett; Earp, Madalene

    2016-01-01

    RNA editing in mammals is a form of post-transcriptional modification in which adenosine is converted to inosine by the adenosine deaminases acting on RNA (ADAR) family of enzymes. Based on evidence of altered ADAR expression in epithelial ovarian cancers (EOC), we hypothesized that single nucleo......, including rs1127313 (G/A), a SNP in the 3' untranslated region. In summary, germline variation involving RNA editing genes may influence EOC susceptibility, warranting further investigation of inherited and acquired alterations affecting RNA editing.......RNA editing in mammals is a form of post-transcriptional modification in which adenosine is converted to inosine by the adenosine deaminases acting on RNA (ADAR) family of enzymes. Based on evidence of altered ADAR expression in epithelial ovarian cancers (EOC), we hypothesized that single...... nucleotide polymorphisms (SNPs) in ADAR genes modify EOC susceptibility, potentially by altering ovarian tissue gene expression. Using directly genotyped and imputed data from 10,891 invasive EOC cases and 21,693 controls, we evaluated the associations of 5,303 SNPs in ADAD1, ADAR, ADAR2, ADAR3, and SND1...

  9. A-to-I RNA editing: the "ADAR" side of human cancer.

    Science.gov (United States)

    Galeano, Federica; Tomaselli, Sara; Locatelli, Franco; Gallo, Angela

    2012-05-01

    Carcinogenesis is a complex, multi-stage process depending on both endogenous and exogenous factors. In the past years, DNA mutations provided important clues to the comprehension of the molecular pathways involved in numerous cancers. Recently, post-transcriptional modification events, such as RNA editing, are emerging as new players in several human diseases, including tumours. A-to-I RNA editing changes the nucleotide sequence of target RNAs, introducing A-to-I/G "mutations". Since ADAR enzymes catalyse this nucleotide conversion, their expression/activity is essential and finely regulated in normal cells. This review summarizes the available knowledge on A-to-I RNA editing in the cancer field, giving a new view on how ADARs may play a role in carcinogenesis. Copyright © 2011 Elsevier Ltd. All rights reserved.

  10. Conjugation and Evaluation of Triazole?Linked Single Guide RNA for CRISPR?Cas9 Gene Editing

    OpenAIRE

    He, Kaizhang; Chou, Eldon T.; Begay, Shawn; Anderson, Emily M.; van?Brabant?Smith, Anja

    2016-01-01

    Abstract The CRISPR?Cas9 gene editing system requires Cas9 endonuclease and guide RNAs (either the natural dual RNA consisting of crRNA and tracrRNA or a chimeric single guide RNA) that direct site?specific double?stranded DNA cleavage. This communication describes a click ligation approach that uses alkyne?azide cycloaddition to generate a triazole?linked single guide RNA (sgRNA). The conjugated sgRNA shows efficient and comparable genome editing activity to natural dual RNA and unmodified s...

  11. ADAR RNA editing in human disease; more to it than meets the I.

    Science.gov (United States)

    Gallo, Angela; Vukic, Dragana; Michalík, David; O'Connell, Mary A; Keegan, Liam P

    2017-09-01

    We review the structures and functions of ADARs and their involvements in human diseases. ADAR1 is widely expressed, particularly in the myeloid component of the blood system, and plays a prominent role in promiscuous editing of long dsRNA. Missense mutations that change ADAR1 residues and reduce RNA editing activity cause Aicardi-Goutières Syndrome, a childhood encephalitis and interferonopathy that mimics viral infection and resembles an extreme form of Systemic Lupus Erythmatosus (SLE). In Adar1 mouse mutant models aberrant interferon expression is prevented by eliminating interferon activation signaling from cytoplasmic dsRNA sensors, indicating that unedited cytoplasmic dsRNA drives the immune induction. On the other hand, upregulation of ADAR1 with widespread promiscuous RNA editing is a prominent feature of many cancers and particular site-specific RNA editing events are also affected. ADAR2 is most highly expressed in brain and is primarily required for site-specific editing of CNS transcripts; recent findings indicate that ADAR2 editing is regulated by neuronal excitation for synaptic scaling of glutamate receptors. ADAR2 is also linked to the circadian clock and to sleep. Mutations in ADAR2 could contribute to excitability syndromes such as epilepsy, to seizures, to diseases involving neuronal plasticity defects, such as autism and Fragile-X Syndrome, to neurodegenerations such as ALS, or to astrocytomas or glioblastomas in which reduced ADAR2 activity is required for oncogenic cell behavior. The range of human disease associated with ADAR1 mutations may extend further to include other inflammatory conditions while ADAR2 mutations may affect psychiatric conditions.

  12. The expression of apoB mRNA editing factors is not the sole determinant for the induction of editing in differentiating Caco-2 cells

    International Nuclear Information System (INIS)

    Galloway, Chad A.; Smith, Harold C.

    2010-01-01

    Apolipoprotein B mRNA is edited at cytidine 6666 in the enterocytes lining the small intestine of all mammals; converting a CAA codon to a UAA stop codon. The conversion is ∼80% efficient in this tissue and leads to the expression of the truncated protein, ApoB48, essential for secretion of dietary lipid as chylomicrons. Caco-2 cell raft cultures have been used as an in vitro model for the induction of editing activity during human small intestinal cell differentiation. This induction of apoB mRNA editing has been ascribed to the expression of APOBEC-1. In agreement our data demonstrated differentiation-dependent induction of expression of the editing enzyme APOBEC-1 and in addition we show alternative splicing of the essential auxiliary factor ACF. However, transfection of these editing factors in undifferentiated proliferating Caco-2 cells was not sufficient to induce robust apoB mRNA editing activity. Only differentiation of Caco-2 cells could induce more physiological like levels of apoB mRNA editing. The data suggested that additional regulatory mechanism(s) were induced by differentiation that controlled the functional activity of editing factors.

  13. New Insights into the Biological Role of Mammalian ADARs; the RNA Editing Proteins

    Directory of Open Access Journals (Sweden)

    Niamh Mannion

    2015-09-01

    Full Text Available The ADAR proteins deaminate adenosine to inosine in double-stranded RNA which is one of the most abundant modifications present in mammalian RNA. Inosine can have a profound effect on the RNAs that are edited, not only changing the base-pairing properties, but can also result in recoding, as inosine behaves as if it were guanosine. In mammals there are three ADAR proteins and two ADAR-related proteins (ADAD expressed. All have a very similar modular structure; however, both their expression and biological function differ significantly. Only two of the ADAR proteins have enzymatic activity. However, both ADAR and ADAD proteins possess the ability to bind double-strand RNA. Mutations in ADARs have been associated with many diseases ranging from cancer, innate immunity to neurological disorders. Here, we will discuss in detail the domain structure of mammalian ADARs, the effects of RNA editing, and the role of ADARs in human diseases.

  14. New Insights into the Biological Role of Mammalian ADARs; the RNA Editing Proteins

    Science.gov (United States)

    Mannion, Niamh; Arieti, Fabiana; Gallo, Angela; Keegan, Liam P.; O’Connell, Mary A.

    2015-01-01

    The ADAR proteins deaminate adenosine to inosine in double-stranded RNA which is one of the most abundant modifications present in mammalian RNA. Inosine can have a profound effect on the RNAs that are edited, not only changing the base-pairing properties, but can also result in recoding, as inosine behaves as if it were guanosine. In mammals there are three ADAR proteins and two ADAR-related proteins (ADAD) expressed. All have a very similar modular structure; however, both their expression and biological function differ significantly. Only two of the ADAR proteins have enzymatic activity. However, both ADAR and ADAD proteins possess the ability to bind double-strand RNA. Mutations in ADARs have been associated with many diseases ranging from cancer, innate immunity to neurological disorders. Here, we will discuss in detail the domain structure of mammalian ADARs, the effects of RNA editing, and the role of ADARs in human diseases. PMID:26437436

  15. The ADAR RNA editing enzyme controls neuronal excitability in Drosophila melanogaster

    Science.gov (United States)

    Li, Xianghua; Overton, Ian M.; Baines, Richard A.; Keegan, Liam P.; O’Connell, Mary A.

    2014-01-01

    RNA editing by deamination of specific adenosine bases to inosines during pre-mRNA processing generates edited isoforms of proteins. Recoding RNA editing is more widespread in Drosophila than in vertebrates. Editing levels rise strongly at metamorphosis, and Adar5G1 null mutant flies lack editing events in hundreds of CNS transcripts; mutant flies have reduced viability, severely defective locomotion and age-dependent neurodegeneration. On the other hand, overexpressing an adult dADAR isoform with high enzymatic activity ubiquitously during larval and pupal stages is lethal. Advantage was taken of this to screen for genetic modifiers; Adar overexpression lethality is rescued by reduced dosage of the Rdl (Resistant to dieldrin), gene encoding a subunit of inhibitory GABA receptors. Reduced dosage of the Gad1 gene encoding the GABA synthetase also rescues Adar overexpression lethality. Drosophila Adar5G1 mutant phenotypes are ameliorated by feeding GABA modulators. We demonstrate that neuronal excitability is linked to dADAR expression levels in individual neurons; Adar-overexpressing larval motor neurons show reduced excitability whereas Adar5G1 null mutant or targeted Adar knockdown motor neurons exhibit increased excitability. GABA inhibitory signalling is impaired in human epileptic and autistic conditions, and vertebrate ADARs may have a relevant evolutionarily conserved control over neuronal excitability. PMID:24137011

  16. CRISPR/Cas9-mediated noncoding RNA editing in human cancers.

    Science.gov (United States)

    Yang, Jie; Meng, Xiaodan; Pan, Jinchang; Jiang, Nan; Zhou, Chengwei; Wu, Zhenhua; Gong, Zhaohui

    2018-01-02

    Cancer is characterized by multiple genetic and epigenetic alterations, including a higher prevalence of mutations of oncogenes and/or tumor suppressors. Mounting evidences have shown that noncoding RNAs (ncRNAs) are involved in the epigenetic regulation of cancer genes and their associated pathways. The clustered regularly interspaced short palindromic repeats (CRISPR)-associated nuclease 9 (CRISPR/Cas9) system, a revolutionary genome-editing technology, has shed light on ncRNA-based cancer therapy. Here, we briefly introduce the classifications and mechanisms of CRISPR/Cas9 system. Importantly, we mainly focused on the applications of CRISPR/Cas9 system as a molecular tool for ncRNA (microRNA, long noncoding RNA and circular RNA, etc.) editing in human cancers, and the novel techniques that are based on CRISPR/Cas9 system. Additionally, the off-target effects and the corresponding solutions as well as the challenges toward CRISPR/Cas9 were also evaluated and discussed. Long- and short-ncRNAs have been employed as targets in precision oncology, and CRISPR/Cas9-mediated ncRNA editing may provide an excellent way to cure cancer.

  17. Modulation of microRNA editing, expression and processing by ADAR2 deaminase in glioblastoma.

    Science.gov (United States)

    Tomaselli, Sara; Galeano, Federica; Alon, Shahar; Raho, Susanna; Galardi, Silvia; Polito, Vinicia Assunta; Presutti, Carlo; Vincenti, Sara; Eisenberg, Eli; Locatelli, Franco; Gallo, Angela

    2015-01-13

    ADAR enzymes convert adenosines to inosines within double-stranded RNAs, including microRNA (miRNA) precursors, with important consequences on miRNA retargeting and expression. ADAR2 activity is impaired in glioblastoma and its rescue has anti-tumoral effects. However, how ADAR2 activity may impact the miRNome and the progression of glioblastoma is not known. By integrating deep-sequencing and array approaches with bioinformatics analyses and molecular studies, we show that ADAR2 is essential to edit a small number of mature miRNAs and to significantly modulate the expression of about 90 miRNAs in glioblastoma cells. Specifically, the rescue of ADAR2 activity in cancer cells recovers the edited miRNA population lost in glioblastoma cell lines and tissues, and rebalances expression of onco-miRNAs and tumor suppressor miRNAs to the levels observed in normal human brain. We report that the major effect of ADAR2 is to reduce the expression of a large number of miRNAs, most of which act as onco-miRNAs. ADAR2 can edit miR-222/221 and miR-21 precursors and decrease the expression of the corresponding mature onco-miRNAs in vivo and in vitro, with important effects on cell proliferation and migration. Our findings disclose an additional layer of complexity in miRNome regulation and provide information to better understand the impact of ADAR2 editing enzyme in glioblastoma. We propose that ADAR2 is a key factor for maintaining edited-miRNA population and balancing the expression of several essential miRNAs involved in cancer.

  18. Guide totheNomenclatureofKinetoplastidRNA Editing: AProposal

    Czech Academy of Sciences Publication Activity Database

    Simpson, L.; Aphasizhev, R.; Lukeš, Julius; Cruz-Reyes, J.

    2010-01-01

    Roč. 161, č. 1 (2010), s. 2-6 ISSN 1434-4610 Institutional research plan: CEZ:AV0Z60220518 Keywords : TRYPANOSOMA-BRUCEI MITOCHONDRIA * BINDING COMPLEX * EDITOSOME INTEGRITY * MESSENGER-RNA * U-DELETION * LEISHMANIA Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.329, year: 2010

  19. Efficient CRISPR/Cas9-Mediated Genome Editing Using a Chimeric Single-Guide RNA Molecule

    KAUST Repository

    Butt, Haroon

    2017-08-24

    The CRISPR/Cas9 system has been applied in diverse eukaryotic organisms for targeted mutagenesis. However, targeted gene editing is inefficient and requires the simultaneous delivery of a DNA template for homology-directed repair (HDR). Here, we used CRISPR/Cas9 to generate targeted double-strand breaks and to deliver an RNA repair template for HDR in rice (Oryza sativa). We used chimeric single-guide RNA (cgRNA) molecules carrying both sequences for target site specificity (to generate the double-strand breaks) and repair template sequences (to direct HDR), flanked by regions of homology to the target. Gene editing was more efficient in rice protoplasts using repair templates complementary to the non-target DNA strand, rather than the target strand. We applied this cgRNA repair method to generate herbicide resistance in rice, which showed that this cgRNA repair method can be used for targeted gene editing in plants. Our findings will facilitate applications in functional genomics and targeted improvement of crop traits.

  20. DEAH-RHA helicase•Znf cofactor systems in kinetoplastid RNA editing and evolutionarily distant RNA processes

    Science.gov (United States)

    Cruz-Reyes, Jorge; Mooers, Blaine H.M.; Abu-Adas, Zakaria; Kumar, Vikas; Gulati, Shelly

    2016-01-01

    Multi-zinc finger proteins are an emerging class of cofactors in DEAH-RHA RNA helicases across highly divergent eukaryotic lineages. DEAH-RHA helicase•zinc finger cofactor partnerships predate the split of kinetoplastid protozoa, which include several human pathogens, from other eukaryotic lineages 100–400 Ma. Despite a long evolutionary history, the prototypical DEAH-RHA domains remain highly conserved. This short review focuses on a recently identified DEAH-RHA helicase•zinc finger cofactor system in kinetoplastid RNA editing, and its potential functional parallels with analogous systems in embryogenesis control in nematodes and antivirus protection in humans. PMID:27540585

  1. Auto-Regulatory RNA Editing Fine-Tunes mRNA Re-Coding and Complex Behaviour in Drosophila

    Science.gov (United States)

    Savva, Yiannis A.; Jepson, James E.C; Sahin, Asli; Sugden, Arthur U.; Dorsky, Jacquelyn S.; Alpert, Lauren; Lawrence, Charles; Reenan, Robert A.

    2014-01-01

    Auto-regulatory feedback loops are a common molecular strategy used to optimize protein function. In Drosophila many mRNAs involved in neuro-transmission are re-coded at the RNA level by the RNA editing enzyme dADAR, leading to the incorporation of amino acids that are not directly encoded by the genome. dADAR also re-codes its own transcript, but the consequences of this auto-regulation in vivo are unclear. Here we show that hard-wiring or abolishing endogenous dADAR auto-regulation dramatically remodels the landscape of re-coding events in a site-specific manner. These molecular phenotypes correlate with altered localization of dADAR within the nuclear compartment. Furthermore, auto-editing exhibits sexually dimorphic patterns of spatial regulation and can be modified by abiotic environmental factors. Finally, we demonstrate that modifying dAdar auto-editing affects adaptive complex behaviors. Our results reveal the in vivo relevance of auto-regulatory control over post-transcriptional mRNA re-coding events in fine-tuning brain function and organismal behavior. PMID:22531175

  2. RNA interference analyses suggest a transcript-specific regulatory role for mitochondrial RNA-binding proteins MRP1 and MRP2 in RNA editing and other RNA processing in Trypanosoma brucei

    NARCIS (Netherlands)

    Vondrusková, Eva; van den Burg, Janny; Zíková, Alena; Ernst, Nancy Lewis; Stuart, Kenneth; Benne, Rob; Lukes, Julius

    2005-01-01

    Mitochondrial RNA-binding proteins MRP1 and MRP2 occur in a heteromeric complex that appears to play a role in U-insertion/deletion editing in trypanosomes. Reduction in the levels of MRP1 (gBP21) and/or MRP2 (gBP25) mRNA by RNA interference in procyclic Trypanosoma brucei resulted in severe growth

  3. Small RNA and A-to-I Editing in Autism Spectrum Disorders

    Science.gov (United States)

    Eran, Alal

    One in every 88 children is diagnosed with Autism Spectrum Disorders (ASDs), a set of neurodevelopmental conditions characterized by social impairments, communication deficits, and repetitive behavior. ASDs have a substantial genetic component, but the specific cause of most cases remains unknown. Understanding gene-environment interactions underlying ASD is essential for improving early diagnosis and identifying critical targets for intervention and prevention. Towards this goal, we surveyed adenosine-to-inosine (A-to-I) RNA editing in autistic brains. A-to-I editing is an epigenetic mechanism that fine-tunes synaptic function in response to environmental stimuli, shown to modulate complex behavior in animals. We used ultradeep sequencing to quantify A-to-I receding of candidate synaptic genes in postmortem cerebella from individuals with ASD and neurotypical controls. We found unexpectedly wide distributions of human A-to-I editing levels, whose extremes were consistently populated by individuals with ASD. We correlated A-to-I editing with isoform usage, identified clusters of correlated sites, and examined differential editing patterns. Importantly, we found that individuals with ASD commonly use a dysfunctional form of the editing enzyme ADARB1. We next profiled small RNAs thought to regulate A-to-I editing, which originate from one of the most commonly altered loci in ASD, 15q11. Deep targeted sequencing of SNORD115 and SNORD116 transcripts enabled their high-resolution detection in human brains, and revealed a strong gender bias underlying their expression. The consistent 2-fold upregulation of 15q11 small RNAs in male vs. female cerebella could be important in delineating the role of this locus in ASD, a male dominant disorder. Overall, these studies provide an accurate population-level view of small RNA and A-to-I editing in human cerebella, and suggest that A-to-I editing of synaptic genes may be informative for assessing the epigenetic risk for autism

  4. RNA editing differently affects protein-coding genes in D. melanogaster and H. sapiens.

    Science.gov (United States)

    Grassi, Luigi; Leoni, Guido; Tramontano, Anna

    2015-07-14

    When an RNA editing event occurs within a coding sequence it can lead to a different encoded amino acid. The biological significance of these events remains an open question: they can modulate protein functionality, increase the complexity of transcriptomes or arise from a loose specificity of the involved enzymes. We analysed the editing events in coding regions that produce or not a change in the encoded amino acid (nonsynonymous and synonymous events, respectively) in D. melanogaster and in H. sapiens and compared them with the appropriate random models. Interestingly, our results show that the phenomenon has rather different characteristics in the two organisms. For example, we confirm the observation that editing events occur more frequently in non-coding than in coding regions, and report that this effect is much more evident in H. sapiens. Additionally, in this latter organism, editing events tend to affect less conserved residues. The less frequently occurring editing events in Drosophila tend to avoid drastic amino acid changes. Interestingly, we find that, in Drosophila, changes from less frequently used codons to more frequently used ones are favoured, while this is not the case in H. sapiens.

  5. RNA-Generated and Gene-Edited Induced Pluripotent Stem Cells for Disease Modeling and Therapy.

    Science.gov (United States)

    Kehler, James; Greco, Marianna; Martino, Valentina; Pachiappan, Manickam; Yokoe, Hiroko; Chen, Alice; Yang, Miranda; Auerbach, Jonathan; Jessee, Joel; Gotte, Martin; Milanesi, Luciano; Albertini, Alberto; Bellipanni, Gianfranco; Zucchi, Ileana; Reinbold, Rolland A; Giordano, Antonio

    2017-06-01

    Cellular reprogramming by epigenomic remodeling of chromatin holds great promise in the field of human regenerative medicine. As an example, human-induced Pluripotent Stem Cells (iPSCs) obtained by reprograming of patient somatic cells are sufficiently similar to embryonic stem cells (ESCs) and can generate all cell types of the human body. Clinical use of iPSCs is dependent on methods that do not utilize genome altering transgenic technologies that are potentially unsafe and ethically unacceptable. Transient delivery of exogenous RNA into cells provides a safer reprogramming system to transgenic approaches that rely on exogenous DNA or viral vectors. RNA reprogramming may prove to be more suitable for clinical applications and provide stable starting cell lines for gene-editing, isolation, and characterization of patient iPSC lines. The introduction and rapid evolution of CRISPR/Cas9 gene-editing systems has provided a readily accessible research tool to perform functional human genetic experiments. Similar to RNA reprogramming, transient delivery of mRNA encoding Cas9 in combination with guide RNA sequences to target specific points in the genome eliminates the risk of potential integration of Cas9 plasmid constructs. We present optimized RNA-based laboratory procedure for making and editing iPSCs. In the near-term these two powerful technologies are being harnessed to dissect mechanisms of human development and disease in vitro, supporting both basic, and translational research. J. Cell. Physiol. 232: 1262-1269, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  6. Reciprocal regulation of A-to-I RNA editing and the vertebrate nervous system

    Directory of Open Access Journals (Sweden)

    Andrew Charles Penn

    2013-04-01

    Full Text Available The fine control of molecules mediating communication in the nervous system is key to adjusting neuronal responsiveness during development and in maintaining the stability of established networks in the face of altered sensory input. To prevent culmination of pathological recurrent network excitation or debilitating periods of quiescence, adaptive alterations occur in the signalling molecules and ion channels that control membrane excitability and synaptic transmission. However, rather than encoding (and thus ‘hardwiring’ modified gene copies, the nervous systems of metazoa have opted for expanding on post-transcriptional pre-mRNA splicing by altering key encoded amino acids using a conserved mechanism of A-to-I RNA editing: the enzymatic deamination of adenosine resulting in a change in the nucleotide to inosine. Inosine exhibits similar base-pairing properties to guanosine with respect to tRNA codon recognition, replication by polymerases and RNA secondary structure forming capacity. In addition to recoding within the open reading frame, adenosine deamination also occurs with high frequency throughout the non-coding transcriptome, where it affects multiple aspects of RNA metabolism and gene expression. We will describe here the recoding function of key RNA editing targets in the mammalian central nervous system (CNS and their potential to be regulated. We will then discuss how interactions of A-to-I editing with gene expression and alternative splicing could play a wider role in regulating the neuronal transcriptome. Finally, we will highlight the increasing complexity of this multifaceted control hub by summarising new findings from high-throughput studies.

  7. Alternative splicing and extensive RNA editing of human TPH2 transcripts.

    Directory of Open Access Journals (Sweden)

    Maik Grohmann

    Full Text Available Brain serotonin (5-HT neurotransmission plays a key role in the regulation of mood and has been implicated in a variety of neuropsychiatric conditions. Tryptophan hydroxylase (TPH is the rate-limiting enzyme in the biosynthesis of 5-HT. Recently, we discovered a second TPH isoform (TPH2 in vertebrates, including man, which is predominantly expressed in brain, while the previously known TPH isoform (TPH1 is primarly a non-neuronal enzyme. Overwhelming evidence now points to TPH2 as a candidate gene for 5-HT-related psychiatric disorders. To assess the role of TPH2 gene variability in the etiology of psychiatric diseases we performed cDNA sequence analysis of TPH2 transcripts from human post mortem amygdala samples obtained from individuals with psychiatric disorders (drug abuse, schizophrenia, suicide and controls. Here we show that TPH2 exists in two alternatively spliced variants in the coding region, denoted TPH2a and TPH2b. Moreover, we found evidence that the pre-mRNAs of both splice variants are dynamically RNA-edited in a mutually exclusive manner. Kinetic studies with cell lines expressing recombinant TPH2 variants revealed a higher activity of the novel TPH2B protein compared with the previously known TPH2A, whereas RNA editing was shown to inhibit the enzymatic activity of both TPH2 splice variants. Therefore, our results strongly suggest a complex fine-tuning of central nervous system 5-HT biosynthesis by TPH2 alternative splicing and RNA editing. Finally, we present molecular and large-scale linkage data evidencing that deregulated alternative splicing and RNA editing is involved in the etiology of psychiatric diseases, such as suicidal behaviour.

  8. Dual core processing: MRB1 is an emerging kinetoplast RNA editing complex

    Czech Academy of Sciences Publication Activity Database

    Hashimi, Hassan; Zimmer, S.L.; Ammerman, M. L.; Read, L. K.; Lukeš, Julius

    2013-01-01

    Roč. 29, č. 2 (2013), s. 91-99 ISSN 1471-4922 R&D Projects: GA ČR GAP305/12/2261; GA ČR GA204/09/1667 Institutional support: RVO:60077344 Keywords : kinetoplastida * trypanosome * RNA editing * protein complexes * RECC * MRB1 Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 6.217, year: 2013 http://www.sciencedirect.com/science/article/pii/S1471492212001985

  9. A core MRB1 complex component is indispensable for RNA editing in insect and human infective stages of Trypanosoma brucei.

    Directory of Open Access Journals (Sweden)

    Michelle L Ammerman

    Full Text Available Uridine insertion/deletion RNA editing is a unique and vital process in kinetoplastids, required for creation of translatable open reading frames in most mitochondrially-encoded RNAs. Emerging as a key player in this process is the mitochondrial RNA binding 1 (MRB1 complex. MRB1 comprises an RNA-independent core complex of at least six proteins, including the GAP1/2 guide RNA (gRNA binding proteins. The core interacts in an RNA-enhanced or -dependent manner with imprecisely defined TbRGG2 subcomplexes, Armadillo protein MRB10130, and additional factors that comprise the dynamic MRB1 complex. Towards understanding MRB1 complex function in RNA editing, we present here functional characterization of the pentein domain-containing MRB1 core protein, MRB11870. Inducible RNAi studies demonstrate that MRB11870 is essential for proliferation of both insect vector and human infective stage T. brucei. MRB11870 ablation causes a massive defect in RNA editing, affecting both pan-edited and minimally edited mRNAs, but does not substantially affect mitochondrial RNA stability or processing of precursor transcripts. The editing defect in MRB1-depleted cells occurs at the initiation stage of editing, as pre-edited mRNAs accumulate. However, the gRNAs that direct editing remain abundant in the knockdown cells. To examine the contribution of MRB11870 to MRB1 macromolecular interactions, we tagged core complexes and analyzed their composition and associated proteins in the presence and absence of MRB11870. These studies demonstrated that MRB11870 is essential for association of GAP1/2 with the core, as well as for interaction of the core with other proteins and subcomplexes. Together, these data support a model in which the MRB1 core mediates functional interaction of gRNAs with the editing machinery, having GAP1/2 as its gRNA binding constituents. MRB11870 is a critical component of the core, essential for its structure and function.

  10. Genes (including RNA editing information) - RMG | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available t tested T: transcribed N: not transcribed Editing site Editing site N: not transcribed Previous reports on ...editing sites Previous reports on editing sites Strand Strand S: sense A: antisense exon1 start Start positi

  11. Cell-type-specific genome editing with a microRNA-responsive CRISPR-Cas9 switch.

    Science.gov (United States)

    Hirosawa, Moe; Fujita, Yoshihiko; Parr, Callum J C; Hayashi, Karin; Kashida, Shunnichi; Hotta, Akitsu; Woltjen, Knut; Saito, Hirohide

    2017-07-27

    The CRISPR-Cas9 system is a powerful genome-editing tool useful in a variety of biotechnology and biomedical applications. Here we developed a synthetic RNA-based, microRNA (miRNA)-responsive CRISPR-Cas9 system (miR-Cas9 switch) in which the genome editing activity of Cas9 can be modulated through endogenous miRNA signatures in mammalian cells. We created miR-Cas9 switches by using a miRNA-complementary sequence in the 5΄-UTR of mRNA encoding Streptococcus pyogenes Cas9. The miR-21-Cas9 or miR-302-Cas9 switches selectively and efficiently responded to miR-21-5p in HeLa cells or miR-302a-5p in human induced pluripotent stem cells, and post-transcriptionally attenuated the Cas9 activity only in the target cells. Moreover, the miR-Cas9 switches could differentially control the genome editing by sensing endogenous miRNA activities within a heterogeneous cell population. Our miR-Cas9 switch system provides a promising framework for cell-type selective genome editing and cell engineering based on intracellular miRNA information. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. Cell-type-specific genome editing with a microRNA-responsive CRISPR–Cas9 switch

    Science.gov (United States)

    Hirosawa, Moe; Fujita, Yoshihiko; Parr, Callum J. C.; Hayashi, Karin; Kashida, Shunnichi; Hotta, Akitsu; Woltjen, Knut

    2017-01-01

    Abstract The CRISPR–Cas9 system is a powerful genome-editing tool useful in a variety of biotechnology and biomedical applications. Here we developed a synthetic RNA-based, microRNA (miRNA)-responsive CRISPR–Cas9 system (miR-Cas9 switch) in which the genome editing activity of Cas9 can be modulated through endogenous miRNA signatures in mammalian cells. We created miR-Cas9 switches by using a miRNA-complementary sequence in the 5΄-UTR of mRNA encoding Streptococcus pyogenes Cas9. The miR-21-Cas9 or miR-302-Cas9 switches selectively and efficiently responded to miR-21-5p in HeLa cells or miR-302a-5p in human induced pluripotent stem cells, and post-transcriptionally attenuated the Cas9 activity only in the target cells. Moreover, the miR-Cas9 switches could differentially control the genome editing by sensing endogenous miRNA activities within a heterogeneous cell population. Our miR-Cas9 switch system provides a promising framework for cell-type selective genome editing and cell engineering based on intracellular miRNA information. PMID:28525578

  13. Molecular modeling and molecular dynamics simulation study of archaeal leucyl-tRNA synthetase in complex with different mischarged tRNA in editing conformation.

    Science.gov (United States)

    Rayevsky, A V; Sharifi, M; Tukalo, M A

    2017-09-01

    Aminoacyl-tRNA synthetases (aaRSs) play important roles in maintaining the accuracy of protein synthesis. Some aaRSs accomplish this via editing mechanisms, among which leucyl-tRNA synthetase (LeuRS) edits non-cognate amino acid norvaline mainly by post-transfer editing. However, the molecular basis for this pathway for eukaryotic and archaeal LeuRS remain unclear. In this study, a complex of archaeal P. horikoshii LeuRS (PhLeuRS) with misacylated tRNA Leu was modeled wherever tRNA's acceptor stem was oriented directly into the editing site. To understand the distinctive features of organization we reconstructed a complex of PhLeuRS with tRNA and visualize post-transfer editing interactions mode by performing molecular dynamics (MD) simulation studies. To study molecular basis for substrate selectivity by PhLeuRS's editing site we utilized MD simulation of the entire LeuRS complexes using a diverse charged form of tRNAs, namely norvalyl-tRNA Leu and isoleucyl-tRNA Leu . In general, the editing site organization of LeuRS from P.horikoshii has much in common with bacterial LeuRS. The MD simulation results revealed that the post-transfer editing substrate norvalyl-A76, binds more strongly than isoleucyl-A76. Moreover, the branched side chain of isoleucine prevents water molecules from being closer and hence the hydrolysis reaction slows significantly. To investigate a possible mechanism of the post-transfer editing reaction, by PhLeuRS we have determined that two water molecules (the attacking and assisting water molecules) are localized near the carbonyl group of the amino acid to be cleaved off. These water molecules approach the substrate from the opposite side to that observed for Thermus thermophilus LeuRS (TtLeuRS). Based on the results obtained, it was suggested that the post-transfer editing mechanism of PhLeuRS differs from that of prokaryotic TtLeuRS. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. Gene Editing With CRISPR/Cas9 RNA-Directed Nuclease.

    Science.gov (United States)

    Doetschman, Thomas; Georgieva, Teodora

    2017-03-03

    Genetic engineering of model organisms and cultured cells has for decades provided important insights into the mechanisms underlying cardiovascular development and disease. In the past few years the development of several nuclease systems has broadened the range of model/cell systems that can be engineered. Of these, the CRISPR (clustered regularly interspersed short palindromic repeats)/Cas9 (CRISPR-associated protein 9) system has become the favorite for its ease of application. Here we will review this RNA-guided nuclease system for gene editing with respect to its usefulness for cardiovascular studies and with an eye toward potential therapy. Studies on its off-target activity, along with approaches to minimize this activity will be given. The advantages of gene editing versus gene targeting in embryonic stem cells, including the breadth of species and cell types to which it is applicable, will be discussed. We will also cover its use in iPSC for research and possible therapeutic purposes; and we will review its use in muscular dystrophy studies where considerable progress has been made toward dystrophin correction in mice. The CRISPR/Ca9s system is also being used for high-throughput screening of genes, gene regulatory regions, and long noncoding RNAs. In addition, the CRISPR system is being used for nongene-editing purposes such as activation and inhibition of gene expression, as well as for fluorescence tagging of chromosomal regions and individual mRNAs to track their cellular location. Finally, an approach to circumvent the inability of post-mitotic cells to support homologous recombination-based gene editing will be presented. In conclusion, applications of the CRISPR/Cas system are expanding at a breath-taking pace and are revolutionizing approaches to gain a better understanding of human diseases. © 2017 American Heart Association, Inc.

  15. Low noise SQUIDs

    Science.gov (United States)

    de Waal, V. J.

    1983-02-01

    The present investigation deals with the design, fabrication, and limitations of very sensitive SQUID (Superconducting Quantum Interference Device) magnetometers. The SQUID magnetometer is based on a utilization of the Josephson effect. A description of the theoretical background is provided, and high performance DC SQUIDs with submicron niobium Josephson junctions are discussed, taking into account design considerations, fabrication, junction characterization, the performance of the SQUID and input coil, and the gradiometer performance. The simulation and optimization of a DC SQUID with finite capacitance is considered, giving attention to the implementation of a simulation procedure on a hybrid computer.

  16. Low noise SQUIDs

    Energy Technology Data Exchange (ETDEWEB)

    De Waal, V.J.

    1983-01-01

    The present investigation deals with the design, fabrication, and limitations of very sensitive SQUID (Superconducting Quantum Interference Device) magnetometers. The SQUID magnetometer is based on a utilization of the Josephson effect. A description of the theoretical background is provided, and high performance DC SQUIDs with submicron niobium Josephson junctions are discussed, taking into account design considerations, fabrication, junction characterization, the performance of the SQUID and input coil, and the gradiometer performance. The simulation and optimization of a DC SQUID with finite capacitance is considered, giving attention to the implementation of a simulation procedure on a hybrid computer. 129 references.

  17. Targeted Genome Editing Using DNA-Free RNA-Guided Cas9 Ribonucleoprotein for CHO Cell Engineering.

    Science.gov (United States)

    Shin, Jongoh; Lee, Namil; Cho, Suhyung; Cho, Byung-Kwan

    2018-01-01

    Recent advances in the CRISPR/Cas9 system have dramatically facilitated genome engineering in various cell systems. Among the protocols, the direct delivery of the Cas9-sgRNA ribonucleoprotein (RNP) complex into cells is an efficient approach to increase genome editing efficiency. This method uses purified Cas9 protein and in vitro transcribed sgRNA to edit the target gene without vector DNA. We have applied the RNP complex to CHO cell engineering to obtain desirable phenotypes and to reduce unintended insertional mutagenesis and off-target effects. Here, we describe our routine methods for RNP complex-mediated gene deletion including the protocols to prepare the purified Cas9 protein and the in vitro transcribed sgRNA. Subsequently, we also describe a protocol to confirm the edited genomic positions using the T7E1 enzymatic assay and next-generation sequencing.

  18. Is plant mitochondrial RNA editing a source of phylogenetic incongruence? An answer from in silico and in vivo data sets

    Directory of Open Access Journals (Sweden)

    Quagliariello Carla

    2008-03-01

    Full Text Available Abstract Background In plant mitochondria, the post-transcriptional RNA editing process converts C to U at a number of specific sites of the mRNA sequence and usually restores phylogenetically conserved codons and the encoded amino acid residues. Sites undergoing RNA editing evolve at a higher rate than sites not modified by the process. As a result, editing sites strongly affect the evolution of plant mitochondrial genomes, representing an important source of sequence variability and potentially informative characters. To date no clear and convincing evidence has established whether or not editing sites really affect the topology of reconstructed phylogenetic trees. For this reason, we investigated here the effect of RNA editing on the tree building process of twenty different plant mitochondrial gene sequences and by means of computer simulations. Results Based on our simulation study we suggest that the editing ‘noise’ in tree topology inference is mainly manifested at the cDNA level. In particular, editing sites tend to confuse tree topologies when artificial genomic and cDNA sequences are generated shorter than 500 bp and with an editing percentage higher than 5.0%. Similar results have been also obtained with genuine plant mitochondrial genes. In this latter instance, indeed, the topology incongruence increases when the editing percentage goes up from about 3.0 to 14.0%. However, when the average gene length is higher than 1,000 bp (rps3, matR and atp1 no differences in the comparison between inferred genomic and cDNA topologies could be detected. Conclusions Our findings by the here reported in silico and in vivo computer simulation system seem to strongly suggest that editing sites contribute in the generation of misleading phylogenetic trees if the analyzed mitochondrial gene sequence is highly edited (higher than 3.0% and reduced in length (shorter than 500 bp. In the current lack of direct experimental evidence the results

  19. RED: A Java-MySQL Software for Identifying and Visualizing RNA Editing Sites Using Rule-Based and Statistical Filters.

    Directory of Open Access Journals (Sweden)

    Yongmei Sun

    Full Text Available RNA editing is one of the post- or co-transcriptional processes that can lead to amino acid substitutions in protein sequences, alternative pre-mRNA splicing, and changes in gene expression levels. Although several methods have been suggested to identify RNA editing sites, there remains challenges to be addressed in distinguishing true RNA editing sites from its counterparts on genome and technical artifacts. In addition, there lacks a software framework to identify and visualize potential RNA editing sites. Here, we presented a software - 'RED' (RNA Editing sites Detector - for the identification of RNA editing sites by integrating multiple rule-based and statistical filters. The potential RNA editing sites can be visualized at the genome and the site levels by graphical user interface (GUI. To improve performance, we used MySQL database management system (DBMS for high-throughput data storage and query. We demonstrated the validity and utility of RED by identifying the presence and absence of C→U RNA-editing sites experimentally validated, in comparison with REDItools, a command line tool to perform high-throughput investigation of RNA editing. In an analysis of a sample data-set with 28 experimentally validated C→U RNA editing sites, RED had sensitivity and specificity of 0.64 and 0.5. In comparison, REDItools had a better sensitivity (0.75 but similar specificity (0.5. RED is an easy-to-use, platform-independent Java-based software, and can be applied to RNA-seq data without or with DNA sequencing data. The package is freely available under the GPLv3 license at http://github.com/REDetector/RED or https://sourceforge.net/projects/redetector.

  20. RED: A Java-MySQL Software for Identifying and Visualizing RNA Editing Sites Using Rule-Based and Statistical Filters.

    Science.gov (United States)

    Sun, Yongmei; Li, Xing; Wu, Di; Pan, Qi; Ji, Yuefeng; Ren, Hong; Ding, Keyue

    2016-01-01

    RNA editing is one of the post- or co-transcriptional processes that can lead to amino acid substitutions in protein sequences, alternative pre-mRNA splicing, and changes in gene expression levels. Although several methods have been suggested to identify RNA editing sites, there remains challenges to be addressed in distinguishing true RNA editing sites from its counterparts on genome and technical artifacts. In addition, there lacks a software framework to identify and visualize potential RNA editing sites. Here, we presented a software - 'RED' (RNA Editing sites Detector) - for the identification of RNA editing sites by integrating multiple rule-based and statistical filters. The potential RNA editing sites can be visualized at the genome and the site levels by graphical user interface (GUI). To improve performance, we used MySQL database management system (DBMS) for high-throughput data storage and query. We demonstrated the validity and utility of RED by identifying the presence and absence of C→U RNA-editing sites experimentally validated, in comparison with REDItools, a command line tool to perform high-throughput investigation of RNA editing. In an analysis of a sample data-set with 28 experimentally validated C→U RNA editing sites, RED had sensitivity and specificity of 0.64 and 0.5. In comparison, REDItools had a better sensitivity (0.75) but similar specificity (0.5). RED is an easy-to-use, platform-independent Java-based software, and can be applied to RNA-seq data without or with DNA sequencing data. The package is freely available under the GPLv3 license at http://github.com/REDetector/RED or https://sourceforge.net/projects/redetector.

  1. Optimized paired-sgRNA/Cas9 cloning and expression cassette triggers high-efficiency multiplex genome editing in kiwifruit.

    Science.gov (United States)

    Wang, Zupeng; Wang, Shuaibin; Li, Dawei; Zhang, Qiong; Li, Li; Zhong, Caihong; Liu, Yifei; Huang, Hongwen

    2018-01-13

    Kiwifruit is an important fruit crop; however, technologies for its functional genomic and molecular improvement are limited. The clustered regulatory interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) system has been successfully applied to genetic improvement in many crops, but its editing capability is variable depending on the different combinations of the synthetic guide RNA (sgRNA) and Cas9 protein expression devices. Optimizing conditions for its use within a particular species is therefore needed to achieve highly efficient genome editing. In this study, we developed a new cloning strategy for generating paired-sgRNA/Cas9 vectors containing four sgRNAs targeting the kiwifruit phytoene desaturase gene (AcPDS). Comparing to the previous method of paired-sgRNA cloning, our strategy only requires the synthesis of two gRNA-containing primers which largely reduces the cost. We further compared efficiencies of paired-sgRNA/Cas9 vectors containing different sgRNA expression devices, including both the polycistronic tRNA-sgRNA cassette (PTG) and the traditional CRISPR expression cassette. We found the mutagenesis frequency of the PTG/Cas9 system was 10-fold higher than that of the CRISPR/Cas9 system, coinciding with the relative expressions of sgRNAs in two different expression cassettes. In particular, we identified large chromosomal fragment deletions induced by the paired-sgRNAs of the PTG/Cas9 system. Finally, as expected, we found both systems can successfully induce the albino phenotype of kiwifruit plantlets regenerated from the G418-resistance callus lines. We conclude that the PTG/Cas9 system is a more powerful system than the traditional CRISPR/Cas9 system for kiwifruit genome editing, which provides valuable clues for optimizing CRISPR/Cas9 editing system in other plants. © 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons

  2. Differential Binding of Mitochondrial Transcripts by MRB8170 and MRB4160 Regulates Distinct Editing Fates of Mitochondrial mRNA in Trypanosomes

    Directory of Open Access Journals (Sweden)

    Sameer Dixit

    2017-01-01

    Full Text Available A dozen mRNAs are edited by multiple insertions and/or deletions of uridine residues in the mitochondrion of Trypanosoma brucei. Several protein complexes have been implicated in performing this type of RNA editing, including the mitochondrial RNA-binding complex 1 (MRB1. Two paralogous novel RNA-binding proteins, MRB8170 and MRB4160, are loosely associated with the core MRB1 complex. Their roles in RNA editing and effects on target mRNAs are so far not well understood. In this study, individual-nucleotide-resolution UV-cross-linking and affinity purification (iCLAP revealed a preferential binding of both proteins to mitochondrial mRNAs, which was positively correlated with their extent of editing. Integrating additional in vivo and in vitro data, we propose that binding of MRB8170 and/or MRB4160 onto pre-mRNA marks it for the initiation of editing and that initial binding of both proteins may facilitate the recruitment of other components of the RNA editing/processing machinery to ensure efficient editing. Surprisingly, MRB8170 also binds never-edited mRNAs, suggesting that at least this paralog has an additional role outside RNA editing to shape the mitochondrial transcriptome.

  3. The Extent of mRNA Editing Is Limited in Chicken Liver and Adipose, but Impacted by Tissular Context, Genotype, Age, and Feeding as Exemplified with a Conserved Edited Site in COG3

    Directory of Open Access Journals (Sweden)

    Pierre-François Roux

    2016-02-01

    Full Text Available RNA editing is a posttranscriptional process leading to differences between genomic DNA and transcript sequences, potentially enhancing transcriptome diversity. With recent advances in high-throughput sequencing, many efforts have been made to describe mRNA editing at the transcriptome scale, especially in mammals, yielding contradictory conclusions regarding the extent of this phenomenon. We show, by detailed description of the 25 studies focusing so far on mRNA editing at the whole-transcriptome scale, that systematic sequencing artifacts are considered in most studies whereas biological replication is often neglected and multi-alignment not properly evaluated, which ultimately impairs the legitimacy of results. We recently developed a rigorous strategy to identify mRNA editing using mRNA and genomic DNA sequencing, taking into account sequencing and mapping artifacts, and biological replicates. We applied this method to screen for mRNA editing in liver and white adipose tissue from eight chickens and confirm the small extent of mRNA recoding in this species. Among the 25 unique edited sites identified, three events were previously described in mammals, attesting that this phenomenon is conserved throughout evolution. Deeper investigations on five sites revealed the impact of tissular context, genotype, age, feeding conditions, and sex on mRNA editing levels. More specifically, this analysis highlighted that the editing level at the site located on COG3 was strongly regulated by four of these factors. By comprehensively characterizing the mRNA editing landscape in chickens, our results highlight how this phenomenon is limited and suggest regulation of editing levels by various genetic and environmental factors.

  4. High-efficiency targeted editing of large viral genomes by RNA-guided nucleases.

    Science.gov (United States)

    Bi, Yanwei; Sun, Le; Gao, Dandan; Ding, Chen; Li, Zhihua; Li, Yadong; Cun, Wei; Li, Qihan

    2014-05-01

    A facile and efficient method for the precise editing of large viral genomes is required for the selection of attenuated vaccine strains and the construction of gene therapy vectors. The type II prokaryotic CRISPR-Cas (clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas)) RNA-guided nuclease system can be introduced into host cells during viral replication. The CRISPR-Cas9 system robustly stimulates targeted double-stranded breaks in the genomes of DNA viruses, where the non-homologous end joining (NHEJ) and homology-directed repair (HDR) pathways can be exploited to introduce site-specific indels or insert heterologous genes with high frequency. Furthermore, CRISPR-Cas9 can specifically inhibit the replication of the original virus, thereby significantly increasing the abundance of the recombinant virus among progeny virus. As a result, purified recombinant virus can be obtained with only a single round of selection. In this study, we used recombinant adenovirus and type I herpes simplex virus as examples to demonstrate that the CRISPR-Cas9 system is a valuable tool for editing the genomes of large DNA viruses.

  5. High-efficiency targeted editing of large viral genomes by RNA-guided nucleases.

    Directory of Open Access Journals (Sweden)

    Yanwei Bi

    2014-05-01

    Full Text Available A facile and efficient method for the precise editing of large viral genomes is required for the selection of attenuated vaccine strains and the construction of gene therapy vectors. The type II prokaryotic CRISPR-Cas (clustered regularly interspaced short palindromic repeats (CRISPR-associated (Cas RNA-guided nuclease system can be introduced into host cells during viral replication. The CRISPR-Cas9 system robustly stimulates targeted double-stranded breaks in the genomes of DNA viruses, where the non-homologous end joining (NHEJ and homology-directed repair (HDR pathways can be exploited to introduce site-specific indels or insert heterologous genes with high frequency. Furthermore, CRISPR-Cas9 can specifically inhibit the replication of the original virus, thereby significantly increasing the abundance of the recombinant virus among progeny virus. As a result, purified recombinant virus can be obtained with only a single round of selection. In this study, we used recombinant adenovirus and type I herpes simplex virus as examples to demonstrate that the CRISPR-Cas9 system is a valuable tool for editing the genomes of large DNA viruses.

  6. Low noise SQUIDS

    International Nuclear Information System (INIS)

    Waal, V.J. de.

    1983-01-01

    The design, fabrication and limitations of very sensitive SQUID magnetometers are described. The SQUID magnetometer is based on the Josephson effect. A very low-noise niobium SQUID is described. It is fabricated with ultra-small niobium junctions with an overlapping area smaller than 1 μm 2 . The photolithographic technique developed for its fabrication, is described. Also an integrated system with a SQUID and a first-order gradiometer on a single substrate is presented. Calculations of the resolution of a dc SQUID containing ideal Josephson junctions according to the RSJ model are presented including a parasitic capacitance. The usefulness of the fabricated SQUIDS as well as some remarks on their performance is considered. (Auth.)

  7. Substrate specificity and catalysis by the editing active site of alanyl-tRNA synthetase from Escherichia coli†

    Science.gov (United States)

    Pasman, Zvi; Robey-Bond, Susan; Mirando, Adam C.; Smith, Gregory J.; Lague, Astrid; Francklyn, Christopher S.

    2011-01-01

    Aminoacyl-tRNA synthetases (ARSs) enhance the fidelity of protein synthesis through multiple mechanisms, including hydrolysis of the adenylate and cleavage of misacylated tRNA. Alanyl-tRNA synthetase (AlaRS) limits misacylation with glycine and serine by use of a dedicated editing domain, and a mutation in this activity has been genetically linked to a mouse model of a progressive neurodegenerative disease. Using the free standing P. horikoshii AlaX editing domain complexed with serine as a model and both Ser-tRNAAla and Ala-tRNAAla as substrates, the deacylation activities of the wild type and five different E. coli AlaRS editing site substitution mutants were characterized. The wild type AlaRS editing domain deacylated Ser-tRNAAla with a kcat/KM of 6.6 × 105 M−1 s−1, equivalent to a rate enhancement of 6000 over the rate of enzyme-independent deacylation, but only 12.2-fold greater than the rate with Ala-tRNAAla. While the E664A and T567G substitutions only minimally decreased kcat/KM, Q584H, I667E, and C666A AlaRS were more compromised in activity, with decreases in kcat/KM in the range of 6-, 7.3-, and 15-fold. C666A AlaRS was 1.4-fold more active on Ala-tRNAAla relative to Ser-tRNAAla, providing the only example of a true reversal of substrate specificity and highlighting a potential role of the coordinated zinc in editing substrate specificity. Along with the potentially serious physiological consequences of serine mis-incorporation, the relatively modest specificity of the AlaRS editing domain may provide a rationale for the widespread phylogenetic distribution of AlaX free standing editing domains, thereby contributing a further mechanism to lower concentrations of misacylated tRNAAla. PMID:21241052

  8. The essential role of AMPA receptor GluR2 subunit RNA editing in the normal and diseased brain

    Directory of Open Access Journals (Sweden)

    Amanda Lorraine Wright

    2012-04-01

    Full Text Available AMPA receptors are comprised of different combinations of GluR1-GluR4 (also known as GluA1-GluA4 and GluR-A to GluR-D subunits. The GluR2 subunit is subject to Q/R site RNA editing by the ADAR2 enzyme, which converts a codon for glutamine (Q, present in the GluR2 gene, to a codon for arginine (R found in the mRNA. AMPA receptors are calcium (Ca2+-permeable if they contain the unedited GluR2(Q subunit or if they lack the GluR2 subunit. While most AMPA receptors in the brain contain the edited GluR2(R subunit and are therefore Ca2+-impermeable, recent evidence suggests that Ca2+-permeable GluR2-lacking AMPA receptors are important in synaptic plasticity and learning. However, the presence of Ca2+-permeable AMPA receptors containing unedited GluR2 leads to excitotoxic cell loss. Recent studies have indicated that RNA editing of GluR2 is deregulated in diseases, such as amyotrophic lateral sclerosis (ALS, as well in acute neurodegenerative conditions, such as ischemia. More recently, studies have investigated the regulation of RNA editing and possible causes for its deregulation during disease. In this review, we will explore the role of GluR2 RNA editing in the healthy and diseased brain and outline new insights into the mechanisms that control this process.

  9. Heterologous and endogenous U6 snRNA promoters enable CRISPR/Cas9 mediated genome editing in Aspergillus niger.

    Science.gov (United States)

    Zheng, Xiaomei; Zheng, Ping; Sun, Jibin; Kun, Zhang; Ma, Yanhe

    2018-01-01

    U6 promoters have been used for single guide RNA (sgRNA) transcription in the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas9) genome editing system. However, no available U6 promoters have been identified in Aspergillus niger, which is an important industrial platform for organic acid and protein production. Two CRISPR/Cas9 systems established in A. niger have recourse to the RNA polymerase II promoter or in vitro transcription for sgRNA synthesis, but these approaches generally increase cloning efforts and genetic manipulation. The validation of functional RNA polymerase II promoters is therefore an urgent need for A. niger . Here, we developed a novel CRISPR/Cas9 system in A. niger for sgRNA expression, based on one endogenous U6 promoter and two heterologous U6 promoters. The three tested U6 promoters enabled sgRNA transcription and the disruption of the polyketide synthase albA gene in A. niger . Furthermore, this system enabled highly efficient gene insertion at the targeted genome loci in A. niger using donor DNAs with homologous arms as short as 40-bp. This study demonstrated that both heterologous and endogenous U6 promoters were functional for sgRNA expression in A. niger . Based on this result, a novel and simple CRISPR/Cas9 toolbox was established in A. niger, that will benefit future gene functional analysis and genome editing.

  10. A-to-I RNA editing in the rat brain is age-dependent, region-specific and sensitive to environmental stress across generations.

    Science.gov (United States)

    Zaidan, Hiba; Ramaswami, Gokul; Golumbic, Yaela N; Sher, Noa; Malik, Assaf; Barak, Michal; Galiani, Dalia; Dekel, Nava; Li, Jin B; Gaisler-Salomon, Inna

    2018-01-08

    Adenosine-to-inosine (A-to-I) RNA editing is an epigenetic modification catalyzed by adenosine deaminases acting on RNA (ADARs), and is especially prevalent in the brain. We used the highly accurate microfluidics-based multiplex PCR sequencing (mmPCR-seq) technique to assess the effects of development and environmental stress on A-to-I editing at 146 pre-selected, conserved sites in the rat prefrontal cortex and amygdala. Furthermore, we asked whether changes in editing can be observed in offspring of stress-exposed rats. In parallel, we assessed changes in ADARs expression levels. In agreement with previous studies, we found editing to be generally higher in adult compared to neonatal rat brain. At birth, editing was generally lower in prefrontal cortex than in amygdala. Stress affected editing at the serotonin receptor 2c (Htr2c), and editing at this site was significantly altered in offspring of rats exposed to prereproductive stress across two generations. Stress-induced changes in Htr2c editing measured with mmPCR-seq were comparable to changes measured with Sanger and Illumina sequencing. Developmental and stress-induced changes in Adar and Adarb1 mRNA expression were observed but did not correlate with editing changes. Our findings indicate that mmPCR-seq can accurately detect A-to-I RNA editing in rat brain samples, and confirm previous accounts of a developmental increase in RNA editing rates. Our findings also point to stress in adolescence as an environmental factor that alters RNA editing patterns several generations forward, joining a growing body of literature describing the transgenerational effects of stress.

  11. SQUID in NDT

    International Nuclear Information System (INIS)

    Rashdi Shah Ahmad

    2001-01-01

    Superconducting Quantum Interference Device (SQUID) is the most sensitive magnetic flux sensor. It has been used to map the magnetic field on the scalp of human being generated by the brain activity. Currently, a number of groups have tried using SQUID for some special NDT application. This paper reviews some of these work. (Author)

  12. 5S rRNA Promoter for Guide RNA Expression Enabled Highly Efficient CRISPR/Cas9 Genome Editing in Aspergillus niger.

    Science.gov (United States)

    Zheng, Xiaomei; Zheng, Ping; Zhang, Kun; Cairns, Timothy C; Meyer, Vera; Sun, Jibin; Ma, Yanhe

    2018-04-30

    The CRISPR/Cas9 system is a revolutionary genome editing tool. However, in eukaryotes, search and optimization of a suitable promoter for guide RNA expression is a significant technical challenge. Here we used the industrially important fungus, Aspergillus niger, to demonstrate that the 5S rRNA gene, which is both highly conserved and efficiently expressed in eukaryotes, can be used as a guide RNA promoter. The gene editing system was established with 100% rates of precision gene modifications among dozens of transformants using short (40-bp) homologous donor DNA. This system was also applicable for generation of designer chromosomes, as evidenced by deletion of a 48 kb gene cluster required for biosynthesis of the mycotoxin fumonisin B1. Moreover, this system also facilitated simultaneous mutagenesis of multiple genes in A. niger. We anticipate that the use of the 5S rRNA gene as guide RNA promoter can broadly be applied for engineering highly efficient eukaryotic CRISPR/Cas9 toolkits. Additionally, the system reported here will enable development of designer chromosomes in model and industrially important fungi.

  13. The SQUID Handbook

    CERN Document Server

    Braginski, Alex I

    2006-01-01

    This two-volume handbook offers a comprehensive and well coordinated presentation of SQUIDs (Superconducting Quantum Interference Devices), including device fundamentals, design, technology, system construction and multiple applications. It is intended to bridge the gap between fundamentals and applications, and will be a valuable textbook reference for graduate students and for professionals engaged in SQUID research and engineering. It will also be of use to specialists in multiple fields of practical SQUID applications, from human brain research and heart diagnostics to airplane and nuclear

  14. Phosphorylation and Dephosphorylation of the Presequence of Precursor MULTIPLE ORGANELLAR RNA EDITING FACTOR3 during Import into Mitochondria from Arabidopsis

    OpenAIRE

    SUN, F; CHENG, S; GUAN, X; ZHANG, R; LAW, YS; Duncan, O; Murcha, M; Whelan, J; Lim, BL

    2015-01-01

    The nuclear-encoded mitochondrial-targeted proteins, multiple organellar RNA editing factors (MORF3, MORF5, MORF6) interact with AtPAP2 (Purple acid phosphatase 2) located on the chloroplast and mitochondrial outer membranes in a presequence dependent manner. Phosphorylation of the presequence of the precursor MORF3 (pMORF3) by endogenous kinases in wheat germ translation lysate, leaf extracts, or STY kinases, but not in rabbit reticulocyte translation lysate, resulted in the inhibition of pr...

  15. The assembly of F1FO-ATP synthase is disrupted upon interference of RNA editing in Trypanosoma brucei

    Czech Academy of Sciences Publication Activity Database

    Hashimi, Hassan; Benkovičová, V.; Čermáková, P.; Lai, De Hua; Horváth, A.; Lukeš, Julius

    2010-01-01

    Roč. 40, č. 1 (2010), s. 45-54 ISSN 0020-7519 R&D Projects: GA ČR GA204/06/1558; GA AV ČR IAA500960705 Institutional research plan: CEZ:AV0Z60220518 Keywords : RNA editing * ATP synthase * mitochondrion * Trypanosoma * respiratory complex * membrane potential Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.822, year: 2010

  16. Market Squid Ecology Dataset

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This dataset contains ecological information collected on the major adult spawning and juvenile habitats of market squid off California and the US Pacific Northwest....

  17. Market Squid Population Dynamics

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This dataset contains population dynamics data on paralarvae, juvenile and adult market squid collected off California and the US Pacific Northwest. These data were...

  18. Vortex electronis and squids

    CERN Document Server

    2003-01-01

    Understanding the nature of vortices in high-Tc superconductors is a crucial subject for research on superconductive electronics, especially for superconducting interference devices (SQUIDs), it is also a fundamental problem in condensed-matter physics. Recent technological progress in methods for both direct and indirect observation of vortices, e.g. scanning SQUID, terahertz imaging, and microwave excitation, has led to new insights into vortex physics, the dynamic behavior of vortices in junctions and related questions of noise. This book presents the current status of research activity and provides new information on the applications of SQUIDs, including magnetocardiography, immunoassays, and laser-SQUID microscopes, all of which are close to being commercially available.

  19. Crystallization and X-ray diffraction analysis of the Trp/amber editing site of hepatitis delta virus (+)RNA: a case of rational design

    International Nuclear Information System (INIS)

    MacElrevey, Celeste; Wedekind, Joseph E.

    2005-01-01

    Well diffracting decamer crystals of the hepatitis delta virus RNA-editing site were prepared, but exhibited merohedral twinning and base averaging owing to duplex symmetry. A longer asymmetric construct that includes additional flanking RNA sequences has been crystallized that does not appear to exhibit these defects. RNA editing by mammalian ADAR1 (Adenosine Deaminase Acting on RNA) is required for the life cycle of the hepatitis delta virus (HDV). Editing extends the single viral open reading frame to yield two protein products of alternate length. ADARs are believed to recognize double-stranded RNA substrates via a ‘structure-based’ readout mechanism. Crystals of 10-mer duplexes representing the HDV RNA-editing site diffracted to 1.35 Å resolution, but suffered from merohedral twinning and averaging of the base registry. Expansion of the construct to include two flanking 3 × 1 internal loops yielded crystals in the primitive tetragonal space group P4 1 2 1 2 or P4 3 2 1 2. X-ray diffraction data were collected to 2.8 Å resolution, revealing a unit cell with parameters a = 62.5, c = 63.5 Å. The crystallization and X-ray analysis of multiple forms of the HDV RNA-editing substrate, encounters with common RNA crystal-growth defects and a strategy to overcome these problems are reported

  20. SQUID application research in Japan

    International Nuclear Information System (INIS)

    Itozaki, Hideo

    2003-01-01

    Japanese research activities using SQUIDs are reviewed in this paper. Low-T c SQUIDs are applied to multi-channel systems for magnetoencephalogram (MEG) and magnetocardiogram (MCG). High-T c SQUIDs are applied to MCG, nondestructive evaluation (NDE), SQUID microscopy, biological testing using fine magnetic markers, geological surveying, food inspection, large-scale integration (LSI) defect analysis and SQUID-NQR (nuclear quadrupole resonance). These applications of SQUIDs are being researched and developed actively and some of them are expected to be in the commercial market in the near future

  1. Effect of apolipoprotein B mRNA-editing catalytic polypeptide-like protein-3G in cervical cancer.

    Science.gov (United States)

    Xu, Yanhua; Leng, Junhong; Xue, Fang; Dong, Ruiqian

    2015-01-01

    Cervical cancer is one of the most common gynecologic cancers. The role of apolipoprotein B mRNA-editing catalytic polypeptide-like protein-3G (APCBEC-3G) in cervical cancer has yet to be elucidated. This study intends to explore the effect of APCBEC-3G on cervical cancer cell proliferation and invasion. In vitro, the cervical cancer cell line Hela was transfected by APCBEC-3G plasmid. The mRNA and protein expression levels of APCBEC-3G were detected by Real-time PCR and Western blot, respectively. Cervical cancer cell proliferation was determined by MTT. Transwell assay was applied to measure the effect of APCBEC-3G on cell invasion. APCBEC-3G mRNA and protein increased significantly after transfection (P3G serves as a suppressor of cervical cancer cell proliferation and invasion. Our research provides theoretical basis for further investigation APOBEC-3G effect in cervical cancer occurrence and development.

  2. Orthogonal Cas9 proteins for RNA-guided gene regulation and editing

    Science.gov (United States)

    Church, George M.; Esvelt, Kevin; Mali, Prashant

    2017-03-07

    Methods of modulating expression of a target nucleic acid in a cell are provided including use of multiple orthogonal Cas9 proteins to simultaneously and independently regulate corresponding genes or simultaneously and independently edit corresponding genes.

  3. Ribosomal incorporation of backbone modified amino acids via an editing-deficient aminoacyl-tRNA synthetase.

    Science.gov (United States)

    Iqbal, Emil S; Dods, Kara K; Hartman, Matthew C T

    2018-02-14

    The ability to incorporate non-canonical amino acids (ncAA) using translation offers researchers the ability to extend the functionality of proteins and peptides for many applications including synthetic biology, biophysical and structural studies, and discovery of novel ligands. Here we describe the high promiscuity of an editing-deficient valine-tRNA synthetase (ValRS T222P). Using this enzyme, we demonstrate ribosomal translation of 11 ncAAs including those with novel side chains, α,α-disubstitutions, and cyclic β-amino acids.

  4. EdiPy: a resource to simulate the evolution of plant mitochondrial genes under the RNA editing.

    Science.gov (United States)

    Picardi, Ernesto; Quagliariello, Carla

    2006-02-01

    EdiPy is an online resource appropriately designed to simulate the evolution of plant mitochondrial genes in a biologically realistic fashion. EdiPy takes into account the presence of sites subjected to RNA editing and provides multiple artificial alignments corresponding to both genomic and cDNA sequences. Each artificial data set can successively be submitted to main and widespread evolutionary and phylogenetic software packages such as PAUP, Phyml, PAML and Phylip. As an online bioinformatic resource, EdiPy is available at the following web page: http://biologia.unical.it/py_script/index.html.

  5. Efficient CRISPR/Cas9-Mediated Genome Editing Using a Chimeric Single-Guide RNA Molecule

    KAUST Repository

    Butt, Haroon; Eid, Ayman; Ali, Zahir; Atia, Mohamed A. M.; Mokhtar, Morad M.; Hassan, Norhan; Lee, Ciaran M.; Bao, Gang; Mahfouz, Magdy M.

    2017-01-01

    used CRISPR/Cas9 to generate targeted double-strand breaks and to deliver an RNA repair template for HDR in rice (Oryza sativa). We used chimeric single-guide RNA (cgRNA) molecules carrying both sequences for target site specificity (to generate

  6. Multifunctional G-rich and RRM-containing domains of TbRGG2 perform separate yet essential functions in trypanosome RNA editing.

    Science.gov (United States)

    Foda, Bardees M; Downey, Kurtis M; Fisk, John C; Read, Laurie K

    2012-09-01

    Efficient editing of Trypanosoma brucei mitochondrial RNAs involves the actions of multiple accessory factors. T. brucei RGG2 (TbRGG2) is an essential protein crucial for initiation and 3'-to-5' progression of editing. TbRGG2 comprises an N-terminal G-rich region containing GWG and RG repeats and a C-terminal RNA recognition motif (RRM)-containing domain. Here, we perform in vitro and in vivo separation-of-function studies to interrogate the mechanism of TbRGG2 action in RNA editing. TbRGG2 preferentially binds preedited mRNA in vitro with high affinity attributable to its G-rich region. RNA-annealing and -melting activities are separable, carried out primarily by the G-rich and RRM domains, respectively. In vivo, the G-rich domain partially complements TbRGG2 knockdown, but the RRM domain is also required. Notably, TbRGG2's RNA-melting activity is dispensable for RNA editing in vivo. Interactions between TbRGG2 and MRB1 complex proteins are mediated by both G-rich and RRM-containing domains, depending on the binding partner. Overall, our results are consistent with a model in which the high-affinity RNA binding and RNA-annealing activities of the G-rich domain are essential for RNA editing in vivo. The RRM domain may have key functions involving interactions with the MRB1 complex and/or regulation of the activities of the G-rich domain.

  7. The Stationary SQUID

    Science.gov (United States)

    Berger, Jorge

    2018-06-01

    In the customary mode of operation of a SQUID, the electromagnetic field in the SQUID is an oscillatory function of time. In this situation, electromagnetic radiation is emitted and couples to the sample. This is a back action that can alter the state that we intend to measure. A circuit that could perform as a stationary SQUID consists of a loop of superconducting material that encloses the magnetic flux, connected to a superconducting and to a normal electrode. This circuit does not contain Josephson junctions, or any other miniature feature. We study the evolution of the order parameter and of the electrochemical potential in this circuit; they converge to a stationary regime, and the voltage between the electrodes depends on the enclosed flux. We obtain expressions for the power dissipation and for the heat transported by the electric current; the validity of these expressions does not rely on a particular evolution model for the order parameter. We evaluate the influence of fluctuations. For a SQUID perimeter of the order of 1μ m and temperature 0.9T_c, we obtain a flux resolution of the order of 10^{-5}Φ _0/Hz^{1/2}; the resolution is expected to improve as the temperature is lowered.

  8. Tipping the balance of RNA stability by 3' editing of the transcriptome.

    Science.gov (United States)

    Chung, Christina Z; Seidl, Lauren E; Mann, Mitchell R; Heinemann, Ilka U

    2017-11-01

    The regulation of active microRNAs (miRNAs) and maturation of messenger RNAs (mRNAs) that are competent for translation is a crucial point in the control of all cellular processes, with established roles in development and differentiation. Terminal nucleotidyltransferases (TNTases) are potent regulators of RNA metabolism. TNTases promote the addition of single or multiple nucleotides to an RNA transcript that can rapidly alter transcript stability. The well-known polyadenylation promotes transcript stability while the newly discovered but ubiquitious 3'-end polyuridylation marks RNA for degradation. Monoadenylation and uridylation are essential control mechanisms balancing mRNA and miRNA homeostasis. This review discusses the multiple functions of non-canonical TNTases, focusing on their substrate range, biological functions, and evolution. TNTases directly control mRNA and miRNA levels, with diverse roles in transcriptome stabilization, maturation, silencing, or degradation. We will summarize the current state of knowledge on non-canonical nucleotidyltransferases and their function in regulating miRNA and mRNA metabolism. We will review the discovery of uridylation as an RNA degradation pathway and discuss the evolution of nucleotidyltransferases along with their use in RNA labeling and future applications as therapeutic targets. The biochemically and evolutionarily highly related adenylyl- and uridylyltransferases play antagonizing roles in the cell. In general, RNA adenylation promotes stability, while uridylation marks RNA for degradation. Uridylyltransferases evolved from adenylyltransferases in multiple independent evolutionary events by the insertion of a histidine residue into the active site, altering nucleotide, but not RNA specificity. Understanding the mechanisms regulating RNA stability in the cell and controlling the transcriptome is essential for efforts aiming to influence cellular fate. Selectively enhancing or reducing RNA stability allows for

  9. Functional and structural insights revealed by molecular dynamics simulations of an essential RNA editing ligase in Trypanosoma brucei.

    Directory of Open Access Journals (Sweden)

    Rommie E Amaro

    2007-11-01

    Full Text Available RNA editing ligase 1 (TbREL1 is required for the survival of both the insect and bloodstream forms of Trypanosoma brucei, the parasite responsible for the devastating tropical disease African sleeping sickness. The type of RNA editing that TbREL1 is involved in is unique to the trypanosomes, and no close human homolog is known to exist. In addition, the high-resolution crystal structure revealed several unique features of the active site, making this enzyme a promising target for structure-based drug design. In this work, two 20 ns atomistic molecular dynamics (MD simulations are employed to investigate the dynamics of TbREL1, both with and without the ATP substrate present. The flexibility of the active site, dynamics of conserved residues and crystallized water molecules, and the interactions between TbREL1 and the ATP substrate are investigated and discussed in the context of TbREL1's function. Differences in local and global motion upon ATP binding suggest that two peripheral loops, unique to the trypanosomes, may be involved in interdomain signaling events. Notably, a significant structural rearrangement of the enzyme's active site occurs during the apo simulations, opening an additional cavity adjacent to the ATP binding site that could be exploited in the development of effective inhibitors directed against this protozoan parasite. Finally, ensemble averaged electrostatics calculations over the MD simulations reveal a novel putative RNA binding site, a discovery that has previously eluded scientists. Ultimately, we use the insights gained through the MD simulations to make several predictions and recommendations, which we anticipate will help direct future experimental studies and structure-based drug discovery efforts against this vital enzyme.

  10. Trypanosome RNA editing: the complexity of getting U in and taking U out

    Czech Academy of Sciences Publication Activity Database

    Read, L. K.; Lukeš, Julius; Hashimi, Hassan

    2016-01-01

    Roč. 7, č. 1 (2016), s. 33-51 ISSN 1757-7004 R&D Projects: GA ČR GA15-21974S EU Projects: European Commission(XE) 289007 Institutional support: RVO:60077344 Keywords : messenger RNA * guide RNA * mitochondria Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.838, year: 2016

  11. Cryostats for SQUID magnetometers

    International Nuclear Information System (INIS)

    Testard, O.A.; Locatelli, M.

    1982-05-01

    A non metallic and non magnetic cryostat, with a very low thermal budget and a container type autonomy was developed, to condition S.Q.U.I.D. magnetometers which maximum sensitivity reaches 10 -14 Tesla Hertzsup(-1/2). This instrumentation puts in hand new concepts of composite materials, thermal shock and vibration resistant, multilayer thermal radiative insulation also to the prouve of vibrations with thermal equivalent emissivity lower than 10 -3

  12. Oligophrenin-1 (OPHN1, a gene involved in X-linked intellectual disability, undergoes RNA editing and alternative splicing during human brain development.

    Directory of Open Access Journals (Sweden)

    Sabina Barresi

    Full Text Available Oligophrenin-1 (OPHN1 encodes for a Rho-GTPase-activating protein, important for dendritic morphogenesis and synaptic function. Mutations in this gene have been identified in patients with X-linked intellectual disability associated with cerebellar hypoplasia. ADAR enzymes are responsible for A-to-I RNA editing, an essential post-transcriptional RNA modification contributing to transcriptome and proteome diversification. Specifically, ADAR2 activity is essential for brain development and function. Herein, we show that the OPHN1 transcript undergoes post-transcriptional modifications such as A-to-I RNA editing and alternative splicing in human brain and other tissues. We found that OPHN1 editing is detectable already at the 18th week of gestation in human brain with a boost of editing at weeks 20 to 33, concomitantly with OPHN1 expression increase and the appearance of a novel OPHN1 splicing isoform. Our results demonstrate that multiple post-transcriptional events occur on OPHN1, a gene playing an important role in brain function and development.

  13. Gene Loss and Error-Prone RNA Editing in the Mitochondrion of Perkinsela, an Endosymbiotic Kinetoplastid

    Czech Academy of Sciences Publication Activity Database

    David, Vojtěch; Flegontov, P.; Gerasimov, E.; Tanifuji, G.; Hashimi, Hassan; Logacheva, M.D.; Maruyama, S.; Onodera, N. T.; Gray, M.W.; Archibald, J.M.; Lukeš, Julius

    2015-01-01

    Roč. 6, č. 6 (2015), e01498-15 ISSN 2150-7511 R&D Projects: GA MŠk LH12104; GA ČR GAP305/12/2261 EU Projects: European Commission(XE) 316304; European Commission(XE) 289007 Institutional support: RVO:60077344 Keywords : kinetoplastid * protist * RNA-seq Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 6.975, year: 2015

  14. Activity-regulated RNA editing in select neuronal subfields in hippocampus

    Czech Academy of Sciences Publication Activity Database

    Balík, Aleš; Penn, A.C.; Nemoda, Z.; Greger, I. H.

    2013-01-01

    Roč. 41, č. 2 (2013), s. 1124-1134 ISSN 0305-1048 R&D Projects: GA ČR(CZ) GBP304/12/G069 Grant - others:Rada Programu interní podpory projektů mezinárodní spolupráce AV ČR(CZ) M200110971; Medical Research Council(GB) U105174197 Institutional support: RVO:67985823 Keywords : hippocampus * RNA * adenosine Subject RIV: ED - Physiology Impact factor: 8.808, year: 2013

  15. SQUID technology for geophysical exploration

    International Nuclear Information System (INIS)

    Meyer, Hans-Georg; Stolz, R.; Chwala, A.; Schulz, M.

    2005-01-01

    We report on successful tests of planar LTS SQUID gradiometers on airborne platforms such as helicopter and aircraft. The system works stable and allows profile work without any constraints. In mobile applications the gradient resolution at low frequencies is dominated by motion noise, since the parasitic areas of the SQUID gradiometer lead to strong disturbances if the gradiometer is tilted in the homogenous Earth's magnetic field. The balance can be improved further by software using data of a SQUID magnetometer triple. (copyright 2005 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  16. Comparison of Various Nuclear Localization Signal-Fused Cas9 Proteins and Cas9 mRNA for Genome Editing in Zebrafish.

    Science.gov (United States)

    Hu, Peinan; Zhao, Xueying; Zhang, Qinghua; Li, Weiming; Zu, Yao

    2018-03-02

    The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system has been proven to be an efficient and precise genome editing technology in various organisms. However, the gene editing efficiencies of Cas9 proteins with a nuclear localization signal (NLS) fused to different termini and Cas9 mRNA have not been systematically compared. Here, we compared the ability of Cas9 proteins with NLS fused to the N-, C-, or both the N- and C-termini and N-NLS-Cas9-NLS-C mRNA to target two sites in the tyr gene and two sites in the gol gene related to pigmentation in zebrafish. Phenotypic analysis revealed that all types of Cas9 led to hypopigmentation in similar proportions of injected embryos. Genome analysis by T7 Endonuclease I (T7E1) assays demonstrated that all types of Cas9 similarly induced mutagenesis in four target sites. Sequencing results further confirmed that a high frequency of indels occurred in the target sites ( tyr1 > 66%, tyr2 > 73%, gol1 > 50%, and gol2 > 35%), as well as various types (more than six) of indel mutations observed in all four types of Cas9-injected embryos. Furthermore, all types of Cas9 showed efficient targeted mutagenesis on multiplex genome editing, resulting in multiple phenotypes simultaneously. Collectively, we conclude that various NLS-fused Cas9 proteins and Cas9 mRNAs have similar genome editing efficiencies on targeting single or multiple genes, suggesting that the efficiency of CRISPR/Cas9 genome editing is highly dependent on guide RNAs (gRNAs) and gene loci. These findings may help to simplify the selection of Cas9 for gene editing using the CRISPR/Cas9 system. Copyright © 2018 Hu et al.

  17. c-Jun amino-terminal kinase-1 mediates glucose-responsive upregulation of the RNA editing enzyme ADAR2 in pancreatic beta-cells.

    Directory of Open Access Journals (Sweden)

    Liu Yang

    Full Text Available A-to-I RNA editing catalyzed by the two main members of the adenosine deaminase acting on RNA (ADAR family, ADAR1 and ADAR2, represents a RNA-based recoding mechanism implicated in a variety of cellular processes. Previously we have demonstrated that the expression of ADAR2 in pancreatic islet β-cells is responsive to the metabolic cues and ADAR2 deficiency affects regulated cellular exocytosis. To investigate the molecular mechanism by which ADAR2 is metabolically regulated, we found that in cultured β-cells and primary islets, the stress-activated protein kinase JNK1 mediates the upregulation of ADAR2 in response to changes of the nutritional state. In parallel with glucose induction of ADAR2 expression, JNK phosphorylation was concurrently increased in insulin-secreting INS-1 β-cells. Pharmacological inhibition of JNKs or siRNA knockdown of the expression of JNK1 prominently suppressed glucose-augmented ADAR2 expression, resulting in decreased efficiency of ADAR2 auto-editing. Consistently, the mRNA expression of Adar2 was selectively reduced in the islets from JNK1 null mice in comparison with that of wild-type littermates or JNK2 null mice, and ablation of JNK1 diminished high-fat diet-induced Adar2 expression in the islets from JNK1 null mice. Furthermore, promoter analysis of the mouse Adar2 gene identified a glucose-responsive region and revealed the transcription factor c-Jun as a driver of Adar2 transcription. Taken together, these results demonstrate that JNK1 serves as a crucial component in mediating glucose-responsive upregulation of ADAR2 expression in pancreatic β-cells. Thus, the JNK1 pathway may be functionally linked to the nutrient-sensing actions of ADAR2-mediated RNA editing in professional secretory cells.

  18. Molecular docking and molecular dynamics simulation studies on Thermus thermophilus leucyl-tRNA synthetase complexed with different amino acids and pre-transfer editing substrates

    OpenAIRE

    Rayevsky A. V.; Tukalo M. A.

    2016-01-01

    Aim. To investigate the structural bases for the amino acid selectivity of the Thermus thermophilus leucyl-tRNA synthetase (LeuRSTT) aminoacylation site and to disclose the binding pattern of pre-transfer editing substrates. Methods. Eight amino acids proposed as semi-cognate substrates for aminoacylation and eight aminoacyl-adenylates (formed from AMP and eight amino acids) were prepared in zwitterions form. The protein structure with a co-crystallized substrate in the aminoacylation site [P...

  19. MRB3010 is a core component of the MRB1 complex that facilitates an early step of the kinetoplastid RNA editing process

    Czech Academy of Sciences Publication Activity Database

    Ammerman, M. L.; Hashimi, Hassan; Novotná, Lucie; Číčová, Zdeňka; Mcevoy, S. M.; Lukeš, Julius; Read, L. K.

    2011-01-01

    Roč. 17, č. 5 (2011), 865-877 ISSN 1355-8382 R&D Projects: GA ČR GA204/09/1667; GA MŠk 2B06129; GA MŠk LC07032 Institutional research plan: CEZ:AV0Z60220518 Keywords : RNA editing * trypanosome * MRB1 complex * mitochondria * kinetoplast Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.095, year: 2011

  20. The Arabidopsis thaliana RNA editing factor SLO2, which affects the mitochondrial electron transport chain, participates in multiple stress and hormone responses.

    Science.gov (United States)

    Zhu, Qiang; Dugardeyn, Jasper; Zhang, Chunyi; Mühlenbock, Per; Eastmond, Peter J; Valcke, Roland; De Coninck, Barbara; Oden, Sevgi; Karampelias, Michael; Cammue, Bruno P A; Prinsen, Els; Van Der Straeten, Dominique

    2014-02-01

    Recently, we reported that the novel mitochondrial RNA editing factor SLO2 is essential for mitochondrial electron transport, and vital for plant growth through regulation of carbon and energy metabolism. Here, we show that mutation in SLO2 causes hypersensitivity to ABA and insensitivity to ethylene, suggesting a link with stress responses. Indeed, slo2 mutants are hypersensitive to salt and osmotic stress during the germination stage, while adult plants show increased drought and salt tolerance. Moreover, slo2 mutants are more susceptible to Botrytis cinerea infection. An increased expression of nuclear-encoded stress-responsive genes, as well as mitochondrial-encoded NAD genes of complex I and genes of the alternative respiratory pathway, was observed in slo2 mutants, further enhanced by ABA treatment. In addition, H2O2 accumulation and altered amino acid levels were recorded in slo2 mutants. We conclude that SLO2 is required for plant sensitivity to ABA, ethylene, biotic, and abiotic stress. Although two stress-related RNA editing factors were reported very recently, this study demonstrates a unique role of SLO2, and further supports a link between mitochondrial RNA editing events and stress response.

  1. Transcriptional Slippage and RNA Editing Increase the Diversity of Transcripts in Chloroplasts: Insight from Deep Sequencing of Vigna radiata Genome and Transcriptome.

    Directory of Open Access Journals (Sweden)

    Ching-Ping Lin

    Full Text Available We performed deep sequencing of the nuclear and organellar genomes of three mungbean genotypes: Vigna radiata ssp. sublobata TC1966, V. radiata var. radiata NM92 and the recombinant inbred line RIL59 derived from a cross between TC1966 and NM92. Moreover, we performed deep sequencing of the RIL59 transcriptome to investigate transcript variability. The mungbean chloroplast genome has a quadripartite structure including a pair of inverted repeats separated by two single copy regions. A total of 213 simple sequence repeats were identified in the chloroplast genomes of NM92 and RIL59; 78 single nucleotide variants and nine indels were discovered in comparing the chloroplast genomes of TC1966 and NM92. Analysis of the mungbean chloroplast transcriptome revealed mRNAs that were affected by transcriptional slippage and RNA editing. Transcriptional slippage frequency was positively correlated with the length of simple sequence repeats of the mungbean chloroplast genome (R2=0.9911. In total, 41 C-to-U editing sites were found in 23 chloroplast genes and in one intergenic spacer. No editing site that swapped U to C was found. A combination of bioinformatics and experimental methods revealed that the plastid-encoded RNA polymerase-transcribed genes psbF and ndhA are affected by transcriptional slippage in mungbean and in main lineages of land plants, including three dicots (Glycine max, Brassica rapa, and Nicotiana tabacum, two monocots (Oryza sativa and Zea mays, two gymnosperms (Pinus taeda and Ginkgo biloba and one moss (Physcomitrella patens. Transcript analysis of the rps2 gene showed that transcriptional slippage could affect transcripts at single sequence repeat regions with poly-A runs. It showed that transcriptional slippage together with incomplete RNA editing may cause sequence diversity of transcripts in chloroplasts of land plants.

  2. The absence of A-to-I editing in the anticodon of plant cytoplasmic tRNA (Arg) ACG demands a relaxation of the wobble decoding rules.

    Science.gov (United States)

    Aldinger, Carolin A; Leisinger, Anne-Katrin; Gaston, Kirk W; Limbach, Patrick A; Igloi, Gabor L

    2012-10-01

    It is a prevalent concept that, in line with the Wobble Hypothesis, those tRNAs having an adenosine in the first position of the anticodon become modified to an inosine at this position. Sequencing the cDNA derived from the gene coding for cytoplasmic tRNA (Arg) ACG from several higher plants as well as mass spectrometric analysis of the isoacceptor has revealed that for this kingdom an unmodified A in the wobble position of the anticodon is the rule rather than the exception. In vitro translation shows that in the plant system the absence of inosine in the wobble position of tRNA (Arg) does not prevent decoding. This isoacceptor belongs to the class of tRNA that is imported from the cytoplasm into the mitochondria of higher plants. Previous studies on the mitochondrial tRNA pool have demonstrated the existence of tRNA (Arg) ICG in this organelle. In moss the mitochondrial encoded distinct tRNA (Arg) ACG isoacceptor possesses the I34 modification. The implication is that for mitochondrial protein biosynthesis A-to-I editing is necessary and occurs by a mitochondrion-specific deaminase after import of the unmodified nuclear encoded tRNA (Arg) ACG.

  3. Paleomagnetic Analysis Using SQUID Microscopy

    Science.gov (United States)

    Weiss, Benjamin P.; Lima, Eduardo A.; Fong, Luis E.; Baudenbacher, Franz J.

    2007-01-01

    Superconducting quantum interference device (SQUID) microscopes are a new generation of instruments that map magnetic fields with unprecedented spatial resolution and moment sensitivity. Unlike standard rock magnetometers, SQUID microscopes map magnetic fields rather than measuring magnetic moments such that the sample magnetization pattern must be retrieved from source model fits to the measured field data. In this paper, we presented the first direct comparison between paleomagnetic analyses on natural samples using joint measurements from SQUID microscopy and moment magnetometry. We demonstrated that in combination with apriori geologic and petrographic data, SQUID microscopy can accurately characterize the magnetization of lunar glass spherules and Hawaiian basalt. The bulk moment magnitude and direction of these samples inferred from inversions of SQUID microscopy data match direct measurements on the same samples using moment magnetometry. In addition, these inversions provide unique constraints on the magnetization distribution within the sample. These measurements are among the most sensitive and highest resolution quantitative paleomagnetic studies of natural remanent magnetization to date. We expect that this technique will be able to extend many other standard paleomagnetic techniques to previously inaccessible microscale samples.

  4. Tracking Electromagnetic Energy With SQUIDs

    Science.gov (United States)

    2005-01-01

    A superconducting quantum interference device (SQUID) is a gadget used to measure extremely weak signals, specifically magnetic flux. It can detect subtle changes in energy, up to 100 billion times weaker than the electromagnetic energy required to move a compass needle. SQUIDs are used for a variety of testing procedures where extreme sensitivity is required and where the test instrument need not come into direct contact with the test subject. NASA uses SQUIDs for remote, noncontact sensing in a variety of venues, including monitoring the Earth s magnetic field and tracking brain activity of pilots. Scientists at NASA s Goddard Space Flight Center have been making extensive use of this technology, from astrophysical research, to tracking the navigational paths of bees in flight to determine if they are using internal compasses. These very sensitive measurement devices have a wide variety of uses within NASA and even more uses within the commercial realm.

  5. SQUID-based measuring systems

    Indian Academy of Sciences (India)

    field produced by a given two-dimensional current density distribution is inverted using the Fourier transform technique. Keywords ... Superconducting quantum interference devices (SQUIDs) are the most sensitive detectors for measurement of ... omagnetic prospecting, detection of gravity waves etc. Judging the importance ...

  6. Compact integrated dc SQUID gradiometer

    Science.gov (United States)

    de Waal, V. J.; Klapwijk, T. M.

    1982-10-01

    An all-niobium integrated system of first-order gradiometer and dc suprconducting quantum interference device (SQUID) has been developed. It is relatively simple to fabricate, has an overall size of 17×12 mm and a sensitivity of 3.5×10-12 T m-1 Hz-1/2.

  7. Compact integrated dc SQUID gradiometer

    Energy Technology Data Exchange (ETDEWEB)

    de Waal, V.J.; Klapwijk, T.M.

    1982-10-01

    An all-niobium integrated system of first-order gradiometer and dc suprconducting quantum interference device (SQUID) has been developed. It is relatively simple to fabricate, has an overall size of 17 x 12 mm and a sensitivity of 3.5 x 10/sup -12/ T m/sup -1/ Hz/sup -1/2/.

  8. Squids: applications outside the laboratory

    Energy Technology Data Exchange (ETDEWEB)

    Falco, C M

    1978-07-01

    Originally thought to be rather esoteric, SQUIDS (superconducting quantum interference devices) have moved from the realms of theory to practical application since 1962. The promise for the not-too-distant future is a superconducting computer, with 10/sup 5/ logic elements in a 1cm cube.

  9. STM-SQUID probe microscope

    International Nuclear Information System (INIS)

    Hayashi, Tadayuki; Tachiki, Minoru; Itozaki, Hideo

    2007-01-01

    We have developed a STM-SQUID probe microscope. A high T C SQUID probe microscope was combined with a scanning tunneling microscope for investigation of samples at room temperature in air. A high permeability probe needle was used as a magnetic flux guide to improve the spatial resolution. The probe with tip radius of less than 100 nm was prepared by microelectropolishing. The probe was also used as a scanning tunneling microscope tip. Topography of the sample surface could be measured by the scanning tunneling microscope with high spatial resolution prior to observation by SQUID microscopy. The SQUID probe microscope image could be observed while keeping the distance from the sample surface to the probe tip constant. We observed a topographic image and a magnetic image of Ni fine pattern and also a magnetically recorded hard disk. Furthermore we have investigated a sample vibration method of the static magnetic field emanating from a sample with the aim of achieving a higher signal-to-noise (S/N) ratio

  10. Cold SQUIDs and hot samples

    Energy Technology Data Exchange (ETDEWEB)

    Lee, T.S.C. [Univ. of California, Berkeley, CA (United States). Dept. of Physics]|[Lawrence Berkeley national Lab., CA (United States). Materials Sciences Div.

    1997-05-01

    Low transition temperature (low-{Tc}) and high-{Tc} Superconducting QUantum Interference Devices (SQUIDs) have been used to perform high-resolution magnetic measurements on samples whose temperatures are much higher than the operating temperatures of the devices. Part 1 of this work focuses on measurements of the rigidity of flux vortices in high-{Tc} superconductors using two low-{Tc} SQUIDs, one on either side of a thermally-insulated sample. The correlation between the signals of the SQUIDs is a direct measure of the extent of correlation between the movements of opposite ends of vortices. These measurements were conducted under the previously-unexplored experimental conditions of nominally-zero applied magnetic field, such that vortex-vortex interactions were unimportant, and with zero external current. At specific temperatures, the authors observed highly-correlated noise sources, suggesting that the vortices moved as rigid rods. At other temperatures, the noise was mostly uncorrelated, suggesting that the relevant vortices were pinned at more than one point along their length. Part 2 describes the design, construction, performance, and applications of a scanning high-{Tc} SQUID microscope optimized for imaging room-temperature objects with very high spatial resolution and magnetic source sensitivity.

  11. Properties of high temperature SQUIDS

    International Nuclear Information System (INIS)

    Falco, C.M.; Wu, C.T.

    1978-01-01

    A review is given of the present status of weak links and dc and rf biased SQUIDs made with high temperature superconductors. A method for producing reliable, reproducible devices using Nb 3 Sn is outlined, and comments are made on directions future work should take

  12. Cold SQUIDs and hot samples

    International Nuclear Information System (INIS)

    Lee, T.S.C.; Lawrence Berkeley national Lab., CA

    1997-05-01

    Low transition temperature (low-T c ) and high-T c Superconducting QUantum Interference Devices (SQUIDs) have been used to perform high-resolution magnetic measurements on samples whose temperatures are much higher than the operating temperatures of the devices. Part 1 of this work focuses on measurements of the rigidity of flux vortices in high-T c superconductors using two low-T c SQUIDs, one on either side of a thermally-insulated sample. The correlation between the signals of the SQUIDs is a direct measure of the extent of correlation between the movements of opposite ends of vortices. These measurements were conducted under the previously-unexplored experimental conditions of nominally-zero applied magnetic field, such that vortex-vortex interactions were unimportant, and with zero external current. At specific temperatures, the authors observed highly-correlated noise sources, suggesting that the vortices moved as rigid rods. At other temperatures, the noise was mostly uncorrelated, suggesting that the relevant vortices were pinned at more than one point along their length. Part 2 describes the design, construction, performance, and applications of a scanning high-T c SQUID microscope optimized for imaging room-temperature objects with very high spatial resolution and magnetic source sensitivity

  13. Efficient genome editing in hematopoietic stem cells with helper-dependent Ad5/35 vectors expressing site-specific endonucleases under microRNA regulation

    Directory of Open Access Journals (Sweden)

    Kamola Saydaminova

    Full Text Available Genome editing with site-specific endonucleases has implications for basic biomedical research as well as for gene therapy. We generated helper-dependent, capsid-modified adenovirus (HD-Ad5/35 vectors for zinc-finger nuclease (ZFN– or transcription activator-like effector nuclease (TALEN–mediated genome editing in human CD34+ hematopoietic stem cells (HSCs from mobilized adult donors. The production of these vectors required that ZFN and TALEN expression in HD-Ad5/35 producer 293-Cre cells was suppressed. To do this, we developed a microRNA (miRNA-based system for regulation of gene expression based on miRNA expression profiling of 293-Cre and CD34+ cells. Using miR-183-5p and miR-218-5p based regulation of transgene gene expression, we first produced an HD-Ad5/35 vector expressing a ZFN specific to the HIV coreceptor gene ccr5. We demonstrated that HD-Ad5/35.ZFNmiR vector conferred ccr5 knock out in primitive HSC (i.e., long-term culture initiating cells and NOD/SCID repopulating cells. The ccr5 gene disruption frequency achieved in engrafted HSCs found in the bone marrow of transplanted mice is clinically relevant for HIV therapy considering that these cells can give rise to multiple lineages, including all the lineages that represent targets and reservoirs for HIV. We produced a second HD-Ad5/35 vector expressing a TALEN targeting the DNase hypersensitivity region 2 (HS2 within the globin locus control region. This vector has potential for targeted gene correction in hemoglobinopathies. The miRNA regulated HD-Ad5/35 vector platform for expression of site-specific endonucleases has numerous advantages over currently used vectors as a tool for genome engineering of HSCs for therapeutic purposes.

  14. Structure of a putative trans-editing enzyme for prolyl-tRNA synthetase from Aeropyrum pernix K1 at 1.7 Å resolution

    International Nuclear Information System (INIS)

    Murayama, Kazutaka; Kato-Murayama, Miyuki; Katsura, Kazushige; Uchikubo-Kamo, Tomomi; Yamaguchi-Hirafuji, Machiko; Kawazoe, Masahito; Akasaka, Ryogo; Hanawa-Suetsugu, Kyoko; Hori-Takemoto, Chie; Terada, Takaho; Shirouzu, Mikako; Yokoyama, Shigeyuki

    2004-01-01

    The three-dimensional structure of the APE2540 protein from A. pernix K1 has been determined by the multiple anomalous dispersion method at 1.7 Å resolution. The structure includes two monomers in the asymmetric unit and shares structural similarity with the YbaK protein or cysteinyl-tRNA Pro deacylase from H. influenzae. The crystal structure of APE2540, the putative trans-editing enzyme ProX from Aeropyrum pernix K1, was determined in a high-throughput manner. The crystal belongs to the monoclinic space group P2 1 , with unit-cell parameters a = 47.4, b = 58.9, c = 53.6 Å, β = 106.8°. The structure was solved by the multiwavelength anomalous dispersion method at 1.7 Å and refined to an R factor of 16.8% (R free = 20.5%). The crystal structure includes two protein molecules in the asymmetric unit. Each monomer consists of eight β-strands and seven α-helices. A structure-homology search revealed similarity between the trans-editing enzyme YbaK (or cysteinyl-tRNA Pro deacylase) from Haemophilus influenzae (HI1434; 22% sequence identity) and putative ProX proteins from Caulobacter crescentus (16%) and Agrobacterium tumefaciens (21%)

  15. Genome Editing for Cancer Therapy: Delivery of Cas9 Protein/sgRNA Plasmid via a Gold Nanocluster/Lipid Core-Shell Nanocarrier.

    Science.gov (United States)

    Wang, Peng; Zhang, Lingmin; Xie, Yangzhouyun; Wang, Nuoxin; Tang, Rongbing; Zheng, Wenfu; Jiang, Xingyu

    2017-11-01

    The type II bacterial clustered, regularly interspaced, short palindromic repeats (CRISPR)-Cas9 (CRISPR-associated protein) system (CRISPR-Cas9) is a powerful toolbox for gene-editing, however, the nonviral delivery of CRISPR-Cas9 to cells or tissues remains a key challenge. This paper reports a strategy to deliver Cas9 protein and single guide RNA (sgRNA) plasmid by a nanocarrier with a core of gold nanoclusters (GNs) and a shell of lipids. By modifying the GNs with HIV-1-transactivator of transcription peptide, the cargo (Cas9/sgRNA) can be delivered into cell nuclei. This strategy is utilized to treat melanoma by designing sgRNA targeting Polo-like kinase-1 ( Plk1 ) of the tumor. The nanoparticle (polyethylene glycol-lipid/GNs/Cas9 protein/sgPlk1 plasmid, LGCP) leads to >70% down-regulation of Plk1 protein expression of A375 cells in vitro. Moreover, the LGCP suppresses melanoma progress by 75% on mice. Thus, this strategy can deliver protein-nucleic acid hybrid agents for gene therapy.

  16. Gene editing by co-transformation of TALEN and chimeric RNA/DNA oligonucleotides on the rice OsEPSPS gene and the inheritance of mutations.

    Directory of Open Access Journals (Sweden)

    Mugui Wang

    Full Text Available Although several site-specific nucleases (SSNs, such as zinc-finger nucleases (ZFNs, transcription activator-like effector nucleases (TALENs, and the clustered regularly interspaced short palindromic repeat (CRISPR/Cas, have emerged as powerful tools for targeted gene editing in many organisms, to date, gene targeting (GT in plants remains a formidable challenge. In the present study, we attempted to substitute a single base in situ on the rice OsEPSPS gene by co-transformation of TALEN with chimeric RNA/DNA oligonucleotides (COs, including different strand composition such as RNA/DNA (C1 or DNA/RNA (C2 but contained the same target base to be substituted. In contrast to zero GT event obtained by the co-transformation of TALEN with homologous recombination plasmid (HRP, we obtained one mutant showing target base substitution although accompanied by undesired deletion of 12 bases downstream the target site from the co-transformation of TALEN and C1. In addition to this typical event, we also obtained 16 mutants with different length of base deletions around the target site among 105 calli lines derived from transformation of TALEN alone (4/19 as well as co-transformation of TELAN with either HRP (5/30 or C1 (2/25 or C2 (5/31. Further analysis demonstrated that the homozygous gene-edited mutants without foreign gene insertion could be obtained in one generation. The induced mutations in transgenic generation were also capable to pass to the next generation stably. However, the genotypes of mutants did not segregate normally in T1 population, probably due to lethal mutations. Phenotypic assessments in T1 generation showed that the heterozygous plants with either one or three bases deletion on target sequence, called d1 and d3, were more sensitive to glyphosate and the heterozygous d1 plants had significantly lower seed-setting rate than wild-type.

  17. Identification of four squid species by quantitative real-time polymerase chain reaction.

    Science.gov (United States)

    Ye, Jian; Feng, Junli; Liu, Shasha; Zhang, Yanping; Jiang, Xiaona; Dai, Zhiyuan

    2016-02-01

    Squids are distributed worldwide, including many species of commercial importance, and they are often made into varieties of flavor foods. The rapid identification methods for squid species especially their processed products, however, have not been well developed. In this study, quantitative real-time PCR (qPCR) systems based on specific primers and TaqMan probes have been established for rapid and accurate identification of four common squid species (Ommastrephes bartramii, Dosidicus gigas, Illex argentinus, Todarodes pacificus) in Chinese domestic market. After analyzing mitochondrial genes reported in GenBank, the mitochondrial cytochrome b (Cytb) gene was selected for O. bartramii detection, cytochrome c oxidase subunit I (COI) gene for D. gigas and T. Pacificus detection, ATPase subunit 6 (ATPase 6) gene for I. Argentinus detection, and 12S ribosomal RNA (12S rDNA) gene for designing Ommastrephidae-specific primers and probe. As a result, all the TaqMan systems are of good performance, and efficiency of each reaction was calculated by making standard curves. This method could detect target species either in single or mixed squid specimen, and it was applied to identify 12 squid processed products successfully. Thus, it would play an important role in fulfilling labeling regulations and squid fishery control. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. NanoSQUIDs: Basics & recent advances

    Science.gov (United States)

    José Martínez-Pérez, Maria; Koelle, Dieter

    2017-08-01

    Superconducting Quantum Interference Devices (SQUIDs) are one of the most popular devices in superconducting electronics. They combine the Josephson effect with the quantization of magnetic flux in superconductors. This gives rise to one of the most beautiful manifestations of macroscopic quantum coherence in the solid state. In addition, SQUIDs are extremely sensitive sensors allowing us to transduce magnetic flux into measurable electric signals. As a consequence, any physical observable that can be converted into magnetic flux, e.g., current, magnetization, magnetic field or position, becomes easily accessible to SQUID sensors. In the late 1980s it became clear that downsizing the dimensions of SQUIDs to the nanometric scale would encompass an enormous increase of their sensitivity to localized tiny magnetic signals. Indeed, nanoSQUIDs opened the way to the investigation of, e.g., individual magnetic nanoparticles or surface magnetic states with unprecedented sensitivities. The purpose of this chapter is to present a detailed survey of microscopic and nanoscopic SQUID sensors. We will start by discussing the principle of operation of SQUIDs, placing the emphasis on their application as ultrasensitive detectors for small localized magnetic signals. We will continue by reviewing a number of existing devices based on different kinds of Josephson junctions and materials, focusing on their advantages and drawbacks. The last sections are left for applications of nanoSQUIDs in the fields of scanning SQUID microscopy and magnetic particle characterization, placing special stress on the investigation of individual magnetic nanoparticles.

  19. RNA.

    Science.gov (United States)

    Darnell, James E., Jr.

    1985-01-01

    Ribonucleic acid (RNA) converts genetic information into protein and usually must be processed to serve its function. RNA types, chemical structure, protein synthesis, translation, manufacture, and processing are discussed. Concludes that the first genes might have been spliced RNA and that humans might be closer than bacteria to primitive…

  20. RNA editing makes mistakes in plant mitochondria: editing loses sense in transcripts of a rps19 pseudogene and in creating stop codons in coxI and rps3 mRNAs of Oenothera.

    Science.gov (United States)

    Schuster, W; Brennicke, A

    1991-01-01

    An intact gene for the ribosomal protein S19 (rps19) is absent from Oenothera mitochondria. The conserved rps19 reading frame found in the mitochondrial genome is interrupted by a termination codon. This rps19 pseudogene is cotranscribed with the downstream rps3 gene and is edited on both sides of the translational stop. Editing, however, changes the amino acid sequence at positions that were well conserved before editing. Other strange editings create translational stops in open reading frames coding for functional proteins. In coxI and rps3 mRNAs CGA codons are edited to UGA stop codons only five and three codons, respectively, downstream to the initiation codon. These aberrant editings in essential open reading frames and in the rps19 pseudogene appear to have been shifted to these positions from other editing sites. These observations suggest a requirement for a continuous evolutionary constraint on the editing specificities in plant mitochondria. Images PMID:1762921

  1. A new integrated microwave SQUID circuit design

    International Nuclear Information System (INIS)

    Erne, S.N.; Finnegan, T.F.

    1980-01-01

    In this paper we consider the design and operation of a planar thin-film rf-SQUID circuit which can be realized via microwave-integrated-circuit (MIC) techniques and which differs substantially from pervious microwave SQUID configurations involving either mechanical point-contact or cylindrical thin-film micro-bridge geometries. (orig.)

  2. Review of SQUID Sensors for Measuring Magnetocardiography

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Y. H.; Kim, J. M.; Yu, K. K.; Kim, K.; Kwon, H. [Brain and Cognition Measurement Lab, Korea Research Institute of Standards and Science, Daejeon (Korea, Republic of)

    2011-08-15

    Measurement of magnetic signals generated from electric activity of myocardium provides useful information for the functional diagnosis of heart diseases. Key technical component of the magnetocardiography (MCG) technology is SQUID. To measure MCG signals with high signal-to-noise ratio, sensitive SQUID magnetic field sensors are needed. Present magnetic field sensors based on Nb SQUIDs have field sensitivity good enough to measure most of MCG signals. However, for accurate measurement of fine signal pattern or detection of local atrial fibrillation signals, we may need higher field sensitivity. In addition to field sensitivity, economic aspect of the SQUID system is also important. To simplify the SQUID readout electronics, the output voltage or flux-to-voltage transfer of SQUID should be large enough so that direct measurement of SQUID output can be done using room-temperature preamplifiers. Double relaxation oscillation SQUID (DROS), having about 10 times larger flux-to-voltage transfers than those of DC-SQUIDs, was shown to be a good choice to make the electronics compact. For effective cancellation of external noise inside a thin economic shielded room, first-order axial gradiometer with high balance, simple structure and long-baseline is needed. We developed a technology to make the axial gradiometer compact using direct bonding of superconductive wires between pickup coil and input coil. Conventional insert has mechanical support to hold the gradiometer array, and the dewar neck has equal diameter with the dewar bottom. Boiling of the liquid He can generate mechanical vibrations in the gradiometer array due to mechanical connection structure. Elimination of the mechanical support, and direct mounting of the gradiometer array into the dewar bottom can reduce the dewar neck diameter, resulting in the reduction of liquid He consumption.

  3. Squid based beam current meter

    International Nuclear Information System (INIS)

    Kuchnir, M.

    1983-01-01

    A SQUID based beam current meter has the capability of measuring the current of a beam with as little as 30 x 155 antiprotons (with a signal to noise ratio of 2). If low noise dc current is used to cancel most of the beam or an up-down counter is used to count auto-resets this sensitivity will be available at any time in the acumulation process. This current meter will therefore be a unique diagnostic tool for optimizing the performance of several Tev I components. Besides requiring liquid helium it seems that its only drawback is not to follow with the above sensitivity a sudden beam change larger than 16 μA, something that could be done using a second one in a less sensitive configuration

  4. New version of toroidal SQUID sensor

    International Nuclear Information System (INIS)

    Zarembinski, S.; Kachniarz, J.

    1983-01-01

    A report is given on the design and fabrication of a mechanically stable and thermal shock resistant SQUID sensor. The sensor is vacuum sealed while the access to the adjustment of its point contact is left open

  5. Host apolipoprotein B messenger RNA-editing enzyme catalytic polypeptide-like 3G is an innate defensive factor and drug target against hepatitis C virus.

    Science.gov (United States)

    Peng, Zong-Gen; Zhao, Zhi-Yun; Li, Yan-Ping; Wang, Yu-Ping; Hao, Lan-Hu; Fan, Bo; Li, Yu-Huan; Wang, Yue-Ming; Shan, Yong-Qiang; Han, Yan-Xing; Zhu, Yan-Ping; Li, Jian-Rui; You, Xue-Fu; Li, Zhuo-Rong; Jiang, Jian-Dong

    2011-04-01

    Host cellular factor apolipoprotein B messenger RNA (mRNA)-editing enzyme catalytic polypeptide-like 3G (hA3G) is a cytidine deaminase that inhibits a group of viruses including human immunodeficiency virus-1 (HIV-1). In the continuation of our research on hA3G, we found that hA3G stabilizing compounds significantly inhibited hepatitis C virus (HCV) replication. Therefore, this study investigated the role of hA3G in HCV replication. Introduction of external hA3G into HCV-infected Huh7.5 human hepatocytes inhibited HCV replication; knockdown of endogenous hA3G enhanced HCV replication. Exogenous HIV-1 virion infectivity factor (Vif) decreased intracellular hA3G and therefore enhanced HCV proliferation, suggesting that the presence of Vif might be an explanation for the HIV-1/HCV coinfection often observed in HIV-1(+) individuals. Treatment of the HCV-infected Huh7.5 cells with RN-5 or IMB-26, two known hA3G stabilizing compounds, increased intracellular hA3G and accordingly inhibited HCV replication. The compounds inhibit HCV through increasing the level of hA3G incorporated into HCV particles, but not through inhibiting HCV enzymes. However, G/A hypermutation in the HCV genome were not detected, suggesting a new antiviral mechanism of hA3G in HCV, different from that in HIV-1. Stabilization of hA3G by RN-5 was safe in vivo. hA3G appears to be a cellular restrict factor against HCV and could be a potential target for drug discovery. 2011 American Association for the Study of Liver Diseases.

  6. YBCO SQUIDs with unconventional current phase relation

    International Nuclear Information System (INIS)

    Bauch, T.; Johansson, J.; Cedergren, K.; Lindstroem, T.; Lombardi, F.

    2007-01-01

    We have studied the dynamics of YBa 2 Cu 3 O 7-δ (YBCO) dc sperconducting quantum interference devices (SQUIDs) characterized by an unconventional Josephson current phase relation (CPR). We have focused on SQUID configurations with Josephson junctions where the lobe of the order parameter in one electrode is facing a node in the other electrode. This order parameter arrangement should enhance the appearance of a sin(2φ) term in the CPR. The response of the critical current of the dc SQUID, under the effect of an external magnetic field, has been measured in temperature, down to 20 mK. Our experimental data have been compared with numerical simulations of the SQUIDs dynamics by considering a CPR of a single junction of the form I(φ) = I I sin(φ) - I II sin(2φ) where I I and I II are, respectively, the first and second harmonic component. In our devices the values of the sin(2φ) term are such that the fundamental state of the SQUID is naturally double degenerate. This is of great relevance for applications of d-wave SQUIDs in quantum information processing

  7. An anti-HIV-1 compound that increases steady-state expression of apoplipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3G.

    Science.gov (United States)

    Ejima, Tomohiko; Hirota, Mayuko; Mizukami, Tamio; Otsuka, Masami; Fujita, Mikako

    2011-10-01

    Human apoplipoprotein B mRNA-editing enzyme-catalytic polypeptide-like (APOBEC) 3G (A3G) is an antiviral protein that blocks HIV-1 replication. However, the antiviral activity of A3G is overcome by the HIV-1 protein Vif. This inhibitory function of Vif is related to its ability to degrade A3G in the proteasome. This finding prompted us to examine the activities of 4-(dimethylamino)-2,6-bis[(N-(2-[(2-nitrophenyl)dithio]ethyl)amino)methyl]pyridine (SN-2) and SN-3. We found that 5 µM SN-2 increases the expression of A3G to a level much higher than that observed in the absence of Vif, without affecting the level of Vif expression. The proteasome inhibitor MG-132 increased the level of both A3G and Vif expression. These results demonstrate that A3G is ubiquitinated and degraded in the proteasome by a factor other than Vif, and that SN-2 selectively inhibits these processes. Furthermore, 5 µM SN-2 significantly inhibited the MAGI cell infectivity of wild-type HIV-1. These findings may contribute to the development of a novel anti-HIV-1 drug.

  8. The inhibitory effect of apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3G (APOBEC3G) and its family members on the activity of cellular microRNAs.

    Science.gov (United States)

    Zhang, Hui

    2010-01-01

    The apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3G (APOBEC3G or APOBEC3G) and its fellow cytidine deaminase family members are potent restrictive factors for human immunodeficiency virus type 1 (HIV-1) and many other retroviruses. However, the cellular function of APOBEC3G remains to be further clarified. It has been reported that APOBEC3s can restrict the mobility of endogenous retroviruses and LTR-retrotransposons, suggesting that they can maintain stability in host genomes. However, APOBEC3G is normally cytoplasmic. Further studies have demonstrated that it is associated with an RNase-sensitive high molecular mass (HMM) and located in processing bodies (P-bodies) of replicating T-cells, indicating that the major cellular function of APOBEC3G seems to be related to P-body-related RNA processing and metabolism. As the function of P-body is closely related to miRNA activity, APOBEC3G could affect the miRNA function. Recent studies have demonstrated that APOBEC3G and its family members counteract miRNA-mediated repression of protein translation. Further, APOBEC3G enhances the association of miRNA-targeted mRNA with polysomes, and facilitates the dissociation of miRNA-targeted mRNA from P-bodies. As such, APOBEC3G regulate the activity of cellular miRNAs. Whether this function is related to its potent antiviral activity remains to be further determined.

  9. The genome editing revolution

    DEFF Research Database (Denmark)

    Stella, Stefano; Montoya, Guillermo

    2016-01-01

    -Cas system has become the main tool for genome editing in many laboratories. Currently the targeted genome editing technology has been used in many fields and may be a possible approach for human gene therapy. Furthermore, it can also be used to modifying the genomes of model organisms for studying human......In the last 10 years, we have witnessed a blooming of targeted genome editing systems and applications. The area was revolutionized by the discovery and characterization of the transcription activator-like effector proteins, which are easier to engineer to target new DNA sequences than...... sequence). This ribonucleoprotein complex protects bacteria from invading DNAs, and it was adapted to be used in genome editing. The CRISPR ribonucleic acid (RNA) molecule guides to the specific DNA site the Cas9 nuclease to cleave the DNA target. Two years and more than 1000 publications later, the CRISPR...

  10. Radiation detection from phase-locked serial dc SQUID arrays

    DEFF Research Database (Denmark)

    Kaplunenko, V. K.; Mygind, Jesper; Pedersen, Niels Falsig

    1993-01-01

    We report on synchronous operation of series arrays of inductively coupled superconducting quantum interference devices (SQUIDs). Each array consisted of N=3 or 11 dc SQUIDs with common inductances providing a strong interaction between neighboring cells. Externally shunted (betac[approximately-e......We report on synchronous operation of series arrays of inductively coupled superconducting quantum interference devices (SQUIDs). Each array consisted of N=3 or 11 dc SQUIDs with common inductances providing a strong interaction between neighboring cells. Externally shunted (betac...

  11. Squids: principles and basic applications in experimental physics

    International Nuclear Information System (INIS)

    Ocio, M.

    1990-01-01

    The basic principles and the description of the technical aspects of SQUIDs (Superconducting Quantum Interference Devices) are described. The applications of SQUIDs in experimental researches and low temperature physics experiments are given. The concepts of fluxoid quantization in a superconductor and Josephson tunnelling are reviewed. The principles, the operation, the noise and the different configurations of r.f. and direct current bias SQUIDs are summarized. The principal characteristics of several SQUIDs are reported

  12. The investigation of rf-squids at liquid nitrogen temperatures

    Energy Technology Data Exchange (ETDEWEB)

    Polushkin, V N; Vasiliev, B V [Joint Inst. for Nuclear Research, Dubna (USSR)

    1989-12-01

    One- and two-hole YBCO ceramic rf-squids operating at liquid nitrogen temperatures have been developed. The main squid parameters: self-inductance, white noise level and magnetic flux resolution were measured. The directly measured external field sensitivity for one-hole squid was at the level of 100 fT/{radical}Hz. (orig.).

  13. The use of (double) relaxation oscillation SQUIDs as a sensor

    NARCIS (Netherlands)

    van Duuren, M.J.; Brons, G.C.S.; Kattouw, H.; Flokstra, Jakob; Rogalla, Horst

    1997-01-01

    Relaxation Oscillation SQUIDs (ROSs) and Double Relaxation Oscillation SQUIDs (DROSs) are based on relaxation oscillations that are induced in hysteretic dc SQUIDs by an external L-R shunt. The relaxation frequency of a ROS varies with the applied flux Φ, whereas the output of a DROS is a dc

  14. Computer model for noise in the dc Squid

    International Nuclear Information System (INIS)

    Tesche, C.D.; Clarke, J.

    1976-08-01

    A computer model for the dc SQUID is described which predicts signal and noise as a function of various SQUID parameters. Differential equations for the voltage across the SQUID including the Johnson noise in the shunted junctions are integrated stepwise in time

  15. Well coupled, low noise, dc SQUIDS

    International Nuclear Information System (INIS)

    Muhlfelder, B.; Beall, J.A.; Cromar, M.W.; Johnson, W.W.; Ono, R.H.

    1985-01-01

    The authors have designed, fabricated, and tested a Double Transformer (DT) coupled dc SQUID (Superconducting Quantum Interference Device) with low noise, an input inductance of 1μH and a smooth input-output characteristic. A transmission line model is presented to explain a resonance in the input-output characteristic of early versions of this device. Guided by the results of numerical simulations a new version of this device has been built and tested. Experimental results are presented that show that the resonance can be moved to a higher voltage by reducing the area of the SQUID loop. The voltage-external flux characteristic of some of these new devices agrees to within 10% with computer simulations. The minimum detectable energy per unit bandwidth (MDE) referred to the SQUID loop, is 10h, where h is Planck's constant. Computer simulations indicate an MDE of 6h

  16. Parameter tolerance of the SQUID bootstrap circuit

    International Nuclear Information System (INIS)

    Zhang Guofeng; Dong Hui; Xie Xiaoming; Jiang Mianheng; Zhang Yi; Krause, Hans-Joachim; Braginski, Alex I; Offenhäusser, Andreas

    2012-01-01

    We recently demonstrated and analysed the voltage-biased SQUID bootstrap circuit (SBC) conceived to suppress the preamplifier noise contribution in the absence of flux modulation readout. Our scheme contains both the additional voltage and current feedbacks. In this study, we analysed the tolerance of the SBC noise suppression performance to spreads in SQUID and SBC circuit parameters. Analytical results were confirmed by experiments. A one-time adjustable current feedback can be used to extend the tolerance to spreads such as those caused by the integrated circuit fabrication process. This should help to improve the fabrication yield of SBC devices integrated on one chip—as required for multi-channel SQUID systems.

  17. Fasting decreases apolipoprotein B mRNA editing and the secretion of small molecular weight apoB by rat hepatocytes: Evidence that the total amount of apoB secreted is regulated post-transcriptionally

    International Nuclear Information System (INIS)

    Leighton, J.K.; Joyner, J.; Zamarripa, J.; Deines, M.; Davis, R.A.

    1990-01-01

    Two different molecular weight forms of apoB are produced from a common initial transcript via editing of a Gln codon (CAA) to a stop codon (UAA), leading to a truncated translation product (apo BS) that consists of the amino terminal half of the larger form (apoBL). Previous studies have shown that fasting coordinately decreases lipogenesis and the secretion of very low density lipoprotein (VLDL) lipids and apoBS. Secretion of the apoBL is unaffected by fasting. We studied whether editing of apoB RNA is repressed by fasting, thus accounting for the selective decreased secretion of apoBS. Column chromatography of [35S]methionine-labeled lipoproteins secreted by hepatocytes from fed rats showed that essentially all of apoBL is secreted in the VLDL fraction, whereas a significant amount (15%) of apoBS is secreted associated as lipoproteins eluting in the HDL fractions. Fasting decreased the relative amount of apoBS that eluted in the VLDL fractions and increased the amount secreted in the HDL fractions. Consistent with previous results, hepatocytes from fasted rats show a selective twofold decrease in apoBS secretion. Fasting did not affect the relative abundance of apoB RNA, determined by slot blot hybridization assays using two different 32P-labeled cDNA probes coding either for both molecular weight forms or for only the large molecular weight form. However, quantitative of the editing of apoB RNA showed that fasting caused a 60% decrease in the amount of apoB RNA possessing the stop codon. These data show that the editing of apoB RNA is sensitive to metabolic state (i.e., fasting) resulting in a selective decrease in the secretion of apoBS. However, since the total secretion of apoB was decreased by fasting, while apoB mRNA levels remained constant, additional (post-transcriptional) mechanisms play a role in regulating apoB secretion

  18. High Tc Josephson Junctions, SQUIDs and magnetometers

    International Nuclear Information System (INIS)

    Clarke, J.

    1991-01-01

    There has recently been considerable progress in the state-of-the-art of high-T c magnetometers based on dc SQUIDs (Superconducting Quantum Interference Devices). This progress is due partly to the development of more manufacturable Josephson junctions, making SQUIDs easier to fabricate, and partly to the development of multiturn flux transformers that convert the high sensitivity of SQUIDs to magnetic flux to a correspondingly high sensitivity to magnetic field. Needless to say, today's high-T c SQUIDs are still considerably less sensitive than their low-T c counterparts, particularly at low frequencies (f) where their level of 1/f noise remains high. Nonetheless, the performance of the high-T c devices has now reached the point where they are adequate for a number of the less demanding applications; furthermore, as we shall see, at least modest improvements in performance are expected in the near future. In this article, the author outlines these various developments. This is far from a comprehensive review of the field, however, and, apart from Sec. 2, he describes largely his own work. He begins in Sec. 2 with an overview of the various types of Josephson junctions that have been investigated, and in Sec. 3, he describes some of the SQUIDs that have been tested, and assess their performance. Section 4 discuss the development of the multilayer structures essential for an interconnect technology, and, in particular, for crossovers and vias. Section 5 shows how this technology enables one to fabricate multiturn flux transformers which, in turn, can be coupled to SQUIDs to make magnetometers. The performance and possible future improvements in these magnetometers are assessed, and some applications mentioned

  19. Design of a hysteretic SQUID as the readout for a dc SQUID

    International Nuclear Information System (INIS)

    Gershenson, M.

    1991-01-01

    This paper present a design for an optimal hysteretic SQUID readout circuit for a DC SQUID, thus eliminating the need for bulky output transformers or resonance matching circuits. The hysteretic readout system, which is based in part on standard sampling theory, is compared to another similar system and shown to be superior in terms of slew rate and immunity of electromagnetic interference. The circuit will be useful in optimizing the performance of biomagnetic systems

  20. Double-barrier junction based dc SQUID

    NARCIS (Netherlands)

    Bartolomé, M.E.; Brinkman, Alexander; Flokstra, Jakob; Golubov, Alexandre Avraamovitch; Rogalla, Horst

    2000-01-01

    dc SQUIDs based on double-barrier Nb/Al/AlOx/Al/AlOx/Al/Nb junctions (DBSQs) have been fabricated and tested for the first time. The current–voltage curves have been measured at temperatures down to 1.4 K. The critical current, Ic, dependence on the temperature T is partially described by the

  1. One Period of Exploration with the Squid.

    Science.gov (United States)

    Bradley, James V.; Ng, Andrew

    1997-01-01

    Presents a lab that can be offered after students have learned the basic anatomy and physiology of the various phyla, the primary objective of which is to explore and apply their acquired knowledge to a new situation. Involves exploring the anatomy and life-style of the squid. (JRH)

  2. Squid Dissection: From Pen to Ink.

    Science.gov (United States)

    Brown, Cindy; Kisiel, Jim

    2003-01-01

    Introduces students to dissection, which is an important part of scientific discovery. Students not only gain an understanding of the anatomy of a squid, but also develop a sense of responsibility and respect for the animal that they are using as a learning tool. (Author/SOE)

  3. Molecular docking and molecular dynamics simulation studies on Thermus thermophilus leucyl-tRNA synthetase complexed with different amino acids and pre-transfer editing substrates

    Directory of Open Access Journals (Sweden)

    Rayevsky A. V.

    2016-02-01

    Full Text Available Aim. To investigate the structural bases for the amino acid selectivity of the Thermus thermophilus leucyl-tRNA synthetase (LeuRSTT aminoacylation site and to disclose the binding pattern of pre-transfer editing substrates. Methods. Eight amino acids proposed as semi-cognate substrates for aminoacylation and eight aminoacyl-adenylates (formed from AMP and eight amino acids were prepared in zwitterions form. The protein structure with a co-crystallized substrate in the aminoacylation site [PDBID: 1OBH] was taken from RCSB. Docking settings and evaluation of substrate efficiency were followed by twofold docking function analysis for each conformation with Gold CCDC. The molecular dynamics simulation was performed using Gromacs. The procedures of relaxation and binding study were separated in two different subsequent simulations for 50ns and 5ns. Results. The evaluation of substrate efficiency for 8 amino acids by twofold docking function analysis, based on score values,has shown that the ligands of LeuRSTT can be positioned in the following order: Leu>Nva>Hcy>Nle>Met>Cys>Ile >Val. MD simulation has revealed lower electrostatic interactions of isoleucine with the active site of the enzyme compared with those for norvaline and leucine. In the case of aminoacyl-adenylates no significant differences were found based on score values for both GoldScore and Asp functions. Molecular dynamics of leucyl-, isoleucyl- and norvalyl-adenylates showed that the most stable and conformationally favorable is leucine, then follow norvaline and isoleucine. It has been also found that the TYR43 of the active site covers carboxyl group of leucine and norvaline like a shield and deflected towards isoleucine, allowing water molecules to come closer. Conclusions. In this study we revealed some structural basis for screening unfavorable substrates by shape, size and flexibility of a radical. The results obtained for different amino acids by molecular docking and MD studies

  4. SISTEM OTENTIKASI UNTUK SQUID BERBASIS WEB

    Directory of Open Access Journals (Sweden)

    Febriliyan Samopa

    2006-07-01

    Full Text Available Dalam sebuah jaringan komputer terdapat bermacam-macam tipe user dengan berbagi tingkatan yang berbeda yang juga dibutuhkan perlakuan yang berbeda pada tiap user yang disesuaikan dengan kebutuhan dalam menggunakan akses web, baik berupa http, ftp, gopher, dan lain-lain. Dimana masing-masing user memiliki skala prioritas dalam penggunaan bandwidth, jumlah koneksi maksimum, waktu koneksi, ukuran file maksimum, situs yang tidak boleh diakses dan lain-lain. Tujuan dari penelitian ini adalah membuat sebuah perangkat lunak yang dapat melakukan otentikasi user berdasarkan data konfigurasi yang disimpan dalam basisdata. Selain itu, perangkat lunak yang dibuat dapat memproses request dari client berdasarkan data konfigurasi dengan lebih cepat. Permasalahan yang mucul adalah bagaimana merancang dan membuat suatu perangkat lunak yang dapat melakukan otentikasi user berdasarkan data konfigurasi yang diambil dari basisdata, serta dapat memproses request dari client dengan lebih cepat berdasarkan hak akses yang dimilikinya.Dalam penelitian ini didesain dan diimplementasikan suatu sistem otentikasi user dengan mengambil data user yang tersimpan dalam basisdata MySQL. Disamping itu, dilakukan rekayasa pada beberapa rutin proses yang terdapat dalam squid proxy, supaya proses-proses dapat melakukan pengambilan data konfigurasi yang dialihkan dan disimpan dalam basisdata MySQL. Data konfigurasi ini didasarkan pada pembagian hak akses yang dimiliki oleh masing-masing grup user. Antarmuka berbasis web digunakan sebagai salah satu layanan bagi admin untuk mempermudah pengelolaan dan pengolahan data konfigurasi yang dibuat.Berdasarkan uji coba yang telah dilakukan, terbukti sistem yang dibuat dapat bekerja dengan baik dan tidak melenceng dari fungsi asli sebelum dilakukan perubahan. Bahkan pada penanganan request client yang berukuran besar, kinerja squid mengalami peningkatan dalam hal kecepatan proses yang dibutuhkan. Sebagai contoh, request client pada  file

  5. Image processing for HTS SQUID probe microscope

    International Nuclear Information System (INIS)

    Hayashi, T.; Koetitz, R.; Itozaki, H.; Ishikawa, T.; Kawabe, U.

    2005-01-01

    An HTS SQUID probe microscope has been developed using a high-permeability needle to enable high spatial resolution measurement of samples in air even at room temperature. Image processing techniques have also been developed to improve the magnetic field images obtained from the microscope. Artifacts in the data occur due to electromagnetic interference from electric power lines, line drift and flux trapping. The electromagnetic interference could successfully be removed by eliminating the noise peaks from the power spectrum of fast Fourier transforms of line scans of the image. The drift between lines was removed by interpolating the mean field value of each scan line. Artifacts in line scans occurring due to flux trapping or unexpected noise were removed by the detection of a sharp drift and interpolation using the line data of neighboring lines. Highly detailed magnetic field images were obtained from the HTS SQUID probe microscope by the application of these image processing techniques

  6. Macroscopic quantum tunneling in a dc SQUID

    International Nuclear Information System (INIS)

    Chen, Y.C.

    1986-01-01

    The theory of macroscopic quantum tunneling is applied to a current-biased dc SQUID whose dynamics can be described by a two-dimensional mechanical system with a dissipative environment. Based on the phenomenological model proposed by Caldeira and Leggett, the dissipative environment is represented by a set of harmonic oscillators coupling to the system. After integrating out the environmental degrees of freedom, an effective Euclidean action is found for the two-dimensional system. The action is used to provide the quantum tunneling rate formalism for the dc SQUID. Under certain conditions, the tunneling rate reduces to that of a single current-biased Josephson junction with an adjustable effective critical current

  7. Fundamental characteristics of the QFP measured by the dc SQUID

    International Nuclear Information System (INIS)

    Shimizu, N.; Harada, Y.; Miyamoto, N.; Hosoya, M.; Goto, E.

    1989-01-01

    This paper describes the fundamental characteristics of the Quantum Flux Parametron (QFP) measured by a new method in which the output signals of the QFP are detected with a dc SQUID. The dc SQUID linearly and continuously converts the output current of the QFP to voltage, allowing the output signal of the QFP to be measured as the voltage of the dc SQUID. Thus, the fundamental characteristics of the QFP have been experimentally confirmed in detail

  8. Hot electron effect in the dc SQUID

    International Nuclear Information System (INIS)

    Wellstood, F.C.; Clarke, J.; Urbina, C.

    1989-01-01

    The authors have investigated the temperature dependence of the noise in thin-film dc Superconducting Quantum Interference Devices (SQUIDs) down to 20 mK. The white noise measured in the early versions of our SQUIDs did not decrease as the bath temperature was lowered below 150 mK. They have attributed this saturation to a hot electron effect in the thin-film AuCu resistors shunting the Josephson junctions. A theoretical investigation showed that the temperature of the electrons in the shunts should be given by T/sub e/ = (P/ΣΩ)/sup 1/5/, where P is the power dissipated in the shunts, Ω is the shunt volume, and Σ is a proportionality constant. Experimentally, the authors found Σ=(2.4+-0.6)X10/sup 9/WK/sup -5/m/sup -3/. They have redesigned the shunts, adding large thin-film cooling fins, to increase their volume substantially. This technique has reduced T/sub e/ to about 50 mK, with a corresponding improvement in the sensitivity of the SQUIDs

  9. Directly coupled YBCO dc SQUID magnetometers

    International Nuclear Information System (INIS)

    Petersen, P.R.E.; Shen, Y.Q.; Holst, T.; Larsen, B.H.; Sager, M.P.; Bindslev Hansen, J.

    1999-01-01

    YBa 2 Cu 3 O 7- x magnetometers have been made on 10mmx10mm MgO substrates by directly coupling the magnetometer pick-up loop to a dc SQUID with narrow strip lines. The dc SQUIDs were made with YBa 2 Cu 3 O 7-x step-edge Josephson junctions. The layout of the magnetometer pick-up loop was chosen as a compromise between maximizing the loop effective area and minimizing the loop inductance. The SQUID was designed to have L S ∼100 pH in order to obtain β L =2I 0 L S /Φ 0 approx.= 1 with the single-junction critical current I 0 ∼10 μA. We have made magnetometers with white noise levels down to 55 fT Hz -1/2 and a 1/f knee at 1 Hz (ac biased). Noise measurements were made on a field-cooled magnetometer. The noise measured at 1 Hz when cooled in 'zero field' was 175 fT Hz -1/2 . When cooled in magnetic fields of B = 50 μT and B = 100 μT we measured the noise at 1 Hz to be 430 fT Hz -1 2 and 1.3 pT Hz -1/2 , respectively. (author)

  10. Recent advancements in the SQUID magnetospinogram system

    Science.gov (United States)

    Adachi, Yoshiaki; Kawai, Jun; Haruta, Yasuhiro; Miyamoto, Masakazu; Kawabata, Shigenori; Sekihara, Kensuke; Uehara, Gen

    2017-06-01

    In this study, a new superconducting quantum interference device (SQUID) biomagnetic measurement system known as magnetospinogram (MSG) is developed. The MSG system is used for observation of a weak magnetic field distribution induced by the neural activity of the spinal cord over the body surface. The current source reconstruction for the observed magnetic field distribution provides noninvasive functional imaging of the spinal cord, which enables medical personnel to diagnose spinal cord diseases more accurately. The MSG system is equipped with a uniquely shaped cryostat and a sensor array of vector-type SQUID gradiometers that are designed to detect the magnetic field from deep sources across a narrow observation area over the body surface of supine subjects. The latest prototype of the MSG system is already applied in clinical studies to develop a diagnosis protocol for spinal cord diseases. Advancements in hardware and software for MSG signal processing and cryogenic components aid in effectively suppressing external magnetic field noise and reducing the cost of liquid helium that act as barriers with respect to the introduction of the MSG system to hospitals. The application of the MSG system is extended to various biomagnetic applications in addition to spinal cord functional imaging given the advantages of the MSG system for investigating deep sources. The study also includes a report on the recent advancements of the SQUID MSG system including its peripheral technologies and wide-spread applications.

  11. Analysis of Squid Net Fisheries Business Production

    Directory of Open Access Journals (Sweden)

    Herna Octivia Damayanti

    2017-03-01

    Full Text Available Squid net is one of alternatives to replace trawl net in Pati regency. The purposes of the research are 1 to determine the influence factors, 2 to analyze the return to scale, 3 to analyze cost and return.The research location in Juwana Subdistrict particularly Bakaran Kulon, Dukutalit, Bajomulyo and Bendar Villages. The research conducted on October 2015 to June 2016. The number of final samples was 36, while the formulation of management strategies used 15 samples by snowball sampling. Data analysis techniques used 1 Cobb Douglas production function, 2 revenue-cost ratio analysis. The results of the research are 1 significant inputs for production factor are long trip, Solar fuel, the number of crew and lights. 2 the return to scale of squid net bussiness in Juwana subdistrict Pati regency is -0.231 means decreasing to scale. 3 the R/C ratio of scenario II more profitable for squid net crews than  scenario I.

  12. Preliminary report on the PIXE analysis of the squid statoliths

    International Nuclear Information System (INIS)

    Ikeda, Yuzuru; Arai, Nobuaki; Sakamoto, Wataru; Murayama, Tatsuro; Maeda, Kuniko; Yoshida, Koji.

    1996-01-01

    Micro trace elements in the squid statolith, a calcareous stone which acts as a balancer and hearing, was analyzed with Particle Induced X-ray Emission (PIXE) for the Japanese common squid for the first time. Calcium is the main component of the squid statoliths, which means that squid statolith is the pure calcified structure similar to the fish otolith. Beside Ca, Sr was detected with strong dosage, and some other elements as Mn, Fe, Cu, Zn and As were also detected. Possible assumption of intake of microelements to the statoliths and the suitability of PIXE for statoliths analysis are discussed. (author)

  13. Low noise niobium dc SQUID with a planar input coil

    Science.gov (United States)

    de Waal, V. J.; van den Hamer, P.; Klapwijk, T. M.

    1983-02-01

    A practical all-niobium dc superconducting quantum interference device (SQUID) with a niobium spiral input coil has been developed. The SQUID utilizes submicron Josephson junctions. The best intrinsic energy resolution obtained with a 1-nH SQUID is 4×10-32 J/Hz. A 20-turn 1.2-μH input coil is coupled to a 2.3-nH SQUID with an efficiency of 0.5. The energy resolution with respect to the coil is 1×10-30 J/Hz.

  14. Low noise niobium dc SQUID with a planar input coil

    Energy Technology Data Exchange (ETDEWEB)

    de Waal, V.J.; van den Hamer, P.; Klapwijk, T.M.

    1983-02-15

    A practical all-niobium dc superconducting quantum interference device (SQUID) with a niobium spiral input coil has been developed. The SQUID utilizes submicron Josephson junctions. The best intrinsic energy resolution obtained with a 1-nH SQUID is 4 x 10/sup -32/ J/Hz. A 20-turn 1.2-..mu..H input coil is coupled to a 2.3-nH SQUID with an efficiency of 0.5. The energy resolution with respect to the coil is 1 x 10/sup -30/ J/Hz.

  15. SQUIDs for the readout of metallic magnetic calorimeters

    Energy Technology Data Exchange (ETDEWEB)

    Ferring, Anna; Wegner, Mathias; Fleischmann, Andreas; Gastaldo, Loredana; Kempf, Sebastian; Enss, Christian [Kirchhoff-Institute for Physics, Heidelberg University (Germany)

    2015-07-01

    Superconducting quantum interference devices (SQUIDs) are the devices of choice to read out metallic magnetic calorimeters (MMCs). Here, the temperature change of the detector upon the absorption of an energetic particle is measured as a magnetization change of a paramagnetic temperature sensor that is situated in a weak magnetic field. Driven by the need for devices that allow for the readout of large-scale detector arrays with hundreds or even thousands of individual detectors as well as of single channel detectors with sub-eV energy resolution, we have recently started the development of low-T{sub c} current-sensing SQUIDs. In particular, we are developing cryogenic frequency-domain multiplexers based on non-hysteretic rf-SQUIDs for detector array readout as well as dc-SQUIDs for single channel detector readout. We discuss our SQUID designs and the performance of prototype SQUIDs. We particularly focus on the frequency and temperature dependence of the SQUID noise as well as the reliability of our SQUID fabrication process for Nb/Al-AlO{sub x}/Nb Josephson junctions. Additionally, we demonstrate experimentally that state-of-the-art MMCs can successfully be read out with our current devices. Finally, we discuss different strategies to improve the SQUID and detector performance aiming to reach sub-eV energy resolution for individual detectors as well as for detector arrays.

  16. Antioxidant and antimicrobial activities of squid ink powder

    OpenAIRE

    Fatimah Zaharah, M.Y.; Rabeta, M.S.

    2017-01-01

    Economic development in Malaysia has led to increasing quantity and complexity of generated waste or by-product. The main objective of this study is to investigate the antioxidant and antimicrobial activities of squid ink powder. The squid ink was collected from fresh squid and dried using freeze dryer before it was ground into powder. The yield of squid ink was 22.82% after freeze-drying which was 69.37g in amount. Proximate composition analysis as well as two total antioxidant activity assa...

  17. Allometry indicates giant eyes of giant squid are not exceptional.

    Science.gov (United States)

    Schmitz, Lars; Motani, Ryosuke; Oufiero, Christopher E; Martin, Christopher H; McGee, Matthew D; Gamarra, Ashlee R; Lee, Johanna J; Wainwright, Peter C

    2013-02-18

    The eyes of giant and colossal squid are among the largest eyes in the history of life. It was recently proposed that sperm whale predation is the main driver of eye size evolution in giant squid, on the basis of an optical model that suggested optimal performance in detecting large luminous visual targets such as whales in the deep sea. However, it is poorly understood how the eye size of giant and colossal squid compares to that of other aquatic organisms when scaling effects are considered. We performed a large-scale comparative study that included 87 squid species and 237 species of acanthomorph fish. While squid have larger eyes than most acanthomorphs, a comparison of relative eye size among squid suggests that giant and colossal squid do not have unusually large eyes. After revising constants used in a previous model we found that large eyes perform equally well in detecting point targets and large luminous targets in the deep sea. The eyes of giant and colossal squid do not appear exceptionally large when allometric effects are considered. It is probable that the giant eyes of giant squid result from a phylogenetically conserved developmental pattern manifested in very large animals. Whatever the cause of large eyes, they appear to have several advantages for vision in the reduced light of the deep mesopelagic zone.

  18. Inductance-dependent characteristics of HTS dc-SQUID amplifiers

    International Nuclear Information System (INIS)

    Mitchell, E.E.; Tilbrook, D.L.; Foley, C.P.; MacFarlane, J.

    2002-01-01

    Full text: We have experimentally determined the transfer function V Φ and noise S Φ of several high temperature superconducting (HTS) dc SQUIDs of increasing loop size, while they were operated (without input flux transformer) in a small-signal-amplifier (open-loop) mode. A primary aim of our investigation was to provide reliable inductance data to aid our design of subsequent magnetometer devices. Flux was induced by means of current injection via a well-defined stripline directly into the SQUID loop. The loop size was systematically incremented in a range of otherwise similar SQUIDs. For each SQUID, the ratio between the induced flux and the injection current (which we define as the coupling inductance of the device, L c ) was measured as a function of the injection path length and the SQUID loop dimensions. Both L c and the derived SQUID self-inductance, L sq , were then compared with theoretical values, and contributions due to kinetic inductance and junction inductance were estimated. Correlations between the inductance data and our measured values of transfer function V Φ and noise S Φ were compared with previous results. Guidelines for optimisation of gradiometer SQUIDs were established, and in particular, the importance of achieving a large value transfer function together with a relatively small inductance was demonstrated. The strong influence of an enhanced transfer function was further emphasised when an order-of-magnitude reduction in noise was achieved by subjecting one of our SQUIDs to an in-house 'ion-beam trimming' process

  19. SQUID magnetometry from nanometer to centimeter length scales

    International Nuclear Information System (INIS)

    Hatridge, Michael J.

    2010-01-01

    The development of Superconducting QUantum Interference Device (SQUID)-based magnetometer for two applications, in vivo prepolarized, ultra-low field MRI of humans and dispersive readout of SQUIDs for micro- and nano-scale magnetometery, are the focus of this thesis.

  20. SQUID magnetometry from nanometer to centimeter length scales

    Energy Technology Data Exchange (ETDEWEB)

    Hatridge, Michael J. [Univ. of California, Berkeley, CA (United States)

    2010-06-01

    The development of Superconducting QUantum Interference Device (SQUID)-based magnetometer for two applications, in vivo prepolarized, ultra-low field MRI of humans and dispersive readout of SQUIDs for micro- and nano-scale magnetometery, are the focus of this thesis.

  1. Halide peroxidase in tissues that interact with bacteria in the host squid Euprymna scolopes.

    Science.gov (United States)

    Small, A L; McFall-Ngai, M J

    1999-03-15

    An enzyme with similarities to myeloperoxidase, the antimicrobial halide peroxidase in mammalian neutrophils, occurs abundantly in the light organ tissue of Euprymna scolopes, a squid that maintains a beneficial association with the luminous bacterium Vibrio fischeri. Using three independent assays typically applied to the analysis of halide peroxidase enzymes, we directly compared the activity of the squid enzyme with that of human myeloperoxidase. One of these methods, the diethanolamine assay, confirmed that the squid peroxidase requires halide ions for its activity. The identification of a halide peroxidase in a cooperative bacterial association suggested that this type of enzyme can function not only to control pathogens, but also to modulate the interactions of host animals with their beneficial partners. To determine whether the squid peroxidase functions under both circumstances, we examined its distribution in a variety of host tissues, including those that typically interact with bacteria and those that do not. Tissues interacting with bacteria included those that have specific cooperative associations with bacteria (i.e., the light organ and accessory nidamental gland) and those that have transient nonspecific interactions with bacteria (i.e., the gills, which clear the cephalopod circulatory system of invading microorganisms). These bacteria-associated tissues were compared with the eye, digestive gland, white body, and ink-producing tissues, which do not typically interact directly with bacteria. Peroxidase enzyme assays, immunocytochemical localization, and DNA-RNA hybridizations showed that the halide-dependent peroxidase is consistently expressed in high concentration in tissues that interact bacteria. Elevated levels of the peroxidase were also found in the ink-producing tissues, which are known to have enzymatic pathways associated with antimicrobial activity. Taken together, these data suggest that the host uses a common biochemical response to

  2. Universal mechanisms of decoherence of qubit states in a SQUID

    Science.gov (United States)

    Kuklov, A. B.; Chudnovsky, E. M.

    2003-03-01

    Fundamental conservation laws mandate parameter-free generic mechanisms of decoherence of quantum oscillations of the superconducting current in a SQUID [1]. The very fact that the current flows with respect to the ion lattice is shown to result in a decoherence via emission of the transverse sound at the oscillation frequency. For SQUIDs larger than the wavelength of the phonons, this effect can significantly limit the quality factor. The decohering effects of the external mechanical and magnetic noise are shown to be proportional to the total magnetic moment of the SQUID, making small SQUIDs less susceptible to the noise than large SQUIDs. Decoherence due to the emission of photons into the open space and in the presence of the metal shielding has been studied as well. Suggestions of experimental setups with low decoherence have been made. [1] E. M. Chudnovsky and A. B. Kuklov, arXiv:cond-mat/0211246.

  3. Drag force and jet propulsion investigation of a swimming squid

    Directory of Open Access Journals (Sweden)

    Tabatabaei Mahdi

    2015-01-01

    Full Text Available In this study, CAD model of a squid was obtained by taking computer tomography images of a real squid. The model later placed into a computational domain to calculate drag force and performance of jet propulsion. The drag study was performed on the CAD model so that drag force subjected to real squid was revealed at squid’s different swimming speeds and comparison has been made with other underwater creatures (e.g., a dolphin, sea lion and penguin. The drag coefficient (referenced to total wetted surface area of squid is 0.0042 at Reynolds number 1.6x106 that is a %4.5 difference from Gentoo penguin. Besides, jet flow of squid was simulated to observe the flow region generated in the 2D domain utilizing dynamic mesh method to mimic the movement of squid’s mantle cavity.

  4. Current-phase relations and noise in rf biased SQUIDS

    International Nuclear Information System (INIS)

    Jackel, L.D.; Clark, T.D.; Buhrman, R.A.

    1975-01-01

    An investigation was made of the effect of the weak link current-phase relation on noise in rf biased SQUIDs. Non-sinusoidal current-phase relations were observed in various weak links, and these non-sinusoidal relations were correlated with significantly increased intrinsic noise in the SQUID ring. The current-phase relation was also found to affect the amplitude of the rf SQUID ring dissipation. The result of an rf SQUID system noise analysis shows that, due to increased intrinsic noise and reduced ring dissipation, the minimum attainable noise for a SQUID ring having a very non-sinusoidal current-phase relation is considerably greater than for a ring with a sinusoidal relation

  5. Cluster editing

    DEFF Research Database (Denmark)

    Böcker, S.; Baumbach, Jan

    2013-01-01

    . The problem has been the inspiration for numerous algorithms in bioinformatics, aiming at clustering entities such as genes, proteins, phenotypes, or patients. In this paper, we review exact and heuristic methods that have been proposed for the Cluster Editing problem, and also applications......The Cluster Editing problem asks to transform a graph into a disjoint union of cliques using a minimum number of edge modifications. Although the problem has been proven NP-complete several times, it has nevertheless attracted much research both from the theoretical and the applied side...

  6. Evolution of a pseudogene: exclusive survival of a functional mitochondrial nad7 gene supports Haplomitrium as the earliest liverwort lineage and proposes a secondary loss of RNA editing in Marchantiidae.

    Science.gov (United States)

    Groth-Malonek, Milena; Wahrmund, Ute; Polsakiewicz, Monika; Knoop, Volker

    2007-04-01

    Gene transfer from the mitochondrion into the nucleus is a corollary of the endosymbiont hypothesis. The frequent and independent transfer of genes for mitochondrial ribosomal proteins is well documented with many examples in angiosperms, whereas transfer of genes for components of the respiratory chain is a rarity. A notable exception is the nad7 gene, encoding subunit 7 of complex I, in the liverwort Marchantia polymorpha, which resides as a full-length, intron-carrying and transcribed, but nonspliced pseudogene in the chondriome, whereas its functional counterpart is nuclear encoded. To elucidate the patterns of pseudogene degeneration, we have investigated the mitochondrial nad7 locus in 12 other liverworts of broad phylogenetic distribution. We find that the mitochondrial nad7 gene is nonfunctional in 11 of them. However, the modes of pseudogene degeneration vary: whereas point mutations, accompanied by single-nucleotide indels, predominantly introduce stop codons into the reading frame in marchantiid liverworts, larger indels introduce frameshifts in the simple thalloid and leafy jungermanniid taxa. Most notably, however, the mitochondrial nad7 reading frame appears to be intact in the isolated liverwort genus Haplomitrium. Its functional expression is shown by cDNA analysis identifying typical RNA-editing events to reconstitute conserved codon identities and also confirming functional splicing of the 2 liverwort-specific group II introns. We interpret our results 1) to indicate the presence of a functional mitochondrial nad7 gene in the earliest land plants and strongly supporting a basal placement of Haplomitrium among the liverworts, 2) to indicate different modes of pseudogene degeneration and chondriome evolution in the later branching liverwort clades, 3) to suggest a surprisingly long maintenance of a nonfunctional gene in the presumed oldest group of land plants, and 4) to support the model of a secondary loss of RNA-editing activity in marchantiid

  7. High speed non-latching squid binary ripple counter

    International Nuclear Information System (INIS)

    Silver, A.H.; Phillips, R.R.; Sandell, R.D.

    1985-01-01

    High speed, single flux quantum (SFQ) binary scalers are important components in superconducting analog-to-digital converters (ADC). This paper reviews the concept for a SQUID ADC and the design of an SFQ binary ripple counter, and reports the simulation of key components, and fabrication and performance of non-latching SQUID scalers and SFQ binary ripple counters. The SQUIDs were fabricated with Nb/Nb 2 O 5 /PbIn junctions and interconnected by monolithic superconducting transmission lines and isolation resistors. Each SQUID functioned as a bistable flip-flop with the input connected to the center of the device and the output across one junction. All junctions were critically damped to optimize the pulse response. Operation was verified by observing the dc I-V curves of successive SQUIDs driven by a cw pulse train generated on the same chip. Each SQUID exhibited constant-voltage current steps at 1/2 the voltage of the preceding device as expected from the Josephson voltage-to-frequency relation. Steps were observed only for the same voltage polarity of successive devices and for proper phase bias of the SQUID. Binary frequency division was recorded up to 40GHz for devices designed to operate to 28GHz

  8. Antioxidant and antimicrobial activities of squid ink powder

    Directory of Open Access Journals (Sweden)

    Fatimah Zaharah, M.Y.

    2017-10-01

    Full Text Available Economic development in Malaysia has led to increasing quantity and complexity of generated waste or by-product. The main objective of this study is to investigate the antioxidant and antimicrobial activities of squid ink powder. The squid ink was collected from fresh squid and dried using freeze dryer before it was ground into powder. The yield of squid ink was 22.82% after freeze-drying which was 69.37g in amount. Proximate composition analysis as well as two total antioxidant activity assays named 2,2-diphenyl-1-picrylhydrazyl (DPPH assay and Ferric Reducing Antioxidant Power (FRAP assay, and antimicrobial analysis were done on the powdered squid ink. The proximate results of squid ink powder were 4.43 ± 0.29% moisture, 62.46 ± 0.62% protein, 3.96 ± 0.08% fat, and 9.29 ± 0.05% ash. Results of DPPH assay showed that water extraction of squid ink powder has the highest 94.87 ± 4.87%, followed by ethanol 67.57 ± 7.55%, and hexane extract 2.10 ± 1.18%. FRAP assay result presented the same trend with water extraction had the highest value of 929.67 ± 2.31 μmol Fe (II / g of sample extract, followed by ethanol extract 201.00 ± 26.29 μmol Fe (II per gram sample and hexane 79.67 ± 12.66 μmol Fe (II / g of sample extract. Both water and ethanol extract showed antimicrobial properties with inhibition range of 7 to 15 mm, respectively. Fresh squid ink had 1.254 × 103 colony forming unit per gram of sample of microbial content. Squid ink powder had protein as major compound and microbial content was below from standard value of fisheries products as stated in Food Act 1983 and Regulation 1985.

  9. High transcript abundance, RNA editing, and small RNAs in intergenic regions within the massive mitochondrial genome of the angiosperm Silene noctiflora

    Czech Academy of Sciences Publication Activity Database

    Wu, Z.; Stone, James D.; Štorchová, Helena; Sloan, D.B.

    2015-01-01

    Roč. 16, NOV 14 (2015), s. 938 ISSN 1471-2164 R&D Projects: GA MŠk(CZ) EE2.3.30.0048 Institutional support: RVO:61389030 Keywords : Antisense RNA * Junk DNA * mtDNA Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.867, year: 2015

  10. RNA SURVEILLANCE– AN EMERGING ROLE FOR RNA REGULATORY NETWORKS IN AGING

    OpenAIRE

    Montano, Monty; Long, Kimberly

    2010-01-01

    In this review, we describe recent advances in the field of RNA regulatory biology and relate these advances to aging science. We introduce a new term, RNA surveillance, an RNA regulatory process that is conserved in metazoans, and describe how RNA surveillance represents molecular cross-talk between two emerging RNA regulatory systems – RNA interference and RNA editing. We discuss how RNA surveillance mechanisms influence mRNA and microRNA expression and activity during lifespan. Additionall...

  11. A SQUID Bootstrap Circuit with a Large Parameter Tolerance

    International Nuclear Information System (INIS)

    Zhang Guo-Feng; Kong Xiang-Yan; Xie Xiao-Ming; Zhang Yi; Krause Hans-Joachim; Offenhäusser Andreas

    2013-01-01

    The voltage biased (SQUID) bootstrap circuit (SBC) was recently introduced as an effective means to reduce the preamplifier noise contribution. We analyze the tolerances of the SBC noise suppression performance to spreads in SQUID and SBC circuit parameters. It is found that the tolerance to spread mainly caused by the integrated circuit fabrication process could be extended by a one-time adjustable current feedback. A helium-cooled niobium SQUID with a loop inductance of 350 pH is employed to experimentally verify the analysis. From this work, design criteria for fully integrated SBC devices with a high yield can be derived

  12. SQUIDs in thermal detectors of weakly interacting particles

    International Nuclear Information System (INIS)

    Trofimov, V.N.

    1991-01-01

    The application of four different types of SQUID-assisted thermometers for cryogenic thermal detectors of weakly interacting particles is analyzed with two of them for the first time. The classic resistive thermometer is considered as well for the comparison. Original results of testing the detector with working temperature of 1K and thermocouple thermometer with SQUID are given. The conclusion is made that temperature resolution of 10 -10 kHz -1/2 or energy sensitivity of 1-10 eV per 1 kg of detector mass can be achieved when using the SQUID-assisted thermometers. 12 refs.; 7 figs.; 1 tab

  13. rf SQUID system as tunable flux qubit

    Energy Technology Data Exchange (ETDEWEB)

    Ruggiero, B. [Istituto di Cibernetica ' E. Caianiello' del Consiglio Nazionale delle Ricerche, I-80078 Pozzuoli (Italy)]. E-mail: b.ruggiero@cib.na.cnr.it; Granata, C. [Istituto di Cibernetica ' E. Caianiello' del Consiglio Nazionale delle Ricerche, I-80078 Pozzuoli (Italy); Vettoliere, A. [Istituto di Cibernetica ' E. Caianiello' del Consiglio Nazionale delle Ricerche, I-80078 Pozzuoli (Italy); Rombetto, S. [Istituto di Cibernetica ' E. Caianiello' del Consiglio Nazionale delle Ricerche, I-80078 Pozzuoli (Italy); Russo, R. [Istituto di Cibernetica ' E. Caianiello' del Consiglio Nazionale delle Ricerche, I-80078 Pozzuoli (Italy); Russo, M. [Istituto di Cibernetica ' E. Caianiello' del Consiglio Nazionale delle Ricerche, I-80078 Pozzuoli (Italy); Corato, V. [Dipartimento di Ingegneria dell' Informazione, Seconda Universita di Napoli, I-81031 Aversa (Italy); Istituto di Cibernetica ' E. Caianiello' del Consiglio Nazionale delle Ricerche, I-80078 Pozzuoli (Italy); Silvestrini, P. [Dipartimento di Ingegneria dell' Informazione, Seconda Universita di Napoli, I-81031 Aversa (Italy); Istituto di Cibernetica ' E. Caianiello' del Consiglio Nazionale delle Ricerche, I-80078 Pozzuoli (Italy)

    2006-08-21

    We present a fully integrated rf SQUID-based system as flux qubit with a high control of the flux transfer function of the superconducting transformer modulating the coupling between the flux qubit and the readout system. The control of the system is possible by including into the superconducting flux transformer a vertical two-Josephson-junctions interferometer (VJI) in which the Josephson current is precisely modulated from a maximum to zero by a transversal magnetic field parallel to the flux transformer plane. The proposed system can be also used in a more general configuration to control the off-diagonal terms in the Hamiltonian of the flux qubit and to turn on and off the coupling between two or more qubits.

  14. Differential Binding of Mitochondrial Transcripts by MRB8170 and MRB4160 Regulates Distinct Editing Fates of Mitochondrial mRNA in Trypanosomes

    Czech Academy of Sciences Publication Activity Database

    Dixit, Sameer; Mueller-McNicoll, M.; David, Vojtěch; Zarnack, K.; Ule, J.; Hashimi, Hassan; Lukeš, Julius

    2017-01-01

    Roč. 8, č. 1 (2017), č. článku e02288-16. ISSN 2150-7511 R&D Projects: GA ČR GA15-21974S Institutional support: RVO:60077344 Keywords : guide RNA * ribonucleoprotein complexes * nucleotide resolution * proteins * DNA * replication * tbrgg2 * subcomplexes * translation Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Biochemistry and molecular biology Impact factor: 6.956, year: 2016

  15. No link of serotonin 2C receptor editing to serotonin transporter genotype

    NARCIS (Netherlands)

    Lyddon, R.; Cuppen, E.; Haroutunian, V.; Siever, L.J.; Dracheva, S.

    2010-01-01

    RNA editing is a post-transcriptional process, which has the potential to alter the function of encoded proteins. In particular, serotonin 2C receptor (5-HT2cR) mRNA editing can produce 24 protein isoforms of varying functionality. Rodent studies have shown that 5-HT2cR editing is dynamically

  16. Can understanding squid life-history strategies and recruitment ...

    African Journals Online (AJOL)

    Can understanding squid life-history strategies and recruitment improve management? ... range of potentially limiting conditions in different years, they store genetic diversity and stabilize recruitment in time. ... AJOL African Journals Online.

  17. Negative inductance SQUID qubit operating in a quantum regime

    Science.gov (United States)

    Liu, W. Y.; Su, F. F.; Xu, H. K.; Li, Z. Y.; Tian, Ye; Zhu, X. B.; Lu, Li; Han, Siyuan; Zhao, S. P.

    2018-04-01

    Two-junction SQUIDs with negative mutual inductance between their two arms, called nSQUIDs, have been proposed for significantly improving quantum information transfer but their quantum nature has not been experimentally demonstrated. We have designed, fabricated, and characterized superconducting nSQUID qubits. Our results provide clear evidence of the quantum coherence of the device, whose properties are well described by theoretical calculations using parameters determined from spectroscopic measurement. In addition to their future application for fast quantum information transfer, the nSQUID qubits exhibit rich characteristics in their tunable two-dimensional (2D) potentials, energy levels, wave function symmetries, and dipole matrix elements, which are essential to the study of a wide variety of macroscopic quantum phenomena such as tunneling in 2D potential landscapes.

  18. Reactive probing of macroscopically quantum mechanical SQUID rings

    International Nuclear Information System (INIS)

    Prance, R.J.; Clark, T.D.; Whiteman, R.; Diggins, J.; Ralph, J.F.; Prance, H.; Spiller, T.P.; Widom, A.; Srivastava, Y.

    1994-01-01

    In this paper we demonstrate that the energy level structure of ultra small capacitance SQUID rings can be probed adiabatically at radio frequency using both dynamical and quasistatic reactive techniques. ((orig.))

  19. Gear Selectivity of a Longfin Squid Bottom Trawl

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Loligo pealeii (longfin inshore squid) co-occurs with Atlantic butterfish (Peprilus triacanthus) throughout the year and discarding in the L. pealeii bottom trawl...

  20. Forecasting chokka squid Loligo vulgaris reynaudii catches and ...

    African Journals Online (AJOL)

    spamer

    2017-11-11

    Nov 11, 2017 ... on ambient water temperature (Augustyn et al. 1992,. A. Oosthuisen, University of ..... from tagged squid and the supply of continuous environ- mental data. ... should a leak develop, and to provide insulation for the electronics.

  1. Dc-SQUID sensor system for multichannel neuromagnetometry

    Energy Technology Data Exchange (ETDEWEB)

    Houwman, E.P.; Veldhuis, D.; Flokstra, ter Brake, H.J.M.; Jaszczuk, W.; Rogalla, H. (Univ. of Twente, Faculty of Applied Physics, P.O. Box 217, 7500 AE Enschede (NL)); Martinez, A. (Universidad de Zaragoza, E.T.S.I.I. Maria Zambrano 50, 50015 Zaragoza (ES))

    1991-03-01

    This paper reports on various DC-SQUID sensor configurations developed for use in the authors' 19-channel neuromagetometer. Apart from the standard type, resistively and indictively shunted SQUIDs were made, allowing for a large screening factor {beta} ({gt}1). In this way signal coupling from the pick-up coil to the SQUID is facilitated and capactive coupling between the input coil and the SQUID washer can be decreased. The number of turns of the input coil is decreased further by allowing for an inductance mismatch in the input circuit. Although theoretically both measures give rise to an increased field noise of the sensor, they may lead to a reduction of the excess noise and the noise balance may become positive.

  2. Symposium on applications of superconducting quantum interference devices (SQUIDS)

    International Nuclear Information System (INIS)

    1978-01-01

    The abstracts are given of thirteen papers presented at a ''SQUID Symposium'' organized by the Division of Materials Sciences of the U.S. Department of Energy and held March 23--25, 1978, at the University of Virginia. Since SQUID systems have already been utilized in feasibility demonstration in geothermal reservoir exploration, it was recognized that these devices also hold great potential for many other important scientific measurements. Many of these are energy-related, and others include forefront investigations in a diverse group of scientific areas, from biomedical to earthquake monitoring. Research in SQUIDs has advanced so rapidly in recent years that it was felt that a symposium to review the current status and future prospects of the devices would be timely. The abstracts given present an overview of work in this area and hopefully provide an opportunity to increase awareness among basic and applied scientists of the inherent implications of the extreme measurement sensitivity in advanced SQUID systems

  3. Nondestructive evaluation of metallic structures using a SQUID magnetometer

    International Nuclear Information System (INIS)

    Weinstock, H.; Nisenoff, M.

    1985-01-01

    We present one of the first reports of the use of SQUID instrumentation for nondestructive evaluation of electrically conducting and ferromagnetic specimens. We report preliminary experiments on the use of SQUIDs for the detection of defects (such as cracks, holes, weld seams, variations in wall thickness, effects of corrosion, etc.) in the walls of a hollow pipe, and for monitoring the magnetic state of a ferromagnetic sample under stress-strain loading conditions. (orig./BUD)

  4. High-performance DC SQUIDs with submicrometer niobium Josephson junctions

    Energy Technology Data Exchange (ETDEWEB)

    de Waal, V.J.; Klapwijk, T.M.; van den Hamer, P.

    1983-11-01

    We report on the fabrication and performance of low-noise, all-niobium, thin-film planar dc SQUIDs with submicrometer Josephson junctions. The junctions are evaporated obliquely through a metal shadow evaporation mask, which is made using optical lithography with 0.5 ..mu..m tolerance. The Josephson junction barrier is formed by evaporating a thin silicon film and with a subsequent oxidation in a glow discharge. The junction parameters can be reproduced within a factor of two. Typical critical currents of the SQUIDs are about 3 ..mu..A and the resistances are about 100 ..cap omega... With SQUIDs having an inductance of 1 nH the voltage modulation is a least 60 ..mu..V. An intrinsic energy resolution of 4 x 10/sup -32/ J/Hz has been reached. The SQUIDs are coupled to wire-wound input coils or with thin-film input coils. The thin-film input coil consists of a niobium spiral of 20 turns on a separate substrate. In both cases the coil is glued onto a 2-nH SQUID with a coupling efficiency of at least 0.5. Referred to the thin-film input coil, the best coupled energy resolution achieved is 1.2 x 10/sup -30/ J/Hz measured in a flux-locked loop at frequencies above 10 Hz. As far as we know, this is the best figure achieved with an all-refractory-metal thin-film SQUID. The fabrication technique used is suited for making circuits with SQUID and pickup coil on the same substrate. We describe a compact, planar, first-order gradiometer integrated with a SQUID on a single substrate. The gradient noise of this device is 3 x 10/sup -12/ Tm/sup -1/. The gradiometer has a size of 12 mm x 17 mm, is simple to fabricate, an is suitable for biomedical applications.

  5. High-performance dc SQUIDs with submicrometer niobium Josephson junctions

    Science.gov (United States)

    de Waal, V. J.; Klapwijk, T. M.; van den Hamer, P.

    1983-11-01

    We report on the fabrication and performance of low-noise, all-niobium, thin-film planar dc SQUIDs with submicrometer Josephson junctions. The junctions are evaporated obliquely through a metal shadow evaporation mask, which is made using optical lithography with 0.5 µm tolerance. The Josephson junction barrier is formed by evaporating a thin silicon film and with a subsequent oxidation in a glow discharge. The junction parameters can be reproduced within a factor of two. Typical critical currents of the SQUIDs are about 3 µA and the resistances are about 100 Ω. With SQUIDs having an inductance of 1 nH the voltage modulation is at least 60 µV. An intrinsic energy resolution of 4×10-32 J/Hz has been reached. The SQUIDs are coupled to wire-wound input coils or with thin-film input coils. The thin-film input coil consists of a niobium spiral of 20 turns on a separate substrate. In both cases the coil is glued onto a 2-nH SQUID with a coupling efficiency of at least 0.5. Referred to the thin-film input coil, the best coupled energy resolution achieved is 1.2×10-30 J/Hz measured in a flux-locked loop at frequencies above 10 Hz. As far as we know, this is the best figure achieved with an all-refractory-metal thin-film SQUID. The fabrication technique used is suited for making circuits with SQUID and pickup coil on the same substrate. We describe a compact, planar, first-order gradiometer integrated with a SQUID on a single substrate. The gradient noise of this device is 3×10-12 T m-1. The gradiometer has a size of 12 mm×17 mm, is simple to fabricate, and is suitable for biomedical applications.

  6. High transition-temperature SQUID magnetometers and practical applications

    International Nuclear Information System (INIS)

    Dantsker, E.; Lawrence Berkeley National Lab., CA

    1997-05-01

    The design, fabrication and performance of SQUID magnetometers based on thin films of the high-transition temperature superconductor YBa 2 Cu 3 O 7-x (YBCO) are described. Essential to the achieving high magnetic field resolution at low frequencies is the elimination of 1/f flux noise due to thermally activated hopping of flux vortices between pinning sites in the superconducting films. Through improvements in processing, 1/f noise in single layer YBCO thin films and YBCO-SrTiO 3 -YBCO trilayers was systematically reduced to allow fabrication of sensitive SQUID magnetometers. Both single-layer directly coupled SQUID magnetometers and multilayer magnetometers were fabricated, based on the dc SQUID with bicrystal grain boundary Josephson junctions. Multilayer magnetometers had a lower magnetic field noise for a given physical size due to greater effective sensing areas. A magnetometer consisting of a SQUID inductively coupled to the multiturn input coil of a flux transformer in a flip-chip arrangement had a field noise of 27 fT Hz -1/2 at 1 Hz and 8.5 fT Hz -1/2 at 1 kHz. A multiloop multilayer SQUID magnetometer had a field noise of 37 fT Hz -1/2 at 1 Hz and 18 fT Hz -1/2 at 1 kHz. A three-axis SQUID magnetometer for geophysical applications was constructed and operated in the field in the presence of 60 Hz and radiofrequency noise. Clinical quality magnetocardiograms were measured using multilayer SQUID magnetometers in a magnetically shielded room

  7. High transition-temperature SQUID magnetometers and practical applications

    Energy Technology Data Exchange (ETDEWEB)

    Dantsker, Eugene [Univ. of California, Berkeley, CA (United States). Dept. of Physics

    1997-05-01

    The design, fabrication and performance of SQUID magnetometers based on thin films of the high-transition temperature superconductor YBa2Cu3O7-x (YBCO) are described. Essential to the achieving high magnetic field resolution at low frequencies is the elimination of 1/f flux noise due to thermally activated hopping of flux vortices between pinning sites in the superconducting films. Through improvements in processing, 1/f noise in single layer YBCO thin films and YBCO-SrTiO3-YBCO trilayers was systematically reduced to allow fabrication of sensitive SQUID magnetometers. Both single-layer directly coupled SQUID magnetometers and multilayer magnetometers were fabricated, based on the dc SQUID with bicrystal grain boundary Josephson junctions. Multilayer magnetometers had a lower magnetic field noise for a given physical size due to greater effective sensing areas. A magnetometer consisting of a SQUID inductively coupled to the multiturn input coil of a flux transformer in a flip-chip arrangement had a field noise of 27 fT Hz-1/2 at 1 Hz and 8.5 fT Hz-1/2 at 1 kHz. A multiloop multilayer SQUID magnetometer had a field noise of 37 fT Hz-1/2 at 1 Hz and 18 fT Hz-1/2 at 1 kHz. A three-axis SQUID magnetometer for geophysical applications was constructed and operated in the field in the presence of 60 Hz and radiofrequency noise. Clinical quality magnetocardiograms were measured using multilayer SQUID magnetometers in a magnetically shielded room.

  8. Characterization of thermal aging of duplex stainless steel by SQUID

    International Nuclear Information System (INIS)

    Isobe, Y.; Kamimura, A.; Aoki, K.; Nakayasu, F.

    1995-01-01

    Thermal aging is a growing concern for long-term-aged duplex stainless steel piping in nuclear power plants. Superconducting QUantum Interference Device (SQUID) was used for the detection of thermal aging of SUS329 rolled duplex stainless steel and SCS16 cast duplex stainless steel. It was found that the SQUID output signal pattern in the presence of AC magnetic field applied to the specimen was sensitive to the changes in electromagnetic properties due to thermal aging

  9. Nb nanoSQUIDs for detection of small spin systems

    Energy Technology Data Exchange (ETDEWEB)

    Woelbing, R.; Nagel, J.; Kemmler, M.; Kleiner, R.; Koelle, D. [Physikalisches Institut, Universitaet Tuebingen (Germany); Kieler, O.; Weimann, T.; Kohlmann, J.; Zorin, A. [Fachbereich 2.4 ' ' Quantenelektronik' ' , PTB Braunschweig (Germany); Buchter, A.; Xue, F.; Poggio, M. [Department of Physics, University of Basel (Switzerland); Rueffer, D.; Russo-Averchi, E.; Fontcuberta i Morral, A. [Laboratoire des Materiaux Semiconducteurs, EPF Lausanne (Switzerland); Huber, R.; Berberich, P. [Physik-Department E10, Technische Universitaet Muenchen (Germany); Grundler, D. [Laboratoire des Materiaux Semiconducteurs, EPF Lausanne (Switzerland); Physik-Department E10, Technische Universitaet Muenchen (Germany)

    2013-07-01

    We report on the realization of highly sensitive dc nanoSQUIDs for the investigation of small spin systems in moderate magnetic fields. The Nb SQUIDs are based on normal metal Josephson junctions made of HfTi and patterned by e-beam lithography. We demonstrate stable operation up to B = ± 50 mT without degradation of rms flux noise (S{sub Φ}{sup 1/2} ≤ 280 nΦ{sub 0}/√(Hz)). We also present a multifunctional system combining a Nb nanoSQUID and a low-temperature magnetic force microscope (LTMFM) with a Ni nanotube as a scanning tip. This system allows for magnetization measurements of the Ni tube by using both, LTMFM and SQUID readout. Furthermore, the measurement of magnetic flux Φ vs. position of the particle provides an experimental determination of the coupling factor φ{sub μ} = Φ/μ between SQUID and Ni tube with magnetic moment μ. The results confirm our predictions from numerical simulations, taking into account the SQUID geometry.

  10. The low fault HTSL-SQUID cooling system. Final report; Stoerarmes HTSL-SQUID-Kuehlsystem. Abschlussbericht

    Energy Technology Data Exchange (ETDEWEB)

    Binneberg, A.; Spoerl, G.; Buschmann, H.

    1997-03-01

    In the context of the research project, work was done for HTSL-SQUID on (1) the development of a thermo-siphon cooler (low fault and continuously working) and (2) the development of a latent storage cooler (low fault and discontinuously working). Two development versions of the latent storage cooler were followed up, the development of a spherical latent storage cooler and the development of an annular vessel latent storage cooler. A further precondition for the construction of the cooler was the use of split Stirling refrigerators as units producing the cold. The experimental sample was built up with refrigerators which could produce a nominal cooling output of 1.2 W at 80 K. Two samples of the thermo-siphon cooler were built, tested and improved. The second sample was developed further as a demonstration model, introduced at meetings and prepared for testing the cooling of HTSL-SQUIDs. The thermo-siphon cooler can be designed for cooling output up to about 2 W at 80 K and can be used controlled for a temperature range of 90 K to 66 K. (orig./MM) [Deutsch] Im Rahmen des Forschungsvorhabens wurde fuer HTSL-SQUID`s an der (1) Entwicklung eines Thermosiphon-Kuehlers (stoerarm und kontinuierlich arbeitend) und (2) Entwicklung eines Latentspeicher-Kuehlers (stoerfrei und diskontinuierlich arbeitend) gearbeitet. Bei dem Latentspeicher-Kuehler wurden zwei Entwicklungsversionen verfolgt, und zwar Entwicklung eines Kugel-Latentspeicher-Kuehlers und Entwicklung eines Ringgefaess-Latentspeicher-Kuehlers. Eine weitere Praemisse zum Aufbau der Kuehler war der Einsatz von Split-Stirling-Kaeltemaschinen als kaelteerzeugende Baugruppe. Die Versuchsmuster wurden mit Kaeltemaschinen aufgebaut, die eine Nennkuehlleistung von 1,2 W bei 80 K erzeugen konnten. Der Thermosiphon-Kuehler wurde in zwei Musterexemplaren aufgebaut, erprobt und verbessert. Das Zweitmuster wurde als Demonstrator weiterentwickelt, zu Fachtagungen vorgestellt und zur Testung der Kuehlung von HTSL-SQUIDs

  11. Measurements of the dynamic input impedance of a dc SQUID

    International Nuclear Information System (INIS)

    Hilbert, C.; Clarke, J.

    1985-01-01

    The impedance of a circuit coupled magnetically via a mutual inductance M/sub i/ to a dc SQUID of geometric inductance L is modified by the dynamic input impedance of the SQUID, which can be characterized by the flux-to-current transfer function J/sub Phi/approx. =partialJ/partialPhi; J is the current circulating in the SQUID loop and ∫ is the flux applied to the loop. At the same time, the SQUID is modified by the presence of the input circuit in the lumped circuit approximation, one expects its inductance to be reduced to L'(1-α/sub e/ 2 )L, where α/sub e/ is an effective coupling coefficient. Calculations of J/sub Phi/ using an analog simulator are described and presented in the form of a dynamic inductance L and a dynamic resistance R versus bias current I and Phi. Experimental measurements of L and R were made on a planar, thin-film SQUID tightly coupled to a spiral input coil that was connected in series with a capacitor C/sub i/ to form a resonant circuit. Thus, J/sub Phi/ was determined from the change in the resonant frequency and quality factor of this circuit as a function of I and Phi. At low bias currents (low Josephson frequencies) the measured values of L were in reasonable agreement with values simulated for the reduced SQUID, while at higher bias currents (higher Josephson frequencies) the measured values were in better agreement with values simulated for the unscreened SQUID. Similar conclusions were reached in the comparison of the experimental and simulated values of the flux-to-voltage transfer function V/sub Phi/

  12. Nuclear magnetic resonance experiments with dc SQUID amplifiers

    International Nuclear Information System (INIS)

    Heaney, M.B.

    1990-11-01

    The development and fabrication of dc SQUIDs (Superconducting QUantum Interference Devices) with Nb/Al 2 O 3 /Nb Josephson junctions is described. A theory of the dc SQUID as a radio-frequency amplifier is presented, with an optimization strategy that accounts for the loading and noise contributions of the postamplifier and maximizes the signal-to-noise ratio of the total system. The high sensitivity of the dc SQUID is extended to high field NMR. A dc SQUID is used as a tuned radio-frequency amplifier to detect pulsed nuclear magnetic resonance at 32 MHz from a metal film in a 3.5 Tesla static field. A total system noise temperature of 11 K has been achieved, at a bath temperature of 4.2 K. The minimum number of nuclear Bohr magnetons observable from a free precession signal after a single pulse is about 2 x 10 17 in a bandwidth of 25 kHz. In a separate experiment, a dc SQUID is used as a rf amplifier in a NQR experiment to observe a new resonance response mechanism. The net electric polarization of a NaClO 3 crystal due to the precessing electric quadrupole moments of the Cl nuclei is detected at 30 MHz. The sensitivity of NMR and NQR spectrometers using dc SQUID amplifiers is compared to the sensitivity of spectrometers using conventional rf amplifiers. A SQUID-based spectrometer has a voltage sensitivity which is comparable to the best achieved by a FET-based spectrometer, at these temperatures and operating frequencies

  13. SQUID use for Geophysics: finding billions of dollars

    Science.gov (United States)

    Foley, Catherine

    2014-03-01

    Soon after their discovery, Jim Zimmerman saw the potential of using Superconducting Quantum Interference Devices, SQUIDs, for the study of Geophysics and undertook experiments to understand the magnetic phenomena of the Earth. However his early experiments were not successful. Nevertheless up to the early 1980's, some research effort in the use of SQUIDs for geophysics continued and many ideas of how you could use SQUIDs evolved. Their use was not adopted by the mining industry at that time for a range of reasons. The discovery of high temperature superconductors started a reinvigoration in the interest to use SQUIDs for mineral exploration. Several groups around the world worked with mining companies to develop both liquid helium and nitrogen cooled systems. The realisation of the achievable sensitivity that contributed to successful mineral discoveries and delineation led to real financial returns for miners. By the mid 2000's, SQUID systems for geophysics were finally being offered for sale by several start-up companies. This talk will tell the story of SQUID use in geophysics. It will start with the early work of the SQUID pioneers including that of Jim Zimmerman and John Clarke and will also cover the development since the early 1990's up to today of a number of magnetometers and gradiometers that have been successfully commercialised and used to create significant impact in the global resources industry. The talk will also cover some of the critical technical challenges that had to be overcome to succeed. It will focus mostly on magnetically unshielded systems used in the field although some laboratory-based systems will be discussed.

  14. Non-GMO genetically edited crop plants.

    Science.gov (United States)

    Kanchiswamy, Chidananda Nagamangala; Malnoy, Mickael; Velasco, Riccardo; Kim, Jin-Soo; Viola, Roberto

    2015-09-01

    Direct delivery of purified Cas9 protein with guide RNA into plant cells, as opposed to plasmid-mediated delivery, displays high efficiency and reduced off-target effects. Following regeneration from edited cells, the ensuing plant is also likely to bypass genetically modified organism (GMO) legislation as the genome editing complex is degraded in the recipient cells. Copyright © 2015 Elsevier Ltd. All rights reserved.

  15. A to I editing in disease is not fake news.

    Science.gov (United States)

    Bajad, Prajakta; Jantsch, Michael F; Keegan, Liam; O'Connell, Mary

    2017-09-02

    Adenosine deaminases acting on RNA (ADARs) are zinc-containing enzymes that deaminate adenosine bases to inosines within dsRNA regions in transcripts. In short, structured dsRNA hairpins individual adenosine bases may be targeted specifically and edited with up to one hundred percent efficiency, leading to the production of alternative protein variants. However, the majority of editing events occur within longer stretches of dsRNA formed by pairing of repetitive sequences. Here, many different adenosine bases are potential targets but editing efficiency is usually much lower. Recent work shows that ADAR-mediated RNA editing is also required to prevent aberrant activation of antiviral innate immune sensors that detect viral dsRNA in the cytoplasm. Missense mutations in the ADAR1 RNA editing enzyme cause a fatal auto-inflammatory disease, Aicardi-Goutières syndrome (AGS) in affected children. In addition RNA editing by ADARs has been observed to increase in many cancers and also can contribute to vascular disease. Thus the role of RNA editing in the progression of various diseases can no longer be ignored. The ability of ADARs to alter the sequence of RNAs has also been used to artificially target model RNAs in vitro and in cells for RNA editing. Potentially this approach may be used to repair genetic defects and to alter genetic information at the RNA level. In this review we focus on the role of ADARs in disease development and progression and on their potential use to artificially modify RNAs in a targeted manner.

  16. The agents of natural genome editing.

    Science.gov (United States)

    Witzany, Guenther

    2011-06-01

    The DNA serves as a stable information storage medium and every protein which is needed by the cell is produced from this blueprint via an RNA intermediate code. More recently it was found that an abundance of various RNA elements cooperate in a variety of steps and substeps as regulatory and catalytic units with multiple competencies to act on RNA transcripts. Natural genome editing on one side is the competent agent-driven generation and integration of meaningful DNA nucleotide sequences into pre-existing genomic content arrangements, and the ability to (re-)combine and (re-)regulate them according to context-dependent (i.e. adaptational) purposes of the host organism. Natural genome editing on the other side designates the integration of all RNA activities acting on RNA transcripts without altering DNA-encoded genes. If we take the genetic code seriously as a natural code, there must be agents that are competent to act on this code because no natural code codes itself as no natural language speaks itself. As code editing agents, viral and subviral agents have been suggested because there are several indicators that demonstrate viruses competent in both RNA and DNA natural genome editing.

  17. High-Tc SQUIDs: Noise and applications

    Energy Technology Data Exchange (ETDEWEB)

    Cho, Hsiao-Mei [Univ. of Houston, TX (United States)

    2001-08-01

    A major challenge in the design and operation of high transition temperature (Tc ) Superconducting Quantum Interference Devices (SQUIDs) is their potential to exhibit substantially higher levels of noise at low frequency f when exposed to earth’s magnetic field. To investigate this problem, we studied the noise of high-Tc SQUIDs, directly coupled magnetometers and multilayer magnetometers in both static and changing magnetic fields. The directly coupled magnetometer consists of a dc SQUID connected to a large area pickup loop in parallel. The multilayer magnetometer involves a multiturn flux transformer inductively coupled to a dc SQUID on a separate substrate. All the devices are made of thin films of the high-Tc superconductor YBa2Cu3O7-δ, patterned into 4 μm linewidths. After cooling in a magnetic field, the devices showed no increase in 1/f noise for fields up to threshold values well above the earth’s magnetic field. The devices were also cooled in a magnetic field that was subsequently turned off. The 1/f noise of bare SQUIDs was unchanged for fields up to 12 μT. The addition of the flux transformer containing flux dams increased the sensitivity to magnetic field by a factor of 43 while reducing the threshold field only moderately, to 5 μT. This result implies that the multilayer magnetometer can be rotated in the earth’s magnetic field through an angle of up to 26o without increasing the low frequency noise. The results of these studies were incorporated into a 5-channel high-Tc magnetocardiography system involving two first-derivative SQUID gradiometers and three reference SQUIDs. Each planar gradiometer consists of a directly coupled SQUID magnetometer inductively coupled to the smaller coil of an asymmetric, two-loop flux transformer. The reference SQUIDs are patterned into 4 μm lines. The outputs of the five channels were subtracted in software to form a second-derivative gradiometer. Its

  18. Editing modifies the GABA(A) receptor subunit alpha3

    DEFF Research Database (Denmark)

    Ohlson, Johan; Pedersen, Jakob Skou; Haussler, David

    2007-01-01

    Adenosine to inosine (A-to-I) pre-mRNA editing by the ADAR enzyme family has the potential to increase the variety of the proteome. This editing by adenosine deamination is essential in mammals for a functional brain. To detect novel substrates for A-to-I editing we have used an experimental method...... to find selectively edited sites and combined it with bioinformatic techniques that find stem-loop structures suitable for editing. We present here the first verified editing candidate detected by this screening procedure. We show that Gabra-3, which codes for the alpha3 subunit of the GABA(A) receptor......, is a substrate for editing by both ADAR1 and ADAR2. Editing of the Gabra-3 mRNA recodes an isoleucine to a methionine. The extent of editing is low at birth but increases with age, reaching close to 100% in the adult brain. We therefore propose that editing of the Gabra-3 mRNA is important for normal brain...

  19. SQUIDs De-fluxing Using a Decaying AC Magnetic Field

    Energy Technology Data Exchange (ETDEWEB)

    Matlashov, Andrei Nikolaevich [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Semenov, Vasili Kirilovich [State Univ. of New York (SUNY), Plattsburgh, NY (United States); Anderson, Bill [Senior Scientific, LLC, Albuquerque, NM (United States)

    2016-06-08

    Flux trapping is the Achilles’ heel of all superconductor electronics. The most direct way to avoid flux trapping is a prevention of superconductor circuits from exposure to magnetic fields. Unfortunately this is not feasible if the circuits must be exposed to a strong DC magnetic field even for a short period of time. For example, such unavoidable exposures take place in superparamagnetic relaxation measurements (SPMR) and ultra-low field magnetic resonance imaging (ULF MRI) using unshielded thin-film SQUID-based gradiometers. Unshielded SQUIDs stop working after being exposed to DC magnetic fields of only a few Gauss in strength. In this paper we present experimental results with de-fluxing of planar thin-film LTS SQUID-based gradiometers using a strong decaying AC magnetic field. We used four commercial G136 gradiometers for SPMR measurements with up to a 10 mT magnetizing field. Strong 12.9 kHz decaying magnetic field pulses reliably return SQUIDs to normal operation 50 ms after zeroing the DC magnetizing field. This new AC de-fluxing method was also successfully tested with seven other different types of LTS SQUID sensors and has been shown to dissipate extremely low energy.

  20. Fabrication and characterization of hybrid Nb-YBCO dc SQUIDs

    International Nuclear Information System (INIS)

    Frack, E.K.; Drake, R.E.; Patt, R.; Radparvar, M.

    1991-01-01

    This paper reports on the fabrication of hybrid low T c /high T c dc SQUIDs of two flavors. The first kind utilizes niobium tunnel junctions and a YBCO film strip as the most inductive portion of the SQUID loop. This configuration allows a direct measurement of the inductance of the YBCO microstrip from which the effective penetration depth can be calculated. The successful fabrication of these SQUIDs has required 1. superconducting Nb-to-YBCO contacts, 2. deposition and patterning of an SiO 2 insulation layer over YBCO, and 3. selective patterning of niobium and SiO 2 relative to YBCO. All these process steps are pertinent to the eventual use of YBCO thin films in electronic devices

  1. Dipole location using SQUID based measurements: Application to magnetocardiography

    Science.gov (United States)

    Mariyappa, N.; Parasakthi, C.; Sengottuvel, S.; Gireesan, K.; Patel, Rajesh; Janawadkar, M. P.; Sundar, C. S.; Radhakrishnan, T. S.

    2012-07-01

    We report a method of inferring the dipole location using iterative nonlinear least square optimization based on Levenberg-Marquardt algorithm, wherein, we use different sets of pseudo-random numbers as initial parameter values. The method has been applied to (i) the simulated data representing the calculated magnetic field distribution produced by a point dipole placed at a known position, (ii) the experimental data from SQUID based measurements of the magnetic field distribution produced by a source coil carrying current, and (iii) the actual experimentally measured magnetocardiograms of human subjects using a SQUID based system.

  2. Application of squids in the Iwate create project

    International Nuclear Information System (INIS)

    Yoshizawa, M.; He, D.F.; Nakai, K.; Kobayashi, K.; Nakamura, Y.; Yaegashi, M.; Ito, M.; Yashiro, H.; Daibo, M.; Simizu, T.; Uchikawa, Y.; Noto, K.

    2005-01-01

    We have developed a 64-channel magnetocardiograph (MCG) system for the diagnosis of heart disease. The MCG is characterized by its display of a unique three-dimensional image of bio-currents flowing inside the human body. The outline of the heart can be displayed without use of MRI. A mobile SQUID-based non-distractive evaluation apparatus was realized by the active shielding technique. The system can offer information from beneath the surface of the specimen by using a saw-wave excitation method. This mobile technology enables us to inspect ferromagnetic materials, whose high magnetic field rules out the use of a conventional SQUID apparatus near them

  3. Scanning high-Tc SQUID imaging system for magnetocardiography

    International Nuclear Information System (INIS)

    Yang, H-C; Wu, T-Y; Horng, H-E; Wu, C-C; Yang, S Y; Liao, S-H; Wu, C-H; Jeng, J T; Chen, J C; Chen, Kuen-Lin; Chen, M J

    2006-01-01

    A scanning magnetocardiography (MCG) system constructed from SQUID sensors offers potential to basic or clinical research in biomagnetism. In this work, we study a first order scanning electronic high-T c (HTS) SQUID MCG system for biomagnetic signals. The scanning MCG system was equipped with an x-y translation bed powered by step motors. Using noise cancellation and μ-metal shielding, we reduced the noise level substantially. The established scanning HTS MCG system was used to study the magnetophysiology of hypercholesterolaemic (HC) rabbits. The MCG data of HC rabbits were analysed. The MCG contour map of HC rabbits provides experimental models for the interpretation of human cardiac patterns

  4. Zinc-mediated binding of a low-molecular-weight stabilizer of the host anti-viral factor apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G.

    Science.gov (United States)

    Radwan, Mohamed O; Sonoda, Sachiko; Ejima, Tomohiko; Tanaka, Ayumi; Koga, Ryoko; Okamoto, Yoshinari; Fujita, Mikako; Otsuka, Masami

    2016-09-15

    Apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G (APOBEC3G, A3G), is a human anti-virus restriction protein which works deaminase-dependently and -independently. A3G is known to be ubiquitinated by HIV-1 viral infectivity factor (Vif) protein, leading to proteasomal degradation. A3G contains two zinc ions at the N-terminal domain and the C-terminal domain. Four lysine residues, K(297), K(301), K(303), and K(334), are known to be required for Vif-mediated A3G ubiquitination and degradation. Previously, we reported compound SN-1, a zinc chelator that increases steady-state expression level of A3G in the presence of Vif. In this study, we prepared Biotin-SN-1, a biotinylated derivative of SN-1, to study the SN-1-A3G interaction. A pull-down assay revealed that Biotin-SN-1 bound A3G. A zinc-abstraction experiment indicated that SN-1 binds to the zinc site of A3G. We carried out a SN-1-A3G docking study using molecular operating environment. The calculations revealed that SN-1 binds to the C-terminal domain through Zn(2+), H(216), P(247), C(288), and Y(315). Notably, SN-1-binding covers the H(257), E(259), C(288), and C(291) residues that participate in zinc-mediated deamination, and the ubiquitination regions of A3G. The binding of SN-1 presumably perturbs the secondary structure between C(288) and Y(315), leading to less efficient ubiquitination. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. Potential roles of placental human beta-defensin-3 and apolipoprotein B mRNA-editing enzyme catalytic polypeptide 3G in prevention of intrauterine transmission of hepatitis B virus.

    Science.gov (United States)

    Bai, Xiaoxia; Tian, Ting; Wang, Peng; Yang, Xiaofu; Wang, Zhengping; Dong, Minyue

    2015-03-01

    Approximately 5% of newborns were infected by hepatitis B virus (HBV) via intrauterine transmission and this is the main reason for high prevalence of HBV in endemic regions. However, the mechanisms by which intrauterine transmission is avoided in most cases remain elusive and placental natural anti-microbial factors may play a role in the prevention of HBV intrauterine transmission. The expression levels of human β-defensin-3 (HBD-3), apolipoprotein B mRNA-editing enzyme catalytic polypeptide 3G (A3G) and mannose binding lectin (MBL) were determined in the placenta of 30 HBV-seronegative pregnant women (controls), 7 HBV-seropositive pregnant women with infants infected via intrauterine transmission (infected group) and 30 HBV-seropositive pregnant women with non-infected infants (non-infected group). The expression of HBD-3, A3G, and MBL of placental trophoblast cell line Swan71 was determined after exposed to HBV. There were significant differences in placental HBD-3 and A3G levels among three groups, but the expression of MBL did not significantly differ. The expressions of HBD-3 and A3G were higher in non-infected group than controls and infected group, but not significantly different between infected group and controls. The exposure to HBV increased significantly the expression of HBD-3, A3G, and MBL by Swan 71. It may be concluded HBV up-regulates HBD-3 and A3G expression in vivo and in vitro in placental trophoblast and lack of this up-regulation is possibly associated with intrauterine transmission of HBV. © 2014 Wiley Periodicals, Inc.

  6. Can understanding squid life-history strategies and recruitment ...

    African Journals Online (AJOL)

    Current views of the links between life-history strategies and recruitment processes in fish are contrasted with the pattern emerging for squid. A general perspective is that the roles of space and time are reversed in the two groups, suggesting that management strategies also should differ. The space/time reversal appears to ...

  7. Scanning SQUID susceptometers with sub-micron spatial resolution

    International Nuclear Information System (INIS)

    Kirtley, John R.; Rosenberg, Aaron J.; Palmstrom, Johanna C.; Holland, Connor M.; Moler, Kathryn A.; Paulius, Lisa; Spanton, Eric M.; Schiessl, Daniel; Jermain, Colin L.; Gibbons, Jonathan; Fung, Y.-K.K.; Gibson, Gerald W.; Huber, Martin E.; Ralph, Daniel C.; Ketchen, Mark B.

    2016-01-01

    Superconducting QUantum Interference Device (SQUID) microscopy has excellent magnetic field sensitivity, but suffers from modest spatial resolution when compared with other scanning probes. This spatial resolution is determined by both the size of the field sensitive area and the spacing between this area and the sample surface. In this paper we describe scanning SQUID susceptometers that achieve sub-micron spatial resolution while retaining a white noise floor flux sensitivity of ≈2μΦ_0/Hz"1"/"2. This high spatial resolution is accomplished by deep sub-micron feature sizes, well shielded pickup loops fabricated using a planarized process, and a deep etch step that minimizes the spacing between the sample surface and the SQUID pickup loop. We describe the design, modeling, fabrication, and testing of these sensors. Although sub-micron spatial resolution has been achieved previously in scanning SQUID sensors, our sensors not only achieve high spatial resolution but also have integrated modulation coils for flux feedback, integrated field coils for susceptibility measurements, and batch processing. They are therefore a generally applicable tool for imaging sample magnetization, currents, and susceptibilities with higher spatial resolution than previous susceptometers.

  8. The magnapinnidae, a newly discovered family of oceanic Squid ...

    African Journals Online (AJOL)

    A peculiar squid paralarva from Hawaiian waters was described by Young (1991, Bull. mar. Sci. 49(1–2): 162–185), but it could not be assigned to any known family. Two larger juvenile specimens have now been obtained, one collected near the surface in the eastern Pacific Ocean and the other rehydrated from a dried ...

  9. A mass stranding of the squid martialia hyadesi Rochebrune and ...

    African Journals Online (AJOL)

    1997-02-11

    Feb 11, 1997 ... All animals were immature, with females in lower stages of maturity than males. No predatory marine mammals were seen in the area during or after the stranding event. An interpretation of the stranding is presented with reference to historical reports of squid strandings worldwide. Evidence suggests some ...

  10. Review of Magneto cardiography Technology based on SQUID

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Y. H.; Kwon, H.; Kim, J. M.; Kim, K.; Yu, K. K.; Park, Y. K. [Brain and Cognition Measurement Lab, Korea Research Institute of Standards and Science, Daejeon (Korea, Republic of)

    2012-04-15

    Electric activity of cardiac muscles generates magnetic fields. Magnetocardiography (or MCG) technology, measuring these magnetic signals, can provide useful information for the diagnosis of heart diseases. It is already about 40 years ago that the first measurement of MCG signals was done by D. Cohen using SQUID (superconducting quantum interference device) sensor inside a magnetically shielded room. In the early period of MCG history, bulky point-contact RF-SQUID was used as the magnetic sensor. Thanks to the development of Nb-based Josephson junction technology in mid 1980s and new design of tightly-coupled DC-SQUID, low-noise SQUID sensors could be developed in late 1980s. In around 1990, several groups developed multi-channel MCG systems and started clinical study. However, it is quite recent years that the true usefulness of MCG was verified in clinical practice, for example, in the diagnosis of coronary artery disease. For the practical MCG system, technical elements of MCG system should be optimized in terms of performance, fabrication cost and operation cost. In this review, development history, technical issue, and future development direction of MCG technology are described.

  11. Scanning SQUID susceptometers with sub-micron spatial resolution

    Energy Technology Data Exchange (ETDEWEB)

    Kirtley, John R., E-mail: jkirtley@stanford.edu; Rosenberg, Aaron J.; Palmstrom, Johanna C.; Holland, Connor M.; Moler, Kathryn A. [Department of Applied Physics, Stanford University, Stanford, California 94305-4045 (United States); Paulius, Lisa [Department of Physics, Western Michigan University, Kalamazoo, Michigan 49008-5252 (United States); Spanton, Eric M. [Department of Physics, Stanford University, Stanford, California 94305-4045 (United States); Schiessl, Daniel [Attocube Systems AG, Königinstraße 11A, 80539 Munich (Germany); Jermain, Colin L.; Gibbons, Jonathan [Department of Physics, Cornell University, Cornell, Ithaca, New York 14853 (United States); Fung, Y.-K.K.; Gibson, Gerald W. [IBM Research Division, T. J. Watson Research Center, Yorktown Heights, New York 10598 (United States); Huber, Martin E. [Department of Physics, University of Colorado Denver, Denver, Colorado 80217-3364 (United States); Ralph, Daniel C. [Department of Physics, Cornell University, Cornell, Ithaca, New York 14853 (United States); Kavli Institute at Cornell, Ithaca, New York 14853 (United States); Ketchen, Mark B. [OcteVue, Hadley, Massachusetts 01035 (United States)

    2016-09-15

    Superconducting QUantum Interference Device (SQUID) microscopy has excellent magnetic field sensitivity, but suffers from modest spatial resolution when compared with other scanning probes. This spatial resolution is determined by both the size of the field sensitive area and the spacing between this area and the sample surface. In this paper we describe scanning SQUID susceptometers that achieve sub-micron spatial resolution while retaining a white noise floor flux sensitivity of ≈2μΦ{sub 0}/Hz{sup 1/2}. This high spatial resolution is accomplished by deep sub-micron feature sizes, well shielded pickup loops fabricated using a planarized process, and a deep etch step that minimizes the spacing between the sample surface and the SQUID pickup loop. We describe the design, modeling, fabrication, and testing of these sensors. Although sub-micron spatial resolution has been achieved previously in scanning SQUID sensors, our sensors not only achieve high spatial resolution but also have integrated modulation coils for flux feedback, integrated field coils for susceptibility measurements, and batch processing. They are therefore a generally applicable tool for imaging sample magnetization, currents, and susceptibilities with higher spatial resolution than previous susceptometers.

  12. A contribution to the biology of the ommastrephid squid Martialia ...

    African Journals Online (AJOL)

    Updated knowledge on the distribution and biology of the ommastrephid squid Martialia hyadesi in the South-West Atlantic Ocean is presented. Although the species has an Antarctic circumpolar distribution, its most frequent area of appearance is in the South-West Atlantic, where commercial catches have been made.

  13. Reducing systematic errors in measurements made by a SQUID magnetometer

    International Nuclear Information System (INIS)

    Kiss, L.F.; Kaptás, D.; Balogh, J.

    2014-01-01

    A simple method is described which reduces those systematic errors of a superconducting quantum interference device (SQUID) magnetometer that arise from possible radial displacements of the sample in the second-order gradiometer superconducting pickup coil. By rotating the sample rod (and hence the sample) around its axis into a position where the best fit is obtained to the output voltage of the SQUID as the sample is moved through the pickup coil, the accuracy of measuring magnetic moments can be increased significantly. In the cases of an examined Co 1.9 Fe 1.1 Si Heusler alloy, pure iron and nickel samples, the accuracy could be increased over the value given in the specification of the device. The suggested method is only meaningful if the measurement uncertainty is dominated by systematic errors – radial displacement in particular – and not by instrumental or environmental noise. - Highlights: • A simple method is described which reduces systematic errors of a SQUID. • The errors arise from a radial displacement of the sample in the gradiometer coil. • The procedure is to rotate the sample rod (with the sample) around its axis. • The best fit to the SQUID voltage has to be attained moving the sample through the coil. • The accuracy of measuring magnetic moment can be increased significantly

  14. A method of background noise cancellation for SQUID applications

    International Nuclear Information System (INIS)

    He, D F; Yoshizawa, M

    2003-01-01

    When superconducting quantum inference devices (SQUIDs) operate in low-cost shielding or unshielded environments, the environmental background noise should be reduced to increase the signal-to-noise ratio. In this paper we present a background noise cancellation method based on a spectral subtraction algorithm. We first measure the background noise and estimate the noise spectrum using fast Fourier transform (FFT), then we subtract the spectrum of background noise from that of the observed noisy signal and the signal can be reconstructed by inverse FFT of the subtracted spectrum. With this method, the background noise, especially stationary inferences, can be suppressed well and the signal-to-noise ratio can be increased. Using high-T C radio-frequency SQUID gradiometer and magnetometer, we have measured the magnetic field produced by a watch, which was placed 35 cm under a SQUID. After noise cancellation, the signal-to-noise ratio could be greatly increased. We also used this method to eliminate the vibration noise of a cryocooler SQUID

  15. Flicker (1/f) noise in tunnel junction DC SQUIDS

    International Nuclear Information System (INIS)

    Koch, R.H.; Clarke, J.; Goubau, W.M.; Martinis, J.M.; Pegrum, C.M.; Van Harlingen, D.J.

    1983-01-01

    We have measured the spectral density of the 1/f voltage noise in current-biased resistively shunted Josephson tunnel junctions and dc SQUIDs. A theory in which fluctuations in the temperature give rise to fluctuations in the critical current and hence in the voltage predicts the magnitude of the noise quite accurately for junctions with areas of about 2 x 10 4 μm 2 , but significantly overestimates the noise for junctions with areas of about 6 μm 2 . DC SQUIDs fabricated from these two types of junctions exhibit substantially more 1/f voltage noise than would be predicted from a model in which the noise arises from critical current fluctuations in the junctions. This result was confirmed by an experiment involving two different bias current and flux modulation schemes, which demonstrated that the predominant 1/f voltage noise arises not from critical current fluctuations, but from some unknown source that can be regarded as an apparent 1/f flux noise. Measurements on five different configurations of dc SQUIDs fabricated with thin-film tunnel junctions and with widely varying areas, inductances, and junction capacitances show that the spectral density of the 1/f equivalent flux noise is roughtly constant, within a factor of three of (10 -10 /f)phi 2 0 Hz -1 . It is emphasized that 1/f flux noise may not be the predominant source of 1/f noise in SQUIDS fabricated with other technologies

  16. SQUID developments for the gravitational wave antenna MiniGRAIL

    NARCIS (Netherlands)

    Pleikies, J.; Usenko, O.; Kuit, K.H.; Flokstra, Jakob; de Waard, A.; de Waard, A.; Frossati, G.

    2007-01-01

    We designed two different sensor SQUIDs for the readout of the resonant mass gravitational wave detector MiniGRAIL. Both designs have integrated input inductors in the order of 1.5 muH and are planned for operation in the mK temperature range. Cooling fins were added to the shunt resistors. The

  17. The biomass and ecology of chokka squid Loligo vulgaris reynaudii ...

    African Journals Online (AJOL)

    Migration, stock size and ecology of chokka squid Loligo vulgaris reynaudii off the West Coast of South Africa were studied and their relationship to other regions compared by analysis of distributional, biomass, and size composition, and biological data collected from biannual research cruises from 1983-1987. Biomass ...

  18. spawning grounds for chokka squid Loligo vulgaris reynaudii, using

    African Journals Online (AJOL)

    denise

    Swimming movements in relation to egg beds have been studied using acoustic micro-electronic transmitters implanted in squid and tracked via 3-D radio-linked acoustic positioning telemetry (O'Dor et al. 1996, 1998, Sauer et al. 1997). Most of these methods are either impractical or would be severely limited on the deeper ...

  19. Multiplex editing system

    DEFF Research Database (Denmark)

    2015-01-01

    The present invention relates to a multiplex editing system. The system allows multiple editing of nucleic acid sequences such as genomic sequences, such as knockins of genes of interest in a genome, knockouts of genomic sequences and/or allele replacement. Also provided herein are a method...... for editing nucleic acids and a cell comprising a stably integrated endonuclease....

  20. Characterisation of micro and nano SQUIDs at variable temperature and magnetic field

    Energy Technology Data Exchange (ETDEWEB)

    Koehn, Claudia; Storm, Jan-Hendrik; Bechstein, Sylke; Schurig, Thomas [Physikalisch-Technische Bundesanstalt, Abbestrasse 2-12, 10587 Berlin (Germany)

    2015-07-01

    SQUIDs are highly suited to investigate the magnetic properties of samples with small dimensions, such as nanoparticles, or to read out nanoelectromechanical systems (NEMS). Due to the small sample size, SQUIDs with dimensions in the μm or nm regime are desirable. These micro or nano SQUIDs should have a low noise and no hysteresis in the current-voltage-characteristic, even when operated in high magnetic fields of up to several 100 mT. To investigate such SQUID, we developed measurement setups which can simulate the measurement conditions of the intended SQUID application. The design and performance of two measurement setups will be shown and compared. One setup uses a dipstick that is immersed in liquid helium and can be evacuated to provide SQUID temperatures between 4.5 K and 10 K. The other one uses an evaporation cryostat so that the temperature can be varied from 2 K to 60 K. Both setups are equipped with coils to enable SQUID operation in variable magnetic field. To minimize noise, the output of the SQUID under test is preamplified by a SQUID series array which is operated at 4.2 K. First results of the characterisation of micro and nano SQUIDs will be presented.

  1. Magnetic shield effect simulation of superconducting film shield covering directly coupled HTS dc-SQUID magnetometer

    International Nuclear Information System (INIS)

    Terauchi, N.; Noguchi, S.; Igarashi, H.

    2011-01-01

    A superconducting film shield over a SQUID ring improves the robustness of the SQUID with respect to magnetic noise. Supercurrent in the SQUID magnetometer and the superconducting film shield were simulated. The superconducting film shield reduces the influence of the external magnetic field on the SQUID ring. An HTS SQUID is a high sensitive magnetic sensor. In recent years, the HTS SQUID is widely used in various applications. In some applications, high robustness with respect to magnetic noise is required to realize stable operation at outside of a magnetic shielding room. The target of this paper is a directly coupled HTS dc-SQUID magnetometer. To enhance the robustness of the SQUID magnetometer, use of a superconducting thin film shield has been proposed. The magnetic field directly penetrating the SQUID ring causes the change of the critical current of Josephson junction, and then the SQUID magnetometer transitions into inoperative state. In order to confirm the magnetic shield effect of the superconducting film shield, electromagnetic field simulation with 3D edge finite element method was performed. To simulate the high temperature superconductor, E-J characteristics and c-axis anisotropy are considered. To evaluate the effect of the superconducting film shield, an external magnetic field which is supposed to be a magnetic noise is applied. From the simulation results, the time transition of the magnetic flux penetrating the SQUID ring is investigated and the effect of the superconducting film shield is confirmed. The amplitude of the magnetic flux penetrating the SQUID ring can be reduced to about one-sixth since the superconducting film shield prevents the magnetic noise from directly penetrating the SQUID ring.

  2. Nanobridge SQUIDs as calorimetric inductive particle detectors

    International Nuclear Information System (INIS)

    Gallop, John; Cox, David; Hao, Ling

    2015-01-01

    Superconducting transition edge sensors (TESs) have made dramatic progress since their invention some 65 years ago (Andrews et al 1949 Phys. Rev. 76 154–155; Irwin and Hilton 2005 Topics Appl. Phys. 99 63–149) until now there are major imaging arrays of TESs with as many as 7588 separate sensors. These are extensively used by astronomers for some ground-breaking observations (Hattori et al 2013 Nucl. Instrum. Methods Phys. Res. A 732 299–302). The great success of TES systems has tended to overshadow other superconducting sensor developments. However there are other types (Sobolewski et al 2003 IEEE Trans. Appl. Supercond. 13 1151–7; Hadfield 2009 Nat. Photonics 3 696–705) which are discussed in papers within this special edition of the journal. Here we describe a quite different type of detector, also applicable to single photon detection but possessing possible advantages (higher sensitivity, higher operating temperature) over the conventional TES, at least for single detectors. (paper)

  3. SQUIDs in biomagnetism: a roadmap towards improved healthcare

    Science.gov (United States)

    Körber, Rainer; Storm, Jan-Hendrik; Seton, Hugh; Mäkelä, Jyrki P.; Paetau, Ritva; Parkkonen, Lauri; Pfeiffer, Christoph; Riaz, Bushra; Schneiderman, Justin F.; Dong, Hui; Hwang, Seong-min; You, Lixing; Inglis, Ben; Clarke, John; Espy, Michelle A.; Ilmoniemi, Risto J.; Magnelind, Per E.; Matlashov, Andrei N.; Nieminen, Jaakko O.; Volegov, Petr L.; Zevenhoven, Koos C. J.; Höfner, Nora; Burghoff, Martin; Enpuku, Keiji; Yang, S. Y.; Chieh, Jen-Jei; Knuutila, Jukka; Laine, Petteri; Nenonen, Jukka

    2016-11-01

    Globally, the demand for improved health care delivery while managing escalating costs is a major challenge. Measuring the biomagnetic fields that emanate from the human brain already impacts the treatment of epilepsy, brain tumours and other brain disorders. This roadmap explores how superconducting technologies are poised to impact health care. Biomagnetism is the study of magnetic fields of biological origin. Biomagnetic fields are typically very weak, often in the femtotesla range, making their measurement challenging. The earliest in vivo human measurements were made with room-temperature coils. In 1963, Baule and McFee (1963 Am. Heart J. 55 95-6) reported the magnetic field produced by electric currents in the heart (‘magnetocardiography’), and in 1968, Cohen (1968 Science 161 784-6) described the magnetic field generated by alpha-rhythm currents in the brain (‘magnetoencephalography’). Subsequently, in 1970, Cohen et al (1970 Appl. Phys. Lett. 16 278-80) reported the recording of a magnetocardiogram using a Superconducting QUantum Interference Device (SQUID). Just two years later, in 1972, Cohen (1972 Science 175 664-6) described the use of a SQUID in magnetoencephalography. These last two papers set the scene for applications of SQUIDs in biomagnetism, the subject of this roadmap. The SQUID is a combination of two fundamental properties of superconductors. The first is flux quantization—the fact that the magnetic flux Φ in a closed superconducting loop is quantized in units of the magnetic flux quantum, Φ0 ≡ h/2e, ≈ 2.07 × 10-15 Tm2 (Deaver and Fairbank 1961 Phys. Rev. Lett. 7 43-6, Doll R and Näbauer M 1961 Phys. Rev. Lett. 7 51-2). Here, h is the Planck constant and e the elementary charge. The second property is the Josephson effect, predicted in 1962 by Josephson (1962 Phys. Lett. 1 251-3) and observed by Anderson and Rowell (1963 Phys. Rev. Lett. 10 230-2) in 1963. The Josephson junction consists of two weakly coupled superconductors

  4. Robot-arm-based mobile HTS SQUID system for NDE of structures

    Energy Technology Data Exchange (ETDEWEB)

    Yotsugi, K; Hatsukade, Y; Tanaka, S [Department of Ecological Engineering, Toyohashi University of Technology, 1-1 Hibarigaoka, Tenpaku-cho, Toyohashi, Aichi 441-8580 (Japan)], E-mail: hatukade@eco.tut.ac.jp

    2008-02-01

    A robot-arm-based mobile HTS SQUID system was developed for NDE of fixed targets. To realize the system, active magnetic shielding technique using fluxgate as reference sensor for ambient field was applied to a cryocooler-based HTS SQUID gradiometer that was mounted on commercial robot-arm. In this technique, ambient field noise and pulse noise of 550 nT from robot were measured by the fluxgate near the SQUID, and then the fluxgate output was negatively fed back to generate compensation field around the SQUID and fluxgate. The noise from robot was reduced by a factor of about 20 and the shielding technique enabled the HTS SQUID to move in unshielded environment by the robot-arm without flux-trapping or unlocking at 10 mm/s. System noise measurement and inspection of hidden cracks in multi-layer composite-metal structure were demonstrated using the mobile SQUID-NDE system.

  5. Design consideration for dc SQUIDs fabricated in deep sub-micron technology

    International Nuclear Information System (INIS)

    Ketchen, M.B.

    1991-01-01

    Design rules for scaling dc SQUID junctions to optimize SQUID performance have been well known for over a decade, and verified down to the sub-micron regime. Practical SQUIDs having well coupled input coils of usable inductance have generally been fabricated at the 2-5 μm level of lithography. Other technologies, silicon in particular, are now routinely practiced at the 0.5 μm level of lithography with impressive demonstrations at the 0.1-0.25 μm level not uncommon. In this paper the implications of applying such fabrication capability to advance dc SQUID technology are explored. In particular the issues of scaling practical dc SQUIDs down to the 0.1-0.25 μm regime are examined, using as a prototype design the basic washer SQUID with a spiral input coil

  6. Two-stage SQUID systems and transducers development for MiniGRAIL

    International Nuclear Information System (INIS)

    Gottardi, L; Podt, M; Bassan, M; Flokstra, J; Karbalai-Sadegh, A; Minenkov, Y; Reinke, W; Shumack, A; Srinivas, S; Waard, A de; Frossati, G

    2004-01-01

    We present measurements on a two-stage SQUID system based on a dc-SQUID as a sensor and a DROS as an amplifier. We measured the intrinsic noise of the dc-SQUID at 4.2 K. A new dc-SQUID has been fabricated. It was specially designed to be used with MiniGRAIL transducers. Cooling fins have been added in order to improve the cooling of the SQUID and the design is optimized to achieve the quantum limit of the sensor SQUID at temperatures above 100 mK. In this paper we also report the effect of the deposition of a Nb film on the quality factor of a small mass Al5056 resonator. Finally, the results of Q-factor measurements on a capacitive transducer for the current MiniGRAIL run are presented

  7. A SQUID gradiometer module with wire-wound pickup antenna and integrated voltage feedback circuit

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Guofeng [State Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology (SIMIT), Chinese Academy of Sciences (CAS), Shanghai 200050 (China); Peter Gruenberg Institute (PGI-8), Forschungszentrum Juelich (FZJ), D-52425 Juelich (Germany); Joint Research Laboratory on Superconductivity and Bioelectronics, Collaboration between CAS-Shanghai and FZJ, Shanghai 200050 (China); Graduate University of the Chinese Academy of Sciences, Beijing 100049 (China); Zhang, Yi, E-mail: y.zhang@fz-juelich.de [Peter Gruenberg Institute (PGI-8), Forschungszentrum Juelich (FZJ), D-52425 Juelich (Germany); Joint Research Laboratory on Superconductivity and Bioelectronics, Collaboration between CAS-Shanghai and FZJ, Shanghai 200050 (China); Zhang Shulin [State Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology (SIMIT), Chinese Academy of Sciences (CAS), Shanghai 200050 (China); Joint Research Laboratory on Superconductivity and Bioelectronics, Collaboration between CAS-Shanghai and FZJ, Shanghai 200050 (China); Krause, Hans-Joachim [Peter Gruenberg Institute (PGI-8), Forschungszentrum Juelich (FZJ), D-52425 Juelich (Germany); Joint Research Laboratory on Superconductivity and Bioelectronics, Collaboration between CAS-Shanghai and FZJ, Shanghai 200050 (China); and others

    2012-10-15

    The performance of the direct readout schemes for dc SQUID, Additional Positive Feedback (APF), noise cancellation (NC) and SQUID bootstrap circuit (SBC), have been studied in conjunction with planar SQUID magnetometers. In this paper, we examine the NC technique applied to a niobium SQUID gradiometer module with an Nb wire-wound antenna connecting to a dual-loop SQUID chip with an integrated voltage feedback circuit for suppression of the preamplifier noise contribution. The sensitivity of the SQUID gradiometer module is measured to be about 1 fT/(cm {radical}Hz) in the white noise range in a magnetically shielded room. Using such gradiometer, both MCG and MEG signals are recorded.

  8. A three-axis SQUID-based absolute vector magnetometer

    Energy Technology Data Exchange (ETDEWEB)

    Schönau, T.; Schmelz, M.; Stolz, R.; Anders, S.; Linzen, S.; Meyer, H.-G. [Department of Quantum Detection, Leibniz Institute of Photonic Technology, Jena 07745 (Germany); Zakosarenko, V.; Meyer, M. [Supracon AG, An der Lehmgrube 11, Jena 07751 (Germany)

    2015-10-15

    We report on the development of a three-axis absolute vector magnetometer suited for mobile operation in the Earth’s magnetic field. It is based on low critical temperature dc superconducting quantum interference devices (LTS dc SQUIDs) with sub-micrometer sized cross-type Josephson junctions and exhibits a white noise level of about 10 fT/Hz{sup 1/2}. The width of superconducting strip lines is restricted to less than 6 μm in order to avoid flux trapping during cool-down in magnetically unshielded environment. The long-term stability of the flux-to-voltage transfer coefficients of the SQUID electronics is investigated in detail and a method is presented to significantly increase their reproducibility. We further demonstrate the long-term operation of the setup in a magnetic field varying by about 200 μT amplitude without the need for recalibration.

  9. The squid-Vibrio symbioses: from demes to genes.

    Science.gov (United States)

    Kimbell, Jennifer R; McFall-Ngai, Margaret J

    2003-04-01

    The monospecific light organ association between the Hawaiian sepiolid squid Euprymna scolopes and the marine luminous bacterium Vibrio fischeri has been used as a model for the study of the most common type of coevolved animal-bacterial interaction; i.e., the association of Gram-negative bacteria with the extracellular apical surfaces of polarized epithelia. Analysis of the squid-vibrio symbiosis has ranged from characterizations of the harvesting mechanisms by which the host ensures colonization by the appropriate symbiont to identification of bacteria-induced changes in host gene expression that accompany the establishment and maintenance of the relationship. Studies of this model have been enhanced by extensive collaboration with microbiologists, who are able to manipulate the genetics of the bacterial symbiont. The results of our studies have indicated that initiation and persistence of the association requires a complex, reciprocal molecular dialogue between these two phylogenetically distant partners.

  10. On-site detection of packaged squid freshness

    Science.gov (United States)

    Ahmad, Noor Azizah; Heng, Lee Yook; Salam, Faridah; Hanifah, Sharina Abu

    2018-04-01

    The development of indicator label for detection of total volatile basic nitrogen (TVB-N) is described. Dye extract from edible plants containing anthocyanins was immobilized onto iota-carrageenan as polymer matrix. TVB-N detection worked based on pH increase as the basic deterioration volatile amines generated in the package headspace. Results showed that the indicator label has changed color from blue to green after 12 hours of storage at ambient conditions. The TVB-N value was 38.9648 mg /100 g which is exceeded of acceptability level for seafood products. The pH value of squid flesh has also increased during storage. The colour values of L * and a * negative increases while b* negative decrease with increasing storage time. The indicator label is potentially used as freshness indicator for squid at ambient conditions.

  11. Magnetic evaluation of a solar panel using HTS-SQUID

    Energy Technology Data Exchange (ETDEWEB)

    Kiwa, Toshihiko, E-mail: kiwa@okayama-u.ac.jp; Fukudome, Yohei; Miyazaki, Shingo; Saari, Mohd Mawardi; Sakai, Kenji; Tsukada, Keiji

    2013-11-15

    Highlights: •The magnetic evaluation system of a solar panel using HTS-SQUID has been developed. •The electric circuits made by the discrete devices on the circuit board were visualized. •The electric properties of the commercial solar panels were demonstrated. -- Abstract: The magnetic evaluation system of a solar panel using HTS-SQUID has been proposed and developed. A normal pick-up coil was applied to detect the tangential magnetic field to the panel surface. Since the detected field could be related to the currents of the solar panels, the electric properties of the solar panels could be evaluated. In this work, the evaluation of the electric properties of the commercial solar panels as well as the electric circuits made by the discrete devices on the circuit board was visualized.

  12. Magnetic evaluation of a solar panel using HTS-SQUID

    International Nuclear Information System (INIS)

    Kiwa, Toshihiko; Fukudome, Yohei; Miyazaki, Shingo; Saari, Mohd Mawardi; Sakai, Kenji; Tsukada, Keiji

    2013-01-01

    Highlights: •The magnetic evaluation system of a solar panel using HTS-SQUID has been developed. •The electric circuits made by the discrete devices on the circuit board were visualized. •The electric properties of the commercial solar panels were demonstrated. -- Abstract: The magnetic evaluation system of a solar panel using HTS-SQUID has been proposed and developed. A normal pick-up coil was applied to detect the tangential magnetic field to the panel surface. Since the detected field could be related to the currents of the solar panels, the electric properties of the solar panels could be evaluated. In this work, the evaluation of the electric properties of the commercial solar panels as well as the electric circuits made by the discrete devices on the circuit board was visualized

  13. Coherent arrays of planar dc-SQUIDS based on thin-film Josephson microbridges

    International Nuclear Information System (INIS)

    Hansen, J.B.

    1982-01-01

    Phase-locking and voltage-locking in systems consisting of two planar dc-SQUIDs located close together in the same superconducting film have been investigated. The locking strength was found to be strongly dependent on the fluxoid state of both SQUIDs. A simple model for the inductive coupling between two such dc-SQUIDs is presented and the prediction of the model is compared with the experimental results. (Auth.)

  14. Size increment of jumbo flying squid Dosidicus gigas mature females in Peruvian waters, 1989-2004

    Science.gov (United States)

    Argüelles, Juan; Tafur, Ricardo; Taipe, Anatolio; Villegas, Piero; Keyl, Friedeman; Dominguez, Noel; Salazar, Martín

    2008-10-01

    Changes in population structure of the jumbo flying squid Dosidicus gigas in Peruvian waters were studied based on size-at-maturity from 1989 to 2004. From 1989 to 1999, mature squid belonging to the medium-sized group prevailed, but from 2001 on, mature squids were larger. This change is not related to the changes in sea surface temperature and we hypothesized that it was caused by the population increase of mesopelagic fishes as prey.

  15. Absolute calibration and beam background of the Squid Polarimeter

    International Nuclear Information System (INIS)

    Blaskiewicz, M.M.; Cameron, P.R.; Shea, T.J.

    1996-01-01

    The problem of beam background in Squid Polarimetry is not without residual benefits. The authors may deliberately generate beam background by gently kicking the beam at the spin tune frequency. This signal may be used to accomplish a simple and accurate absolute calibration of the polarimeter. The authors present details of beam background calculations and their application to polarimeter calibration, and suggest a simple proof-of-principle accelerator experiment

  16. Symplectin evolved from multiple duplications in bioluminescent squid

    DEFF Research Database (Denmark)

    Francis, Warren R.; Christianson, Lynne M.; Haddock, Steven H.D.

    2017-01-01

    The squid Sthenoteuthis oualaniensis, formerly Symplectoteuthis oualaniensis, generates light using the luciferin coelenterazine and a unique enzyme, symplectin. Genetic information is limited for bioluminescent cephalopod species, so many proteins, including symplectin, occur in public databases...... functioning is conserved across essentially all members of the protein family, even those unlikely to be used for bioluminescence. Conversely, active site residues involved in pantetheinase catalysis are also conserved across essentially all of these proteins, suggesting that symplectin may have multiple...

  17. Antibacterial Activity of Melanin from Cuttlefish and Squid Ink

    OpenAIRE

    Yuspihana Fitrial; Iin Khusnul Khotimah

    2017-01-01

    Marine environment comprises of many organism which are known to posses bioactive compound as a common means of self-defense or for the protection of eggs and embryos. Class Cephalopods (such as squidand cuttlefish) are notable for their defences, such as jetting escape movements, changes in colouration, toxic venom and inking.This study aims to compare the antibacterial activity of melanin from cuttlefish ink (Sepia sp.) with squid ink (Loligo sp.) against E. coli. Extraction and purificatio...

  18. Detecting damage in steel with scanning SQUID microscopy

    International Nuclear Information System (INIS)

    Lee, Tae-Kyu; Clatterbuck, D.M.; Morris, J.W. Jr.; Shaw, T.J.; Lee, Seungkyun; Clarke, John

    2002-01-01

    A 'Holy Grail' of NDE research is a non-destructive method for measuring fatigue damage prior to crack initiation. High-Tc scanning SQUID microscopy may be a useful tool. Because of the exceptional magnetic sensitivity of this technique, fatigue damage can be detected well before microcrack initiation, and in the absence of other obvious microstructure or property changes. Given the spatial resolution of the technique, undamaged material can be located and used to set internal standards

  19. Detecting damage in steel with scanning SQUID microscopy

    International Nuclear Information System (INIS)

    Lee, Tae-Kyu; Clatterbuck, David; Morris Jr., J.W.; Shaw, T.J.; McDermott R.; Clarke, John

    2001-01-01

    A ''Holy Grail'' of NDE research is a non-destructive method for measuring fatigue damage prior to crack initiation. High-Tc scanning SQUID microscopy may be a useful tool. Because of the exceptional magnetic sensitivity of this technique, fatigue damage can be detected well before microcrack initiation, and in the absence of other obvious microstructure or property changes. Given the spatial resolution of the technique, undamaged material can be located and used to set internal standards

  20. SQUID sensor application for small metallic particle detection

    International Nuclear Information System (INIS)

    Tanaka, Saburo; Hatsukade, Yoshimi; Ohtani, Takeyoshi; Suzuki, Shuichi

    2009-01-01

    High-Tc superconducting quantum interference device (SQUID) is an ultra-sensitive magnetic sensor. Since the performance of the SQUID is improved and stabilized, now it is ready for application. One strong candidate for application is a detection system of magnetic foreign matters in industrial products or beverages. There is a possibility that ultra-small metallic foreign matter has been accidentally mixed with industrial products such as lithium ion batteries. If this happens, the manufacturer of the product suffers a great loss recalling products. The outer dimension of metallic particles less than 100 μm cannot be detected by an X-ray imaging, which is commonly used for the inspection. Ionization of the material is also a big issue for beverages in the case of the X-ray imaging. Therefore a highly sensitive and safety detection system for small foreign matters is required. We developed detection systems based on high-Tc SQUID with a high-performance magnetic shield. We could successfully measure small iron particles of 100 μm on a belt conveyer and stainless steel balls of 300 μm in water. These detection levels were hard to be achieved by a conventional X-ray detection or other methods

  1. Simulation and optimization of a dc SQUID with finite capacitance

    Energy Technology Data Exchange (ETDEWEB)

    de Waal, V.J.; Schrijner, P.; Llurba, R.

    1984-02-01

    This paper deals with the calculations of the noise an the optimization of the energy resolution of a dc SQUID with finite junction capacitance. Up to now noise calculations of dc SQUIDs were performed using a model without parasitic capacitances across the Josephson junctions. As the capacitances limit the performance of the SQUID, for a good optimization one must take them into account. The model consists of two coupled nonlinear second-order differential equations. The equations are very suitable for simulation with an analog circuit. We implemented the model on a hybrid computer. The noise spectrum from the model is calculated with a fast Fourier transform. A calculation of the energy resolution for one set of parameters takes about 6 min of computer time. Detailed results of the optimization are given for products of inductance and temperature of LT = 1.2 and 5 nHK. Within a range of ..beta.. and ..beta../sub c/ between 1 and 2, which is optimum, the energy resolution is nearly independent of these variables. In this region the energy resolution is near the value calculated without parasitic capacitances. Results of the optimized energy resolution are given as a function of LT between 1.2 and 10 nHK.

  2. Simulation and optimization of a dc SQUID with finite capacitance

    Science.gov (United States)

    de Waal, V. J.; Schrijner, P.; Llurba, R.

    1984-02-01

    This paper deals with the calculations of the noise and the optimization of the energy resolution of a dc SQUID with finite junction capacitance. Up to now noise calculations of dc SQUIDs were performed using a model without parasitic capacitances across the Josephson junctions. As the capacitances limit the performance of the SQUID, for a good optimization one must take them into account. The model consists of two coupled nonlinear second-order differential equations. The equations are very suitable for simulation with an analog circuit. We implemented the model on a hybrid computer. The noise spectrum from the model is calculated with a fast Fourier transform. A calculation of the energy resolution for one set of parameters takes about 6 min of computer time. Detailed results of the optimization are given for products of inductance and temperature of LT=1.2 and 5 nH K. Within a range of β and β c between 1 and 2, which is optimum, the energy resolution is nearly independent of these variables. In this region the energy resolution is near the value calculated without parasitic capacitances. Results of the optimized energy resolution are given as a function of LT between 1.2 and 10 mH K.

  3. Transfer of 60Co from midwater squid to sperm whales

    International Nuclear Information System (INIS)

    Umezu, Takeshi; Minamisako, Yoko; Ebihara, Hiroshi; Watanabe, Hiroshi.

    1984-01-01

    Sperm whales are notable squid-eaters. They feed mainly on medium to large-sized cephalopods at midwater levels and defecate near the surface. This suggests the existence of an upward transport of 60 Co by sperm whales from the mesopelagic zone (150-1,200m). To elucidate this squid-whale route for this artificial radionuclide, 60 Co content was determined in squid and in predator whales captured by commercial whaling. In the Cephalopoda livers 60 Co levels of 30-500 mBq kg -1 wet were found and in the viscera of Odontoceti (toothed whales) 15-40 mBq kg -1 wet. About 0.3% of 60 Co ingested was estimated to be retained in a 23-year-old male sperm whale. In the livers of Bryde's whales, 60 Co levels of 40-80 mBq kg -1 wet were detected, but not in euphausiids and sardines, their possible prey. The level of Co in sperm whales was nearly the same as in Bryde's whales. Specific radioactivity 60 Co/ 59 Co in mBq μg -1 was several times higher in sperm whale (1.1-1.6) than in cephalopods (0.19-0.77). Eating prey with a high content of 60 Co in the 1960's may have contributed to the present body burden in sperm whales with a long-life span. However, the origin of 60 Co in Bryde's whales is unknown. (author)

  4. Thermoelectric SQUID method for the detection of segregations

    Science.gov (United States)

    Hinken, Johann H.; Tavrin, Yury

    2000-05-01

    Aero engine turbine discs are most critical parts. Material inhomogeneities can cause disc fractures during the flight with fatal air disasters. Nondestructive testing (NDT) of the discs in various machining steps is necessary and performed as well as possible. Conventional NDT methods, however, like eddy current testing and ultrasonic testing have unacceptable limits. For example, subsurface segregations often cannot be detected directly but only indirectly in such cases when cracks already have developed from them. This may be too late. A new NDT method, which we call the Thermoelectric SQUID Method, has been developed. It allows for the detection of metallic inclusions within non-ferromagnetic metallic base material. This paper describes the results of a feasibility study on aero engine turbine discs made from Inconel® 718. These contained segregations that had been detected before by anodic etching. With the Thermoelectric SQUID Method, these segregations were detected again, and further segregations below the surfaces have been found, which had not been detected before. For this new NDT method the disc material is quasi-transparent. The Thermoelectric SQUID Method is also useful to detect distributed and localized inhomogeneities in pure metals like niobium sheets for particle accelerators.

  5. Low-frequency nuclear quadrupole resonance with a dc SQUID

    International Nuclear Information System (INIS)

    Chang, J.W.

    1991-07-01

    Conventional pure nuclear quadrupole resonance (NQR) is a technique well suited for the study of very large quadrupolar interactions. Numerous nuclear magnetic resonance (NMR) techniques have been developed for the study of smaller quadrupolar interactions. However, there are many nuclei which have quadrupolar interactions of intermediate strength. Quadrupolar interactions in this region have traditionally been difficult or unfeasible to detect. This work describes the development and application of a SQUID NQR technique which is capable of measuring intermediate strength quadrupolar interactions, in the range of a few hundred kilohertz to several megahertz. In this technique, a dc SQUID (Superconducting QUantum Interference Device) is used to monitor the longitudinal sample magnetization, as opposed to the transverse magnetization, as a rf field is swept in frequency. This allows the detection of low-frequency nuclear quadrupole resonances over a very wide frequency range with high sensitivity. The theory of this NQR technique is discussed and a description of the dc SQUID system is given. In the following chapters, the spectrometer is discussed along with its application to the study of samples containing half-odd-integer spin quadrupolar nuclei, in particular boron-11 and aluminum-27. The feasibility of applying this NQR technique in the study of samples containing integer spin nuclei is discussed in the last chapter. 140 refs., 46 figs., 6 tabs

  6. SQUID-based noise thermometer for sub-Millikelvin refrigerators

    Energy Technology Data Exchange (ETDEWEB)

    Schmidt, Marco; Beyer, Joern; Klemm, Monique [Physikalisch-Technische Bundesanstalt, Abbestrasse 2-12, 10587 Berlin (Germany); Alivaliollahi, Sassan; Barthelmess, Henry [Magnicon GmbH, Barkhausenweg 11, 22339 Hamburg (Germany)

    2015-07-01

    The magnetic field fluctuation thermometer (MFFT) is a high-accuracy SQUID-based noise thermometer suitable for sub-Kelvin thermometry. A highly sensitive low-Tc SQUID magnetometer detects inductively the magnetic field fluctuation above a metal surface. The fluctuations are generated by the thermal activated noise currents inside the metal body that is thermally anchored to the temperature stage to be measured. The spectral shape is independent of temperature as the electrical conductivity is constant and the geometry is fixed. The magnetic noise power spectral amplitudes at any frequencies are directly proportional to temperature. Hence, only one reference measurement at a known temperature is required for calibration. A complete MFFT thermometer system for the temperature range of ca. 4 K down to <10 mK is commercially available. We have now developed an integrated MFFT with an extended range of operation down to <1 mK. For this purpose the sensitivity of the SQUID sensor has been increased, the metal body geometry modified and the magnetic shielding of the MFFT module improved. These modifications make it possible to obtain a thermometer noise temperature of <10 μK. We discuss the rationale for our MFFT configuration and present numerical simulations and experimental results.

  7. Trophic niche of squids: Insights from isotopic data in marine systems worldwide

    Science.gov (United States)

    Navarro, Joan; Coll, Marta; Somes, Christoper J.; Olson, Robert J.

    2013-10-01

    Cephalopods are an important prey resource for fishes, seabirds, and marine mammals, and are also voracious predators on crustaceans, fishes, squid and zooplankton. Because of their high feeding rates and abundance, squids have the potential to exert control on the recruitment of commercially important fishes. In this review, we synthesize the available information for two intrinsic markers (δ15N and δ13C isotopic values) in squids for all oceans and several types of ecosystems to obtain a global view of the trophic niches of squids in marine ecosystems. In particular, we aimed to examine whether the trophic positions and trophic widths of squid species vary among oceans and ecosystem types. To correctly compare across systems, we adjusted squid δ15N values for the isotopic variability of phytoplankton at the base of the food web provided by an ocean circulation-biogeochemistry-isotope model. Studies that focused on the trophic ecology of squids using isotopic techniques were few, and most of the information on squids was from studies on their predators. Our results showed that squids occupy a large range of trophic positions and exploit a large range of trophic resources, reflecting the versatility of their feeding behavior and confirming conclusions from food-web models. Clear differences in both trophic position and trophic width were found among oceans and ecosystem types. The study also reinforces the importance of considering the natural variation in isotopic values when comparing the isotopic values of consumers inhabiting different ecosystems.

  8. General edition program

    International Nuclear Information System (INIS)

    Vaturi, Sylvain

    1969-01-01

    Computerized edition is essential for data processing exploitation. When a more or less complex edition program is required for each task, then the need for a general edition program become obvious. The aim of this study is to create a general edition program. Universal programs are capable to execute numerous and varied tasks. For a more precise processing, the execution of which is frequently required, the use of a specialized program is preferable because, contradictory to the universal program, it goes straight to the point [fr

  9. Effect of the squid viscera hydrolysate on growth performance and digestion in the red sea bream Pagrus major.

    Science.gov (United States)

    Kondo, Fumitaka; Ohta, Takashi; Iwai, Toshiharu; Ido, Atsushi; Miura, Chiemi; Miura, Takeshi

    2017-12-01

    The improvement in feed efficiency is one of the most important subjects in fish culture. The development of feed, in terms of good intake, high growth performance, and high feed efficiency is needed. Squid viscera are one of the candidates for alternative material in improving feed efficiency in fish culture. In the present study, we described the dietary effect of the squid viscera hydrolysate (SVH) on the growth performance of the red sea bream. The addition of SVH to feed caused significant increases in feed intake, fork length, and body weight and produced a marked improvement in feed conversion after 4 weeks of feeding. Furthermore, the results of this feeding revealed that low dietary levels of SVH promote growth performance in the red sea bream. We physiologically analyzed digestion and appetite in fish fed diet containing SVH. SVH promoted the activity of hepatic trypsin and lipase, gene expression of stomach pepsin, hepatic lipase, and pyloric caeca trypsin, thereby improving the nutrient availability in red sea bream. Moreover, the mRNA expression of appetite regulating factor, such as brain NPY and stomach ghrelin was significantly improved by dietary SVH. Our current results indicate that dietary SVH as alternative material produced excellent effects on growth performance, which is dependent on the promoting effect on digestion and appetite in red sea bream.

  10. 76 FR 68642 - Fisheries of the Northeastern United States; Atlantic Mackerel, Squid, and Butterfish Fisheries...

    Science.gov (United States)

    2011-11-07

    ... update to essential fish habitat designations for all life stages of mackerel, longfin squid, Illex squid... issued a mackerel permit may not fish for, possess, or land more than 20,000 lb (9.08 mt) of mackerel per trip, and that, during any closure that occurs after June 1, vessels may not fish for, possess, or land...

  11. [In silico CRISPR-based sgRNA design].

    Science.gov (United States)

    Wang, Yuanli; Chuai, Guohui; Yan, Jifang; Shi, Lei; Liu, Qi

    2017-10-25

    CRISPR-based genome editing has been widely implemented in various cell types. In-silico single guide RNA (sgRNA) design is a key step for successful gene editing using CRISPR system. Continuing efforts are made to refine in-silico sgRNA design with high on-target efficacy and reduced off-target effects. In this paper, we summarize the present sgRNA design tools, and show that efficient in-silico models can be built that integrate current heterogeneous genome-editing data to derive unbiased sgRNA design rules and identify key features for improving sgRNA design. Our review shows that systematic comparisons and evaluation of on-target and off-target effects of sgRNA will allow more precise genome editing and gene therapies using the CRISPR system.

  12. Noise characteristics of a dc SQUID with a resistively shunted inductance

    International Nuclear Information System (INIS)

    Enpuku, K.; Muta, T.; Yoshida, K.; Irie, F.

    1985-01-01

    Noise characteristics of a dc SQUID with an inductance shunted by a damping resistance are studied numerically. It is shown that the damping resistance improves considerably the resolution of the SQUID in the case of large β, where β = 2LI 0 /Phi 0 , I 0 is a critical current, L is a loop inductance and Phi 0 is the flux quantum. The energy resolutions for β = 4 and β = 10 are only about 2 and 4 times larger than that for β = 1, respectively. Furthermore, the ranges of both the bias current and the external flux, where good resolution is obtained, become very wide compared with the conventional SQUID. Therefore, the SQUID with the damping resistance can be used for large β (or L) without the significant degradation of the resolution, and will much improve the coupling properties between the SQUID and the input circuitry. The numerical simulation results are also compared with analytical ones, and a reasonable agreement is obtained

  13. Correlation between fluxgate and SQUID magnetometer data sets for geomagnetic storms

    Directory of Open Access Journals (Sweden)

    Matladi Thabang

    2014-01-01

    Full Text Available There has always been a need to monitor the near Earth's magnetic field, as this monitoring provides understanding and possible predictions of Space Weather events such as geomagnetic storms. Conventional magnetometers such as fluxgates have been used for decades for Space Weather research. The use of highly sensitive magnetometers such as Superconducting QUantum Interference Devices (SQUIDs, promise to give more insight into Space Weather. SQUIDs are relatively recent types of magnetometers that exploit the superconductive effects of flux quantization and Josephson tunneling to measure magnetic flux. SQUIDs have a very broad bandwidth compared to most conventional magnetometers and can measure magnetic flux as low as a few femtotesla. Since SQUIDs have never been used in Space Weather research, unshielded, it is necessary to investigate if they can be reliable Space Weather instruments. The validation is performed by comparing the frequency content of the SQUID and fluxgate magnetometers, as reported by Phiri.

  14. Low-frequency flux noise in YBCO dc SQUIDs cooled in static magnetic fields

    International Nuclear Information System (INIS)

    Sager, M.P.; Bindslev Hansen, J.; Petersen, P.R.E.; Holst, T.; Shen, Y.Q.

    1999-01-01

    The low-frequency flux noise in bicrystal and step-edge YBa 2 Cu 3 O x dc SQUIDs has been investigated. The width, w, of the superconducting strips forming the SQUID frame was varied from 4 to 42 μm. The SQUIDs were cooled in static magnetic fields up to 150 μT. Two types of low-frequency noise dominated, namely 1/f-like noise and random telegraph noise giving a Lorentzian frequency spectrum. The 1/f noise performance of the w = 4, 6 and 7 μm SQUIDs was almost identical, while the SQUIDs with w = 22 and 42 μm showed an order of magnitude higher noise level. Our analysis of the data suggests an exponential increase of the 1/f noise versus the cooling field, exhibiting a characteristic magnetic field around 40 μT. (author)

  15. Robotic 3D SQUID imaging system for practical nondestructive evaluation applications

    International Nuclear Information System (INIS)

    Isawa, K.; Nakayama, S.; Ikeda, M.; Takagi, S.; Tosaka, S.; Kasai, N.

    2005-01-01

    A robotic three-dimensional (3D) scanning superconducting quantum interference device (SQUID) imaging system was developed for practical nondestructive evaluation (NDE) applications. The major feature of this SQUID-NDE system is that the SQUID sensor itself scans in 3D by traveling over the surface of an object during testing without the need for magnetic shielding. This imaging system consists of (i) DC-SQUID gradiometer for effective movement of the sensor, (ii) SQUID sensor manipulator utilizing an articulated-type robot used in industry, (iii) laser charge-coupled-device (CCD) displacement sensor to measure the 3D coordinates of points on the surface of the object, and (iv) computer-aided numerical interpolation scheme for 3D surface reconstruction of the object. The applicability of this system for NDE was demonstrated by successfully detecting artificial damage of cylindrical-shaped steel tubes

  16. Temperature dependence of the effective sensing area of high-Tc dc SQUIDs

    International Nuclear Information System (INIS)

    Brake, H.J.M. ter; Aarnink, W.A.M.; Bosch, P.J. van den; Hilgenkamp, J.W.M.; Flokstra, J.; Rogalla, H.

    1997-01-01

    The effective sensing area of a high-T c dc SQUID depends on temperature. As a consequence, fluctuations in the operating temperature result in apparent magnetic field noise if the SQUID is placed in a background magnetic field. An analysis of this effect for two SQUID types, the square-washer 'Ketchen' type and the inductively shunted type, is performed. For magnetocardiography, the temperature fluctuations (peak to peak) of the latter SQUID type should be below w 0.3 mK at 77 K, and below 2 mK at 55 K, with an earth's field suppression of 40 dB. For the square-washer SQUID the requirements are about 8 times less stringent. (author)

  17. Issues relating to airborne applications of HTS SQUIDs

    CERN Document Server

    Foley, C P; Binks, R A; Lam, S H K; Du, J; Tilbrook, D L; Mitchell, E E; MacFarlane, J C; Lee, J B; Turner, R; Downey, M; Maddever, A

    2002-01-01

    Airborne application of HTS SQUIDs is the most difficult environment for their successful deployment. In order to operate with the sensitivity required for a particular application, there are many issues to be addressed such as the need for very wide dynamic range electronics, motion noise elimination, immunity to large changing magnetic fields and cultural noise sources. This paper reviews what is necessary to achieve an airborne system giving examples in geophysical mineral exploration. It will consider issues relating to device design and fabrication, electronics, dewar design, suspension system requirements and noise elimination methods.

  18. Quantum versus thermally excited fluxoid transitions in a SQUID ring

    International Nuclear Information System (INIS)

    Kurkijaervi, J.

    1980-01-01

    The possibility of quantum tunneling as a mechanism for fluxoid transitions in a SQUID ring is carefully considered neglecting, however, dissipation arising from the quasiparticle current. The tunneling rates are compared with the thermally excited transition rates. The type of experiment Jackel et al. carried out in order to observe the thermal process is analyzed for observing the quantum tunneling. We find the expected result that the temperature at which the quantum process should begin to dominate depends essentially on ω 0 = 1/√LC of the ring. If an underdamped junction with C -13 F can be made the quantum tunneling temperature range should be easy to attain. (orig.)

  19. 3D Inversion of SQUID Magnetic Tensor Data

    DEFF Research Database (Denmark)

    Zhdanov, Michael; Cai, Hongzhu; Wilson, Glenn

    2012-01-01

    Developments in SQUID-based technology have enabled direct measurement of magnetic tensor data for geophysical exploration. For quantitative interpretation, we introduce 3D regularized inversion for magnetic tensor data. For mineral exploration-scale targets, our model studies show that magnetic...... tensor data have significantly improved resolution compared to magnetic vector data for the same model. We present a case study for the 3D regularized inversion of magnetic tensor data acquired over a magnetite skarn at Tallawang, Australia. The results obtained from our 3D regularized inversion agree...

  20. Issues relating to airborne applications of HTS SQUIDs

    International Nuclear Information System (INIS)

    Foley, C P; Leslie, K E; Binks, R A; Lam, S H K; Du, J; Tilbrook, D L; Mitchell, E E; Macfarlane, J C; Lee, J B; Turner, R; Downey, M; Maddever, A

    2002-01-01

    Airborne application of HTS SQUIDs is the most difficult environment for their successful deployment. In order to operate with the sensitivity required for a particular application, there are many issues to be addressed such as the need for very wide dynamic range electronics, motion noise elimination, immunity to large changing magnetic fields and cultural noise sources. This paper reviews what is necessary to achieve an airborne system giving examples in geophysical mineral exploration. It will consider issues relating to device design and fabrication, electronics, dewar design, suspension system requirements and noise elimination methods

  1. Thermal activation and macroscopic quantum tunneling in a DC SQUID

    International Nuclear Information System (INIS)

    Sharifi, F.; Gavilano, J.L.; VanHarlingen, D.J.

    1989-01-01

    The authors report measurements of the transition rate from metastable minima in the two-dimensional 1 of a dc SQUID as a function of applied flux temperature. The authors observe a crossover from energy-activated escape to macroscopic quantum tunneling at a critical temperature. The macroscopic quantum tunneling rate is substantially reduced by damping, and also broadens the crossover region. Most interestingly, the authors observe thermal rates that are suppressed from those predicted by the two-dimensional thermal activation model. The authors discuss possible explanations for this based on the interaction of the macroscopic degree of freedom in the device and energy level effects

  2. Semiautomated improvement of RNA alignments

    DEFF Research Database (Denmark)

    Andersen, Ebbe Sloth; Lind-Thomsen, Allan; Knudsen, Bjarne

    2007-01-01

    connects to external tools to provide a flexible semiautomatic editing environment. A new method, Pcluster, is introduced for dividing the sequences of an RNA alignment into subgroups with secondary structure differences. Pcluster was used to evaluate 574 seed alignments obtained from the Rfam database...... and we identified 71 alignments with significant prediction of inconsistent base pairs and 102 alignments with significant prediction of novel base pairs. Four RNA families were used to illustrate how SARSE can be used to manually or automatically correct the inconsistent base pairs detected by Pcluster......: the mir-399 RNA, vertebrate telomase RNA (vert-TR), bacterial transfer-messenger RNA (tmRNA), and the signal recognition particle (SRP) RNA. The general use of the method is illustrated by the ability to accommodate pseudoknots and handle even large and divergent RNA families. The open architecture...

  3. Flux-coherent series SQUID array magnetometers operating above 77 K with superior white flux noise than single-SQUIDs at 4.2 K

    Science.gov (United States)

    Chesca, Boris; John, Daniel; Mellor, Christopher J.

    2015-10-01

    A very promising direction to improve the sensitivity of magnetometers based on superconducting quantum interference devices (SQUIDs) is to build a series-array of N non-interacting SQUIDs operating flux-coherently, because in this case their voltage modulation depth, ΔV, linearly scales with N whereas the white flux noise SΦ1/2 decreases as 1/N1/2. Here, we report the realization of both these improvements in an advanced layout of very large SQUID arrays made of YBa2Cu3O7. Specially designed with large area narrow flux focusers for increased field sensitivity and improved flux-coherency, our arrays have extremely low values for SΦ1/2 between (0.25 and 0.44) μΦ0/Hz1/2 for temperatures in the range (77-83) K. In this respect, they outperform niobium/aluminium trilayer technology-based single-SQUIDs operating at 4.2 K. Moreover, with values for ΔV and transimpedance in the range of (10-17) mV and (0.3-2.5) kΩ, respectively, a direct connection to a low-noise room temperature amplifier is allowed, while matching for such readout is simplified and the available bandwidth is greatly increased. These landmark performances suggest such series SQUID arrays are ideal candidates to replace single-SQUIDs operating at 4.2 K in many applications.

  4. [CRISPR/CAS9, the King of Genome Editing Tools].

    Science.gov (United States)

    Bannikov, A V; Lavrov, A V

    2017-01-01

    The discovery of CRISPR/Cas9 brought a hope for having an efficient, reliable, and readily available tool for genome editing. CRISPR/Cas9 is certainly easy to use, while its efficiency and reliability remain the focus of studies. The review describes the general principles of the organization and function of Cas nucleases and a number of important issues to be considered while planning genome editing experiments with CRISPR/Cas9. The issues include evaluation of the efficiency and specificity for Cas9, sgRNA selection, Cas9 variants designed artificially, and use of homologous recombination and nonhomologous end joining in DNA editing.

  5. SQUID readout multiplexers for transition-edge sensor arrays

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Adrian T. [Physics Department, University of California, Berkeley, CA 94720 (United States) and Physics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States)]. E-mail: atl@physics.berkeley.edu

    2006-04-15

    Two classes of SQUID multiplexer are being developed for large arrays of cryogenic sensors, distinguished by their operation in either the time domain or frequency domain. Several systems optimized for use with Transition-Edge Sensors (TES) are reaching a high level of maturity, and will be deployed on funded astrophysics experiments in the next several years. A useful technical figure of merit is the product of the number of detectors multplexed multipled by the bandwidth of the detectors, which can be termed the 'total signal bandwidth' of a multiplexer system. This figure of merit is comparable within a factor of two for the mature systems. Several new concepts for increasing the total bandwidth are being developed in the broad class of frequency domain multiplexers. Another notable area of progress is in the level of integration of muliplexer and detector array. The time domain system for SCUBA-II is a sophisticated bump-bonded sandwich structure, and the Jena/MPI group is integrating detectors and a time domain multiplexer on one substrate. Finally, the Kinetic Inductance Detectors (KID)/HEMT (non-SQUID) detector/multiplexer system, will be discussed briefly.

  6. Antibacterial Activity of Melanin from Cuttlefish and Squid Ink

    Directory of Open Access Journals (Sweden)

    Yuspihana Fitrial

    2017-08-01

    Full Text Available Marine environment comprises of many organism which are known to posses bioactive compound as a common means of self-defense or for the protection of eggs and embryos. Class Cephalopods (such as squidand cuttlefish are notable for their defences, such as jetting escape movements, changes in colouration, toxic venom and inking.This study aims to compare the antibacterial activity of melanin from cuttlefish ink (Sepia sp. with squid ink (Loligo sp. against E. coli. Extraction and purification studies were carried out on Sepia and Loligo melanin using a hydrochloric acid 0,5M treatment under mechanical.The melanins were obtained and further evaluated their activity by direct contact methods between melanin and E. coli in nutrient broth.Total microbes was counted by total plate count.Both inks also was tested their activity against E. coli. The results showed that melanin from cuttlefish and squid inks had inhibitory activity at concentrations of 10 mg / ml and 20 mg / mL, respectively reaching 99.99% against E. coli.The inks of both Cephalopods at the same concentration as melanin, did not show any inhibitory activity against E. coli.  The melanin of Sepia sp. have a higher antibacterial activity than the melanin of Loligo sp.

  7. Reduction of environmental MHz noise for SQUID application

    Energy Technology Data Exchange (ETDEWEB)

    Araya, T. [Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531 (Japan)]. E-mail: araya@sup.ee.es.osaka-u.ac.jp; Kitamura, Y. [Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531 (Japan); Kamishiro, M. [Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531 (Japan); Sakuta, K. [Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531 (Japan); Itozaki, H. [Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531 (Japan)]. E-mail: itozaki@ee.es.osaka-u.ac.jp

    2006-10-01

    It is important to remove large environmental noise in measurement using SQUIDs without magnetic shielding. Active noise control (ANC) is an effective method to remove the environmental noise. The environmental noise has been reduced by the ANC system in the radio frequency region around MHz. The anti-phase waves of the environmental noise should be generated by this system. The ANC system including the phase and amplitude control circuit was developed to make the anti-phase waves in the MHz region. In this paper, sinusoidal waves with a MHz frequency were used as the environmental noise. When a coil antenna was used for a receiver antenna, this ANC system suppressed these sinusoidal waves to the white noise level about 40 dB. When we used a SQUID as a receiver antenna, we also cancelled sinusoidal waves to the white noise level by this system. This shows that the ANC system is useful to reduce an environmental noise when this ANC system is developed to cancel multi-frequency noise.

  8. Reduction of environmental MHz noise for SQUID application

    International Nuclear Information System (INIS)

    Araya, T.; Kitamura, Y.; Kamishiro, M.; Sakuta, K.; Itozaki, H.

    2006-01-01

    It is important to remove large environmental noise in measurement using SQUIDs without magnetic shielding. Active noise control (ANC) is an effective method to remove the environmental noise. The environmental noise has been reduced by the ANC system in the radio frequency region around MHz. The anti-phase waves of the environmental noise should be generated by this system. The ANC system including the phase and amplitude control circuit was developed to make the anti-phase waves in the MHz region. In this paper, sinusoidal waves with a MHz frequency were used as the environmental noise. When a coil antenna was used for a receiver antenna, this ANC system suppressed these sinusoidal waves to the white noise level about 40 dB. When we used a SQUID as a receiver antenna, we also cancelled sinusoidal waves to the white noise level by this system. This shows that the ANC system is useful to reduce an environmental noise when this ANC system is developed to cancel multi-frequency noise

  9. Impact of SQUIDs on functional imaging in neuroscience

    International Nuclear Information System (INIS)

    Penna, Stefania Della; Pizzella, Vittorio; Romani, Gian Luca

    2014-01-01

    This paper provides an overview on the basic principles and applications of magnetoencephalography (MEG), a technique that requires the use of many SQUIDs and thus represents one of the most important applications of superconducting electronics. Since the development of the first SQUID magnetometers, it was clear that these devices could be used to measure the ultra-low magnetic signals associated with the bioelectric activity of the neurons of the human brain. Forty years on from the first measurement of magnetic alpha rhythm by David Cohen, MEG has become a fundamental tool for the investigation of brain functions. The simple localization of cerebral sources activated by sensory stimulation performed in the early years has been successively expanded to the identification of the sequence of neuronal pool activations, thus decrypting information of the hierarchy underlying cerebral processing. This goal has been achieved thanks to the development of complex instrumentation, namely whole head MEG systems, allowing simultaneous measurement of magnetic fields all over the scalp with an exquisite time resolution. The latest trends in MEG, such as the study of brain networks, i.e. how the brain organizes itself in a coherent and stable way, are discussed. These sound applications together with the latest technological developments aimed at implementing systems able to record MEG signals and magnetic resonance imaging (MRI) of the head with the same set-up pave the way to high performance systems for brain functional investigation in the healthy and the sick population. (paper)

  10. Selection of tRNA charging quality control mechanisms that increase mistranslation of the genetic code

    DEFF Research Database (Denmark)

    Yadavalli, Srujana S; Ibba, Michael

    2013-01-01

    Mistranslation can follow two events during protein synthesis: production of non-cognate amino acid:transfer RNA (tRNA) pairs by aminoacyl-tRNA synthetases (aaRSs) and inaccurate selection of aminoacyl-tRNAs by the ribosome. Many aaRSs actively edit non-cognate amino acids, but editing mechanisms...

  11. CRISPR Genome Editing

    Science.gov (United States)

    A research article about a technique for gene editing known as CRISPR-Cas9. The technique has made it much easier and faster for cancer researchers to study mutations and test new therapeutic targets.

  12. Temperature-dependent performance of all-NbN DC-SQUID magnetometers

    Science.gov (United States)

    Liu, Quansheng; Wang, Huiwu; Zhang, Qiyu; Wang, Hai; Peng, Wei; Wang, Zhen

    2017-05-01

    Integrated NbN direct current superconducting quantum interference device (DC-SQUID) magnetometers were developed based on high-quality epitaxial NbN/AlN/NbN Josephson junctions for SQUID applications operating at high temperatures. We report the current-voltage and voltage-flux characteristics and the noise performance of the NbN DC-SQUIDs for temperatures ranging from 4.2 to 9 K. The critical current and voltage swing of the DC-SQUIDs decreased by 15% and 25%, respectively, as the temperature was increased from 4.2 to 9 K. The white flux noise of the DC-SQUID magnetometer at 1 kHz increased from 3.9 μΦ0/Hz1/2 at 4.2 K to 4.8 μΦ0/Hz1/2 at 9 K with 23% increase, corresponding to the magnetic field noise of 6.6 and 8.1 fT/Hz1/2, respectively. The results show that NbN DC-SQUIDs improve the tolerance of the operating temperatures and temperature fluctuations in SQUID applications.

  13. Development of an image processing system in splendid squid quality classification

    Science.gov (United States)

    Masunee, Niyada; Chaiprapat, Supapan; Waiyagan, Kriangkrai

    2013-07-01

    Agricultural products typically exhibit high variance in quality characteristics. To assure customer satisfaction and control manufacturing productivity, quality classification is necessary to screen off defective items and to grade the products. This article presents an application of image processing techniques on squid grading and defect discrimination. A preliminary study indicated that surface color was an efficient determinant to justify quality of splendid squids. In this study, a computer vision system (CVS) was developed to examine the characteristics of splendid squids. Using image processing techniques, squids could be classified into three different quality grades as in accordance with an industry standard. The developed system first sifted through squid images to reject ones with black marks. Qualified squids were graded on a proportion of white, pink, and red regions appearing on their bodies by using fuzzy logic. The system was evaluated on 100 images of squids at different quality levels. It was found that accuracy obtained by the proposed technique was 95% compared with sensory evaluation of an expert.

  14. Sensitive YBCO nanoSQUIDs for the investigation of small spin systems

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, Benedikt; Schwarz, Tobias; Woelbing, Roman; Martinez-Perez, Maria Jose; Kleiner, Reinhold; Koelle, Dieter [Tuebingen Univ. (Germany). Physikalisches Inst. and Center for Collective Quantum Phenomena in LISA+; Reiche, Christopher F.; Muehl, Thomas; Buechner, Bernd [Leibniz Institute for Solid State and Materials Research IFW Dresden (Germany)

    2015-07-01

    We report on advances in the realization of dc YBCO nanoSQUIDs for continuous measurement of magnetic nanoparticle magnetization loops in strong magnetic fields up to the Tesla range, applied in the plane of the SQUID loop at temperatures of 4 K and below. Our grain boundary junction based YBCO SQUIDs are patterned by focused ion beam milling and feature a constriction next to the SQUID loop, allowing for on-chip SQUID modulation and bias reversal readout schemes. Using numerical simulations based on London theory, the spin sensitivity S{sub μ}{sup 1/2} = S{sub Φ}{sup 1/2} / φ{sub μ} was improved by optimizing both the flux noise S{sub Φ}{sup 1/2} and the coupling factor φ{sub μ} = Φ / μ (Φ is the magnetic flux coupled into the SQUID loop by a particle with magnetic moment μ). For optimized experimental devices, flux noise levels down to 50 nΦ{sub 0} / Hz{sup 1/2} in the white noise limit have been achieved, corresponding to a calculated spin sensitivity of only a few μ{sub B} / Hz{sup 1/2}. Further, the magnetization reversal of a Fe filled carbon nanotube attached to a YBCO nanoSQUID was traced out.

  15. Neurosurgery. Fourth edition

    International Nuclear Information System (INIS)

    Simon, L.; Thomas, D.G.T.; Clark, W.K.

    1987-01-01

    The Fourth Edition of this volume in the Operative Surgery Series has been considerably revised to accommodate the many changes which have changed the practice of neurosurgery in the past eight years. There have been advances in technology, such as the wider application of CT scanning, in surgical technique, and in the design of new implantable materials. All these developments have substantially affected both the practice of neurosurgery and the prognosis for the patient and are fully reflected in the new edition

  16. Human Germline Genome Editing

    OpenAIRE

    Ormond, Kelly E.; Mortlock, Douglas P.; Scholes, Derek T.; Bombard, Yvonne; Brody, Lawrence C.; Faucett, W. Andrew; Garrison, Nanibaa’ A.; Hercher, Laura; Isasi, Rosario; Middleton, Anna; Musunuru, Kiran; Shriner, Daniel; Virani, Alice; Young, Caroline E.

    2017-01-01

    With CRISPR/Cas9 and other genome-editing technologies, successful somatic and germline genome editing are becoming feasible. To respond, an American Society of Human Genetics (ASHG) workgroup developed this position statement, which was approved by the ASHG Board in March 2017. The workgroup included representatives from the UK Association of Genetic Nurses and Counsellors, Canadian Association of Genetic Counsellors, International Genetic Epidemiology Society, and US National Society of Gen...

  17. Decimal Classification Editions

    Directory of Open Access Journals (Sweden)

    Zenovia Niculescu

    2009-01-01

    Full Text Available The study approaches the evolution of Dewey Decimal Classification editions from the perspective of updating the terminology, reallocating and expanding the main and auxilary structure of Dewey indexing language. The comparative analysis of DDC editions emphasizes the efficiency of Dewey scheme from the point of view of improving the informational offer, through basic index terms, revised and developed, as well as valuing the auxilary notations.

  18. Decimal Classification Editions

    OpenAIRE

    Zenovia Niculescu

    2009-01-01

    The study approaches the evolution of Dewey Decimal Classification editions from the perspective of updating the terminology, reallocating and expanding the main and auxilary structure of Dewey indexing language. The comparative analysis of DDC editions emphasizes the efficiency of Dewey scheme from the point of view of improving the informational offer, through basic index terms, revised and developed, as well as valuing the auxilary notations.

  19. Characteristics of an HTS-SQUID gradiometer with ramp-edge Josephson junctions and its application on robot-based 3D-mobile compact SQUID NDE system

    Energy Technology Data Exchange (ETDEWEB)

    Hatsukade, Y., E-mail: hatukade@ens.tut.ac.jp [Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi 441-8580 (Japan); Hayashi, K.; Shinyama, Y.; Kobayashi, Y. [Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi 441-8580 (Japan); Adachi, S.; Tanabe, K. [International Superconductivity Technology Center/Superconductivity Research Laboratory, 10-13, Shinonome 1-chome, Koto-ku, Tokyo 135-0062 (Japan); Tanaka, S. [Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi 441-8580 (Japan)

    2011-11-15

    We investigated behavior of HTS-dc-SQUID gradiometers with ramp-edge Josephson junctions (JJs) in ac and dc magnetic fields. In the both fields, the gradiometers show higher durability against entry of flux vortices than SQUIDs with bicrystal JJs. A robot-based SQUID NDE system utilizing the gradiometer was developed in an unshielded environment. Detectability of the system to detect non-through cracks in double-layer structures was demonstrated. A new excitation coil was applied to detect cracks that oriented vertical and parallel to the baseline of the gradiometer. In this paper, we investigated detailed behavior of novel HTS-dc-SQUID gradiometers with ramp-edge Josephson junctions (JJs) in both an ac magnetic field and a dc magnetic field. In the both fields, the novel gradiometers shows the superior performance to the conventional YBa{sub 2}Cu{sub 3}O{sub 7-x} (YBCO) HTS-dc-SQUID gradiometer and a bare HTS-dc-SQUID ring with bicrystal JJs concerning durability against entry and hopping of flux vortices, probably due to their differential pickup coils without a grain boundary and multilayer structure of the ramp-edge JJs. A robot-based compact HTS-SQUID NDE system utilizing the novel gradiometer was reviewed, and detectability of the system to detect non-through cracks in a carbon fiber reinforced plastic (CFRP)/Al double-layer structure was demonstrated. A new excitation coil in which the supplied currents flowed in the orthogonal directions was applied to detect cracks that oriented vertical and parallel to the baseline of the gradiometer.

  20. Prospects on the application of HTS SQUID magnetometry to nondestructive evaluation (NDE)

    Science.gov (United States)

    Weinstock, H.

    1993-04-01

    In light of recent advances in the fabrication of low-noise HTS SQUIDs, a review is presented on the use of LTS SQUID magnetometry for nondestructive evaluation (NDE). Examples are given on applications relating to defects in steel, subsurface cracks in aircraft frames, and voids in non-metallic structures. HTS SQUIDs may make a significant difference in the acceptance of these applications because sensing coils will be closer to a sample under test, there will be greater instrument portability and the problem of bringing liquid helium to remote locations will be eliminated.

  1. Radio frequency interference noise reduction using a field programmable gate array for SQUID applications

    International Nuclear Information System (INIS)

    Sakuta, K; Narita, Y; Itozaki, H

    2007-01-01

    It is important to remove large environmental noise in superconducting quantum interference device (SQUID) measurement without magnetic shielding. Active noise control (ANC) is one of the effective methods to reduce environmental noise. Recently, SQUIDs have been used in various applications at high frequencies, such as nuclear quadrupole resonance (NQR). The NQR frequency from explosives is in the range 0.5-5 MHz. In this case, an NQR sensor is exposed to AM radio frequency interference (RFI). The feasibility of the ANC system for RFI that used digital signal processing was studied. Our investigation showed that this digital ANC system can be applied to SQUID measurements for RFI suppression

  2. Mismatch between the eye and the optic lobe in the giant squid.

    Science.gov (United States)

    Liu, Yung-Chieh; Liu, Tsung-Han; Yu, Chun-Chieh; Su, Chia-Hao; Chiao, Chuan-Chin

    2017-07-01

    Giant squids ( Architeuthis ) are a legendary species among the cephalopods. They live in the deep sea and are well known for their enormous body and giant eyes. It has been suggested that their giant eyes are not adapted for the detection of either mates or prey at distance, but rather are best suited for monitoring very large predators, such as sperm whales, at distances exceeding 120 m and at a depth below 600 m (Nilsson et al. 2012 Curr. Biol. 22 , 683-688. (doi:10.1016/j.cub.2012.02.031)). However, it is not clear how the brain of giant squids processes visual information. In this study, the optic lobe of a giant squid ( Architeuthis dux , male, mantle length 89 cm), which was caught by local fishermen off the northeastern coast of Taiwan, was scanned using high-resolution magnetic resonance imaging in order to examine its internal structure. It was evident that the volume ratio of the optic lobe to the eye in the giant squid is much smaller than that in the oval squid ( Sepioteuthis lessoniana ) and the cuttlefish ( Sepia pharaonis ). Furthermore, the cell density in the cortex of the optic lobe is significantly higher in the giant squid than in oval squids and cuttlefish, with the relative thickness of the cortex being much larger in Architeuthis optic lobe than in cuttlefish. This indicates that the relative size of the medulla of the optic lobe in the giant squid is disproportionally smaller compared with these two cephalopod species. This morphological study of the giant squid brain, though limited only to the optic lobe, provides the first evidence to support that the optic lobe cortex, the visual information processing area in cephalopods, is well developed in the giant squid. In comparison, the optic lobe medulla, the visuomotor integration centre in cephalopods, is much less developed in the giant squid than other species. This finding suggests that, despite the giant eye and a full-fledged cortex within the optic lobe, the brain of giant

  3. jSquid: a Java applet for graphical on-line network exploration.

    Science.gov (United States)

    Klammer, Martin; Roopra, Sanjit; Sonnhammer, Erik L L

    2008-06-15

    jSquid is a graph visualization tool for exploring graphs from protein-protein interaction or functional coupling networks. The tool was designed for the FunCoup web site, but can be used for any similar network exploring purpose. The program offers various visualization and graph manipulation techniques to increase the utility for the user. jSquid is available for direct usage and download at http://jSquid.sbc.su.se including source code under the GPLv3 license, and input examples. It requires Java version 5 or higher to run properly. erik.sonnhammer@sbc.su.se Supplementary data are available at Bioinformatics online.

  4. Frequency-domain multiplex with eight-input SQUID and readout electronics over 1MHz

    International Nuclear Information System (INIS)

    Masui, K.; Takei, Y.; Ikeda, H.; Kimura, S.; Mitsuda, K.; Yamasaki, N.Y.

    2006-01-01

    In a magnetic summation method, TES and SQUID driving circuits are isolated and thus small crosstalk and stray impedance are expected. Since a FLL circuit with a large bandwidth and a small noise level is required for a SQUID, we designed and produced an electronics to meet our design of multiplexing with an 8-input SQUID. The FLL circuit achieved an open loop-gain bandwidth product of 8MHz with 1m wire length, which is enough for a TES to be operated with a bias current of 70μA, and a noise level of 30pA/Hz

  5. Step edge Josephson junctions and high temperature superconducting quantum interference device (SQUID) gradiometers

    International Nuclear Information System (INIS)

    Millar, Alasdair J.

    2002-01-01

    This thesis is concerned with the development of Superconducting Quantum Interference Device (SQUID) gradiometers based on the high temperature superconductor YBa 2 Cu 3 O 7-δ (YBCO). A step-edge Josephson junction fabrication process was developed to produce sufficiently steep (>60 deg) step-edges such that junctions exhibited RSJ-like current-voltage characteristics. The mean I C R N product of a sample of twenty step-edge junctions was 130μV. Step-edge dc SQUIDs with inductances between 67pH and 114pH were fabricated. Generally the SQUIDs had an intrinsic white flux noise in the 10-30μΦ 0 /√Hz range, with the best device, a 70pH SQUID, exhibiting a white flux noise of 5μΦ 0 /√Hz. Different first-order SQUID gradiometer designs were fabricated from single layers of YBCO. Two single-layer gradiometer (SLG) designs were fabricated on 10x10mm 2 substrates. The best balance and lowest gradient sensitivity measured for these devices were 1/300 and 308fT/cm√Hz (at 1 kHz) respectively. The larger baseline and larger flux capture area of the pick-up loops in a large area SLG design, fabricated on 30x10mm 2 substrates, resulted in significant improvements in the balance and gradient field sensitivity with 1/1000 and 50fT/cm√Hz (at 1kHz) measured respectively. To reduce the uniform field effective area of SLOs and therefore reduce the direct pick-up of environmental field noise when operated unshielded, a novel gradiometric SQUID (G-SQUID) device was developed. Fabricated from a single layer of YBCO, the G-SQUIDs with inductances of 67pH, had small uniform field effective areas of approximately 2μm 2 - more than two orders of magnitude smaller than the uniform field effective areas of conventional narrow linewidth SQUIDs of similar inductance. Two designs of G-SQUID were fabricated on 10x10mm 2 substrates. Due to their small effective areas, when cooled unshielded these devices showed no increase in their white flux noise. The best balance achieved for a G-SQUID

  6. Integrative omics analysis reveals differentially distributed proteins in dimorphic euspermatozoa of the squid, Loligo bleekeri.

    Science.gov (United States)

    Yoshida, Masa-aki; Yamada, Lixy; Ochi, Hiroe; Iwata, Yoko; Tamura-Nakano, Miwa; Sawada, Hitoshi; Sauer, Warwick H H; Ogura, Atsushi; Hirohashi, Noritaka

    2014-08-01

    In the coastal squid Loligo bleekeri, each male produces one of two types of fertilization-competent spermatozoa (eusperm) that exhibit morphological and behavioral differences. Large "consort" males produce short-tailed spermatozoa that display free-swimming behavior when ejaculated into seawater. Small "sneaker" males, on the other hand, produce long-tailed spermatozoa that exhibit a self-swarming trait after ejaculation. To understand the molecular basis for adaptive traits employed by alternative male mating tactics, we performed the transcriptome deep sequencing (RNA-seq) and proteome analyses to search for differences in testicular mRNAs and sperm proteins, respectively. From mature male testes we identified a total of 236,455 contigs (FPKM ≧1) where 3789 and 2789 were preferentially (≧10-fold) expressed in consort and sneaker testes, respectively. A proteomic analysis detected 4302 proteins in the mature sperm as post-translational products. A strongly biased (≧10-fold) distribution occurred in 55 consort proteins and 61 sneaker proteins. There was no clear mRNA-protein correlation, making a ballpark estimate impossible for not only overall protein abundance but also the degree of biased sperm type expressed in the spermatozoa. A family encoding dynein heavy chain gene, however, was found to be biased towards sneakers, whereas many enzymes involving energy metabolism were heavily biased towards consort spermatozoa. The difference in flagellar length matched exactly the different amount of tubulins. From these results we hypothesize that discrete differential traits in dimorphic eusperm arose from a series of innovative alterations in the intracellular components of spermatozoa. Copyright © 2014 Elsevier Inc. All rights reserved.

  7. Magnetic imaging of unconventional superconductors by scanning SQUID microscopy

    International Nuclear Information System (INIS)

    Hykel, D.

    2011-01-01

    We present the development of a scanning SQUID/AFM microscope and measurements performed on different samples. The microscope can take topographic and magnetic images simultaneously. The magnetic resolution is of the order of 10 -4 Φ 0 √Hz and the spatial resolution of the SQUIDs used in this thesis goes up to 600 nm. The scanning range is 70 μm * 85 μm. The temperature range accessible is between 200 mK and 10 K at the time of writing. Measurements on a thin rhenium film (80 nm) give an estimate of the minimal pinning force of a vortex of about 3.9 * 10 -16 N. Furthermore, the penetration depth λ on this sample was determined as a function of temperature. For T → 0, λ →79 nm. We have for the first time shown local measurements of the domain structure of the superconducting ferromagnet UCoGe and determined the average domain size in the virgin state (10 μm). By magnetic imaging we were capable of determining the magnetic field difference above opposite domains along the c-axis to be 45 G and 16 G along the b-axis. Due to these magnetic field measurements we were able to give an upper limit for the domain wall width (∼ 1μm) and domain reconstruction depth (100 nm). This is supported by simple calculations leading to a domain wall width of several angstroms. Thus UCoGe can be considered an ideal Ising ferromagnet. Different possible domain structures for an Ising ferromagnet have been discussed. The complicated domain structure found in the zero field cooled virgin state corresponds to up domains embedded in larger down domains and vice versa. We have shown evidence for coexistence of superconductivity and ferromagnetism. The weak Meissner effect can be explained by a spontaneous vortex state, put forward by other groups. Numerical simulations suggest that the strong magnetic background signal and the limited spatial and magnetic resolution of the used SQUID made it difficult to resolve the expected spontaneous vortex state. The relaxation of the

  8. Engineered Viruses as Genome Editing Devices

    Science.gov (United States)

    Chen, Xiaoyu; Gonçalves, Manuel A F V

    2016-01-01

    Genome editing based on sequence-specific designer nucleases, also known as programmable nucleases, seeks to modify in a targeted and precise manner the genetic information content of living cells. Delivering into cells designer nucleases alone or together with donor DNA templates, which serve as surrogate homologous recombination (HR) substrates, can result in gene knockouts or gene knock-ins, respectively. As engineered replication-defective viruses, viral vectors are having an increasingly important role as delivery vehicles for donor DNA templates and designer nucleases, namely, zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered, regularly interspaced, short palindromic repeats (CRISPR)-associated Cas9 (CRISPR−Cas9) nucleases, also known as RNA-guided nucleases (RGNs). We review this dual role played by engineered viral particles on genome editing while focusing on their main scaffolds, consisting of lentiviruses, adeno-associated viruses, and adenoviruses. In addition, the coverage of the growing body of research on the repurposing of viral vectors as delivery systems for genome editing tools is complemented with information regarding their main characteristics, pros, and cons. Finally, this information is framed by a concise description of the chief principles, tools, and applications of the genome editing field as a whole. PMID:26336974

  9. Genome Editing in Sugarcane: Challenges ahead

    Directory of Open Access Journals (Sweden)

    Chakravarthi Mohan

    2016-10-01

    Full Text Available Genome editing opens new and unique opportunities for researchers to enhance crop production. Until 2013, the zinc finger nucleases (ZFNs and transcription activator-like effector nucleases (TALENs were the key tools used for genome editing applications. The advent of RNA-guided engineered nucleases - the type II clustered regularly interspaced short palindromic repeat (CRISPR/Cas9 (CRISPR-associated system from Streptococcus pyogenes holds great potential since it is simple, effective and more versatile than ZFNs and TALENs. CRISPR/Cas9 system has already been successfully employed in several crop plants. Use of these techniques is in its infant stage in sugarcane. Jung and Altpeter (2016 have reported TALEN mediated approach for the first time to reduce lignin content in sugarcane to make it amenable for biofuel production. This is so far the only report describing genome editing in sugarcane. Large genome size, polyploidy, low transformation efficiency, transgene silencing and lack of high throughput screening techniques are certainly great challenges for genome editing in sugarcane which would be discussed in detail in this review.

  10. In Silico Meets In Vivo: Towards Computational CRISPR-Based sgRNA Design.

    Science.gov (United States)

    Chuai, Guo-Hui; Wang, Qi-Long; Liu, Qi

    2017-01-01

    CRISPR-based genome editing has been widely implemented in various cell types. In silico single guide RNA (sgRNA) design is a key step for successful gene editing using the CRISPR system, and continuing efforts are aimed at refining in silico sgRNA design with high on-target efficacy and reduced off-target effects. Many sgRNA design tools are available, but careful assessments of their application scenarios and performance benchmarks across different types of genome-editing data are needed. Efficient in silico models can be built that integrate current heterogeneous genome-editing data to derive unbiased sgRNA design rules and identify key features for improving sgRNA design. Comprehensive evaluation of on-target and off-target effects of sgRNA will allow more precise genome editing and gene therapies using the CRISPR system. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Multichannel DC SQUID sensor array for biomagnetic applications

    International Nuclear Information System (INIS)

    Hoenig, H.E.; Daalmans, G.M.; Bar, L.; Bommel, F.; Paulus, A.; Uhl, D.; Weisse, H.J.; Schneider, S.; Seifert, H.; Reichenberger, H.; Abraham-Fuchs, K.

    1991-01-01

    This paper reports on a biomagnetic multichannel system for medical diagnosis of brain and heart KRENIKON has been developed. 37 axial 2st order gradiometers - manufactured as flexible superconducting printed circuits - are arranged in a circular flat array of 19 cm diameter. Additionally, 3 orthogonal magnetometers are provided. The DC SQUIDs are fabricated in all-Nb technology, ten on a chip. The sensor system is operated in a shielded room with two layers of soft magnetic material and one layer of Al. The every day noise level is 10 fT/Hz 1/2 at frequencies above 10 Hz. Within 2 years of operation in a normal urban surrounding, useful clinical applications have been demonstrated (e.g. for epilepsy and heart arrhythmias)

  12. Detection of Rapid Atrial Arrhythmias in SQUID Magnetocardiography

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Ki Woong; Kwon, Hyuk Chan; Kim, Ki Dam; Lee, Yong Ho; Kim, Jin Mok; Kim, In Seon; Lim, Hyun Kyoon; Park, Yong Ki [Biomagnetism Research, Korea Research Institute of Standards and Science, Daejeon (Korea, Republic of); Kim, Doo Sang [Seoul Veterans Hospital, Seoul (Korea, Republic of); Lim, Seung Pyung [Chungnam National University Hospital, Daejeon (Korea, Republic of)

    2005-10-15

    We propose a method to measure atrial arrhythmias (AA) such as atrial fibrillation (Afb) and atrial flutter (Afl) with a SQUID magnetocardiograph (MCG) system. To detect AA is one of challenging topics in MCG. As the AA generally have irregular rhythm and atrio-ventricular conduction, the MCG signal cannot be improved by QRS averaging; therefore a SQUID MCG system having a high SNR is required to measure informative atrial excitation with a single scan. In the case of Afb, diminished f waves are much smaller than normal P waves because the sources are usually located on the posterior wall of the heart. In this study, we utilize an MCG system measuring tangential field components, which is known to be more sensitive to a deeper current source. The average noise spectral density of the whole system in a magnetic shielded room was 10 fT/Hz(a) 1 Hz and 5 fT/Hz(a) 100 Hz. We measured the MCG signals of patients with chronic Afb and Afl. Before the AA measurement, the comparison between the measurements in supine and prone positions for P waves has been conducted and the experiment gave a result that the supine position is more suitable to measure the atrial excitation. Therefore, the AA was measured in subject's supine position. Clinical potential of AA measurement in MCG is to find an aspect of a reentry circuit and to localize the abnormal stimulation noninvasively. To give useful information about the abnormal excitation, we have developed a method, separative synthetic aperture magnetometry (sSAM). The basic idea of sSAM is to visualize current source distribution corresponding to the atrial excitation, which are separated from the ventricular excitation and the Gaussian sensor noises. By using sSAM, we localized the source of an Afl successfully.

  13. SQUID-detected magnetic resonance imaging in microtesla magnetic fields

    International Nuclear Information System (INIS)

    McDermott, Robert; Kelso, Nathan; Lee, SeungKyun; Moessle, Michael; Mueck, Michael; Myers, Whittier; Haken, Bernard ten; Seton, H.C.; Trabesinger, Andreas H.; Pines, Alex; Clarke, John

    2003-01-01

    We describe studies of nuclear magnetic resonance (NMR) spectroscopy and magnetic resonance imaging (MRI) of liquid samples at room temperature in microtesla magnetic fields. The nuclear spins are prepolarized in a strong transient field. The magnetic signals generated by the precessing spins, which range in frequency from tens of Hz to several kHz, are detected by a low-transition temperature dc SQUID (Superconducting QUantum Interference Device) coupled to an untuned, superconducting flux transformer configured as an axial gradiometer. The combination of prepolarization and frequency-independent detector sensitivity results in a high signal-to-noise ratio and high spectral resolution (∼1 Hz) even in grossly inhomogeneous magnetic fields. In the NMR experiments, the high spectral resolution enables us to detect the 10-Hz splitting of the spectrum of protons due to their scalar coupling to a 31P nucleus. Furthermore, the broadband detection scheme combined with a non-resonant field-reversal spin echo allows the simultaneous observation of signals from protons and 31P nuclei, even though their NMR resonance frequencies differ by a factor of 2.5. We extend our methodology to MRI in microtesla fields, where the high spectral resolution translates into high spatial resolution. We demonstrate two-dimensional images of a mineral oil phantom and slices of peppers, with a spatial resolution of about 1 mm. We also image an intact pepper using slice selection, again with 1-mm resolution. In further experiments we demonstrate T1-contrast imaging of a water phantom, some parts of which were doped with a paramagnetic salt to reduce the longitudinal relaxation time T1. Possible applications of this MRI technique include screening for tumors and integration with existing multichannel SQUID systems for brain imaging

  14. Editing Audio with Audacity

    Directory of Open Access Journals (Sweden)

    Brandon Walsh

    2016-08-01

    Full Text Available For those interested in audio, basic sound editing skills go a long way. Being able to handle and manipulate the materials can help you take control of your object of study: you can zoom in and extract particular moments to analyze, process the audio, and upload the materials to a server to compliment a blog post on the topic. On a more practical level, these skills could also allow you to record and package recordings of yourself or others for distribution. That guest lecture taking place in your department? Record it and edit it yourself! Doing so is a lightweight way to distribute resources among various institutions, and it also helps make the materials more accessible for readers and listeners with a wide variety of learning needs. In this lesson you will learn how to use Audacity to load, record, edit, mix, and export audio files. Sound editing platforms are often expensive and offer extensive capabilities that can be overwhelming to the first-time user, but Audacity is a free and open source alternative that offers powerful capabilities for sound editing with a low barrier for entry. For this lesson we will work with two audio files: a recording of Bach’s Goldberg Variations available from MusOpen and another recording of your own voice that will be made in the course of the lesson. This tutorial uses Audacity 2.1.2, released January 2016.

  15. SQUID-Detected Magnetic Resonance Imaging in MicroteslaFields

    Energy Technology Data Exchange (ETDEWEB)

    Moessle, Michael; Hatridge, Michael; Clarke, John

    2006-08-14

    amplitude in MRI using laser polarized noble gases such as {sup 3}He or {sup 129}Xe (10-12). Hyperpolarized gases were used successfully to image the human lung in fields on the order of several mT (13-15). To overcome the sensitivity loss of Faraday detection at low frequencies, ultrasensitive magnetometers based on the Superconducting QUantum Interference Device (SQUID) (16) are used to detect NMR and MRI signals (17-24). Recently, SQUID-based MRI systems capable of acquiring in vivo images have appeared. For example, in the 10-mT system of Seton et al. (18) signals are coupled to a SQUID via a superconducting tuned circuit, while Clarke and coworkers (22, 25, 26) developed a system at 132 {micro}T with an untuned input circuit coupled to a SQUID. In a quite different approach, atomic magnetometers have been used recently to detect the magnetization (27) and NMR signal (28) of hyperpolarized gases. This technique could potentially be used for low-field MRI in the future. The goal of this review is to summarize the current state-of-the-art of MRI in microtesla fields detected with SQUIDs. The principles of SQUIDs and NMR are briefly reviewed. We show that very narrow NMR linewidths can be achieved in low magnetic fields that are quite inhomogeneous, with illustrative examples from spectroscopy. After describing our ultralow-field MRI system, we present a variety of images. We demonstrate that in microtesla fields the longitudinal relaxation T{sub 1} is much more material dependent than is the case in high fields; this results in a substantial improvement in 'T{sub 1}-weighted contrast imaging'. After outlining the first attempts to combine microtesla NMR with magnetoencephalography (MEG) (29), we conclude with a discussion of future directions.

  16. Imaging of current density distributions with a Nb weak-link scanning nano-SQUID microscope

    Science.gov (United States)

    Shibata, Yusuke; Nomura, Shintaro; Kashiwaya, Hiromi; Kashiwaya, Satoshi; Ishiguro, Ryosuke; Takayanagi, Hideaki

    2015-10-01

    Superconducting quantum interference devices (SQUIDs) are accepted as one of the highest magnetic field sensitive probes. There are increasing demands to image local magnetic fields to explore spin properties and current density distributions in a two-dimensional layer of semiconductors or superconductors. Nano-SQUIDs have recently attracting much interest for high spatial resolution measurements in nanometer-scale samples. Whereas weak-link Dayem Josephson junction nano-SQUIDs are suitable to miniaturization, hysteresis in current-voltage (I-V) characteristics that is often observed in Dayem Josephson junction is not desirable for a scanning microscope. Here we report on our development of a weak-link nano-SQUIDs scanning microscope with small hysteresis in I-V curve and on reconstructions of two-dimensional current density vector in two-dimensional electron gas from measured magnetic field.

  17. Technology for SQUID systems for the application in magnetically disturbed environment. Final report

    International Nuclear Information System (INIS)

    Schultze, V.; Fritzsch, L.; Thrum, F.; Stolz, R.; Chwala, A.

    1996-06-01

    International available SQUID systems, as used for example in biomagnetic research, obtain high sensitivities for magnetic fields or magnetic fieldgradients. However, these systems were optimised for operation in magnetically shielded rooms. Goal of this project was to develop SQUIDs suppressing the external noise and therefore are able to operate without external shielding in normal environments. As a consequence, the required Nb/AlO x /Nb technology has also been developed. The resulting planar SQUID gradiometers as produced at the IPHT, reached a suppression of homogeneous fields up to 5 x 10 4 for a magnetic field sensitivity c , project. SQUID gradiometers, produced using YBCO technology, were successfully operated in non shielded eddy current NDE measurements in the lab. (orig.) [de

  18. Growth of juvenile shrimp Metapenaeus monoceros fed with squid and mussel

    Digital Repository Service at National Institute of Oceanography (India)

    Achuthankutty, C.T.; Nair, S.R.S.; Krishnakumari, L.

    Small juveniles of both sexes and females of large juveniles of Metapenaeus monoceros attained faster growth with squid diet. Males of large juveniles registered better growth with mussel diet. No significant difference was observed in moult weights...

  19. High-T /SUB c/ Superconducting integrated circuit: a dc SQUID with input coil

    International Nuclear Information System (INIS)

    Di Iorio, M.S.; Beasley, M.R.

    1985-01-01

    We have fabricated a high transition temperature superconducting integrated circuit consisting of a dc SQUID and an input coupling coil. The purpose is to ascertain the generic problems associated with constructing a high-T /SUB c/ circuit as well as to fabricate a high performance dc SQUID. The superconductor used for both the SQUID and the input coil is Nb 3 Sn which must be deposited at 800 0 C. Importantly, the insulator separating SQUID and input coil maintains its integrity at this elevated temperature. A hole in the insulator permits contact to the innermost winding of the coil. This contact has been achieved without significant degradation of the superconductivity. Consequently, the device operates over a wide temperature range, from below 4.2 K to near T /SUB c/

  20. Performance of a novel SQUID-based superconducting imaging-surface magnetoencephalography system

    Science.gov (United States)

    Kraus, R. H.; Volegov, P.; Maharajh, K.; Espy, M. A.; Matlashov, A. N.; Flynn, E. R.

    2002-03-01

    Performance for a recently completed whole-head magnetoencephalography system using a superconducting imaging surface (SIS) surrounding an array of 150 SQUID magnetometers is reported. The helmet-like SIS is hemispherical in shape with a brim. Conceptually, the SIS images nearby sources onto the SQUIDs while shielding sensors from distant “noise” sources. A finite element method (FEM) description using the as-built geometry was developed to describe the SIS effect on source fields by imposing B⊥( surface)=0 . Sensors consist of 8×8 mm 2 SQUID magnetometers with 0.84 nT/ Φ0 sensitivity and positions and orientations was found. Good agreement was found between modeled and measured shielding of the SQUIDs from sources external to the array showing significant frequency-independent shielding. Phantom localization precision was better than 0.5 mm at all locations with a mean of better than 0.3 mm.

  1. Development of a Flow-Through SQUID System for Non-Destructive Evaluation of MRI Wire

    National Research Council Canada - National Science Library

    Wellstood, Frederick C

    2007-01-01

    ...) superconducting quantum interference device (SQUID) system. The ability to detect small defects in km-long sections of NbTi magnet wire could improve the production yield of high-field magnets for power and medical applications...

  2. Analysis of the ac SQUID with low inductance and low critical current

    DEFF Research Database (Denmark)

    Sørensen, O. H.

    1976-01-01

    The properties of the ac SQUID magnetometer has been analyzed. The results are valid in the low-inductance low-critical-current regime, where the Lri0 producted is belowthe value at which the relation between the enclosed and externally applied magnetic dc flux becomes reentrant. The effects...... of the screening current circulating in the SQUID ring as well as of the SQUID-ring time constant, tau-Lr/R9 are taken into account. Here LR IS THE SQUID-ring inductance, and R is the shunt resistance in the shunted junction model assumed to describe the weak link. It is shown that for finite values of omegatau...... constriuctively with the result that the optimal response occurs at a definite and finite value of omegatau. If omegatau is increased beyond this optimal value the weak link behavior is dominated by the Ohmic current channel implying that only if the shunt conductance contains a term depending...

  3. 76 FR 66260 - Fisheries of the Northeastern United States; Atlantic Mackerel, Squid, and Butterfish Fisheries...

    Science.gov (United States)

    2011-10-26

    ...) of scup, 184,280 lb (83,588 kg) of black sea bass, and 200,000 lb (90,718 kg) of bluefish. Project... summer flounder, scup, black sea bass, longfin squid, butterfish, and Atlantic bluefish, and assessment...

  4. The bases for the development of high-temperature integrated SQUID-systems

    International Nuclear Information System (INIS)

    Polushkin, V.N.

    1992-01-01

    The current state of high-T c superconducting thin-film Josephson junctions and SQUIDs developing is reviewed. The prospects of application of new devices in supersensitive measurement apparatus are analyzed. It is shown that high T c SQUIDs are able seriously to influence further development of information and measurement engineering as on their base the series of microelectronic elements and devices of new generation can be built. 55 refs.; 7 figs.; 2 tabs

  5. The bases for the development of high-temperature integrated squid-systems

    International Nuclear Information System (INIS)

    Polushkin, V.N.

    1992-01-01

    The current state of high-Tc superconducting thinfilm Josepson junctions and SQUIDs developing is reviewed. The prospects of application of new devices in supersensitive measurement apparatus are analyzed. It is shown that high T c SQUIDs are able seriously to influence further development of information and measurement engineering as on their base the series of microelectronic elements and devices of new generation can be built. 84 refs.; 16 figs.; 3 tabs

  6. Targeted CRISPR disruption reveals a role for RNase MRP RNA in human preribosomal RNA processing.

    Science.gov (United States)

    Goldfarb, Katherine C; Cech, Thomas R

    2017-01-01

    MRP RNA is an abundant, essential noncoding RNA whose functions have been proposed in yeast but are incompletely understood in humans. Mutations in the genomic locus for MRP RNA cause pleiotropic human diseases, including cartilage hair hypoplasia (CHH). Here we applied CRISPR-Cas9 genome editing to disrupt the endogenous human MRP RNA locus, thereby attaining what has eluded RNAi and RNase H experiments: elimination of MRP RNA in the majority of cells. The resulting accumulation of ribosomal RNA (rRNA) precursor-analyzed by RNA fluorescent in situ hybridization (FISH), Northern blots, and RNA sequencing-implicates MRP RNA in pre-rRNA processing. Amelioration of pre-rRNA imbalance is achieved through rescue of MRP RNA levels by ectopic expression. Furthermore, affinity-purified MRP ribonucleoprotein (RNP) from HeLa cells cleaves the human pre-rRNA in vitro at at least one site used in cells, while RNP isolated from cells with CRISPR-edited MRP loci loses this activity, and ectopic MRP RNA expression restores cleavage activity. Thus, a role for RNase MRP in human pre-rRNA processing is established. As demonstrated here, targeted CRISPR disruption is a valuable tool for functional studies of essential noncoding RNAs that are resistant to RNAi and RNase H-based degradation. © 2017 Goldfarb and Cech; Published by Cold Spring Harbor Laboratory Press.

  7. Precision genome editing

    DEFF Research Database (Denmark)

    Steentoft, Catharina; Bennett, Eric P; Schjoldager, Katrine Ter-Borch Gram

    2014-01-01

    Precise and stable gene editing in mammalian cell lines has until recently been hampered by the lack of efficient targeting methods. While different gene silencing strategies have had tremendous impact on many biological fields, they have generally not been applied with wide success in the field...... of glycobiology, primarily due to their low efficiencies, with resultant failure to impose substantial phenotypic consequences upon the final glycosylation products. Here, we review novel nuclease-based precision genome editing techniques enabling efficient and stable gene editing, including gene disruption...... by introducing single or double-stranded breaks at a defined genomic sequence. We here compare and contrast the different techniques and summarize their current applications, highlighting cases from the field of glycobiology as well as pointing to future opportunities. The emerging potential of precision gene...

  8. Human Germline Genome Editing.

    Science.gov (United States)

    Ormond, Kelly E; Mortlock, Douglas P; Scholes, Derek T; Bombard, Yvonne; Brody, Lawrence C; Faucett, W Andrew; Garrison, Nanibaa' A; Hercher, Laura; Isasi, Rosario; Middleton, Anna; Musunuru, Kiran; Shriner, Daniel; Virani, Alice; Young, Caroline E

    2017-08-03

    With CRISPR/Cas9 and other genome-editing technologies, successful somatic and germline genome editing are becoming feasible. To respond, an American Society of Human Genetics (ASHG) workgroup developed this position statement, which was approved by the ASHG Board in March 2017. The workgroup included representatives from the UK Association of Genetic Nurses and Counsellors, Canadian Association of Genetic Counsellors, International Genetic Epidemiology Society, and US National Society of Genetic Counselors. These groups, as well as the American Society for Reproductive Medicine, Asia Pacific Society of Human Genetics, British Society for Genetic Medicine, Human Genetics Society of Australasia, Professional Society of Genetic Counselors in Asia, and Southern African Society for Human Genetics, endorsed the final statement. The statement includes the following positions. (1) At this time, given the nature and number of unanswered scientific, ethical, and policy questions, it is inappropriate to perform germline gene editing that culminates in human pregnancy. (2) Currently, there is no reason to prohibit in vitro germline genome editing on human embryos and gametes, with appropriate oversight and consent from donors, to facilitate research on the possible future clinical applications of gene editing. There should be no prohibition on making public funds available to support this research. (3) Future clinical application of human germline genome editing should not proceed unless, at a minimum, there is (a) a compelling medical rationale, (b) an evidence base that supports its clinical use, (c) an ethical justification, and (d) a transparent public process to solicit and incorporate stakeholder input. Copyright © 2017 American Society of Human Genetics. All rights reserved.

  9. Simple Genome Editing of Rodent Intact Embryos by Electroporation.

    Directory of Open Access Journals (Sweden)

    Takehito Kaneko

    Full Text Available The clustered regularly interspaced short palindromic repeat (CRISPR/CRISPR-associated (Cas system is a powerful tool for genome editing in animals. Recently, new technology has been developed to genetically modify animals without using highly skilled techniques, such as pronuclear microinjection of endonucleases. Technique for animal knockout system by electroporation (TAKE method is a simple and effective technology that produces knockout rats by introducing endonuclease mRNAs into intact embryos using electroporation. Using TAKE method and CRISPR/Cas system, the present study successfully produced knockout and knock-in mice and rats. The mice and rats derived from embryos electroporated with Cas9 mRNA, gRNA and single-stranded oligodeoxynucleotide (ssODN comprised the edited targeted gene as a knockout (67% of mice and 88% of rats or knock-in (both 33%. The TAKE method could be widely used as a powerful tool to produce genetically modified animals by genome editing.

  10. Squid-derived chitin oligosaccharides are a chemotactic signal during colonization by Vibrio fischeri.

    Science.gov (United States)

    Mandel, Mark J; Schaefer, Amy L; Brennan, Caitlin A; Heath-Heckman, Elizabeth A C; Deloney-Marino, Cindy R; McFall-Ngai, Margaret J; Ruby, Edward G

    2012-07-01

    Chitin, a polymer of N-acetylglucosamine (GlcNAc), is noted as the second most abundant biopolymer in nature. Chitin serves many functions for marine bacteria in the family Vibrionaceae ("vibrios"), in some instances providing a physical attachment site, inducing natural genetic competence, and serving as an attractant for chemotaxis. The marine luminous bacterium Vibrio fischeri is the specific symbiont in the light-emitting organ of the Hawaiian bobtail squid, Euprymna scolopes. The bacterium provides the squid with luminescence that the animal uses in an antipredatory defense, while the squid supports the symbiont's nutritional requirements. V. fischeri cells are harvested from seawater during each host generation, and V. fischeri is the only species that can complete this process in nature. Furthermore, chitin is located in squid hemocytes and plays a nutritional role in the symbiosis. We demonstrate here that chitin oligosaccharides produced by the squid host serve as a chemotactic signal for colonizing bacteria. V. fischeri uses the gradient of host chitin to enter the squid light organ duct and colonize the animal. We provide evidence that chitin serves a novel function in an animal-bacterial mutualism, as an animal-produced bacterium-attracting synomone.

  11. Editing faces in videos

    OpenAIRE

    Amberg, Brian

    2011-01-01

    Editing faces in movies is of interest in the special effects industry. We aim at producing effects such as the addition of accessories interacting correctly with the face or replacing the face of a stuntman with the face of the main actor. The system introduced in this thesis is based on a 3D generative face model. Using a 3D model makes it possible to edit the face in the semantic space of pose, expression, and identity instead of pixel space, and due to its 3D nature allows...

  12. Genome editing: The efficient tool CRISPR–Cpf1

    KAUST Repository

    Mahfouz, Magdy M.

    2017-01-01

    The novel features of the CRISPR–Cpf1 RNA-guided endonuclease system facilitate precise and efficient genome engineering. Application of CRISPR–Cpf1 in plants shows promise for robust gene editing and regulation, opening exciting possibilities for targeted trait improvement in crops.

  13. Genome editing: The efficient tool CRISPR–Cpf1

    KAUST Repository

    Mahfouz, Magdy M.

    2017-03-01

    The novel features of the CRISPR–Cpf1 RNA-guided endonuclease system facilitate precise and efficient genome engineering. Application of CRISPR–Cpf1 in plants shows promise for robust gene editing and regulation, opening exciting possibilities for targeted trait improvement in crops.

  14. Systematic identification of edited microRNAs in the human brain

    Science.gov (United States)

    Alon, Shahar; Mor, Eyal; Vigneault, Francois; Church, George M.; Locatelli, Franco; Galeano, Federica; Gallo, Angela; Shomron, Noam; Eisenberg, Eli

    2012-01-01

    Adenosine-to-inosine (A-to-I) editing modifies RNA transcripts from their genomic blueprint. A prerequisite for this process is a double-stranded RNA (dsRNA) structure. Such dsRNAs are formed as part of the microRNA (miRNA) maturation process, and it is therefore expected that miRNAs are affected by A-to-I editing. Editing of miRNAs has the potential to add another layer of complexity to gene regulation pathways, especially if editing occurs within the miRNA–mRNA recognition site. Thus, it is of interest to study the extent of this phenomenon. Current reports in the literature disagree on its extent; while some reports claim that it may be widespread, others deem the reported events as rare. Utilizing a next-generation sequencing (NGS) approach supplemented by an extensive bioinformatic analysis, we were able to systematically identify A-to-I editing events in mature miRNAs derived from human brain tissues. Our algorithm successfully identified many of the known editing sites in mature miRNAs and revealed 17 novel human sites, 12 of which are in the recognition sites of the miRNAs. We confirmed most of the editing events using in vitro ADAR overexpression assays. The editing efficiency of most sites identified is very low. Similar results are obtained for publicly available data sets of mouse brain-regions tissues. Thus, we find that A-to-I editing does alter several miRNAs, but it is not widespread. PMID:22499667

  15. Expression of MDM2 mRNA, MDM2, P53 and P16 Proteins in Urothelial Lesions in the View of the WHO 4th Edition Guidelines as A Molecular Insight towards Personalized Medicine

    Directory of Open Access Journals (Sweden)

    Olfat Hammam

    2017-08-01

    Full Text Available AIM: Here we imposed a multimarker molecular panel composed of P53, MDM2 protein & mRNA & P16 with the identification of sensitive and specific cut offs among the Egyptian urothelial carcinomas bilharzial or not emphasize the pathological and molecular classifications, pathways and prognosis as a privilege for adjuvant therapy. METHODS: Three hundred and ten urothelial lesions were pathologically evaluated and grouped as follows: 50 chronic cystitis as benign, 240 urothelial carcinomas and 20 normal bladder tissue as a control. Immunohistochemistry for MDM Protein, P16 & p53 and In Situ Hybridization for MDM2mRNA were done. RESULTS: MDM2mRNA overexpression correlated with low grade low stage non invasive tumors, while P53 > 40% & p16 40% & P16 10% from high grade, high stage invasive urothelial carcinomas (with p53 > 40, p16 40 & p16 < 10%, together with the histopathological features can distinguish in situ urothelial lesions from dysplastic and atypical lesions.

  16. Influence of inductance induced noise in an YBa2Cu3O7 dc-SQUID at high operation temperatures

    DEFF Research Database (Denmark)

    Nilsson, P. Å.; Claeson, T.; Hansen, J. B.

    1994-01-01

    The voltage modulation depth of a high T(c) dc-SQUID was measured at temperatures close to T(c) and compared to a model by Enpuku et al. where the flux noise from the SQUID inductance is taken into account. The device was an YBa2Cu3O7 dc-SQUID made on a bicrystal substrate of SrTiO3. The design w...

  17. Apparatus and method for detecting a magnetic anomaly contiguous to remote location by SQUID gradiometer and magnetometer systems

    Science.gov (United States)

    Overton, W.C. Jr.; Steyert, W.A. Jr.

    1981-05-22

    A superconducting quantum interference device (SQUID) magnetic detection apparatus detects magnetic fields, signals, and anomalies at remote locations. Two remotely rotatable SQUID gradiometers may be housed in a cryogenic environment to search for and locate unambiguously magnetic anomalies. The SQUID magnetic detection apparatus can be used to determine the azimuth of a hydrofracture by first flooding the hydrofracture with a ferrofluid to create an artificial magnetic anomaly therein.

  18. RNA-SSPT: RNA Secondary Structure Prediction Tools.

    Science.gov (United States)

    Ahmad, Freed; Mahboob, Shahid; Gulzar, Tahsin; Din, Salah U; Hanif, Tanzeela; Ahmad, Hifza; Afzal, Muhammad

    2013-01-01

    The prediction of RNA structure is useful for understanding evolution for both in silico and in vitro studies. Physical methods like NMR studies to predict RNA secondary structure are expensive and difficult. Computational RNA secondary structure prediction is easier. Comparative sequence analysis provides the best solution. But secondary structure prediction of a single RNA sequence is challenging. RNA-SSPT is a tool that computationally predicts secondary structure of a single RNA sequence. Most of the RNA secondary structure prediction tools do not allow pseudoknots in the structure or are unable to locate them. Nussinov dynamic programming algorithm has been implemented in RNA-SSPT. The current studies shows only energetically most favorable secondary structure is required and the algorithm modification is also available that produces base pairs to lower the total free energy of the secondary structure. For visualization of RNA secondary structure, NAVIEW in C language is used and modified in C# for tool requirement. RNA-SSPT is built in C# using Dot Net 2.0 in Microsoft Visual Studio 2005 Professional edition. The accuracy of RNA-SSPT is tested in terms of Sensitivity and Positive Predicted Value. It is a tool which serves both secondary structure prediction and secondary structure visualization purposes.

  19. Behaviour Recovery. Second Edition

    Science.gov (United States)

    Rogers, Bill

    2004-01-01

    This second edition of Behaviour Recovery puts emphasis on teaching behaviour concerning children with emotional and behavioural disorders (EBD). These children have many factors in their lives that affect their behaviour over which schools have limited control. This book acknowledges the challenge and explores the practical realities, options and…

  20. Newspaper Editing: English, Journalism.

    Science.gov (United States)

    Bullock, Johanna

    A course designed to groom editors for the newspaper is presented. Editing copy, copyreading and proofreading, principles of headlining, responsibility of the press, libel and slander laws, and problems of censorship are covered. Course objectives include the following: (1) The student will recognize and correct all newspaper items that do not…

  1. Nair handbook. 1995 edition

    International Nuclear Information System (INIS)

    1995-01-01

    This Handbook contains general background, administrative and technical information for those participating in the National Arrangements for Incidents involving Radioactivity (NAIR), updating and replacing the previous edition published in 1987. The overriding need for revision was brought about as a result of changes introduced by British Telecom to the telephone numbers of establishments. (UK)

  2. Tokamaks (Second Edition)

    Energy Technology Data Exchange (ETDEWEB)

    Stott, Peter [JET, UK (United Kingdom)

    1998-10-01

    The first edition of John Wesson's book on tokamaks, published in 1987, established itself as essential reading for researchers in the field of magnetic confinement fusion: it was an excellent introduction for students to tokamak physics and also a valuable reference work for the more experienced. The second edition, published in 1997, has been completely rewritten and substantially enlarged (680 pages compared with 300). The new edition maintains the aim of providing a simple introduction to basic tokamak physics, but also includes discussion of the substantial advances in fusion research during the past decade. The new book, like its predecessor, is well written and commendable for its clarity and accuracy. In fact many of the chapters are written by a series of co-authors bringing the benefits of a wide range of expertise but, by careful editing, Wesson has maintained a uniformity of style and presentation. The chapter headings and coverage for the most part remain the same - but are expanded considerably and brought up to date. The most substantial change is that the single concluding chapter in the first edition on 'Experiments' has been replaced by three chapters: 'Tokamak experiments' which deals with some of the earlier key experiments plus a selection of recent small and medium-sized devices, 'Large experiments' which gives an excellent summary of the main results from the four large tokamaks - TFTR, JET, JT60/JT60U and DIII-D, and 'The future' which gives a very short (possibly too short in my opinion) account of reactors and ITER. This is an excellent book, which I strongly recommend should have a place - on the desk rather than in the bookshelf - of researchers in magnetic confinement fusion. (book review)

  3. Tokamaks (Second Edition)

    International Nuclear Information System (INIS)

    Stott, Peter

    1998-01-01

    The first edition of John Wesson's book on tokamaks, published in 1987, established itself as essential reading for researchers in the field of magnetic confinement fusion: it was an excellent introduction for students to tokamak physics and also a valuable reference work for the more experienced. The second edition, published in 1997, has been completely rewritten and substantially enlarged (680 pages compared with 300). The new edition maintains the aim of providing a simple introduction to basic tokamak physics, but also includes discussion of the substantial advances in fusion research during the past decade. The new book, like its predecessor, is well written and commendable for its clarity and accuracy. In fact many of the chapters are written by a series of co-authors bringing the benefits of a wide range of expertise but, by careful editing, Wesson has maintained a uniformity of style and presentation. The chapter headings and coverage for the most part remain the same - but are expanded considerably and brought up to date. The most substantial change is that the single concluding chapter in the first edition on 'Experiments' has been replaced by three chapters: 'Tokamak experiments' which deals with some of the earlier key experiments plus a selection of recent small and medium-sized devices, 'Large experiments' which gives an excellent summary of the main results from the four large tokamaks - TFTR, JET, JT60/JT60U and DIII-D, and 'The future' which gives a very short (possibly too short in my opinion) account of reactors and ITER. This is an excellent book, which I strongly recommend should have a place - on the desk rather than in the bookshelf - of researchers in magnetic confinement fusion. (book review)

  4. The CRISPR/Cas genome-editing tool: application in improvement of crops

    Directory of Open Access Journals (Sweden)

    SURENDER eKHATODIA

    2016-04-01

    Full Text Available The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR associated Cas9/sgRNA system is a novel fledgling targeted genome-editing technique from bacterial immune system, which is a cheap, easy and most rapidly adopted genome editing tool transforming to revolutionary paradigm. Cas9 protein is an RNA guided endonuclease utilized for creating targeted double stranded breaks with only a short RNA sequence to confer recognition of the target in animals and plants. Development of genetically edited (GE crops similar to those developed by conventional or mutation breeding using this potential technique makes it a promising and extremely versatile tool for providing sustainable productive agriculture for better feeding of rapidly growing population in changing climate. The emerging areas of research for the genome editing in plants are like, interrogating gene function, rewiring the regulatory signaling networks, sgRNA library for high-throughput loss-of-function screening. In this review, we will discuss the broad applicability of the Cas9 nuclease mediated targeted plant genome editing for development of designer crops. The regulatory uncertainty and social acceptance of plant breeding by Cas9 genome editing have also been discussed. The non-GM designer genetically edited plants could prospect climate resilient and sustainable energy agriculture in coming future for maximizing the yield by combating abiotic and biotic stresses with this new innovative plant breeding technique.

  5. Optical parameters of the tunable Bragg reflectors in squid.

    Science.gov (United States)

    Ghoshal, Amitabh; Demartini, Daniel G; Eck, Elizabeth; Morse, Daniel E

    2013-08-06

    Cephalopods (e.g. octopus, squid and cuttlefish) dynamically tune the colour and brightness of their skin for camouflage and communication using specialized skin cells called iridocytes. We use high-resolution microspectrophotometry to investigate individual tunable Bragg structures (consisting of alternating reflectin protein-containing, high-refractive index lamellae and low-refractive index inter-lamellar spaces) in live and chemically fixed iridocytes of the California market squid, Doryteuthis opalescens. This subcellular, single-stack microspectrophotometry allows for spectral normalization, permitting use of a transfer-matrix model of Bragg reflectance to calculate all the parameters of the Bragg stack-the refractive indices, dimensions and numbers of the lamellae and inter-lamellar spaces. Results of the fitting analyses show that eight or nine pairs of low- and high-index layers typically contribute to the observed reflectivity in live cells, whereas six or seven pairs of low- and high-index layers typically contribute to the reflectivity in chemically fixed cells. The reflectin-containing, high-index lamellae of live cells have a refractive index proportional to the peak reflectivity, with an average of 1.405 ± 0.012 and a maximum around 1.44, while the reflectin-containing lamellae in fixed tissue have a refractive index of 1.413 ± 0.015 suggesting a slight increase of refractive index in the process of fixation. As expected, incremental changes in refractive index contribute to the greatest incremental changes in reflectivity for those Bragg stacks with the most layers. The excursions in dimensions required to tune the measured reflected wavelength from 675 (red) to 425 nm (blue) are a decrease from ca 150 to 80 nm for the high-index lamellae and from ca 120 to 50 nm for the low-index inter-lamellar spaces. Fixation-induced dimensional changes also are quantified, leading us to suggest that further microspectrophotometric analyses of this iridocyte

  6. Enlightenment of old ideas from new investigations: more questions regarding the evolution of bacteriogenic light organs in squids.

    Science.gov (United States)

    Nishiguchi, M K; Lopez, J E; Boletzky, S v

    2004-01-01

    Bioluminescence is widespread among many different types of marine organisms. Metazoans contain two types of luminescence production, bacteriogenic (symbiotic with bacteria) or autogenic, via the production of a luminous secretion or the intrinsic properties of luminous cells. Several species in two families of squids, the Loliginidae and the Sepiolidae (Mollusca: Cephalopoda) harbor bacteriogenic light organs that are found central in the mantle cavity. These light organs are exceptional in function, that is, the morphology and the complexity suggests that the organ has evolved to enhance and direct light emission from bacteria that are harbored inside. Although light organs are widespread among taxa within the Sepiolidae, the origin and development of this important feature is not well studied. We compared light organ morphology from several closely related taxa within the Sepiolidae and combined molecular phylogenetic data using four loci (nuclear ribosomal 28S rRNA and the mitochondrial cytochrome c oxidase subunit I and 12S and 16S rRNA) to determine whether this character was an ancestral trait repeatedly lost among both families or whether it evolved independently as an adaptation to the pelagic and benthic lifestyles. By comparing other closely related extant taxa that do not contain symbiotic light organs, we hypothesized that the ancestral state of sepiolid light organs most likely evolved from part of a separate accessory gland open to the environment that allowed colonization of bacteria to occur and further specialize in the eventual development of the modern light organ.

  7. Production of Purified CasRNPs for Efficacious Genome Editing.

    Science.gov (United States)

    Lingeman, Emily; Jeans, Chris; Corn, Jacob E

    2017-10-02

    CRISPR-Cas systems have been harnessed as modular genome editing reagents for functional genomics and show promise to cure genetic diseases. Directed by a guide RNA, a Cas effector introduces a double stranded break in DNA and host cell DNA repair leads to the introduction of errors (e.g., to knockout a gene) or a programmed change. Introduction of a Cas effector and guide RNA as a purified Cas ribonucleoprotein complex (CasRNP) has recently emerged as a powerful approach to alter cell types and organisms. Not only does CasRNP editing exhibit increased efficacy and specificity, it avoids optimization and iteration of species-specific factors such as codon usage, promoters, and terminators. CasRNP editing has been rapidly adopted for research use in many contexts and is quickly becoming a popular method to edit primary cells for therapeutic application. This article describes how to make a Cas9 RNP and outlines its use for gene editing in human cells. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

  8. Microwave SQUID multiplexer demonstration for cosmic microwave background imagers

    Science.gov (United States)

    Dober, B.; Becker, D. T.; Bennett, D. A.; Bryan, S. A.; Duff, S. M.; Gard, J. D.; Hays-Wehle, J. P.; Hilton, G. C.; Hubmayr, J.; Mates, J. A. B.; Reintsema, C. D.; Vale, L. R.; Ullom, J. N.

    2017-12-01

    Key performance characteristics are demonstrated for the microwave superconducting quantum interference device (SQUID) multiplexer (μmux) coupled to transition edge sensor (TES) bolometers that have been optimized for cosmic microwave background (CMB) observations. In a 64-channel demonstration, we show that the μmux produces a white, input referred current noise level of 29 pA/ √{H z } at a microwave probe tone power of -77 dB, which is well below the expected fundamental detector and photon noise sources for a ground-based CMB-optimized bolometer. Operated with negligible photon loading, we measure 98 pA/ √{H z } in the TES-coupled channels biased at 65% of the sensor normal resistance. This noise level is consistent with that predicted from bolometer thermal fluctuation (i.e., phonon) noise. Furthermore, the power spectral density is white over a range of frequencies down to ˜100 mHz, which enables CMB mapping on large angular scales that constrain the physics of inflation. Additionally, we report cross-talk measurements that indicate a level below 0.3%, which is less than the level of cross-talk from multiplexed readout systems in deployed CMB imagers. These measurements demonstrate the μmux as a viable readout technique for future CMB imaging instruments.

  9. Development of improved superconductive axial gradiometers for biomagnetic SQUID applications

    Science.gov (United States)

    Budnyk, M. M.; Minov, Yu. D.; Lyakhno, V. Yu.; Desnenko, V. A.; Linnik, A. S.; Shopen, O. B.

    2018-03-01

    SQUID magnetometers for biomagnetic measurements are equipped with superconductive gradiometers which are required to provide a high signal-to-noise ratio at low frequencies, sufficient mechanical strength and sustained performance under repeated thermal cycles, as well as a low level of intrinsic magnetic noise. This paper describes the design of a gradiometer made with a carbon-fiber reinforced composite material for magnetic cardiography measurements. The thermal coefficient of linear expansion (TCLE) of the carbon fiber composite can be precisely adjusted to match that of the superconducting detector coil wire. This is achieved thanks to the difference in the TCLE of carbon fibers in the longitudinal and transverse directions and is realized by varying the laying directions of the fiber in the composite. The data of magnetic susceptibility measurements on carbon fiber composite are reported, showing the magnetic susceptibility about six times smaller than that of graphite. The presented gradiometer design provides a high degree of balancing and is patented along side other specific techniques.

  10. An interchangeable scanning Hall probe/scanning SQUID microscope

    International Nuclear Information System (INIS)

    Tang, Chiu-Chun; Lin, Hui-Ting; Wu, Sing-Lin; Chen, Tse-Jun; Wang, M. J.; Ling, D. C.; Chi, C. C.; Chen, Jeng-Chung

    2014-01-01

    We have constructed a scanning probe microscope for magnetic imaging, which can function as a scanning Hall probe microscope (SHPM) and as a scanning SQUID microscope (SSM). The scanning scheme, applicable to SHPM and SSM, consists of a mechanical positioning (sub) micron-XY stage and a flexible direct contact to the sample without a feedback control system for the Z-axis. With the interchangeable capability of operating two distinct scanning modes, our microscope can incorporate the advantageous functionalities of the SHPM and SSM with large scan range up to millimeter, high spatial resolution (⩽4 μm), and high field sensitivity in a wide range of temperature (4.2 K-300 K) and magnetic field (10 −7 T-1 T). To demonstrate the capabilities of the system, we present magnetic images scanned with SHPM and SSM, including a RbFeB magnet and a nickel grid pattern at room temperature, surface magnetic domain structures of a La 2/3 Ca 1/3 MnO 3 thin film at 77 K, and superconducting vortices in a striped niobium film at 4.2 K

  11. Development of Contaminant Detection System using HTS SQUIDs

    International Nuclear Information System (INIS)

    Ohtani, T.; Tanaka, S.; Narita, Y.; Ariyoshi, S.; Suzuki, S.

    2015-01-01

    In terms of food safety, mixture of contaminants in food is a serious problem for not only consumers but also manufacturers. In general, the target size of the metallic contaminant to be removed is 0.5 mm. However, it is a difficult task for manufacturers to achieve this target, because of lower system sensitivity. Therefore, we developed a food contaminant detection system based on high-Tc RF superconducting quantum interference devices (SQUIDs), which are highly sensitive magnetic sensors. This study aims to improve the signal to noise ratio (SNR) of the system and detect a 0.5 mm diameter steel ball. Using a real time digital signal processing technique along with analog band-pass filters, we improved the SNR of the system. Owing to the improved SNR, a steel ball with a diameter as small as 0.3 mm, with stand-off distance of 117 mm was successfully detected. These results suggest that the proposed system is a promising candidate for the detection of metallic contaminants in food products

  12. An interchangeable scanning Hall probe/scanning SQUID microscope

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Chiu-Chun; Lin, Hui-Ting; Wu, Sing-Lin [Department of Physics, National Tsing Hua University, Hsinchu 30013, Taiwan (China); Chen, Tse-Jun; Wang, M. J. [Institute of Astronomy and Astrophysics, Academia Sinica, Taipei 10617, Taiwan (China); Ling, D. C. [Department of Physics, Tamkang University, Tamsui Dist., New Taipei City 25137, Taiwan (China); Chi, C. C.; Chen, Jeng-Chung [Department of Physics, National Tsing Hua University, Hsinchu 30013, Taiwan (China); Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 30013, Taiwan (China)

    2014-08-15

    We have constructed a scanning probe microscope for magnetic imaging, which can function as a scanning Hall probe microscope (SHPM) and as a scanning SQUID microscope (SSM). The scanning scheme, applicable to SHPM and SSM, consists of a mechanical positioning (sub) micron-XY stage and a flexible direct contact to the sample without a feedback control system for the Z-axis. With the interchangeable capability of operating two distinct scanning modes, our microscope can incorporate the advantageous functionalities of the SHPM and SSM with large scan range up to millimeter, high spatial resolution (⩽4 μm), and high field sensitivity in a wide range of temperature (4.2 K-300 K) and magnetic field (10{sup −7} T-1 T). To demonstrate the capabilities of the system, we present magnetic images scanned with SHPM and SSM, including a RbFeB magnet and a nickel grid pattern at room temperature, surface magnetic domain structures of a La{sub 2/3}Ca{sub 1/3}MnO{sub 3} thin film at 77 K, and superconducting vortices in a striped niobium film at 4.2 K.

  13. Dynamic Characteristics of S-band DC SQUID Amplifier

    DEFF Research Database (Denmark)

    Prokopenko, G. V.; Shitov, S. V.; Koshelets, I. L. L. V. P.

    2003-01-01

    A low-noise rf amplifier based on a de SQUID (SQA) has been tested in the frequency range 3.0-4.6 GHz in the open-loop configuration. The following parameters have been measured for the single-stage balanced type SQA at 4.0 GHz: gain (12 +/- 1) dB, 3 dB bandwidth of 500 MHz and noise temperature (1.......0 +/- 0.25) K. For the nonbalanced type SQA at 4.0 GHz gain was (15 +/-1) dB, 3 dB bandwidth 200 MHz and noise temperature (0.5 +/- 0.25) K. The improved performance is obtained due to the increased characteristic voltage (approximate to 420 muV) of the small-area (down to 0.7-0.9 mum(2)) high-quality Nb......-AlOx-Nb SIS junctions. The saturation power (normalized to 1 GHz) referred to the input at 1 dB gain compression is estimated as approximate to55 K*GHz at a bias voltage of 60 muV. The reasons for saturation of the SQA are discussed....

  14. Sperm from sneaker male squids exhibit chemotactic swarming to CO₂.

    Science.gov (United States)

    Hirohashi, Noritaka; Alvarez, Luis; Shiba, Kogiku; Fujiwara, Eiji; Iwata, Yoko; Mohri, Tatsuma; Inaba, Kazuo; Chiba, Kazuyoshi; Ochi, Hiroe; Supuran, Claudiu T; Kotzur, Nico; Kakiuchi, Yasutaka; Kaupp, U Benjamin; Baba, Shoji A

    2013-05-06

    Behavioral traits of sperm are adapted to the reproductive strategy that each species employs. In polyandrous species, spermatozoa often form motile clusters, which might be advantageous for competing with sperm from other males. Despite this presumed advantage for reproductive success, little is known about how sperm form such functional assemblies. Previously, we reported that males of the coastal squid Loligo bleekeri produce two morphologically different euspermatozoa that are linked to distinctly different mating behaviors. Consort and sneaker males use two distinct insemination sites, one inside and one outside the female's body, respectively. Here, we show that sperm release a self-attracting molecule that causes only sneaker sperm to swarm. We identified CO2 as the sperm chemoattractant and membrane-bound flagellar carbonic anhydrase as its sensor. Downstream signaling results from the generation of extracellular H(+), intracellular acidosis, and recovery from acidosis. These signaling events elicit Ca(2+)-dependent turning behavior, resulting in chemotactic swarming. These results illuminate the bifurcating evolution of sperm underlying the distinct fertilization strategies of this species. Copyright © 2013 Elsevier Ltd. All rights reserved.

  15. EFFECT OF DETERGENT ON ELECTRICAL PROPERTIES OF SQUID AXON MEMBRANE.

    Science.gov (United States)

    KISHIMOTO, U; ADELMAN, W J

    1964-05-01

    The effects of detergents on squid giant axon action and resting potentials as well as membrane conductances in the voltage clamp have been studied. Anionic detergents (sodium lauryl sulfate, 0.1 to 1.0 mM; dimethyl benzene sulfonate, 1 to 20 mM, pH 7.6) cause a temporary increase and a later decrease of action potential height and the value of the resting potential. Cationic detergent (cetyl trimethyl ammonium chloride, 6 x 10(-5)M or more, pH 7.6) generally brings about immediate and irreversible decreases in the action and resting potentials. Non-ionic detergent (tween 80, 0.1 M, pH 7.6) causes a slight reversible reduction of action potential height without affecting the value of the resting potential. Both anionic and cationic detergents generally decrease the sodium and potassium conductances irreversibly. The effect of non-ionic detergent is to decrease the sodium conductance reversibly, leaving the potassium conductance almost unchanged.

  16. Microwave SQUID Multiplexer Demonstration for Cosmic Microwave Background Imagers.

    Science.gov (United States)

    Dober, B; Becker, D T; Bennett, D A; Bryan, S A; Duff, S M; Gard, J D; Hays-Wehle, J P; Hilton, G C; Hubmayr, J; Mates, J A B; Reintsema, C D; Vale, L R; Ullom, J N

    2017-12-01

    Key performance characteristics are demonstrated for the microwave SQUID multiplexer (µmux) coupled to transition edge sensor (TES) bolometers that have been optimized for cosmic microwave background (CMB) observations. In a 64-channel demonstration, we show that the µmux produces a white, input referred current noise level of [Formula: see text] at -77 dB microwave probe tone power, which is well below expected fundamental detector and photon noise sources for a ground-based CMB-optimized bolometer. Operated with negligible photon loading, we measure [Formula: see text] in the TES-coupled channels biased at 65% of the sensor normal resistance. This noise level is consistent with that predicted from bolometer thermal fluctuation (i.e. phonon) noise. Furthermore, the power spectral density is white over a range of frequencies down to ~ 100 mHz, which enables CMB mapping on large angular scales that constrain the physics of inflation. Additionally, we report cross-talk measurements that indicate a level below 0.3%, which is less than the level of cross-talk from multiplexed readout systems in deployed CMB imagers. These measurements demonstrate the µmux as a viable readout technique for future CMB imaging instruments.

  17. SQUID biosusceptometry in the measurement of hepatic iron

    International Nuclear Information System (INIS)

    Sheth, Sujit

    2003-01-01

    Individuals with primary or secondary abnormalities of iron metabolism, such as hereditary hemochromatosis and transfusional iron loading, may develop potentially lethal systemic iron overload. Over time, this excess iron is progressively deposited in the liver, heart, pancreas, and other organs, resulting in cirrhosis, heart disease, diabetes and other disorders. Unless treated, death usually results from cardiac failure. The amount of iron in the liver is the best indicator of the amount of iron in the whole body. At present, the only sure way to measure the amount of iron in the liver is to remove a sample of the liver by biopsy. Iron stored in the liver can be magnetized to a small degree when placed in a magnetic field. The amount of magnetization is measured by our instrument, called a superconducting quantum interference device (SQUID) susceptometer. In patients with iron overload, our previous studies have shown that magnetic measurements of liver iron in patients with iron overload are quantitatively equivalent to biochemical determinations on tissue obtained by biopsy. The safety, ease, rapidity, and comfort of magnetic measurements make frequent, serial studies technically feasible and practically acceptable to patients. (orig.)

  18. Fan edits and the legacy of The Phantom Edit

    Directory of Open Access Journals (Sweden)

    Joshua Wille

    2014-09-01

    Full Text Available A fan edit can generally be defined as an alternative version of a film or television text created by a fan. It offers a different viewing experience, much as a song remix offers a different listening experience. The contemporary wave of fan edits has emerged during the remix zeitgeist of digital media and at a time when digital video editing technology has become more affordable and popular. The increasing number of alternative versions of films and the works of revisionist Hollywood filmmakers such as George Lucas have contributed to a greater public understanding of cinema as a fluid medium instead of one that exists in a fixed form. The Phantom Edit (2000, a seminal fan edit based on Lucas's Star Wars Episode I: The Phantom Menace (1999, inspired new ranks of fan editors. However, critics have misunderstood fan edits as merely the work of disgruntled fans. In order to provide a critical and historical basis for studies in fan editing as a creative practice, I examine previous interpretations of fan edits in the context of relevant contemporary works, and I use an annotated chronology of The Phantom Edit to trace its influence on subsequent fan editing communities and uncover their relationship with intellectual property disputes.

  19. Identifying Pelagic Habitat Hotspots of Neon Flying Squid in the Temperate Waters of the Central North Pacific.

    Science.gov (United States)

    Alabia, Irene D; Saitoh, Sei-Ichi; Mugo, Robinson; Igarashi, Hiromichi; Ishikawa, Yoichi; Usui, Norihisa; Kamachi, Masafumi; Awaji, Toshiyuki; Seito, Masaki

    2015-01-01

    We identified the pelagic habitat hotspots of the neon flying squid (Ommastrephes bartramii) in the central North Pacific from May to July and characterized the spatial patterns of squid aggregations in relation to oceanographic features such as mesoscale oceanic eddies and the Transition Zone Chlorophyll-a Front (TZCF). The data used for the habitat model construction and analyses were squid fishery information, remotely-sensed and numerical model-derived environmental data from May to July 1999-2010. Squid habitat hotspots were deduced from the monthly Maximum Entropy (MaxEnt) models and were identified as regions of persistent high suitable habitat across the 12-year period. The distribution of predicted squid habitat hotspots in central North Pacific revealed interesting spatial and temporal patterns likely linked with the presence and dynamics of oceanographic features in squid's putative foraging grounds from late spring to summer. From May to June, the inferred patches of squid habitat hotspots developed within the Kuroshio-Oyashio transition zone (KOTZ; 37-40°N) and further expanded north towards the subarctic frontal zone (SAFZ; 40-44°N) in July. The squid habitat hotspots within the KOTZ and areas west of the dateline (160°W-180°) were likely influenced and associated with the highly dynamic and transient oceanic eddies and could possibly account for lower squid suitable habitat persistence obtained from these regions. However, predicted squid habitat hotspots located in regions east of the dateline (180°-160°W) from June to July, showed predominantly higher squid habitat persistence presumably due to their proximity to the mean position of the seasonally-shifting TZCF and consequent utilization of the highly productive waters of the SAFZ.

  20. ADAR2 editing activity in newly diagnosed versus relapsed pediatric high-grade astrocytomas

    International Nuclear Information System (INIS)

    Tomaselli, Sara; Galeano, Federica; Massimi, Luca; Di Rocco, Concezio; Lauriola, Libero; Mastronuzzi, Angela; Locatelli, Franco; Gallo, Angela

    2013-01-01

    High-grade (WHO grade III and IV) astrocytomas are aggressive malignant brain tumors affecting humans with a high risk of recurrence in both children and adults. To date, limited information is available on the genetic and molecular alterations important in the onset and progression of pediatric high-grade astrocytomas and, even less, on the prognostic factors that influence long-term outcome in children with recurrence. A-to-I RNA editing is an essential post-transcriptional mechanism that can alter the nucleotide sequence of several RNAs and is mediated by the ADAR enzymes. ADAR2 editing activity is particularly important in mammalian brain and is impaired in both adult and pediatric high-grade astrocytomas. Moreover, we have recently shown that the recovered ADAR2 activity in high-grade astrocytomas inhibits in vivo tumor growth. The aim of the present study is to investigate whether changes may occur in ADAR2-mediated RNA editing profiles of relapsed high-grade astrocytomas compared to their respective specimens collected at diagnosis, in four pediatric patients. Total RNAs extracted from all tumor samples and controls were tested for RNA editing levels (by direct sequencing on cDNA pools) and for ADAR2 mRNA expression (by qRT-PCR). A significant loss of ADAR2-editing activity was observed in the newly diagnosed and recurrent astrocytomas in comparison to normal brain. Surprisingly, we found a substantial rescue of ADAR2 editing activity in the relapsed tumor of the only patient showing prolonged survival. High-grade astrocytomas display a generalized loss of ADAR2-mediated RNA editing at both diagnosis and relapse. However, a peculiar Case, in complete remission of disease, displayed a total rescue of RNA editing at relapse, intriguingly suggesting ADAR2 activity/expression as a possible marker for long-term survival of patients with high-grade astrocytomas

  1. Opportunistic acoustic recordings of (potential) orangeback flying squid Sthenoteuthis pteropus in the Central Eastern Atlantic

    Science.gov (United States)

    Peña, Marian; Villanueva, Roger; Escánez, Alejandro; Ariza, Alejandro

    2018-03-01

    Squids are fast swimmers that are difficult to catch by nets and to record with echosounders in the open ocean. A rare detection of orangeback flying squid Sthenoteuthis pteropus in the Central Eastern Atlantic Ocean off the coast of Senegal was accomplished during the MAFIA oceanographic survey carried out between Brazil and the Canary Islands in April 2015. Although net sampling did not yield any subadult or adult individuals, dozens were visually detected from the vessel jumping out of the water at night and displaying their characteristic dorsal photophore patch. A few squids were caught with fishing lines and identified at the species level. The acoustic echograms revealed distinctive previously unobserved acoustic echotraces that seemed to be caused by those squids, which were the only new species detected at that station (over a bottom depth ranging from 4010 to 5215 m, between 10° 45‧ N 22° 41‧ W and 10° 53‧ N 22° 40‧ W). The acoustic response and swimming behaviour shown by those echotraces reinforced this hypothesis. The (potentially) squid recordings dove rapidly (0.19 m/s to 0.48 m/s) from around 10 m below the mesopelagic fish layer, which had migrated to the subsurface at night (35 m depth), to depths of 70-95 m, and swam upward, apparently attacking fish from below. The morning squid migration to deeper waters (250-300 m) was also recorded acoustically. Downward movements of squid swimming at speeds of 0.22 m/s were calculated from the echogram, while the mesopelagic migrating fish swam at 0.27 m/s reaching 250 m depth. Sv120 - Sv38 averaged 2.7 ± 3.2 dB for the squid echotraces while the mesopelagic layer showed values of -8.8 ± 0.9 dB. These ranges agreed with values in the literature and from theoretical models. This study provides more insight into the migrating behaviour of oceanic squids, a species group that is poorly represented in the acoustic literature due to challenges in studying them.

  2. Preface to Special Edition

    Directory of Open Access Journals (Sweden)

    Renee Nathanson

    2012-04-01

    Full Text Available Given that reading comprehension is at the forefront of global literacy discourse, this special edition of Per Linguam, the first number that is also published online, features a collection of articles that cover different aspects of reading comprehension and instruction, such as, strategies for comprehending texts, metacognitive awareness, the reciprocity of assessment and comprehension instruction and socio-affective factors that influence comprehension.

  3. Genome Editing of Monkey.

    Science.gov (United States)

    Liu, Zhen; Cai, Yijun; Sun, Qiang

    2017-01-01

    Gene-modified monkey models would be particularly valuable in biomedical and neuroscience research. Virus-based transgenic and programmable nucleases-based site-specific gene editing methods (TALEN, CRISPR-cas9) enable the generation of gene-modified monkeys with gain or loss of function of specific genes. Here, we describe the generation of transgenic and knock-out (KO) monkeys with high efficiency by lentivirus and programmable nucleases.

  4. Mobile HTS-SQUID NDE system with robot arm and active shielding using fluxgate

    Energy Technology Data Exchange (ETDEWEB)

    Hatsukade, Y. [Department of Ecological Engineering, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi 441-8580 (Japan)], E-mail: hatukade@eco.tut.ac.jp; Yotsugi, K.; Tanaka, S. [Department of Ecological Engineering, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi 441-8580 (Japan)

    2008-09-15

    A robot-arm-based mobile HTS-SQUID NDE system was developed for inspection of advanced structures such as hydrogen fuel cell tanks. In order to realize stable operation of HTS-SQUID exposed in Earth's field and robot arm's noise without flux trapping, flux jumping and unlocking during motion, a new active magnetic shielding (AMS) technique using fluxgate was introduced. The high sensitive fluxgate, which could measure magnetic field of up to several 10 {mu}T, was mounted near an HTS-SQUID gradiometer on the robot arm to measure the ambient noise and feed back its output to a compensation coil, which surrounded both SQUID and fluxgate to cancel the ambient noise around them. The AMS technique successfully enabled the HTS-SQUID gradiometer to be moved at 10 mm/s by the robot arm in unshielded environment without flux trapping, jumping and unlocking. Detection of hidden slots in multi-layer composite-metal structures imitating the fuel cell tank was demonstrated.

  5. Vestigial phragmocone in the gladius points to a deepwater origin of squid (Mollusca: Cephalopoda)

    Science.gov (United States)

    Arkhipkin, Alexander I.; Bizikov, Vyacheslav A.; Fuchs, Dirk

    2012-03-01

    The microstructure of the gladius cone was investigated in six species of nektonic squid: shallow-water Loligo gahi (Loliginidae), pelagic eurybathic Illex argentinus, Todarodes pacificus, Dosidicus gigas (Ommastrephidae), and deepwater Onykia ingens (Onychoteuthidae) and Gonatus antarcticus (Gonatidae) using state-of-the-art microscopy. Apart from L. gahi, all other species had septa-like layers in the gladius cone, which for the first time were investigated in detail and compared with those in extinct Cretaceous belemnites Hibolithes sp. and Pachyteuthis sp., and spirulid Cyrtobelus sp. It was found that the organic layers of the gladius cone in recent squid can be homologized with the organic components of the shell in fossil phragmocone-bearing coleoids. The septa-like layers in modern gladius cones therefore represent a vestigial phragmocone composed of organic septal rudiments of the ancestral phragmocone that has lost the siphuncle and gas-filled chambers. The well-developed rostrum in onychoteuthids and small rostrum of the gladius in ommastrephids and gonatids can be seen as homologous with the belemnoid rostrum, which may indicate a close phylogenetic relationship between belemnites and at least some squid. Possible evolutionary pathways of the reduction of the functional phragmocone in squid ancestors are discussed. Several features such as the loss of shell calcification, deep water speciation, and the structure of the equilibrium organ point to a deep-water origin of squids.

  6. Development of Nb nanoSQUIDs based on SNS junctions for operation in high magnetic fields

    Energy Technology Data Exchange (ETDEWEB)

    Morosh, Viacheslav; Kieler, Oliver; Weimann, Thomas; Zorin, Alexander [Physikalisch-Technische Bundesanstalt (PTB), Braunschweig (Germany); Mueller, Benedikt; Martinez-Perez, Maria Jose; Kleiner, Reinhold; Koelle, Dieter [Physikalisches Institut and Center for Quantum Science in LISA+, Universitaet Tuebingen (Germany)

    2016-07-01

    Investigation of the magnetization reversal of single magnetic nanoparticles requires SQUIDs with high spatial resolution, high spin sensitivity (a few Bohr magneton μ{sub B}) and at the same time sufficient stability in high magnetic fields. We fabricated dc nanoSQUIDs comprising overdamped SNS sandwich-type (Nb/HfTi/Nb) Josephson junctions using optimized technology based on combination of electron beam lithography and chemical-mechanical polishing. Our nanoSQUIDs have Josephson junctions with lateral dimensions ≤ 150 nm x 150 nm, effective loop areas < 0.05 μm{sup 2} and the distance between the Josephson junctions ≤ 100 nm. The feeding strip lines of the width ≤ 200 nm have been realized. The nanoSQUIDs have shown stable operation in external magnetic fields at least up to 250 mT. Sufficiently low level of flux noise resulting in spin sensitivity of few tens μ{sub B}/Hz{sup 1/2} has been demonstrated. A further reduction of the nanoSQUID size using our technology is possible.

  7. SQUID magnetometer using sensitivity correction signal for non-magnetic metal contaminants detection

    Energy Technology Data Exchange (ETDEWEB)

    Yagi, Toshifumi, E-mail: sakuta.k@usp.ac.jp; Ohashi, Masaharu; Sakuta, Ken

    2016-11-15

    Highlights: • A high-frequency excitation is necessary to detect nonmagnetic metals using SQUID. • It is possible to detect a high-frequency magnetic field using the open loop technique. • Open loop operation leads to a change in the conversion factor. • Conversion between voltage and magnetic field for open loop operation are examined. - Abstract: Measurement methods with SQUID can accurately detect small magnetic metal contaminants based on their magnetic remanence. But, a high-frequency excitation is necessary to detect nonmagnetic metals, on the base of contrasts in electric conductivity. In this work, an open loop technique is introduced to facilitate this. The SQUID is negative feedback controlled (flux locked loop (FLL) operation) for the low frequency range, which includes significant noise due to the movement of the magnetic body or the change of the ambient magnetic field composed of the geomagnetic field and technical signals, and it operates in an open loop configuration for the high frequency range. When using the open loop technique, negative feedback is not applied to the high frequency range. Consequently, the V–Φ characteristic changes due to various causes, which leads to variations in the conversion factor between the SQUID output voltage and the magnetic field. In this study, conversion techniques for the magnetic field for open loop operation of SQUID in the high frequency range are examined.

  8. NANO-SQUIDs based on niobium Dayem bridges for nanoscale applications

    Energy Technology Data Exchange (ETDEWEB)

    Granata, C; Esposito, E; Nappi, C; Ruggiero, B; Russo, M [Istituto di Cibernetica ' E. Caianiello' del Consiglio Nazionale delle Ricerche, 80078 Pozzuoli (Napoli) (Italy); Vettoliere, A; Walke, P [Also Universita degli Studi di Napoli ' Federico II' , Napoli (Italy); Silvestrini, P, E-mail: c.granata@cib.na.cnr.i [Dipartimento di Ingegneria dell' Informazione, Seconda Universita degli Studi di Napoli, Aversa(Caserta) (Italy)

    2010-06-01

    We report on the design, the fabrication and the performance of an integrated magnetic nano-sensor based on niobium dc-SQUID (Superconducting QUantum Interference Device) for nanoscale applications is presented. The nano-sensors are based on nanometric niobium constrictions (Dayem bridges) inserted in a square loop having a side length of 200 nm. Measurements of voltage-flux characteristic, flux to voltage transfer factor and noise performances are reported. In small signal mode, the sensors have shown a magnetic flux noise spectral density of 1.5 {mu}{Phi}{sub 0}/Hz{sup 1/2} corresponding to a spin sensitivity in unit of Bohr magneton of 60 spin/Hz{sup 1/2}. Supercurrent decay measurements of these devices are also reported. Such measurements provide useful information for applications which employ the SQUID as a trigger where the sensor works on the zero voltage state. The experimental data, have shown an intrinsic current fluctuation less than 0.2% of the critical current at liquid helium temperature, corresponding to an intrinsic sensor magnetic flux resolution of a few m{Phi}{sub 0}. In view of the nano-SQUID employments in the detection of small spin populations, the authors calculated the spin sensitivity and the magnetic response relative to the single spin, as a function of its position within the SQUID hole. The results show that the SQUID response depends strongly on the spin position.

  9. RF SQUID in the nonhysteretic regime with k2Ql>1

    International Nuclear Information System (INIS)

    Dmitrenko, I.M.; Tsoi, G.M.; Shnyrkov, V.I.; Kartsovnik, V.V.

    1982-01-01

    Experimental measurements of current-voltage, current-phase, amplitude-frequency, phase-frequency, and signal characteristics of an rf SQUID operating at a frequency of 30 MHz in the nonhysteretic regime (1 = 2πL 0 I 0 /phi/sub o/ 2 Ql>1. Here I 0 is the critical current of the weak link, L 0 is the SQUID ring inductance, k is the coefficient of coupling of the SQUID ring to a resonant tank circuit of quality Q, and phi 0 is the magnetic flux quantum. A numerical analysis of the above characteristics for all relevant parameter values close to those occurring under experimental conditions was performed for qualitative comparison with theory. The main difference from the traditional nonhysteretic regime of SQUID operation (k 2 Q1 12 V/Wb for the single-valued region of the signal characteristics. The results suggest that considerable improvement of rf SQUID resolution is possible in the regime k 2 Ql>1

  10. SQUID magnetometer using sensitivity correction signal for non-magnetic metal contaminants detection

    International Nuclear Information System (INIS)

    Yagi, Toshifumi; Ohashi, Masaharu; Sakuta, Ken

    2016-01-01

    Highlights: • A high-frequency excitation is necessary to detect nonmagnetic metals using SQUID. • It is possible to detect a high-frequency magnetic field using the open loop technique. • Open loop operation leads to a change in the conversion factor. • Conversion between voltage and magnetic field for open loop operation are examined. - Abstract: Measurement methods with SQUID can accurately detect small magnetic metal contaminants based on their magnetic remanence. But, a high-frequency excitation is necessary to detect nonmagnetic metals, on the base of contrasts in electric conductivity. In this work, an open loop technique is introduced to facilitate this. The SQUID is negative feedback controlled (flux locked loop (FLL) operation) for the low frequency range, which includes significant noise due to the movement of the magnetic body or the change of the ambient magnetic field composed of the geomagnetic field and technical signals, and it operates in an open loop configuration for the high frequency range. When using the open loop technique, negative feedback is not applied to the high frequency range. Consequently, the V–Φ characteristic changes due to various causes, which leads to variations in the conversion factor between the SQUID output voltage and the magnetic field. In this study, conversion techniques for the magnetic field for open loop operation of SQUID in the high frequency range are examined.

  11. Non-destructive inspection using HTS-SQUID on aluminum liner covered by CFRP

    International Nuclear Information System (INIS)

    Hatsukade, Y.; Yotsugi, K.; Sakaguchi, Y.; Tanaka, S.

    2007-01-01

    An eddy-current-based SQUID non-destructive inspection (NDI) system to detect deep-lying cracks in multi-layer composite-Al vessels was developed taking advantage of the uncontested sensitivity of HTS-SQUID in low-frequency range. An HTS-SQUID gradiometer was mounted in a pulse tube cryocooler. A pair of differential coils with C-shaped ferrite cores was employed to induce an enhanced eddy current in an Al vessel wrapped in a carbon fiber reinforced plastic (CFRP) cover. Ellipsoidal dome-shaped Al liners containing through cracks, which were made by pressure cycle tests, in the CFRP covers with total thickness of 6 mm (CFPR 3 mm, and Al 3 mm) were inspected by the system. While inducing eddy currents in the vessels with excitation fields at 100 Hz or 7 kHz, the vessels were rotated under the HTS-SQUID. Above the cracks, anomalous signals due to the cracks were clearly detected at both frequencies. These results suggested the SQUID-NDI technique would be a possible candidate for inspection of high-pressure multi-layer composite-Al vessels

  12. Non-destructive inspection using HTS-SQUID on aluminum liner covered by CFRP

    Energy Technology Data Exchange (ETDEWEB)

    Hatsukade, Y. [Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi 441-8580 (Japan)], E-mail: hatukade@eco.tut.ac.jp; Yotsugi, K. [Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi 441-8580 (Japan); Sakaguchi, Y. [SAMTECH Corporation, 1000-18 Enmyo-cho, Kashiwara City, Osaka 582-0027 (Japan); Tanaka, S. [Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi 441-8580 (Japan)

    2007-10-01

    An eddy-current-based SQUID non-destructive inspection (NDI) system to detect deep-lying cracks in multi-layer composite-Al vessels was developed taking advantage of the uncontested sensitivity of HTS-SQUID in low-frequency range. An HTS-SQUID gradiometer was mounted in a pulse tube cryocooler. A pair of differential coils with C-shaped ferrite cores was employed to induce an enhanced eddy current in an Al vessel wrapped in a carbon fiber reinforced plastic (CFRP) cover. Ellipsoidal dome-shaped Al liners containing through cracks, which were made by pressure cycle tests, in the CFRP covers with total thickness of 6 mm (CFPR 3 mm, and Al 3 mm) were inspected by the system. While inducing eddy currents in the vessels with excitation fields at 100 Hz or 7 kHz, the vessels were rotated under the HTS-SQUID. Above the cracks, anomalous signals due to the cracks were clearly detected at both frequencies. These results suggested the SQUID-NDI technique would be a possible candidate for inspection of high-pressure multi-layer composite-Al vessels.

  13. Phylogenetic characterization of epibiotic bacteria in the accessory nidamental gland and egg capsules of the squid Loligo pealei (Cephalopoda:Loliginidae).

    Science.gov (United States)

    Barbieri, E; Paster, B J; Hughes, D; Zurek, L; Moser, D P; Teske, A; Sogin, M L

    2001-03-01

    Sexually mature female squid Loligo pealei harbour dense bacterial communities in their accessory nidamental glands (ANGs) and in their egg capsules (ECs). This study describes a molecular approach using the 16S rRNA gene (rDNA) to identify bacterial populations within the ANG and the ECs of the North Atlantic squid species L. pealei. Fluorescent in situ hybridization (FISH) and 16S rDNA analysis showed that predominantly alpha- and, to a lesser extent, gamma-proteobacteria were the predominant components of the ANG and EC bacterial communities. Sequencing results showed the presence of alpha-proteobacterial populations affiliated with the Roseobacter group and additional deep-branching alpha-proteobacterial lineages. In contrast, isolates from the ANG and ECs contained only a few alpha-proteobacteria of the Roseobacter group compared with several gamma-proteobacterial isolates, mostly Shewanella and Pseudoalteromonas species. Most of the ANG-associated bacterial populations were also found within the ECs of L. pealei. The molecular approach allowed the visualization of alpha-proteobacteria as major constituents of a bacterial symbiosis within the reproductive system of the Loliginidae.

  14. Thermodynamics of a closed-cycle gas flow system for cooling a HTc dc-SQUID magnetometer

    NARCIS (Netherlands)

    van den Bosch, P.J.; van den Bosch, P.J.; ter Brake, Hermanus J.M.; van den Eijkel, G.C.; Boelens, J.P.; Holland, Herman J.; Verberne, J.F.C.; Rogalla, Horst

    1994-01-01

    A multichannel high-Tc dc-SQUID based heart-magnetometer is currently under development in our laboratory. The system is cooled by a cooler that, due to its magnetic interference, has to be separated from the SQUID unit. In the present prototype system a closed-cycle gas flow was chosen as the

  15. 76 FR 3044 - Fisheries of the Exclusive Economic Zone Off Alaska; Sculpins, Sharks, Squid, and Octopus in the...

    Science.gov (United States)

    2011-01-19

    ..., Squid, and Octopus in the Gulf of Alaska AGENCY: National Marine Fisheries Service (NMFS), National... prohibiting directed fishing for sculpins, sharks, squid, and octopus in the Gulf of Alaska (GOA). This action..., and octopus in the GOA. DATES: Effective 1200 hrs, Alaska local time (A.l.t.), January 13, 2011...

  16. The male reproductive strategy of a deep-sea squid : sperm allocation, continuous production, and long-term storage of spermatophores in Histioteuthis miranda

    NARCIS (Netherlands)

    Hoving, Hendrik Jan T.; Lipinski, Marek R.; Dam, Lammertjan

    2010-01-01

    Squid are semelparous organisms. Much of what we know about squid reproduction relates to females, because few studies have addressed males and, although males are similarly challenged by semelparity, it remains virtually unknown what tactics squid have evolved to allocate sperm to spermatophores.

  17. Research on Intelligent Control System of DC SQUID Magnetometer Parameters for Multi-channel System

    Science.gov (United States)

    Chen, Hua; Yang, Kang; Lu, Li; Kong, Xiangyan; Wang, Hai; Wu, Jun; Wang, Yongliang

    2018-03-01

    In a multi-channel SQUID measurement system, adjusting device parameters to optimal condition for all channels is time-consuming. In this paper, an intelligent control system is presented to determine the optimal working point of devices which is automatic and more efficient comparing to the manual one. An optimal working point searching algorithm is introduced as the core component of the control system. In this algorithm, the bias voltage V_bias is step scanned to obtain the maximal value of the peak-to-peak current value I_pp of the SQUID magnetometer modulation curve. We choose this point as the optimal one. Using the above control system, more than 30 weakly damped SQUID magnetometers with area of 5 × 5 mm^2 or 10 × 10 mm^2 are adjusted and a 36-channel magnetocardiography system perfectly worked in a magnetically shielded room. The average white flux noise is 15 μΦ_0/Hz^{1/2}.

  18. Second order gradiometer and dc SQUID integrated on a planar substrate

    Science.gov (United States)

    van Nieuwenhuyzen, G. J.; de Waal, V. J.

    1985-02-01

    An integrated system of a thin-film niobium dc superconducting quantum interference device (SQUID) and a second order gradiometer on a planar substrate is described. The system consists of a dc SQUID with eight loops in parallel, each sensitive to the second derivative ∂2Bz/∂x2 of the magnetic field. The calculated SQUID inductance is 1.3 nH. With an overall size of 16×16.5 mm2 a sensitivity of 1.5×10-9 Tm-2 Hz-1/2 is obtained. The measured transfer function for uniform fields perpendicular to the plane of the gradiometer is 2.1×10-7 T Φ-10.

  19. Second order gradiometer and dc SQUID integrated on a planar substrate

    Energy Technology Data Exchange (ETDEWEB)

    van Nieuwenhuyzen, G.J.; de Waal, V.J.

    1985-02-15

    An integrated system of a thin-film niobium dc superconducting quantum interference device (SQUID) and a second order gradiometer on a planar substrate is described. The system consists of a dc SQUID with eight loops in parallel, each sensitive to the second derivative partial/sup 2/B/sub z//partialx/sup 2/ of the magnetic field. The calculated SQUID inductance is 1.3 nH. With an overall size of 16 x 16.5 mm/sup 2/ a sensitivity of 1.5 x 10/sup -9/ Tm/sup -2/ Hz/sup -1//sup ///sup 2/ is obtained. The measured transfer function for uniform fields perpendicular to the plane of the gradiometer is 2.1 x 10/sup -7/ T Phi/sup -1//sub 0/.

  20. Routine clinical heart examinations using SQUID magnetocardiography at University of Tsukuba Hospital

    Science.gov (United States)

    Inaba, T.; Nakazawa, Y.; Yoshida, K.; Kato, Y.; Hattori, A.; Kimura, T.; Hoshi, T.; Ishizu, T.; Seo, Y.; Sato, A.; Sekiguchi, Y.; Nogami, A.; Watanabe, S.; Horigome, H.; Kawakami, Y.; Aonuma, K.

    2017-11-01

    A 64-channel Nb-based DC-SQUID magnetocardiography (MCG) system was installed at the University of Tsukuba Hospital (UTH) in March 2007 after obtaining Japanese pharmaceutical approval and insurance reimbursement approval. In the period between 2008 and 2016, the total number of patients was 10 085. The heart diseases diagnosed in fetuses as well as adults are mainly atrial arrhythmia, abnormal repolarization, ventricular arrhythmia, and fetal arrhythmia. In most cases of insufficient diagnostic accuracy with electrocardiography, SQUID MCG precisely revealed these heart diseases as an abnormal electrical current distribution. Based on success in routine examinations, SQUID MCG is now an indispensable clinical instrument with diagnostic software tuned up during routine use at UTH.

  1. A SQUID magnetometry system for a cryogenic neutron electric dipole moment experiment

    Energy Technology Data Exchange (ETDEWEB)

    Henry, S., E-mail: s.henry@physics.ox.ac.uk; Clarke, C.; Cottle, A.; Lynch, A.; Pipe, M.

    2014-11-01

    Precision magnetometry is an essential component of any neutron electric dipole moment experiment in order to correct shifts in the neutron precession frequency due to changes in the magnetic field. We have developed a magnetometry system using 12 SQUID sensors, designed to operate in 0.5 K superfluid helium. The pick-up loops located near the neutron cell are connected to the SQUID sensors by ∼2 m twisted wire pairs. The SQUID readout cables are run via an intermediate stage at 4.2 K. The system has been installed and tested in the cryoEDM apparatus at the ILL, Grenoble, and used to characterise the magnetic environment. Further tests in a suitable low noise environment confirm it meets our requirements.

  2. Squid measurement of the Verwey transition on epitaxial (1 0 0) magnetite thin films

    International Nuclear Information System (INIS)

    Dediu, V.; Arisi, E.; Bergenti, I.; Riminucci, A.; Solzi, M.; Pernechele, C.; Natali, M.

    2007-01-01

    We report results on epitaxial magnetite (Fe 3 O 4 ) thin films grown by electron beam ablation on (1 0 0) MgAl 2 O 4 substrates. At 120 K magnetite undergoes a structural and electronic transition, the so-called Verwey transition, at which magnetic and conducting properties of the material change. We observed the Verwey transition on epitaxial films with a thickness of 50 nm by comparing zero-field cooling (ZFC) and field cooling (FC) curves measured with a superconducting quantum interference device (SQUID) magnetometer. Observation of the Verwey transition by SQUID measurements in the films is sign of their high crystalline quality. Room temperature ferromagnetism has also been found by magneto-optical Kerr rotation (MOKE) and confirmed by SQUID measurements, with a hysteresis loop showing a coercive field of hundreds of Oe

  3. Revising and editing for translators

    CERN Document Server

    Mossop, Brian

    2014-01-01

    Revising and Editing for Translators provides guidance and learning materials for translation students learning to edit texts written by others, and professional translators wishing to improve their self-revision ability or learning to revise the work of others. Editing is understood as making corrections and improvements to texts, with particular attention to tailoring them to the given readership. Revising is this same task applied to draft translations. The linguistic work of editors and revisers is related to the professional situations in which they work. Mossop offers in-depth coverage of a wide range of topics, including copyediting, style editing, structural editing, checking for consistency, revising procedures and principles, and translation quality assessment. This third edition provides extended coverage of computer aids for revisers, and of the different degrees of revision suited to different texts. The inclusion of suggested activities and exercises, numerous real-world examples, a proposed gra...

  4. Direct readout flux locked loop circuit with automatic tuning of bias current and bias flux for high-Tc SQUID

    International Nuclear Information System (INIS)

    Hirano, T.; Nagaishi, T.; Itozaki, H.

    1999-01-01

    Measurement of high-frequency magnetic signals has been required from some SQUID applications. We fabricated a high-T c SQUID magnetic sensor system that can treat high-frequency signals. This system is composed of a SQUID, a preamplifier circuit, a flux locked loop (FLL) circuit with I/O and a personal computer and a PC card. We used the FLL circuit with no modulation to treat the high-frequency signal and to simplify the circuit. This system can treat a signal from dc to 1 MHz. All the sequence from tuning the SQUID to data acquisition can be done by a personal computer. This system successfully realized easy operation of SQUID measurement. (author)

  5. Effect of thermal processing and canning on cadmium and lead levels in California market squid: the role of metallothioneins.

    Science.gov (United States)

    Galitsopoulou, A; Georgantelis, D; Kontominas, M G

    2013-01-01

    The effects of two common seafood preparation practices (roasting and industrial canning) on the heavy metal content--cadmium (Cd) and lead (Pb)--of various tissues of California market squid were studied. Emphasis was placed on the role of metallothioneins (MT) in Cd and Pb behaviour during processing. Cd and Pb analysis was conducted by a Zeeman GTA-AAS atomic absorption spectrometry system; MT analysis was performed by a mercury saturation assay. Results showed that Cd levels in the mantle and whole squid were considerably affected by both processing practices, reaching a 240% increase in mantle and a 40% increase in whole squid. Interestingly, Cd behaviour was associated with MT changes during squid processing. On the other hand, Pb content was not affected from either processing or associated with MT content in the raw or processed squid. Therefore, processing operations may affect Cd and Pb content differently due to the specific metal bioaccumulation and chemical features of each heavy metal type.

  6. Non-destructive testing (NDT) of metal cracks using a high Tc rf-SQUID and eddy current method

    Energy Technology Data Exchange (ETDEWEB)

    Lu, D.F.; Fan, C.; Ruan, J.Z. [Midwest Superconductivity Inc., Lawrence, KS (United States)] [and others

    1994-12-31

    A SQUID is the most sensitive device to detect change in magnetic field. A non-destructive testing (NDT) device using high temperature SQUIDs and eddy current method will be much more sensitive than those currently used eddy current systems, yet much cheaper than one with low temperature SQUIDs. In this paper, we present our study of such a NDT device using a high temperature superconducting rf-SQUID as a gradiometer sensor. The result clearly demonstrates the expected sensitivity of the system, and indicates the feasibility of building a portable HTS SQUID NDT device with the help from cryocooler industry. Such a NDT device will have a significant impact on metal corrosion or crack detection technology.

  7. Trophic relationships between the jumbo squid (Dosidicus gigas and the lightfish (Vinciguerria lucetia in the Humboldt Current System off Peru

    Directory of Open Access Journals (Sweden)

    Rigoberto Rosas-Luis

    2011-04-01

    Full Text Available Acoustic surveys for assessing the biomass and distribution of the jumbo squid (Dosidicus gigas and the lightfish (Vinciguerria lucetia were carried out in the Humboldt Current System of Peru in 2007 and 2008. At the same time, 937 jumbo squid were caught and their stomach contents analyzed. The diet of the jumbo squid was dominated by mesopelagic fish. The first component of their fish diet was V. lucetia and the second component was the myctophid fish Diogenichthys laternatus. Acoustic biomass estimates of these species show that V. lucetia is an important component in aggregative structures in the Humboldt Current System of Peru and its distribution and movements are closely related to the migratory movements of the jumbo squid. The trophic relationship observed between D. gigas and V. lucetia promotes an increase in jumbo squid biomass and, has a positive trophic effect on the ocean ecosystem.

  8. Non-destructive testing (NDT) of metal cracks using a high Tc rf-SQUID and eddy current method

    International Nuclear Information System (INIS)

    Lu, D.F.; Fan, C.; Ruan, J.Z.

    1994-01-01

    A SQUID is the most sensitive device to detect change in magnetic field. A non-destructive testing (NDT) device using high temperature SQUIDs and eddy current method will be much more sensitive than those currently used eddy current systems, yet much cheaper than one with low temperature SQUIDs. In this paper, we present our study of such a NDT device using a high temperature superconducting rf-SQUID as a gradiometer sensor. The result clearly demonstrates the expected sensitivity of the system, and indicates the feasibility of building a portable HTS SQUID NDT device with the help from cryocooler industry. Such a NDT device will have a significant impact on metal corrosion or crack detection technology

  9. Axon-Schwann cell interaction in the squid nerve fibre.

    Science.gov (United States)

    Villegas, J

    1972-09-01

    The electrical properties of Schwann cells and the effects of neuronal impulses on their membrane potential have been studied in the giant nerve fibre of the squid.1. The behaviour of the Schwann cell membrane to current injection into the cell was ohmic. No impulse-like responses were observed with displacements of 35 mV in the membrane potential. The resistance of the Schwann cell membrane was found to be approximately 10(3) Omega cm(2).2. A long-lasting hyperpolarization is observed in the Schwann cells following the conduction of impulse trains by the axon. Whereas the propagation of a single impulse had little effect, prolonged stimulation of the fibre at 250 impulses/sec was followed by a hyperpolarization of the Schwann cell that gradually declined over a period of several minutes.3. The prolonged effects of nerve impulse trains on the Schwann cell were similar to those produced by depolarizing current pulses applied to the axon by the voltage-clamp technique. Thus, a series of depolarizing pulses in the axon was followed by a long-lasting hyperpolarization of the Schwann cells. In contrast, the application of a series of hyperpolarizing 100 mV pulses at a frequency of 1/sec had no apparent effects.4. Changes in the external potassium concentration did not reproduce the long-lasting effects of nerve excitation.5. The hyperpolarizing effects of impulse trains were abolished by the incubation of the nerve fibre in a sea-water solution containing trypsin.6. These findings are discussed in relation to the possible mechanisms that might be responsible for the long-lasting hyperpolarizations of the Schwann cells.

  10. Quantum decay of metastable current states in rf squids

    International Nuclear Information System (INIS)

    Dmitrenko, I.M.; Khlus, V.A.; Tsoj, C.M.; Shnyrkov, V.I.

    1985-01-01

    Quantum decay of metastable current states in a rf SQUID superconducting ring of a hysteresis mode are considered. Point contacts are used as a Josephson weak link. The first derivative of rf IVC, dVsub(T)/dIsub(RF), is measured which gives the dependence of the density of decay probability on the amplitude of magnetic flux oscillations in the ring. The temperature dependence of probability distribution width between 4.2 and 0.5 K suggests that for most of high-ohmic contacts Nb-Nb, Nb-Ag-Nb the quantum mechanisms of decay become dominant beginning with the temperature of about 2 K. The experimental parameters of distribution of decay probability in the quantum limit are compared to those calculated by the theory of macroscopic quantum tunneling in the limit of high and low dissipation. The experimental values of probability density distribution width and characteristic quantum temperature are higher than the theoretical ones, the fact can be attributed to the deviation of current-phase relation of contact from a sinusoidal one. Besides, some contacts seem to correspond to the case of an intermediate value of dissipation. As the frequency of rf oscillations varies from 30 to 6 MHz, the distribution width remains unchanged in accordance with the theory of quantum tunneling decay of metastable current state in the ring in the limit of high damping. At low temperatures (T approximately 0.5 K), and rather small damping coefficient, the density of probability displays anomalous peaks when the amplitude of rf oscillations is lower considerably than the critical vaiue of magnetic flux in the ring

  11. Detection of thermal aging degradation and plastic strain damage for duplex stainless steel using SQUID sensor

    International Nuclear Information System (INIS)

    Otaka, M.; Evanson, S.; Hesegawa, K.; Takaku, K.

    1991-01-01

    An apparatus using a SQUID sensor is developed for nondestructive inspection. The measurements are obtained with the SQUID sensor located approximately 150 mm from the specimen. The degradation of thermal aging and plastic strain for duplex stainless steel is successfully detected independently from the magnetic characterization measurements. The magnetic flux density under high polarizing field is found to be independent of thermal aging. Coercive force increases with thermal aging time. On the other hand, the magnetic flux density under high field increases with the plastic strain. Coercive force is found to be independent of the plastic strain. (author)

  12. RNA Crystallization

    Science.gov (United States)

    Golden, Barbara L.; Kundrot, Craig E.

    2003-01-01

    RNA molecules may be crystallized using variations of the methods developed for protein crystallography. As the technology has become available to syntheisize and purify RNA molecules in the quantities and with the quality that is required for crystallography, the field of RNA structure has exploded. The first consideration when crystallizing an RNA is the sequence, which may be varied in a rational way to enhance crystallizability or prevent formation of alternate structures. Once a sequence has been designed, the RNA may be synthesized chemically by solid-state synthesis, or it may be produced enzymatically using RNA polymerase and an appropriate DNA template. Purification of milligram quantities of RNA can be accomplished by HPLC or gel electrophoresis. As with proteins, crystallization of RNA is usually accomplished by vapor diffusion techniques. There are several considerations that are either unique to RNA crystallization or more important for RNA crystallization. Techniques for design, synthesis, purification, and crystallization of RNAs will be reviewed here.

  13. HMMEditor: a visual editing tool for profile hidden Markov model

    Directory of Open Access Journals (Sweden)

    Cheng Jianlin

    2008-03-01

    Full Text Available Abstract Background Profile Hidden Markov Model (HMM is a powerful statistical model to represent a family of DNA, RNA, and protein sequences. Profile HMM has been widely used in bioinformatics research such as sequence alignment, gene structure prediction, motif identification, protein structure prediction, and biological database search. However, few comprehensive, visual editing tools for profile HMM are publicly available. Results We develop a visual editor for profile Hidden Markov Models (HMMEditor. HMMEditor can visualize the profile HMM architecture, transition probabilities, and emission probabilities. Moreover, it provides functions to edit and save HMM and parameters. Furthermore, HMMEditor allows users to align a sequence against the profile HMM and to visualize the corresponding Viterbi path. Conclusion HMMEditor provides a set of unique functions to visualize and edit a profile HMM. It is a useful tool for biological sequence analysis and modeling. Both HMMEditor software and web service are freely available.

  14. Ribosomal protein S14 transcripts are edited in Oenothera mitochondria.

    Science.gov (United States)

    Schuster, W; Unseld, M; Wissinger, B; Brennicke, A

    1990-01-01

    The gene encoding ribosomal protein S14 (rps14) in Oenothera mitochondria is located upstream of the cytochrome b gene (cob). Sequence analysis of independently derived cDNA clones covering the entire rps14 coding region shows two nucleotides edited from the genomic DNA to the mRNA derived sequences by C to U modifications. A third editing event occurs four nucleotides upstream of the AUG initiation codon and improves a potential ribosome binding site. A CGG codon specifying arginine in a position conserved in evolution between chloroplasts and E. coli as a UGG tryptophan codon is not edited in any of the cDNAs analysed. An inverted repeat 3' of an unidentified open reading frame is located upstream of the rps14 gene. The inverted repeat sequence is highly conserved at analogous regions in other Oenothera mitochondrial loci. Images PMID:2326162

  15. The Craft of Editing

    DEFF Research Database (Denmark)

    Moeran, Brian

    To edit is to make a choice, or series of choices. Will I write a rough draft of this essay in longhand, or hammer it out on my computer? If the latter, what font shall I use? Times New Roman, Book Antiqua, or Garamond? Once I get started, what style shall I adopt: realistic, confessional or impr...... or impressionistic; or a combination of all three (Van Maanen 1988)? Should I try to impress with ‘learned scholarship’, or should I merely outline in conversational English a few thoughts based on my own experiences?...

  16. With this Special Edition

    Directory of Open Access Journals (Sweden)

    Oscar Antonio Martínez Molina

    2017-02-01

    Full Text Available With this Special Edition, the refereed Scientific Magazine, published in February 2017, presents a nourished and multidisciplinary theme, from the relationship of Environmental Education, in this ecological sharing man-environment; the social responsibility from the Management environment and the motivational values ​​conducive to the teaching performance in the different educational levels. Twenty-five (25 articles, generated from research production in university environments at the International level, are a signature of the quality of articles / essays presented in this Special Edition. Several reasons motivate the literary pen of our authors, adjusting to the rhythm of the times and the use of new technologies; and in correspondence with the care of the environment, this way of disseminating and making visible the scientific contents of humanistic and social court, support the care and protection of the forests, being an online production, in the Cloud. Thanks to the support of the Instituto Internacional de Investigación y Desarrollo Tecnológico Educativo INDTEC, CA, Scientific Magazine has been able to develop from the cooperative work of the people who compose its different committees: Editorial Academic Committee, Academic Scientific Committee and the Arbitrators in the review and valuation of the quality of the articles. With these assets, the Scientific Magazine, opening to the general public and especially to the academic new intellectual horizons.

  17. Natural Hazards, Second Edition

    Science.gov (United States)

    Rouhban, Badaoui

    Natural disaster loss is on the rise, and the vulnerability of the human and physical environment to the violent forces of nature is increasing. In many parts of the world, disasters caused by natural hazards such as earthquakes, floods, landslides, drought, wildfires, intense windstorms, tsunami, and volcanic eruptions have caused the loss of human lives, injury, homelessness, and the destruction of economic and social infrastructure. Over the last few years, there has been an increase in the occurrence, severity, and intensity of disasters, culminating with the devastating tsunami of 26 December 2004 in South East Asia.Natural hazards are often unexpected or uncontrollable natural events of varying magnitude. Understanding their mechanisms and assessing their distribution in time and space are necessary for refining risk mitigation measures. This second edition of Natural Hazards, (following a first edition published in 1991 by Cambridge University Press), written by Edward Bryant, associate dean of science at Wollongong University, Australia, grapples with this crucial issue, aspects of hazard prediction, and other issues. The book presents a comprehensive analysis of different categories of hazards of climatic and geological origin.

  18. Instrumental analysis, second edition

    International Nuclear Information System (INIS)

    Christian, G.D.; O'Reilly, J.E.

    1988-01-01

    The second edition of Instrumental Analysis is a survey of the major instrument-based methods of chemical analysis. It appears to be aimed at undergraduates but would be equally useful in a graduate course. The volume explores all of the classical quantitative methods and contains sections on techniques that usually are not included in a semester course in instrumentation (such as electron spectroscopy and the kinetic methods). Adequate coverage of all of the methods contained in this book would require several semesters of focused study. The 25 chapters were written by different authors, yet the style throughout the book is more uniform than in the earlier edition. With the exception of a two-chapter course in analog and digital circuits, the book purports to de-emphasize instrumentation, focusing more on the theory behind the methods and the application of the methods to analytical problems. However, a detailed analysis of the instruments used in each method is by no means absent. The book has the favor of a user's guide to analysis

  19. Verification of the weak equivalence principle of supports and heavy masses using SQUIDs; Ueberpruefung des schwachen Aequivalenzprinzips von Traegern und schwerer Masse mittels Squids

    Energy Technology Data Exchange (ETDEWEB)

    Vodel, W.; Nietzsche, S.; Neubert, R. [Friedrich-Schiller-Universitaet Jena (Germany). Inst. fuer Festkoerperphysik; Dittus, H. [Univ. Bremen (Germany). Zentrum fuer angewandte Raumfahrttechnologie und Mikrogravitation

    2003-07-01

    The weak equivalence principle is one of the fundamental hypotheses of general relativity and one of the key elements of our physical picture of the world, but since Galileo there has been no satisfactory way of verifying it. The new SQUID technology may offer a solution. The contribution presents the experiments of Jena University. Applications are envisaged, e.g., in the STEP space mission of the NASA/ESA. [German] Das Schwache Aequivalenzprinzip ist eine der grundlegenden Hypothesen der Allgemeinen Relativitaetstheorie und damit einer der Grundpfeiler unseres physikalischen Weltbildes. Obwohl es seit den ersten Experimenten von Galileo Galilei am Schiefen Turm zu Pisa im Jahre 1638 bis heute schon zahlreiche und immer praeziser werdende Messungen zur Ueberpruefung der Aequivalenz von schwerer und traeger Masse gegeben hat, ist die strenge Gueltigkeit dieses fundamentalen Prinzips experimentell vergleichsweise unzureichend bestimmt. Neuere Methoden, wie der Einsatz SQUID-basierter Messtechnik und die Durchfuehrung von Experimenten auf Satelliten, lassen Verbesserungen schon in naher Zukunft erwarten, so dass theoretische Ueberlegungen zur Vereinigung aller uns bekannten physikalischen Wechselwirkungen, die eine Verletzung des Schwachen Aequivalenzprinzips voraussagen, experimentell eingegrenzt werden koennten. Der Beitrag gibt einen Ueberblick ueber die an der Universitaet Jena entwickelte SQUID-basierte Messtechnik zum Test des Aequivalenzprinzips und fasst die bisher bei Freifallversuchen am Fallturm Bremen erzielten experimentellen Ergebnisse zusammen. Ein Ausblick auf die geplante Raumfahrtmission STEP der NASA/ESA zum Praezisionstest des Schwachen Aequivalenzprinzips schliesst den Beitrag ab. (orig.)

  20. RNA Origami

    DEFF Research Database (Denmark)

    Sparvath, Steffen Lynge

    introducerede vores gruppe den enkeltstrengede RNA-origami metode, der giver mulighed for cotranscriptional foldning af veldefinerede nanostrukturer, og er en central del af arbejdet præsenteret heri. Denne ph.d.-afhandling udforsker potentielle anvendelser af RNA-origami nanostrukturer, som nanomedicin eller...... biosensorer. Afhandlingen består af en introduktion til RNA-nanoteknologi feltet, en introduktion af enkeltstrenget RNA-origami design, og fire studier, der beskriver design, produktion og karakterisering af både strukturelle og funktionelle RNA-origamier. Flere RNA-origami designs er blevet undersøgt, og...... projekterne, der indgår i denne afhandling, inkluderer de nyeste fremskridt indenfor strukturel RNA-nanoteknologi og udvikling af funktionelle RNA-baserede enheder. Det første studie beskriver konstruktion og karakterisering af en enkeltstrenget 6-helix RNA-origami stuktur, som er den første demonstration af...

  1. Cadmium content in fresh and canned squid (Loligo opalescens) from the Pacific coastal waters of California (USA).

    Science.gov (United States)

    Galitsopoulou, A; Georgantelis, D; Kontominas, M G

    2009-01-01

    Cadmium (Cd) levels were determined in 70 samples of mantle tissue and 70 whole individual squid (Loligo opalescens; commercially known as California squid). Samples were collected from the coastal zones of California (USA) during the period 2007/2008. To further investigate consumer exposure to processed fishery products, cadmium concentration was also determined in 200 canned samples of squid. Cd concentrations in raw mantle were low, between 0.01 and 0.29 mg kg(-1) and below the tolerance limit of current regulations (1 mg kg(-1)). Respective concentrations in whole individuals were significantly higher, ranging from 0.51 to 1.18 mg kg(-1), attributed to the presence of the visceral portion in whole squid samples. Cd concentrations varied in relation to age and sex of squid, indicating that several physiological factors may influence accumulation. Furthermore, canning of squid substantially enhanced Cd levels. Cd concentration ranged 0.17-0.67 mg kg(-1) in canned mantle tissue and 0.86-2.07 mg kg(-1) in canned whole squid samples, due to both concentration after canning and movement of the metal between different tissues. Several biological compounds, including metallothioneins, nucleic acids and enzymes, may affect Cd concentrations in commercial fishery products.

  2. Effects of Gamma Irradiation on Shelf-Life and Sensory Scores of Squid Sundae under Accelerated Storage Conditions

    International Nuclear Information System (INIS)

    Kim, H.J.; Kim, K.B.W.R.; Kim, D.H.; Sunwoo, C.; Jung, S.A.; Jeong, D.H.; Jung, H.Y.; Ahn, D.H.; Kim, J.H.; Lee, J.W.; Do, S.R.; Byun, M.W.

    2012-01-01

    This study was conducted to examine the effects of gamma irradiation on the shelf-life and sensory scores of squid Sundae under accelerated storage conditions. Squid Sundae was stored at 37°C for 35 days following gamma irradiation at doses of 0, 10, and 20 kGy. For total viable cell counts, control and gamma-irradiated (GI) (10 kGy) squid Sundae were already spoiled in 4 days, whereas GI (20 kGy) squid Sundae showed complete suppression of bacterial growth during storage. There were no significant changes in pH values compared to the control. The VBN and TBARS (thiobarbituric acid reactive substance) values of GI (20 kGy) squid Sundae were significantly lower than those of the control. In addition, the induction period of GI (20 kGy) squid Sundae as measured by a Rancimat showed a higher level compared to that of the control. In the sensory evaluation, there were no significant changes between the control and GI samples. These results suggest that a dose of 20 kGy is the optimum and effective dose for preservation of squid Sundae. (author)

  3. Potential use of stable isotope and fatty acid analyses for traceability of geographic origins of jumbo squid (Dosidicus gigas).

    Science.gov (United States)

    Gong, Yi; Li, Yunkai; Chen, Xinjun; Chen, Ling

    2018-04-15

    Squid is an important seafood resource for Asian and European countries. With the continuous development of processed squid products, an effective traceability system has become increasingly prominent. Here, we attempt to trace the fishery products of the main target species, jumbo squid (Dosidicus gigas), by using biochemical tracers. Carbon and nitrogen isotope ratios (δ 13 C and δ 15 N values) and fatty acid profiles were identified in squid from three harvest locations in the eastern Pacific Ocean by isotope ratio mass spectrometry and gas chromatography/mass spectrometry, respectively. Comparative analysis was used to evaluate the geographic variations in tracers and to identify the suitable discriminatory variables among origins. Significant spatial variations were found in isotopic values and fatty acid profiles in squid muscle tissues, possibly because of different food availability and/or oceanographic conditions that each group experiences at a given location. The stepwise discriminant analysis indicated that δ 15 N, C16:1n7, C17:1n7, C18:2n6, C20:1 and C20:4n6 were effective variables at differentiating origin. Combined use of stable isotope ratios and fatty acid analyses could trace geographic origins of jumbo squid. This study provides an alternative approach for improving authenticity evaluation of commercial squid products. Copyright © 2018 John Wiley & Sons, Ltd.

  4. Expression of squid iridescence depends on environmental luminance and peripheral ganglion control.

    Science.gov (United States)

    Gonzalez-Bellido, P T; Wardill, T J; Buresch, K C; Ulmer, K M; Hanlon, R T

    2014-03-15

    Squid display impressive changes in body coloration that are afforded by two types of dynamic skin elements: structural iridophores (which produce iridescence) and pigmented chromatophores. Both color elements are neurally controlled, but nothing is known about the iridescence circuit, or the environmental cues, that elicit iridescence expression. To tackle this knowledge gap, we performed denervation, electrical stimulation and behavioral experiments using the long-fin squid, Doryteuthis pealeii. We show that while the pigmentary and iridescence circuits originate in the brain, they are wired differently in the periphery: (1) the iridescence signals are routed through a peripheral center called the stellate ganglion and (2) the iridescence motor neurons likely originate within this ganglion (as revealed by nerve fluorescence dye fills). Cutting the inputs to the stellate ganglion that descend from the brain shifts highly reflective iridophores into a transparent state. Taken together, these findings suggest that although brain commands are necessary for expression of iridescence, integration with peripheral information in the stellate ganglion could modulate the final output. We also demonstrate that squid change their iridescence brightness in response to environmental luminance; such changes are robust but slow (minutes to hours). The squid's ability to alter its iridescence levels may improve camouflage under different lighting intensities.

  5. Effect of electron beam on the microbiological and sensory characteristics of squid jeotkal and its ingredients

    International Nuclear Information System (INIS)

    Liu Xiande; Piao Linghua

    2012-01-01

    A seasoned squid Jeotkal, Koran traditional fermented seafood, and its ingredients for manufacturing, including red hot pepper powder and ground garlic were irradiated by 0, 0.5, 1, 2 and 5 kGy electron beam and stored at 4 ℃ for 4 weeks to determine the changes of microorganisms and sensory characteristics. The initial contamination of squid Jeotkal such as total aerobic bacteria, yeast and mold, and coliform bacterial were at the levels of 2.88, 3.04 and 4.20 logCFU/g, respectively. However, 5 kGy electron beam irradiation reduced the total aerobic bacteria about 1 logCFU/g. Yeast and mold and coliform bacterial were reduced 1 ∼ 2 logCFU/g after 2 kGy irradiation and reached to undetected level when the sample was irradiated at 5 kGy and following storage at 4 ℃ for 4 weeks. Sensory characteristics showed that 5 kGy electron beam irradiation did not adversely affect overall acceptability of squid Jeotkal and its ingredients during 4 ℃ storage. Therefore, electron beam irradiation is one of the possible methods to improve storage stability of seasoned squid Jeotkal. (authors)

  6. Highly balanced gradiometer systems based on HTS-SQUIDs for the use in magnetically unshielded environment

    NARCIS (Netherlands)

    Borgmann, H.J.R.; Rijpma, A.P.; ter Brake, Hermanus J.M.; Rogalla, Horst; David, P.

    1999-01-01

    Two different concepts for gradiometer formation were tested applying high-temperature rf SQUIDs operated at 77 K in liquid nitrogen. All gradiometer systems are fully based on magnetometers. The first concept applies a compensating magnetometer at different positions to actively cancel the magnetic

  7. Integrated de SQUID magnetometer with high dV/dB

    International Nuclear Information System (INIS)

    Drung, D.; Cantor, R.; Peters, M.; Ryhanen, T.; Kochi, H.

    1991-01-01

    This paper presents a directly coupled dc SQUID magnetometer with very simple feedback electronics. The magnetometer has been integrated on a 7.2 x 7.2 mm 2 chip and fabricated using a four-level Nb/Si x N v /Nb process. Eight pick-up loops are connected in parallel to directly form the SQUID inductance of about 0.4 nH which leads to a high sensitivity B/Φ = 0.47 nT/Φ. An Additional Positive Feedback (APF) circuit on the magnetometer chip has been used to increase the gradient of the V-μ characteristic to dV/dΦ ≅ 300 μV/Φ 0 at the SQUID operating point. The resulting gradient of the transfer function of dV/dB ≅ 640 μV/nT makes it possible to directly read out the SQUID without helium temperature impedance matching circuits or flux modulation techniques

  8. Magnetic properties of thin Ni films measured by a dc SQUID-based magnetic microscope

    DEFF Research Database (Denmark)

    Snigirev, O.V.; Andreev, K.E.; Tishin, A.M.

    1997-01-01

    We have applied a scanning HTS (high-temperature superconductor) de SQUID (superconducting quantum interference device) -based magnetic microscope to study the magnetic properties of Au/Ni/Si(100) films in the thickness range from 8 to 200 Angstrom at T = 77 K. A one-domain structure with in...

  9. The effects of jig color and lunar bright on coastal squid jigging ...

    African Journals Online (AJOL)

    Squid jigging experiments were carried out to determine whether differences occurred between different colors and lunar brightness in Middle Eastern coast of Aegean Sea. Five different colors of jigs (red, blue, green, orange and white) were used together in same angle. According to one-way analysis of variance results, ...

  10. Rotational population patterns and searches for the nuclear SQUID (Superconducting Quantum Interference Device)

    International Nuclear Information System (INIS)

    Canto, L.F.; Donangelo, R.J.; Farhan, A.R.; Guidry, M.W.; Rasmussen, J.O.; Ring, P.; Stoyer, M.A.

    1989-11-01

    This paper presents new theoretical results for rotational population patterns in the nuclear SQUID effect. (The term nuclear SQUID is in analogy to the solid-state Superconducting Quantum Interference Devices.) The SQUID effect is an interesting new twist to an old quest to understand Coriolis anti-pairing (CAP) effects in nuclear rotational bands. Two-neutron transfer reaction cross sections among high-spin states have long been touted as more specific CAP probes than other nuclear properties. Heavy projectiles like Sn or Pb generally are recommended to pump the deformed nucleus to as high spin as possible for transfer. The interference and sign reversal of 2n transfer amplitudes at high spin, as predicted in the early SQUID work imposes the difficult requirement of Coulomb pumping to near back-bending spins at closest approach. For Pb on rare earths we find a dramatic departure from sudden-approximation, so that the population depression occurs as low as final spin 10h. 14 refs., 8 figs

  11. High-Tc SQUID Application for Roll to Roll Metallic Contaminant Detector

    International Nuclear Information System (INIS)

    Tanaka, S.; Kitamura, Y.; Uchida, Y.; Hatsukade, Y.; Ohtani, T.; Suzuki, S.

    2012-01-01

    A sensitive eight-channel high-Tc Superconducting Interference Device (SQUID) detection system for magnetic contaminant in a lithium ion battery anode was developed. Finding ultra-small metallic foreign matter is an important issue for a manufacturer because metallic contaminants carry the risk of an internal short. When contamination occurs, the manufacturer of the product suffers a great loss from recalling the tainted product. Metallic particles with outer dimensions smaller than 100 microns cannot be detected using a conventional X-ray imaging system. Therefore, a highly sensitive detection system for small foreign matter is required. We have already developed a detection system based on a single-channel SQUID gradiometer and horizontal magnetization. For practical use, the detection width of the system should be increased to at least 65 mm by employing multiple sensors. In this paper, we present an 8-ch high-Tc SQUID roll-to-roll system for inspecting a lithium-ion battery anode with a width of 65 mm. A special microscopic type of a cryostat was developed upon which eight SQUID gradiometers were mounted. As a result, small iron particles of 35 microns on a real lithium-ion battery anode with a width of 70 mm were successfully detected. This system is practical for the detection of contaminants in a lithium ion battery anode sheet.

  12. Comparison live adult Artemia and squid meat on the growth of Penaeid shrimp Metapenaeus dobsoni (Miers)

    Digital Repository Service at National Institute of Oceanography (India)

    Nair, S.R.S.; Achuthankutty, C.T.; Royan, J.P.

    An experiment lasting 14 weeks was conducted to compare the efficiency of live adult Artemia with fresh squid meat on growth of penaeid shrimp Metapenaeus dobsoni. The shrimps were found actively feeding on live Artemia and grew 84% more than those...

  13. A simple method for checking the balance of gradiometers used with squids

    International Nuclear Information System (INIS)

    Eghrari, I.R.; Ribeiro, P.C.

    1978-11-01

    A simple technique for detecting the degree of balance of first order gradiometers before connecting them to the SQUID is described. The effect of thermal cycling on this balance is given for different materials used in the construction of the gradiometers [pt

  14. Ocean acidification responses in paralarval squid swimming behavior using a novel 3D tracking system

    KAUST Repository

    Zakroff, Casey J.; Mooney, T. Aran; Wirth, Colin

    2017-01-01

    . pealeii from eggs reared under chronic OA demonstrated measurable impairments to swimming activity and control. This required the development of a novel, cost-effective, and robust method for 3D motion tracking and analysis. Squid eggs were reared in pCO2

  15. Rapid Associative Learning and Stable Long-Term Memory in the Squid Euprymna scolopes.

    Science.gov (United States)

    Zepeda, Emily A; Veline, Robert J; Crook, Robyn J

    2017-06-01

    Learning and memory in cephalopod molluscs have received intensive study because of cephalopods' complex behavioral repertoire and relatively accessible nervous systems. While most of this research has been conducted using octopus and cuttlefish species, there has been relatively little work on squid. Euprymna scolopes Berry, 1913, a sepiolid squid, is a promising model for further exploration of cephalopod cognition. These small squid have been studied in detail for their symbiotic relationship with bioluminescent bacteria, and their short generation time and successful captive breeding through multiple generations make them appealing models for neurobiological research. However, little is known about their behavior or cognitive ability. Using the well-established "prawn-in-the-tube" assay of learning and memory, we show that within a single 10-min trial E. scolopes learns to inhibit its predatory behavior, and after three trials it can retain this memory for at least 12 d. Rapid learning and very long-term retention were apparent under two different training schedules. To our knowledge, this study is the first demonstration of learning and memory in this species as well as the first demonstration of associative learning in any squid.

  16. A nitrogen triple-point thermal storage unit for cooling a SQUID magnetometer

    NARCIS (Netherlands)

    Rijpma, A.P.; Meenderink, D.J.; Reincke, H.A.; Venhorst, G.C.F.; Holland, H.J.; Brake, ter H.J.M.

    2005-01-01

    In order to achieve turnkey operation, the use is planned of cryocoolers to cool a SQUID magnetometer system. To minimize the magnetical and mech. interference from the coolers, they are switched off during the actual measurements. Consequently, a thermal storage unit (TSU) is required with

  17. A nitrogen triple-point thermal storage unit for cooling a SQUID magnetometer

    NARCIS (Netherlands)

    Rijpma, A.P.; Meenderink, D.J.; Reincke, H.A.; Venhorst, G.C.F.; Venhorst, G.C.F.; Holland, Herman J.; ter Brake, Hermanus J.M.

    2005-01-01

    In order to achieve turnkey operation, we plan to use cryocoolers to cool a SQUID magnetometer system. To minimize the magnetical and mechanical interference from the coolers, we intend to switch them off during the actual measurements. Consequently, a thermal storage unit (TSU) is required with

  18. Closed-cycle gas flow system for cooling a HTc dc-SQUID magnetometer

    NARCIS (Netherlands)

    Bosch, van den P.J.; Holland, H.J.; Brake, ter H.J.M.; Rogalla, H.

    1994-01-01

    A closed-cycle gas flow system for cooling a high-crit. temp. d.c.-superconducting quantum interference device (SQUID) magnetometer by means of a cryocooler has been designed, constructed and tested. The magnetometer is aimed to measure heart signals with a sensitivity of 0.1 pT/Hz1/2. The required

  19. Analysis of metal catalyst content in magnetically filtered SWCNTs by SQUID magnetometry

    Czech Academy of Sciences Publication Activity Database

    Pacáková, Barbara; Komínková, Zuzana; Vejpravová, Jana; Kalbáč, Martin

    2015-01-01

    Roč. 50, č. 6 (2015), s. 2544-2553 ISSN 0022-2461 R&D Projects: GA ČR GAP204/10/1677 Institutional support: RVO:68378271 ; RVO:61388955 Keywords : single-wall carbon nanotubes * nanoparticles * magnetic filtration * SQUID Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 2.302, year: 2015

  20. Characterization of single-core magnetite nanoparticles for magnetic imaging by SQUID relaxometry

    International Nuclear Information System (INIS)

    Adolphi, Natalie L; Huber, Dale L; Monson, Todd C; Provencio, Paula P; Bryant, Howard C; Fegan, Danielle L; Tessier, Trace E; Flynn, Edward R; Lim, JitKang; Majetich, Sara A; Trujillo, Jason E; Lovato, Debbie M; Butler, Kimberly S; Larson, Richard S; Hathaway, Helen J

    2010-01-01

    Optimizing the sensitivity of SQUID (superconducting quantum interference device) relaxometry for detecting cell-targeted magnetic nanoparticles for in vivo diagnostics requires nanoparticles with a narrow particle size distribution to ensure that the Neel relaxation times fall within the measurement timescale (50 ms-2 s, in this work). To determine the optimum particle size, single-core magnetite nanoparticles (with nominal average diameters 20, 25, 30 and 35 nm) were characterized by SQUID relaxometry, transmission electron microscopy, SQUID susceptometry, dynamic light scattering and zeta potential analysis. The SQUID relaxometry signal (detected magnetic moment/kg) from both the 25 nm and 30 nm particles was an improvement over previously studied multi-core particles. However, the detected moments were an order of magnitude lower than predicted based on a simple model that takes into account the measured size distributions (but neglects dipolar interactions and polydispersity of the anisotropy energy density), indicating that improved control of several different nanoparticle properties (size, shape and coating thickness) will be required to achieve the highest detection sensitivity. Antibody conjugation and cell incubation experiments show that single-core particles enable a higher detected moment per cell, but also demonstrate the need for improved surface treatments to mitigate aggregation and improve specificity.

  1. Characterization of single-core magnetite nanoparticles for magnetic imaging by SQUID relaxometry

    Energy Technology Data Exchange (ETDEWEB)

    Adolphi, Natalie L [Department of Biochemistry and Molecular Biology, University of New Mexico, Albuquerque, NM 87131 (United States); Huber, Dale L; Monson, Todd C; Provencio, Paula P [Sandia National Laboratories, P. O. Box 5800, Albuquerque, NM 87185 (United States); Bryant, Howard C; Fegan, Danielle L; Tessier, Trace E; Flynn, Edward R [Senior Scientific, LLC, 11109 Country Club NE, Albuquerque, NM 87111 (United States); Lim, JitKang; Majetich, Sara A [Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213 (United States); Trujillo, Jason E; Lovato, Debbie M; Butler, Kimberly S; Larson, Richard S [Department of Pathology, Cancer Research and Treatment Center, University of New Mexico, Albuquerque, NM 87131 (United States); Hathaway, Helen J, E-mail: NAdolphi@salud.unm.ed [Department of Cell Biology and Physiology, University of New Mexico, Albuquerque, NM 87131 (United States)

    2010-10-07

    Optimizing the sensitivity of SQUID (superconducting quantum interference device) relaxometry for detecting cell-targeted magnetic nanoparticles for in vivo diagnostics requires nanoparticles with a narrow particle size distribution to ensure that the Neel relaxation times fall within the measurement timescale (50 ms-2 s, in this work). To determine the optimum particle size, single-core magnetite nanoparticles (with nominal average diameters 20, 25, 30 and 35 nm) were characterized by SQUID relaxometry, transmission electron microscopy, SQUID susceptometry, dynamic light scattering and zeta potential analysis. The SQUID relaxometry signal (detected magnetic moment/kg) from both the 25 nm and 30 nm particles was an improvement over previously studied multi-core particles. However, the detected moments were an order of magnitude lower than predicted based on a simple model that takes into account the measured size distributions (but neglects dipolar interactions and polydispersity of the anisotropy energy density), indicating that improved control of several different nanoparticle properties (size, shape and coating thickness) will be required to achieve the highest detection sensitivity. Antibody conjugation and cell incubation experiments show that single-core particles enable a higher detected moment per cell, but also demonstrate the need for improved surface treatments to mitigate aggregation and improve specificity.

  2. Conversion of Squid Pens to Chitosanases and Proteases via Paenibacillus sp. TKU042

    Directory of Open Access Journals (Sweden)

    Chien Thang Doan

    2018-03-01

    Full Text Available Chitosanases and proteases have received much attention due to their wide range of applications. Four kinds of chitinous materials, squid pens, shrimp heads, demineralized shrimp shells and demineralized crab shells, were used as the sole carbon and nitrogen (C/N source to produce chitosanases, proteases and α-glucosidase inhibitors (αGI by four different strains of Paenibacillus. Chitosanase productivity was highest in the culture supernatants using squid pens as the sole C/N source. The maximum chitosanase activity of fermented squid pens (0.759 U/mL was compared to that of fermented shrimp heads (0.397 U/mL, demineralized shrimp shells (0.201 U/mL and demineralized crab shells (0.216 U/mL. A squid pen concentration of 0.5% was suitable for chitosanase, protease and αGI production via Paenibacillus sp. TKU042. Multi-purification, including ethanol precipitation and column chromatography of Macro-Prep High S as well as Macro-Prep DEAE (diethylaminoethyl, led to the isolation of Paenibacillus sp. TKU042 chitosanase and protease with molecular weights of 70 and 35 kDa, respectively. For comparison, 16 chitinolytic bacteria, including strains of Paenibacillus, were investigated for the production of chitinase, exochitinase, chitosanase, protease and αGI using two kinds of chitinous sources.

  3. Characterization and demonstration results of a SQUID magnetometer system developed for geomagnetic field measurements

    Science.gov (United States)

    Kawai, J.; Miyamoto, M.; Kawabata, M.; Nosé, M.; Haruta, Y.; Uehara, G.

    2017-08-01

    We characterized a low temperature superconducting quantum interference device (SQUID) magnetometer system developed for high-sensitivity geomagnetic field measurement, and demonstrated the detection of weak geomagnetic signals. The SQUID magnetometer system is comprised of three-axis SQUID magnetometers housed in a glass fiber reinforced plastic cryostat, readout electronics with flux locked loop (FLL), a 24-bit data logger with a global positioning system and batteries. The system noise was approximately 0.2 pT √Hz- 1/2 in the 1-50 Hz frequency range. This performance was determined by including the thermal noise and the shielding effect of the copper shield, which covered the SQUID magnetometers to eliminate high-frequency interference. The temperature drift of the system was ˜0.8 pT °C- 1 in an FLL operation. The system operated for a month using 33 l liquid helium. Using this system, we performed the measurements of geomagnetic field in the open-air, far away from the city. The system could detect weak geomagnetic signals such as the Schumann resonance with sixth harmonics, and the ionospheric Alfvén resonance appearing at night, for the north-south and east-west components of the geomagnetic field. We confirm that the system was capable of high-sensitivity measurement of the weak geomagnetic activities.

  4. SQUIDs as detectors in a new experiment to measure the neutron electric dipole moment

    International Nuclear Information System (INIS)

    Espy, M.A.; Cooper, M.; Lamoreaux, S.; Kraus, R.H. Jr.; Matlachov, A.; Ruminer, P.

    1998-01-01

    A new experiment has been proposed at Los Alamos National Laboratory to measure the neutron electric dipole moment (EDM) to 4x10 -28 ecm, a factor of 250 times better than the current experimental limit. Such a measure of the neutron EDM would challenge the theories of supersymmetry and time reversal violation as the origin of the observed cosmological asymmetry in the ratio of baryons to antibaryons. One possible design for this new experiment includes the use of LTC SQUIDs coupled to large (∼100 cm 2 ) pick-up coils to measure the precision frequency of the spin-polarized 3 He atoms that act as polarizer, spin analyzer, detector, and magnetometer for the ultra-cold neutrons used in the experiment. The method of directly measuring the 3 He precession signal eliminates the need for very uniform magnetic fields (a major source of systematic error in these types of experiments). It is estimated that a flux of ∼2x10 -16 Tm 2 (0.1 Φ 0 ) will be coupled into the pick-up coils. To achieve the required signal-to-noise ratio one must have a flux resolution of dΦ SQ = 2x10 -6 Φ 0 /√Hz at 10 Hz. While this is close to the sensitivity available in commercial devices, the effects of coupling to such a large pick-up coil and flux noise from other sources in the experiment still need to be understood. To determine the feasibility of using SQUIDs in such an application the authors designed and built a superconducting test cell, which simulates major features of the proposed EDM experiment, and they developed a two-SQUID readout system that will reduce SQUID noise in the experiment. They present an overview of the EDM experiment with SQUIDs, estimations of required SQUID parameters and experimental considerations. The authors also present the measured performance of a single magnetometer in the test cell as well as the performance of the two SQUID readout technique

  5. Low-frequency noise in high-(Tc) superconductor Josephson junctions, SQUIDs, and magnetometers

    Science.gov (United States)

    Miklich, A. H.

    1994-05-01

    Design and performance of high-T(sub c) dc superconducting quantum interference devices (SQUID's), junctions that comprise them, and magnetometers made from them are described, with attention to sources of 1/f noise. Biepitaxial junctions are found to have large levels of critical current fluctuations which make them unsuitable for low-noise SQUID's; this suggests a poorly connected interface at the grain boundary junction. SQUID's from bicrystal junctions have levels of critical current noise controllable using bias current reversal techniques which leave the noise white down to frequencies of a few Hz. A SQUID with an energy resolution of 1.5 x 10(exp -30) J Hz(exp -1) at 1 Hz is reported. Magnetometers in which a (9 mm)(exp 2) pickup loop is directly coupled to a SQUID body have achieved field resolutions of 93 fT Hz(exp -1/2) down to frequencies below 1 Hz, improving to 39 fT Hz(exp -1/2) at 1 Hz with the addition of a 50mm-diameter single-turn flux transformer. Poor coupling to pickup loop makes it difficult to satisfy competing goals of high field resolution and small detector size necessary for multichannel biomagnetic imaging. Improved coupling is demonstrated by the use of multiturn-input-coil flux transformers, and a resolution of 35 fT Hz(exp -1/2) in the white noise region is reported with a (10 mm)(exp 2) pickup loop. However, additional 1/f noise from processed multilayer structures in the transformer limits the resolution at 1 Hz to 114 fT Hz(exp -1/2). High-T(sub c) SQUID's exhibit additional 1/f noise when cooled in a nonzero static magnetic field because of additional flux vortices trapped in the film, with the noise power at 1 Hz typically increasing by a factor of 10-20 in a field of 0.05mT (0.5 G). Finally, a SQUID-based voltmeter with a resolution of 9.2 pV Hz(exp -1/2) at 10 Hz (24 pV Hz(exp -1/2) at 1 Hz) is described.

  6. Low-Frequency Noise in High-T Superconductor Josephson Junctions, Squids, and Magnetometers.

    Science.gov (United States)

    Miklich, Andrew Hostetler

    The design and performance of high-T_ {rm c} dc superconducting quantum interference devices (SQUIDs), the junctions that comprise them, and magnetometers made from them are described, with special attention paid to sources of 1/f noise. Biepitaxial junctions are found to have large levels of critical current fluctuations which make them unsuitable for low-noise SQUIDs. This noise suggests a poorly connected interface at the grain boundary junction. SQUIDs from bicrystal junctions, in contrast, have levels of critical current noise that are controllable using bias current reversal techniques which leave the noise white down to frequencies of a few Hz. A SQUID with an energy resolution of 1.5times 10^{-30} J Hz^ {-1} at 1 Hz is reported. Magnetometers in which a (9 mm)^2 pickup loop is directly coupled to a SQUID body have achieved field resolutions of 93 fT Hz^{-1/2} down to frequencies below 1 Hz, improving to 39 fT Hz^{-1/2} at 1 Hz with the addition of a 50 mm-diameter single-turn flux transformer. Although the performance of these devices is sufficient for single -channel biomagnetometry or geophysical studies, their relatively poor coupling to the pickup loop makes it difficult to satisfy the competing goals of high field resolution and small detector size necessary for multichannel biomagnetic imaging. Improved coupling is demonstrated by the use of multiturn-input-coil flux transformers, and a resolution of 35 fT Hz^{-1/2} in the white noise region is reported with a (10 mm) ^2 pickup loop. However, additional 1/f noise from the processed multilayer structures in the transformer limits the resolution at 1 Hz to 114 fT Hz^ {-1/2}. High-T_{ rm c} SQUIDs are shown to exhibit additional 1/f noise when they are cooled in a nonzero static magnetic field because of the additional flux vortices trapped in the film, with the noise power at 1 Hz typically increasing by a factor of 10-20 in a field of 0.05 mT (0.5 G). Finally, a SQUID-based voltmeter with a resolution

  7. RNA-DNA Differences Are Generated in Human Cells within Seconds after RNA Exits Polymerase II

    Directory of Open Access Journals (Sweden)

    Isabel X. Wang

    2014-03-01

    Full Text Available RNA sequences are expected to be identical to their corresponding DNA sequences. Here, we found all 12 types of RNA-DNA sequence differences (RDDs in nascent RNA. Our results show that RDDs begin to occur in RNA chains ∼55 nt from the RNA polymerase II (Pol II active site. These RDDs occur so soon after transcription that they are incompatible with known deaminase-mediated RNA-editing mechanisms. Moreover, the 55 nt delay in appearance indicates that they do not arise during RNA synthesis by Pol II or as a direct consequence of modified base incorporation. Preliminary data suggest that RDD and R-loop formations may be coupled. These findings identify sequence substitution as an early step in cotranscriptional RNA processing.

  8. Fundamentals of Welding. Teacher Edition [and] Student Edition [and] Student Workbook. Second Edition.

    Science.gov (United States)

    Fortney, Clarence; Gregory, Mike; New, Larry

    Teacher and student editions and a student workbook for fundamentals of welding comprise the first of six in a series of competency-based instructional materials for welding programs. Introductory pages in the teacher edition are training and competency profile, instructional/task analysis, basic skills icons and classifications, basic skills…

  9. Oxyacetylene Welding and Oxyfuel Cutting. Third Edition. Teacher Edition [and] Student Edition [and] Student Workbook.

    Science.gov (United States)

    Knapp, John; Harper, Eddie

    This Oklahoma curriculum guide, which includes a teacher edition, a student edition, and a student workbook, provides three units for a course on oxyacetylene welding, oxyfuel cutting, and cutting done with alternative fuels such as MAPP, propane, and natural gas. The three units are: "Oxyacetylene Welding"; "Oxyfuel Cutting";…

  10. Residential and Light Commercial HVAC. Teacher Edition and Student Edition. Second Edition.

    Science.gov (United States)

    Stephenson, David

    This package contains teacher and student editions of a residential and light commercial heating, ventilation, and air conditioning (HVAC) course of study. The teacher edition contains information on the following: using the publication; national competencies; competency profile; related academic and workplace skills list; tools, equipment, and…

  11. Volcanoes, Third Edition

    Science.gov (United States)

    Nye, Christopher J.

    It takes confidence to title a smallish book merely “Volcanoes” because of the impliction that the myriad facets of volcanism—chemistry, physics, geology, meteorology, hazard mitigation, and more—have been identified and addressed to some nontrivial level of detail. Robert and Barbara Decker have visited these different facets seamlessly in Volcanoes, Third Edition. The seamlessness comes from a broad overarching, interdisciplinary, professional understanding of volcanism combined with an exceptionally smooth translation of scientific jargon into plain language.The result is a book which will be informative to a very broad audience, from reasonably educated nongeologists (my mother loves it) to geology undergraduates through professional volcanologists. I bet that even the most senior professional volcanologists will learn at least a few things from this book and will find at least a few provocative discussions of subjects they know.

  12. The biology and ecology of the jumbo squid Dosidicus gigas (Cephalopoda in Chilean waters: a review

    Directory of Open Access Journals (Sweden)

    Christian M Ibáñez

    2015-07-01

    Full Text Available ABSTRACT. The jumbo squid Dosidicus gigas is the most abundant cephalopod species in the southeastern Pacific Ocean, which supports the biggest cephalopod fishery in the world. Due to its growing economic importance, the population growth and distributional expansion of this squid is being increasingly studied. Nevertheless, some basic features of the biology of D. gigas are still unknown or have been poorly investigated. In this review we summarize the known information regarding the biology and ecology of this species in the southeastern Pacific Ocean; we focus on the Chilean region in order to propose hypotheses and research lines for a better understanding the life history of this organism. Available data on the size structure, reproduction and genetics of D. gigas allows us to propose hypotheses related to the squid's life history traits. Based on the current literature and publications of colleagues, we propose two hypotheses regarding the effect of spatial variation on the life history of D. gigas. Hypothesis 1: Squids mature at large sizes and spawn in oceanic waters with warm temperatures where paralarvae and juveniles develop. Immature squids migrate near shore to feed, grow and mature, and then return to the offshore sites to spawn. Hypothesis 2: Alternatively, juvenile D. gigas in the oceanic zone do not migrate to coastal waters and mature at small sizes compared to individuals living near the coast that mature at larger size and migrate to oceanic waters to spawn. We provide background information about the feeding behavior and parasitism of this species, suggesting that D. gigas is an important trophic link in the southeastern Pacific marine ecosystem. However, more studies on the feeding habits, reproduction and parasite load are needed not only to test hypotheses proposed in this study, but also to advance the overall knowledge of this species.

  13. Preparation and characterisation of irradiated crab chitosan and New Zealand Arrow squid pen chitosan

    International Nuclear Information System (INIS)

    Shavandi, Amin; Bekhit, Adnan A.; Bekhit, Alaa El-Din A.; Sun, Zhifa; Ali, M. Azam

    2015-01-01

    The properties of chitosan from Arrow squid (Nototodarus sloanii) pen (CHS) and commercial crab shell (CHC) were investigated using FTIR, DSC, SEM and XRD before and after irradiation at the dose of 28 kGy in the presence or absence of 5% water. Also, the viscosity, deacetylation degree, water and oil holding capacities, colour and antimicrobial activities of the chitosan samples were determined. Irradiation decreased (P < 0.05) the viscosity of CHC from 0.21 to 0.03 Pa s and of CHS from 1.71 to 0.23 Pa s. The inclusion of water had no effect on the viscosity of irradiated chitosan. Irradiation did not affect the degree of deacetylation of CHC, but increased the deacetylation degree of CHS from 72.78 to 82.29% in samples with 5% water. Water and oil holding capacities of CHS (1197.30% and 873.3%, respectively) were higher (P < 0.05) than those found in CHC (340.70% and 264.40%, respectively). The water and oil holding capacities were decreased for both types of chitosan irradiation, but were not affected by the addition of water. Squid pen chitosan was whiter in colour (White Index = 90.06%) compared to CHC (White Index = 83.70%). Generally, the CHC samples (control and irradiated) exhibited better antibacterial activity compared to CHS, but the opposite was observed with antifungal activity. - Highlights: • Chitosan prepared from Arrow squid pens (Nototodarus sloanii). • Chitosan samples were gamma irradiated at 28 kGy. • Squid pen chitosan showed high fat and water uptake capacities compared to crab shell chitosan. • Gamma irradiation enhanced the DDA of squid pen chitosan but not crab shell chitosan.

  14. Fishery biology of jumbo flying squid Dosidicus gigas off Costa Rica Dome

    Science.gov (United States)

    Chen, Xinjun; Li, Jianghua; Liu, Bilin; Li, Gang; Lu, Huajie

    2014-06-01

    The jumbo flying squid ( Dosidicus gigas) population was surveyed with the help of Chinese squid jigging vessels off the Costa Rica Dome (4°-11°N, 90°-100°W) in 2009 and 2010. The daily catch of D. gigas in the two survey cruises ranged from 0 to 5.5 t and was mostly obtained from the areas bounded by 6°-9°N and 91°-94°W and by 6°30'-7°30'N and 96°-97°W. The sea surface temperature in the areas yielding the most catch ranged from 27.5 to 29°C. The sex ratio of the total catch was 3.75:1 (female: male). The mantle length of the squid ranged from 211 to 355 mm (male) and from 204 to 429 mm (female) with an average of 297.9 and 306.7 mm, respectively. In the relationship of the mantle length (mm) and body weight (g) of the squid, there was no significant difference between sexes. The female and male were at a similar maturity, and most individuals are maturing or have matured with a few females being spent. The size (mantle length) and age at the first sexual maturity were 297 mm and 195 d in females, and less than 211 mm and 130 d in males, respectively. Most of the sampled stomachs (70.6%) had no food remains. The major preys of the squids were fish, cephalopods and crustaceans, with the most abundant Myctophum orientale and D. gigas. The preys in more than 65% of the non-empty sampled stomachs evidenced the cannibalism of D. gigas. The results improved current understanding of the fishery biology of D. gigas off the Costa Rica Dome, which may facilitate the assessment and management of relative fishery resources.

  15. A non-inheritable maternal Cas9-based multiple-gene editing system in mice

    OpenAIRE

    Takayuki Sakurai; Akiko Kamiyoshi; Hisaka Kawate; Chie Mori; Satoshi Watanabe; Megumu Tanaka; Ryuichi Uetake; Masahiro Sato; Takayuki Shindo

    2016-01-01

    The CRISPR/Cas9 system is capable of editing multiple genes through one-step zygote injection. The preexisting method is largely based on the co-injection of Cas9 DNA (or mRNA) and guide RNAs (gRNAs); however, it is unclear how many genes can be simultaneously edited by this method, and a reliable means to generate transgenic (Tg) animals with multiple gene editing has yet to be developed. Here, we employed non-inheritable maternal Cas9 (maCas9) protein derived from Tg mice with systemic Cas9...

  16. RNA-Binding Proteins in Plant Immunity

    Directory of Open Access Journals (Sweden)

    Virginia Woloshen

    2011-01-01

    Full Text Available Plant defence responses against pathogen infection are crucial to plant survival. The high degree of regulation of plant immunity occurs both transcriptionally and posttranscriptionally. Once transcribed, target gene RNA must be processed prior to translation. This includes polyadenylation, 5′capping, editing, splicing, and mRNA export. RNA-binding proteins (RBPs have been implicated at each level of RNA processing. Previous research has primarily focused on structural RNA-binding proteins of yeast and mammals; however, more recent work has characterized a number of plant RBPs and revealed their roles in plant immune responses. This paper provides an update on the known functions of RBPs in plant immune response regulation. Future in-depth analysis of RBPs and other related players will unveil the sophisticated regulatory mechanisms of RNA processing during plant immune responses.

  17. Flux-coherent series SQUID array magnetometers operating above 77 K with superior white flux noise than single-SQUIDs at 4.2 K

    International Nuclear Information System (INIS)

    Chesca, Boris; John, Daniel; Mellor, Christopher J.

    2015-01-01

    A very promising direction to improve the sensitivity of magnetometers based on superconducting quantum interference devices (SQUIDs) is to build a series-array of N non-interacting SQUIDs operating flux-coherently, because in this case their voltage modulation depth, ΔV, linearly scales with N whereas the white flux noise S Φ 1/2 decreases as 1/N 1/2 . Here, we report the realization of both these improvements in an advanced layout of very large SQUID arrays made of YBa 2 Cu 3 O 7 . Specially designed with large area narrow flux focusers for increased field sensitivity and improved flux-coherency, our arrays have extremely low values for S Φ 1/2 between (0.25 and 0.44) μΦ 0 /Hz 1/2 for temperatures in the range (77–83) K. In this respect, they outperform niobium/aluminium trilayer technology-based single-SQUIDs operating at 4.2 K. Moreover, with values for ΔV and transimpedance in the range of (10–17) mV and (0.3–2.5) kΩ, respectively, a direct connection to a low-noise room temperature amplifier is allowed, while matching for such readout is simplified and the available bandwidth is greatly increased. These landmark performances suggest such series SQUID arrays are ideal candidates to replace single-SQUIDs operating at 4.2 K in many applications

  18. NCCI Medically Unlikely Edits (MUEs)

    Data.gov (United States)

    U.S. Department of Health & Human Services — Medically Unlikely Edits (MUEs) define for each HCPCS / CPT code the maximum units of service (UOS) that a provider would report under most circumstances for a...

  19. The mechanics of locomotion in the squid Loligo pealei: locomotory function and unsteady hydrodynamics of the jet and intramantle pressure.

    Science.gov (United States)

    Anderson, E J; DeMont, M E

    2000-09-01

    High-speed, high-resolution digital video recordings of swimming squid (Loligo pealei) were acquired. These recordings were used to determine very accurate swimming kinematics, body deformations and mantle cavity volume. The time-varying squid profile was digitized automatically from the acquired swimming sequences. Mantle cavity volume flow rates were determined under the assumption of axisymmetry and the condition of incompressibility. The data were then used to calculate jet velocity, jet thrust and intramantle pressure, including unsteady effects. Because of the accurate measurements of volume flow rate, the standard use of estimated discharge coefficients was avoided. Equations for jet and whole-cycle propulsive efficiency were developed, including a general equation incorporating unsteady effects. Squid were observed to eject up to 94 % of their intramantle working fluid at relatively high swimming speeds. As a result, the standard use of the so-called large-reservoir approximation in the determination of intramantle pressure by the Bernoulli equation leads to significant errors in calculating intramantle pressure from jet velocity and vice versa. The failure of this approximation in squid locomotion also implies that pressure variation throughout the mantle cannot be ignored. In addition, the unsteady terms of the Bernoulli equation and the momentum equation proved to be significant to the determination of intramantle pressure and jet thrust. Equations of propulsive efficiency derived for squid did not resemble Froude efficiency. Instead, they resembled the equation of rocket motor propulsive efficiency. The Froude equation was found to underestimate the propulsive efficiency of the jet period of the squid locomotory cycle and to overestimate whole-cycle propulsive efficiency when compared with efficiencies calculated from equations derived with the squid locomotory apparatus in mind. The equations for squid propulsive efficiency reveal that the refill

  20. [Preface for genome editing special issue].

    Science.gov (United States)

    Gu, Feng; Gao, Caixia

    2017-10-25

    Genome editing technology, as an innovative biotechnology, has been widely used for editing the genome from model organisms, animals, plants and microbes. CRISPR/Cas9-based genome editing technology shows its great value and potential in the dissection of functional genomics, improved breeding and genetic disease treatment. In the present special issue, the principle and application of genome editing techniques has been summarized. The advantages and disadvantages of the current genome editing technology and future prospects would also be highlighted.

  1. Marine botany. Second edition

    International Nuclear Information System (INIS)

    Dawes, C.J.

    1998-01-01

    Marine plants are a diverse group that include unicellular algae, seaweeds, seagrasses, salt marshes, and mangrove forests. They carry out a variety of ecological functions and serve as the primary producers in coastal wetlands and oceanic waters. The theme that connects such a wide variety of plants is their ecology, which was also emphasized in the 1981 edition. The goal of this revision is to present taxonomic, physiological, chemical, and ecological aspects of marine plants, their adaptations, and how abiotic and biotic factors interact in their communities. The data are presented in a concise, comparative manner in order to identify similarities and differences between communities such as salt marsh and mangroves or subtidal seaweeds and seagrasses. To accomplish this, the text is organized into five chapters that introduce the marine habitats, consider abiotic and biotic factors, and anthropogenic influences on the communities followed by seven chapters that deal with microalgae, seaweeds, salt marshes, mangroves, seagrasses, and coral reefs. Two appendixes are included; one presents simple field techniques and the other is a summary of seaweed uses

  2. Editörden

    OpenAIRE

    Toprakcı, Erdal

    2017-01-01

    Editörden 2017 yılının ikinci sayısıyla yeniden sizinleyiz. Kaliteye verdiğimiz önem sayesinde, çok kısa sürede adından söz ettiren bir dergiye dönüştük. Kuşkusuz bu süreçte en önemli etken yazarlarımız ve hakemlerimizin titizliğidir.Dergimizin bu sayısında şunlar var: Birinci olarak, YBO’da öğrenim gören öğrencilerin matematiğe yönelik genel tutumların olumlu olduğu, tutum puanlarının sınıf düzeyi, matematik başarısı, matematik öğretmeni sevme düzeyi, matematik önem algısı ve öz-yeterlik baş...

  3. CRISPR/Cas9-mediated genome editing of Epstein-Barr virus in human cells.

    Science.gov (United States)

    Yuen, Kit-San; Chan, Chi-Ping; Wong, Nok-Hei Mickey; Ho, Chau-Ha; Ho, Ting-Hin; Lei, Ting; Deng, Wen; Tsao, Sai Wah; Chen, Honglin; Kok, Kin-Hang; Jin, Dong-Yan

    2015-03-01

    The CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated 9) system is a highly efficient and powerful tool for RNA-guided editing of the cellular genome. Whether CRISPR/Cas9 can also cleave the genome of DNA viruses such as Epstein-Barr virus (EBV), which undergo episomal replication in human cells, remains to be established. Here, we reported on CRISPR/Cas9-mediated editing of the EBV genome in human cells. Two guide RNAs (gRNAs) were used to direct a targeted deletion of 558 bp in the promoter region of BART (BamHI A rightward transcript) which encodes viral microRNAs (miRNAs). Targeted editing was achieved in several human epithelial cell lines latently infected with EBV, including nasopharyngeal carcinoma C666-1 cells. CRISPR/Cas9-mediated editing of the EBV genome was efficient. A recombinant virus with the desired deletion was obtained after puromycin selection of cells expressing Cas9 and gRNAs. No off-target cleavage was found by deep sequencing. The loss of BART miRNA expression and activity was verified, supporting the BART promoter as the major promoter of BART RNA. Although CRISPR/Cas9-mediated editing of the multicopy episome of EBV in infected HEK293 cells was mostly incomplete, viruses could be recovered and introduced into other cells at low m.o.i. Recombinant viruses with an edited genome could be further isolated through single-cell sorting. Finally, a DsRed selectable marker was successfully introduced into the EBV genome during the course of CRISPR/Cas9-mediated editing. Taken together, our work provided not only the first genetic evidence that the BART promoter drives the expression of the BART transcript, but also a new and efficient method for targeted editing of EBV genome in human cells. © 2015 The Authors.

  4. Architecture of the trypanosome RNA editing accessory complex, MRB1

    Czech Academy of Sciences Publication Activity Database

    Ammerman, M. L.; Downey, K. M.; Hashimi, Hassan; Fisk, J. C.; Tomasello, D. L.; Faktorová, Drahomíra; Kafková, L.; King, T.; Lukeš, Julius; Read, L. K.

    2012-01-01

    Roč. 40, č. 12 (2012), s. 5637-5650 ISSN 0305-1048 R&D Projects: GA ČR GA204/09/1667 Institutional support: RVO:60077344 Keywords : BINDING COMPLEX * PROTEIN * BRUCEI * TANDEM * TRANSCRIPTOME * MITOCHONDRIA * INTERACTS * TBRGG2 Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 8.278, year: 2012 http://nar.oxfordjournals.org/content/40/12/5637.full

  5. Influence of gamma irradiation and low temperature storage on the quality and shelf life of squid (Doryteuthis sibogae

    Directory of Open Access Journals (Sweden)

    Manjanaik, B.

    2017-08-01

    Full Text Available Irradiation is considered as an efficient method for the reduction of microorganisms in food. It has been used to improve the safety and shelf life of food products. The present investigation is aimed at studying the influence of gamma irradiation (3 and 5 kGy and subsequent storage at refrigeration temperature (4oC on the chemical, microbial qualities and extended shelf life of squid (Doryteuthis sibogae. The total volatile base nitrogen (TVB-N and trimethyl amine nitrogen values (TMA-N of the irradiated squid samples significantly decreased in comparison with the control (non-irradiated stored at 4oC. The thiobarbituric acid values for the irradiated squid was significantly lower than of the non-irradiated samples stored at 4oC (p<0.05. The pH value of the squid was affected significantly by both, irradiation dose and storage temperature (p<0.05. The total microbial load for the non-irradiated squid samples was higher than those of irradiated samples at 4oC temperature. The results revealed that the combination of irradiation and refrigerated storage resulted in a significant reduction of microbial growth and stabilized the biochemical characteristics of squid.

  6. Studies on the effect of low dose gamma irradiation on the chemical, microbial quality and shelf life of squid

    International Nuclear Information System (INIS)

    Bojayanaik, Manjanaik; Naroth, Kavya; Shetty, Veena; Hiriyur, Somashekarappa

    2014-01-01

    The present investigation was carried out to study the combined effect of low dose gamma irradiation (1, 3 and 5 kGy) and storage at refrigeration (+4℃) and frozen (-18℃) temperatures, on the shelf life extension of fresh squid. The study was based on microbiological and physico-chemical changes occurring in the squid samples. The biochemical parameters such as total volatile base nitrogen and trimethyl amine nitrogen values for irradiated squid samples were significantly lower than non-irradiated samples at both storage temperatures and the rate of decrease was more pronounced in samples irradiated at the higher dose of 3 and 5 kGy (p<0.05). pH values of squid samples were affected by both irradiation dose and storage temperature (p<0.05). Total microbial load for non- irradiated (control) squid samples were higher than the respective irradiated samples at both storage temperatures. The results revealed that the combination of irradiation and low temperature storage resulted in a significant reduction of microbial growth and extend the shelf life of squid at refrigeration and frozen temperature to about 12 and 90 days respectively. (author)

  7. Natural mortality estimation and rational exploitation of purpleback flying squid Sthenoteuthis oualaniensis in the southern South China Sea

    Science.gov (United States)

    Wang, Xuehui; Qiu, Yongsong; Zhang, Peng; Du, Feiyan

    2017-07-01

    Based on the biological data of purpleback flying squid ( Sthenoteuthis oualaniensis) collected by light falling-net in the southern South China Sea (SCS) during September to October 2012 and March to April 2013, growth and mortality of `Medium' and `Dwarf' forms of squid are derived using the Powell-Wetherall, ELEFAN methods and length-converted catch curves (FiSAT package). Given a lack of commercial exploitation, we assume total mortality to be due entirely to natural mortality. We estimate these squid have fast growth, with growth coefficients ( k) ranging from 1.42 to 2.39, and high natural mortality ( M), with estimates ranging from 1.61 to 2.92. To sustainably exploit these squid stocks, yield per recruitment based on growth and natural mortality was determined using the Beverton-Holt dynamic pool model. We demonstrate squid stocks could sustain high fishing mortality and low ages at first capture, with an optimal fishing mortality >3.0, with the optimal age at first capture increased to 0.4-0.6 years when fishing mortality approached optimal levels. On the basis of our analyses and estimates of stock biomass, we believe considerable potential exists to expand the squid fishery into the open SCS, relieving fishing pressure on coastal waters.

  8. Ultra-sensitive sensors for weak electromagnetic fields using high-Tc SQUIDS for biomagnetism, NDE, and corrosion currents

    International Nuclear Information System (INIS)

    Kraus, R.H. Jr.; Flynn, E.R.; Espy, M.; Jia, Q.X.; Wu, X.D.; Reagor, D.

    1998-01-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The research has directly contributed to a new DOE supported project, three patents (one granted and two submitted), and several potential opportunities for new program funding at the Laboratory. The authors report significant developments extending from basic understanding of and fabrication techniques for high critical-temperature (high-T c ) SQUID devices to the development of high-level applications such as the SQUID Microscope. The development of ramp edge geometry and silver-doped YBa 2 Cu 3 O 7-x (YBCO) electrodes has tremendously improved the performance of high-T c SQUIDS. Recent experiments have proven and quantified the LANL-patented superconducting imaging plane gradiometry concept. A SQUID microscope, developed largely under this project, has recently acquired data that demonstrated exceptional sensitivity and resolution. New techniques for background noise suppression, needed to use the extraordinarily sensitive SQUID sensors in unshielded environments, have also been developed. Finally, initial investigations to use SQUIDs in a basic physics experiment to measure the electric dipole moment of the neutron were very successful

  9. Induced electric currents in the Alaska oil pipeline measured by gradient, fluxgate, and SQUID magnetometers

    Science.gov (United States)

    Campbell, W. H.; Zimmerman, J. E.

    1979-01-01

    The field gradient method for observing the electric currents in the Alaska pipeline provided consistent values for both the fluxgate and SQUID method of observation. These currents were linearly related to the regularly measured electric and magnetic field changes. Determinations of pipeline current were consistent with values obtained by a direct connection, current shunt technique at a pipeline site about 9.6 km away. The gradient method has the distinct advantage of portability and buried- pipe capability. Field gradients due to the pipe magnetization, geological features, or ionospheric source currents do not seem to contribute a measurable error to such pipe current determination. The SQUID gradiometer is inherently sensitive enough to detect very small currents in a linear conductor at 10 meters, or conversely, to detect small currents of one amphere or more at relatively great distances. It is fairly straightforward to achieve imbalance less than one part in ten thousand, and with extreme care, one part in one million or better.

  10. Polarization sensitivity and retinal topography of the striped pyjama squid (Sepioloidea lineolata - Quoy/Gaimard 1832).

    Science.gov (United States)

    Talbot, Christopher M; Marshall, Justin

    2010-10-01

    Coleoid cephalopods (octopus, cuttlefish and squid) potentially possess polarization sensitivity (PS) based on photoreceptor structure, but this idea has rarely been tested behaviourally. Here, we use a polarized, striped optokinetic stimulus to demonstrate PS in the striped pyjama squid, Sepioloidea lineolata. This species displayed strong, consistent optokinetic nystagmic eye movements in response to a drum with stripes producing e-vectors set to 0 deg, 45 deg, 90 deg and 135 deg that would only be visible to an animal with PS. This is the first behavioural demonstration of a polarized optokinetic response in any species of cephalopod. This species, which typically sits beneath the substrate surface looking upwards for potential predators and prey, possesses a dorsally shifted horizontal pupil slit. Accordingly, it was found to possess a horizontal strip of high-density photoreceptors shifted ventrally in the retina, suggesting modifications such as a change in sensitivity or resolution to the dorsal visual field.

  11. High-Tc SQUID gradiometer system for magnetocardiography in an unshielded environment

    International Nuclear Information System (INIS)

    Liao, S H; Hsu, S C; Lin, C C; Horng, H E; Chen, J C; Chen, M J; Wu, C H; Yang, H C

    2003-01-01

    We set up an electronic gradiometer for magnetocardiography (MCG) in an unshielded environment. The electronically balanced gradiometer consists of high-temperature radio-frequency superconducting quantum interference device (rf SQUID) magnetometers. The rf SQUID magnetometers are arranged to form the electronic first-order, four-vector gradiometer, or second-order gradiometer. The output of the MCG signal was filtered by a band pass (1-30 Hz) and power line filters. We can reduce the noise to ∼1 pT Hz -1/2 at 1 Hz for second-order or four-vector gradiometers. Two-dimensional MCG imaging is demonstrated. The results are discussed with data measured in the moderate magnetically shielded environment

  12. Habitat and distribution of post-recruit life stages of the squid Loligo forbesii

    Science.gov (United States)

    Smith, Jennifer M.; Macleod, Colin D.; Valavanis, Vasilis; Hastie, Lee; Valinassab, Tooraj; Bailey, Nick; Santos, M. Begoña; Pierce, Graham J.

    2013-10-01

    This study models habitat preferences of the squid Loligo forbesii through its post-recruitment life cycle in waters around Scotland (UK). Trawl survey and market sample data from 1985 to 2004 are used to model seasonal habitats of immature, maturing and mature squid (maturity being inferred from size and season). Squid presence-absence and catch rate in areas of presence were analysed using generalised additive models, relating spatiotemporal patterns of distribution and abundance to ecogeographic variables. For all maturity classes, higher abundance in winter and spring (i.e., quarters 1 and 2) was associated with deeper water while higher abundance in summer and autumn (quarters 3 and 4) was associated with shallower water, consistent with seasonal onshore-offshore migrations but suggesting that most spawning may take place in deeper waters. The preferred SST range was generally 8-8.75 °C while preferred salinity values were below 35‰ in winter and summer and above 35‰ in spring and autumn. Squid were positively associated with gravel substrate and negatively associated with mud. Seasonal changes in habitat use were more clearly evident than changes related to inferred maturity, although the two effects cannot be fully separated due to the annual life cycle. Habitat selection for this species can be satisfactorily modelled on a seasonal basis; predictions based on such models could be useful for fishers to target the species more effectively, and could assist managers wishing to protect spawning grounds. The extent to which this approach may be useful for other cephalopods is discussed.

  13. Ultra-Low Field SQUID-NMR using LN2 Cooled Cu Polarizing Field coil

    Science.gov (United States)

    Demachi, K.; Kawagoe, S.; Ariyoshi, S.; Tanaka, S.

    2017-07-01

    We are developing an Ultra-Low Field (ULF) Magnetic Resonance Imaging (MRI) system using a High-Temperature Superconductor superconducting quantum interference device (HTS rf-SQUID) for food inspection. The advantages of the ULF-NMR (Nuclear Magnetic Resonance) / MRI as compared with a conventional high field MRI are that they are compact and of low cost. In this study, we developed a ULF SQUID-NMR system using a polarizing coil to measure fat of which relaxation time T1 is shorter. The handmade polarizing coil was cooled by liquid nitrogen to reduce the resistance and accordingly increase the allowable current. The measured decay time of the polarizing field was 40 ms. The measurement system consisted of the liquid nitrogen cooled polarizing coil, a SQUID, a Cu wound flux transformer, a measurement field coil for the field of 47 μT, and an AC pulse coil for a 90°pulse field. The NMR measurements were performed in a magnetically shielded room to reduce the environmental magnetic field. The size of the sample was ϕ35 mm × L80 mm. After applying a polarizing field and a 90°pulse, an NMR signal was detected by the SQUID through the flux transformer. As a result, the NMR spectra of fat samples were obtained at 2.0 kHz corresponding to the measurement field Bm of 47 μT. The T1 relaxation time of the mineral oil measured in Bm was 45 ms. These results suggested that the ULF-NMR/MRI system has potential for food inspection.

  14. Limits to the observation of coherent oscillations in a SQUID ring

    International Nuclear Information System (INIS)

    Diggins, J.

    1995-01-01

    Using the quantum mechanical, lumped component model of a SQUID ring we compute the onset of tunnelling and macroscopic superposition behaviour in the parameter space of the ring. In addition, we make a quantitative estimate of the stability required in the environmental flux to sustain a superposition state. Both these features are of crucial importance to the realisation of experiments aimed at revealing such behaviour. (orig.)

  15. Sneaker Male Squid Produce Long-lived Spermatozoa by Modulating Their Energy Metabolism

    OpenAIRE

    Hirohashi, Noritaka; Tamura-Nakano, Miwa; Nakaya, Fumio; Iida, Tomohiro; Iwata, Yoko

    2016-01-01

    Spermatozoa released by males should remain viable until fertilization. Hence, sperm longevity is governed by intrinsic and environmental factors in accordance with the male mating strategy. However, whether intraspecific variation of insemination modes can impact sperm longevity remains to be elucidated. In the squid Heterololigo bleekeri, male dimorphism (consort and sneaker) is linked to two discontinuous insemination modes that differ in place and time. Notably, only sneaker male spermato...

  16. SiGe Integrated Circuit Developments for SQUID/TES Readout

    Science.gov (United States)

    Prêle, D.; Voisin, F.; Beillimaz, C.; Chen, S.; Piat, M.; Goldwurm, A.; Laurent, P.

    2018-03-01

    SiGe integrated circuits dedicated to the readout of superconducting bolometer arrays for astrophysics have been developed since more than 10 years at APC. Whether for Cosmic Microwave Background (CMB) observations with the QUBIC ground-based experiment (Aumont et al. in astro-ph.IM, 2016. arXiv:1609.04372) or for the Hot and Energetic Universe science theme with the X-IFU instrument on-board of the ATHENA space mission (Barret et al. in SPIE 9905, space telescopes & instrumentation 2016: UV to γ Ray, 2016. https://doi.org/10.1117/12.2232432), several kinds of Transition Edge Sensor (TES) (Irwin and Hilton, in ENSS (ed) Cryogenic particle detection, Springer, Berlin, 2005) arrays have been investigated. To readout such superconducting detector arrays, we use time or frequency domain multiplexers (TDM, FDM) (Prêle in JINST 10:C08015, 2016. https://doi.org/10.1088/1748-0221/10/08/C08015) with Superconducting QUantum Interference Devices (SQUID). In addition to the SQUID devices, low-noise biasing and amplification are needed. These last functions can be obtained by using BiCMOS SiGe technology in an Application Specific Integrated Circuit (ASIC). ASIC technology allows integration of highly optimised circuits specifically designed for a unique application. Moreover, we could reach very low-noise and wide band amplification using SiGe bipolar transistor either at room or cryogenic temperatures (Cressler in J Phys IV 04(C6):C6-101, 1994. https://doi.org/10.1051/jp4:1994616). This paper discusses the use of SiGe integrated circuits for SQUID/TES readout and gives an update of the last developments dedicated to the QUBIC telescope and to the X-IFU instrument. Both ASIC called SQmux128 and AwaXe are described showing the interest of such SiGe technology for SQUID multiplexer controls.

  17. Design and Performance of the Multiplexed SQUID/TES Array at Ninety Gigahertz

    Science.gov (United States)

    Stanchfield, Sara; Ade, Peter; Aguirre, James; Brevik, Justus A.; Cho, Hsiao-Mei; Datta, Rahul; Devlin, Mark; Dicker, Simon R.; Dober, Bradley; Duff, Shannon M.; Egan, Dennis; Ford, Pam; Hilton, Gene; Hubmayr, Johannes; Irwin, Kent; Knowles, Kenda; Marganian, Paul; Mason, Brian Scott; Mates, John A. B.; McMahon, Jeff; Mello, Melinda; Mroczkowski, Tony; Romero, Charles; Sievers, Jonathon; Tucker, Carole; Vale, Leila R.; Vissers, Michael; White, Steven; Whitehead, Mark; Ullom, Joel; Young, Alexander

    2018-01-01

    We present the array performance and astronomical images from early science results from MUSTANG-2, a 90 GHz feedhorn-coupled, microwave SQUID-multiplexed TES bolometer array operating on the Robert C. Byrd Green Bank Telescope (GBT). MUSTANG-2 was installed on the GBT on December 2, 2016 and immediately began commissioning efforts, followed by science observations, which are expected to conclude June 2017. The feedhorn and waveguide-probe-coupled detector technology is a mature technology, which has been used on instrument including the South Pole Telescope, the Atacama Cosmology Telescope, and the Atacama B-mode Search telescope. The microwave SQUID readout system developed for MUSTANG-2 currently reads out 66 detectors with a single coaxial cable and will eventually allow thousands of detectors to be multiplexed. This microwave SQUID multiplexer combines the proven abilities of millimeterwave TES detectors with the multiplexing capabilities of KIDs with no degradation in noise performance of the detectors. Each multiplexing device is read out using warm electronics consisting of a commercially available ROACH board, a DAC/ADC card, and an Intermediate Frequency mixer circuit. The hardware was originally developed by the UC Berkeley Collaboration for Astronomy Signal Processing and Electronic Research (CASPER) group, whose primary goal is to develop scalable FPGA-based hardware with the flexibility to be used in a wide range of radio signal processing applications. MUSTANG-2 is the first on-sky instrument to use microwave SQUID multiplexing and is available as a shared-risk/PI instrument on the GBT. In MUSTANG-2's first season 7 separate proposals were awarded a total of 230 hours of telescope time.

  18. K+/Na+-triggered bioluminescence in the oceanic squid Symplectoteuthis oualaniensis

    OpenAIRE

    Tsuji, Frederick I.; Leisman, Gary B.

    1981-01-01

    A distinctive type of luminescent system present in the large dorsal luminous organ of the oceanic squid Symplectoteuthis oualaniensis is described. The organ produces an intense blue flash of light followed by a rapid decay in light intensity. Luminescence originates from numerous oval granules present in the luminous organ. The essential light-emitting components are membrane bound. Intact granules or washed homogenates of the granules are triggered to emit light by monovalent cations such ...

  19. Depressed light emission by symbiotic Vibrio fischeri of the sepiolid squid Euprymna scolopes.

    OpenAIRE

    Boettcher, K J; Ruby, E G

    1990-01-01

    Bioluminescent marine bacteria of the species Vibrio fischeri are the specific light organ symbionts of the sepiolid squid Euprymna scolopes. Although they share morphological and physiological characteristics with other strains of V. fischeri, when cultured away from the light organ association the E. scolopes symbionts depress their maximal luminescence over 1,000-fold. The primary cause of this reduced luminescence is the underproduction by these bacteria of luciferase autoinducer, a molec...

  20. Phylogeographical patterns among Mediterranean sepiolid squids and their Vibrio symbionts: environment drives specificity among sympatric species.

    Science.gov (United States)

    Zamborsky, D J; Nishiguchi, M K

    2011-01-01

    Bobtail squid from the genera Sepiola and Rondeletiola (Cephalopoda: Sepiolidae) form mutualistic associations with luminous Gram-negative bacteria (Gammaproteobacteria: Vibrionaceae) from the genera Vibrio and Photobacterium. Symbiotic bacteria proliferate inside a bilobed light organ until they are actively expelled by the host into the surrounding environment on a diel basis. This event results in a dynamic symbiont population with the potential to establish the symbiosis with newly hatched sterile (axenic) juvenile sepiolids. In this study, we examined the genetic diversity found in populations of sympatric sepiolid squid species and their symbionts by the use of nested clade analysis with multiple gene analyses. Variation found in the distribution of different species of symbiotic bacteria suggests a strong influence of abiotic factors in the local environment, affecting bacterial distribution among sympatric populations of hosts. These abiotic factors include temperature differences incurred by a shallow thermocline, as well as a lack of strong coastal water movement accompanied by seasonal temperature changes in overlapping niches. Host populations are stable and do not appear to have a significant role in the formation of symbiont populations relative to their distribution across the Mediterranean Sea. Additionally, all squid species examined (Sepiola affinis, S. robusta, S. ligulata, S. intermedia, and Rondeletiola minor) are genetically distinct from one another regardless of location and demonstrate very little intraspecific variation within species. These findings suggest that physical boundaries and distance in relation to population size, and not host specificity, are important factors in limiting or defining gene flow within sympatric marine squids and their associated bacterial symbionts in the Mediterranean Sea.

  1. Newer Gene Editing Technologies toward HIV Gene Therapy

    Directory of Open Access Journals (Sweden)

    Premlata Shankar

    2013-11-01

    Full Text Available Despite the great success of highly active antiretroviral therapy (HAART in ameliorating the course of HIV infection, alternative therapeutic approaches are being pursued because of practical problems associated with life-long therapy. The eradication of HIV in the so-called “Berlin patient” who received a bone marrow transplant from a CCR5-negative donor has rekindled interest in genome engineering strategies to achieve the same effect. Precise gene editing within the cells is now a realistic possibility with recent advances in understanding the DNA repair mechanisms, DNA interaction with transcription factors and bacterial defense mechanisms. Within the past few years, four novel technologies have emerged that can be engineered for recognition of specific DNA target sequences to enable site-specific gene editing: Homing Endonuclease, ZFN, TALEN, and CRISPR/Cas9 system. The most recent CRISPR/Cas9 system uses a short stretch of complementary RNA bound to Cas9 nuclease to recognize and cleave target DNA, as opposed to the previous technologies that use DNA binding motifs of either zinc finger proteins or transcription activator-like effector molecules fused to an endonuclease to mediate sequence-specific DNA cleavage. Unlike RNA interference, which requires the continued presence of effector moieties to maintain gene silencing, the newer technologies allow permanent disruption of the targeted gene after a single treatment. Here, we review the applications, limitations and future prospects of novel gene-editing strategies for use as HIV therapy.

  2. Short RNA guides cleavage by eukaryotic RNase III.

    Directory of Open Access Journals (Sweden)

    Bruno Lamontagne

    Full Text Available In eukaryotes, short RNAs guide a variety of enzymatic activities that range from RNA editing to translation repression. It is hypothesized that pre-existing proteins evolved to bind and use guide RNA during evolution. However, the capacity of modern proteins to adopt new RNA guides has never been demonstrated. Here we show that Rnt1p, the yeast orthologue of the bacterial dsRNA-specific RNase III, can bind short RNA transcripts and use them as guides for sequence-specific cleavage. Target cleavage occurred at a constant distance from the Rnt1p binding site, leaving the guide RNA intact for subsequent cleavage. Our results indicate that RNase III may trigger sequence-specific RNA degradation independent of the RNAi machinery, and they open the road for a new generation of precise RNA silencing tools that do not trigger a dsRNA-mediated immune response.

  3. Electronics for a Next-Generation SQUID-Based Time-Domain Multiplexing System

    International Nuclear Information System (INIS)

    Reintsema, C. D.; Doriese, W. R.; Hilton, G. C.; Irwin, K. D.; Krinsky, J. W.; Adams, J. S.; Baker, R.; Bandler, S. R.; Kelly, R. L.; Kilbourne, C. A.; Porter, F. S.; Figueroa-Feliciano, E.; Wikus, P.

    2009-01-01

    A decade has elapsed since the design, development and realization of a SQUID-based time-division multiplexer at NIST. During this time the system has been used extensively for low-temperature-detector-array measurements. Concurrently, there have been substantial advancements both in detector array and commercial electronic component technology. The relevance and applicability of the technology has blossomed as well, often accompanied by more demanding measurement requirements. These factors have motivated a complete redesign of the NIST room-temperature read-out electronics. The redesign has leveraged advancements in component technology to achieve new capabilities better suited to the SQUID multiplexers and detector arrays being realized today. As examples of specific performance enhancements, the overall system bandwidth has been increased by a factor of four (a row switching rate of 6.24 MHz), the compactness has been increased by over a factor of two (a higher number of detector columns and rows per circuit board), and there are two high speed outputs per column (allowing fast switching of SQUID offsets in addition to digital feedback). The system architecture, design implementations, and performance advantages of the new system will be discussed. As an application example, the science chain flight electronics for the Micro-X High Resolution Microcalorimeter X-ray Imaging Rocket will be described as both a motivation for, and a direct implementation of the new system.

  4. SQUID Based Cryogenic Current Comparator for Measurements of the Dark Current of Superconducting Cavities

    CERN Document Server

    Vodel, W; Neubert, R; Nietzsche, S

    2005-01-01

    This contribution presents a LTS-SQUID based Cryogenic Current Comparator (CCC) for detecting dark currents, generated e.g. by superconducting cavities for the upcoming X-FEL project at DESY. To achieve the maximum possible energy the gradients of the superconducting RF cavities should be pushed close to the physical limit of 50 MV/m. The measurement of the undesired field emission of electrons (the so-called dark current) in correlation with the gradient will give a proper value to compare and classify the cavities. The main component of the CCC is a high performance LTS-DC SQUID system which is able to measure extremely low magnetic fields, e.g. caused by the extracted dark current. For this reason the input coil of the SQUID is connected across a special designed toroidal niobium pick-up coil (inner diameter: about 100 mm) for the passing electron beam. A noise limited current resolution of nearly 2 pA/√(Hz) with a measurement bandwidth of up to 70 kHz was achieved without the pick-up coil. Now, ...

  5. HTS-SQUID NDE Technique for Pipes based on Ultrasonic Guided Wave

    International Nuclear Information System (INIS)

    Hatsukade, Y; Masutani, N; Teranishi, S; Masamoto, K; Kanenaga, S; Adachi, S; Tanabe, K

    2017-01-01

    This article describes research on the novel high-temperature superconductor (HTS) superconducting quantum interference device (SQUID) non-destructive evaluation (NDE) technique for metallic pipes based on ultrasonic guided waves. We constructed HTS-SQUID NDE system for pipes based on ultrasonic guided waves, which were generated and received by means of the magnetostrictive effects. Using the system, we measured magnetic signals due to T (0, 1) mode ultrasonic guided waves that transmitted on aluminium pipe, and investigated influences of measurement parameters to the magnetic signals, such as direction of a HTS-SQUID gradiometer, lift-off distance, and intensity and frequency of input current fed to a magnetostrictive transmitter. With the gradiometer oriented parallel to the pipe axis, more than 10 times larger signals were measured compared with that oriented perpendicular to the pipe axis. Magnetic signals measured by the gradiometer were inverse proportional to the power of the list- off distance, and proportional to the intensity of the input current up to 1 A pp . Relation between the frequency of the input current and the measured signal was shown and discussed. (paper)

  6. Optimization of a digital SQUID magnetometer in terms of noise and distortion

    International Nuclear Information System (INIS)

    Haverkamp, I; Toepfer, H; Wetzstein, O; Kunert, J; Stolz, R; Meyer, H-G; Ortlepp, T

    2012-01-01

    The digital SQUID magnetometer takes advantage of flux quantization in a superconducting loop in order to measure magnetic fields. The core element of the digital SQUID is a Josephson comparator with a superconducting antenna loop attached to one of its junctions. Evaluation of the circuit from the system’s point of view requires an analysis in the frequency domain. In order to obtain a high-resolution fast Fourier transform, large datasets are necessary which are difficult to generate with transient simulation tools. In this work we derive a behavioural model for the digital SQUID in order to overcome restrictions imposed by transient simulation. By means of this model the influence of the comparator grey zone and the input loop inductance on the system performance was analysed. In order to assess the system, evaluation criteria based on the power spectral density were applied, which are commonly used for characterization of semiconductor analogue to digital converters. As a result of this study, design guidelines for an optimum antenna inductance depending on the comparator grey zone are derived, allowing us to achieve an optimum system performance in terms of noise and distortion. (paper)

  7. Spawning pattern of the neon flying squid Ommastrephes bartramii (Cephalopoda: Oegopsida around the Hawaiian Islands

    Directory of Open Access Journals (Sweden)

    Dharmamony Vijai

    2014-12-01

    Full Text Available The neon flying squid, Ommastrephes bartramii, is an oceanic squid species that is widely distributed in the North Pacific, with the winter-spring cohort spawning around the Hawaiian Islands. Here, we investigated the spawning characteristics of O. bartramii by analyzing various reproductive parameters of individuals (622 males, 108 females collected in this region. Female spawning status was determined from the somatic indices and histological characteristics of the ovaries. At all developmental stages, the ovaries of spawned females contained oocytes, and oviduct fullness was not correlated with body size. Thus, because the eggs mature asynchronously, with multiple filling and evacuation events, this species is considered an intermittent spawner. Mature males with developed accessory glands were also present within the distribution range of healthy spawned females, indicating that mating occurs between spawning events. Our data indicate that the first spawning event occurs at a mantle length of ~520-540 mm for Hawaiian O. bartramii. Subsequently, the squid forage and grow, and refill the oviducts, before the second spawning event occurs.

  8. Specific accumulation of polychlorinated biphenyls and organochlorine pesticides in Japanese common squid as a bioindicator

    International Nuclear Information System (INIS)

    Ueno, D.; Inoue, S.; Ikeda, K.; Tanaka, H.; Yamada, H.; Tanabe, S.

    2003-01-01

    Japanese common squid is a suitable bioindicator for monitoring organochlorines pollution in waters around Japan. - Organochlorines (OCs) representing Persistent Organic Pollutants (POPs) such as PCBs (polychlorinated biphenyls), DDTs (DDT and its metabolites), CHLs (chlordane compounds), HCHs (hexachlorocyclohexane isomers) and HCB (hexachlorobenzene) were determined in the liver of Japanese common squid (Todarodes pacificus) collected from the waters around Japan (Japan Sea and western North Pacific Ocean). Among OCs concentrations, PCBs (upto 5600 ng/g lipid wt.) were the highest, and those of other OCs were in the order of DDT> CHLs > HCHs > HCB. Studies on growth trend and seasonal variation of OCs in this species suggest a rapid reflection of the pollution levels in seawater where and when they were collected, regardless of body-length and time of collection. These results indicate that Japanese common squid is a suitable bioindicator for monitoring OCs pollution in waters around Japan. With regard to the geographical distribution of OCs in this species collected from waters around Japan, OCs concentrations in specimens from Japan Sea were higher than those from the Pacific Ocean. This result might reflect some existing of local pollution sources of OCs around Japan Sea, and slower water exchange between Japan Sea and open ocean

  9. SQUID magnetometry and magneto-optics of epitaxial EuS

    International Nuclear Information System (INIS)

    Rumpf, K.; Granitzer, P.; Krenn, H.; Kellner, W.; Pascher, H.; Kirchschlager, R.; Janecek, S.

    2004-01-01

    The complicated (H,T)-magnetic phase diagram of EuS is caused by the critical balance between nearest and next nearest neighbour exchange interaction (J NN = 0.119 K and J NNN =-0.1209 K) and leads to various spin arrangements NNSS..., NSN..., NNS, NNN... [NS denotes opposite ferromagnetic order in adjacent (111) planes]. Beside the subtle local exchange of 5d-t 2g electrons and localized holes with neighbouring Eu-4f spins, obviously also the strain status influences the occurrence of these different phases. We investigate the magnetic ordering phenomenon in a strained 2.5 μm EuS film on BaF 2 substrate by SQUID magnetometry and magneto-optics like spectral Faraday- and Kerr-effect measurements for temperatures from 2 K up to 200 K and for magnetic field up to 5 T. The magneto-optical probe monitors the local environment of the photoexcited electron-hole pair, called magnetic exciton, located within a ferromagnetic surrounding (photoinduced magnetic polaron), whereas the integral magnetization measured by SQUID is most sensitive to long-range magnetic ordering. In spite of the dissimilarity of measurement techniques we find an influence of the long-range magnetic order (e.g. of the NNS- or NNN-matrix) on the non-resonant Kerr reflection. The complementarity of SQUID and magneto-optical methods is stringent only in the (resonant) spectral range, where magnetic polarons are formed. (author)

  10. Growth and optical development of the ocular lens of the squid (Sepioteuthis lessoniana).

    Science.gov (United States)

    Sivak, J G; West, J A; Campbell, M C

    1994-09-01

    Lens focal properties (spherical aberration), diameter and relative anterior/posterior proportions were measured photographically for Japanese squid (Sepioteuthis lessoniana) at ages 4-6 weeks, 7-9 weeks and 7-8 months. The measures involved photographing the refractive effects of lenses in a physiological solution, with and without an index matching fluid (polyvinylpyrroloidone solution), on a parallel array of fine helium-neon laser beams. Spherical aberration was determined from measurement of back vertex distance. Similar measurements were made on lenses from the eyes of cuttlefish (Sepia officinalis). The cephalopod lens develops as hemispheric halves from separate ectodermal sources. The posterior component contributes, on average, about 60% of axial lens diameter in S. lessoniana of all ages and 55% in S. officinalis. However, these proportions vary widely in both species. All lenses of both species show that spherical aberration is neutralized, although small variations in back vertex distance (positive and negative spherical aberration) were measured. Preliminary measures indicate that the refractive index distribution within the cephalopod lens varies in a manner reminiscent of teleost lenses. Squid lenses from animals 7-9 weeks of age were optimally corrected for spherical aberration. Some squid of this age, from a separate tank, showed a high incidence of cataract development. In each case, lens opacification was caused by deterioration of the posterior lens component.

  11. Assessment of Heavy Metal Contamination in Squid (Loligo Spp.) Tissues of Kedah-Perlis Waters, Malaysia

    International Nuclear Information System (INIS)

    Jamil, T.; Lias, K.; Norsila, D.; Syafinaz, N.S.

    2014-01-01

    This study was carried out to determine the concentration of selected heavy metals (Cd, Cu, Pb and Zn) in three different tissues collected from the ink-sac, head, and muscle of the squid. Squid samples were caught off the coastal waters of Kedah-Perlis, where only mature squids within the maturity size-range of 13 to 15 cm were used. From this study, the concentration of Zn (35.06 ± 4.06 mg/ kg in dry weight) was found significantly higher in all of the tissues, followed by Cu (15.10 ± 13.28 mg/ kg in dry weight), Cd (4.76 ± 3.77 mg/ kg in dry weight), and Pb with an average value of 4.01 ± 0.08 mg/ kg in dry weight. From this study, it was discovered that Zn and Cu concentrations in the tissues were lower than the maximum limit recommended by the Food and Agriculture Organization, Malaysian Food Regulation (1985), as well as other countries. Meanwhile, both non-essential elements namely Cd and Pb recorded higher values than that of the recommended concentrations. According to the Metal Pollution Index (MPI), the ink-sac indicated medium-range contamination, while the head and muscle tissues showed low contamination levels. (author)

  12. Hypoxia tolerance and antioxidant defense system of juvenile jumbo squids in oxygen minimum zones

    Science.gov (United States)

    Trübenbach, Katja; Teixeira, Tatiana; Diniz, Mário; Rosa, Rui

    2013-10-01

    Jumbo squid (Dosidicus gigas) is a large oceanic squid endemic off the Eastern Tropical Pacific that undertakes diel vertical migrations into mesopelagic oxygen minimum zones. One of the expected physiological effects of such migration is the generation of reactive oxygen species (ROS) at the surface, promoted by the transition between hypoxia and reoxygenation states. The aim of this study was to investigate the energy expenditure rates and the antioxidant stress strategies of juvenile D. gigas under normoxia and hypoxia, namely by quantifying oxygen consumption rates, antioxidant enzyme activities [including superoxide dismutase (SOD), catalase (CAT) and glutathione-S-transferase (GST)], heat shock protein expression (Hsp70/Hsc70), and lipid peroxidation [malondialdehyde (MDA) levels]. A high significant decrease (68%) in squid's metabolic rates was observed during hypoxia (p0.05), with the latter indicating no enhancement of lipid peroxidation (i.e. cellular damage) at the warmer and normoxic surface waters. The understanding of such physiological strategies that are linked to oxygen deprivation and reoxygenation phases may provide valuable information about how this species is quickly responding to the impacts of environmental stressors coupled with global climate change.

  13. SQUID-based Nondestructive Testing Instrument of Dished Niobium Sheets for SRF Cavities

    International Nuclear Information System (INIS)

    Q. S. Shu; I. Ben-Zvi; G. Cheng; I. M. Phipps; J. T. Susta; P. Kneisel; G. Myneni; J. Mast; R. Selim

    2007-01-01

    Currently available technology can only inspect flat sheets and allow the elimination of defective flat sheets before the expensive forming and machining of the SRF cavity half-cells, but it does not eliminate the problem of remaining or uncovered surface impurities after partial chemical etching of the half-cells, nor does it detect any defects that may have been added during the fabrication of the half-cells. AMAC has developed a SQUID scanning system based on eddy current technique that allows the scanning of curved Nb samples that are welded to make superconducting RF cavity half-cells. AMAC SQUID scanning system successfully located the defects (Ta macro particles about 100 mm diameter) in a flat Nb sample (top side) and was able to also locate the defects in a cylindrical surface sample (top side). It is more significant that the system successfully located the defects on the backside of the flat sample and curved sample or 3-mm from the top surface. The 3-D SQUID-based Nondestructive instrument will be further optimized and improved in making SRF cavities and allow inspection and detection during cavity manufacturing for achieving highest accelerating fields

  14. Scanning SQUID microscope with an in-situ magnetization/demagnetization field for geological samples

    Science.gov (United States)

    Du, Junwei; Liu, Xiaohong; Qin, Huafeng; Wei, Zhao; Kong, Xiangyang; Liu, Qingsong; Song, Tao

    2018-04-01

    Magnetic properties of rocks are crucial for paleo-, rock-, environmental-magnetism, and magnetic material sciences. Conventional rock magnetometers deal with bulk properties of samples, whereas scanning microscope can map the distribution of remanent magnetization. In this study, a new scanning microscope based on a low-temperature DC superconducting quantum interference device (SQUID) equipped with an in-situ magnetization/demagnetization device was developed. To realize the combination of sensitive instrument as SQUID with high magnetizing/demagnetizing fields, the pick-up coil, the magnetization/demagnetization coils and the measurement mode of the system were optimized. The new microscope has a field sensitivity of 250 pT/√Hz at a coil-to-sample spacing of ∼350 μm, and high magnetization (0-1 T)/ demagnetization (0-300 mT, 400 Hz) functions. With this microscope, isothermal remanent magnetization (IRM) acquisition and the according alternating field (AF) demagnetization curves can be obtained for each point without transferring samples between different procedures, which could result in position deviation, waste of time, and other interferences. The newly-designed SQUID microscope, thus, can be used to investigate the rock magnetic properties of samples at a micro-area scale, and has a great potential to be an efficient tool in paleomagnetism, rock magnetism, and magnetic material studies.

  15. Preparation and evaluation of squid ink polysaccharide-chitosan as a wound-healing sponge.

    Science.gov (United States)

    Huang, Na; Lin, Jiali; Li, Sidong; Deng, Yifeng; Kong, Songzhi; Hong, Pengzhi; Yang, Ping; Liao, Mingneng; Hu, Zhang

    2018-01-01

    A new type of wound healing agent was developed using two marine biomaterials (squid ink polysaccharide and chitosan) as carriers and calcium chloride as an initiator for coagulation. Based on central composite design-response surface methodology, comprehensive evaluation of appearance quality for composite sponges and water absorbency were used as evaluation indices to identify the optimized preparation conditions and further evaluate the performance of the squid ink polysaccharide-chitosan sponge (SIP-CS). The optimized formulation of SIP-CS was as follows: chitosan concentration, 2.29%; squid ink polysaccharide concentration, 0.55%; and calcium chloride concentration, 2.82%, at a volume ratio of 15:5:2. SIP-CS was conducive to sticking on the wound, characterized by the spongy property, strong absorptivity, and tackiness. Rabbit ear arterial, hepatic, and femoral artery hemorrhage experiments indicated that, compared with chitosan dressings and absorbable gelatin, the hemostatic times were shorter and the bleeding volume was smaller. Furthermore, SIP-CS absorbed a large amount of hemocytes, leading to rapid hemostasis. The healing areas and wound pathological sections in scalded New Zealand rabbits indicated that SIP-CS promoted wound healing more rapidly than chitosan and better than commercially available burn cream. Thus, SIP-CS is a good wound healing agent for rapid hemostasis, promoting burn/scalded skin healing, and protecting from wound infection. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Greatly improved cache update times for conditions data with Frontier/Squid

    Energy Technology Data Exchange (ETDEWEB)

    Dykstra, Dave; Lueking, Lee, E-mail: dwd@fnal.go [Computing Division, Fermilab, Batavia, IL (United States)

    2010-04-01

    The CMS detector project loads copies of conditions data to over 100,000 computer cores worldwide by using a software subsystem called Frontier. This subsystem translates database queries into HTTP, looks up the results in a central database at CERN, and caches the results in an industry-standard HTTP proxy/caching server called Squid. One of the most challenging aspects of any cache system is coherency, that is, ensuring that changes made to the underlying data get propagated out to all clients in a timely manner. Recently, the Frontier system was enhanced to drastically reduce the time for changes to be propagated everywhere without heavily loading servers. The propagation time is now as low as 15 minutes for some kinds of data and no more than 60 minutes for the rest of the data. This was accomplished by taking advantage of an HTTP and Squid feature called If-Modified-Since. In order to use this feature, the Frontier server sends a Last-Modified timestamp, but since modification times are not normally tracked by Oracle databases, a PL/SQL program was developed to track the modification times of database tables. We discuss the details of this caching scheme and the obstacles overcome including database and Squid bugs.

  17. Chitinolytic Bacteria-Assisted Conversion of Squid Pen and Its Effect on Dyes and Pigments Adsorption

    Directory of Open Access Journals (Sweden)

    Tzu-Wen Liang

    2015-07-01

    Full Text Available The aim of this work was to produce chitosanase by fermenting from squid pen, and recover the fermented squid pen for dye removal by adsorption. One chitosanase induced from squid pen powder (SPP-containing medium by Bacillus cereus TKU034 was purified in high purification fold (441 and high yield of activity recovery (51% by ammonium sulfate precipitation and combined column chromatography. The SDS-PAGE results showed its molecular mass to be around 43 kDa. The TKU034 chitosanase used for the chitooligomers preparation was studied. The enzyme products revealed that the chitosanase could degrade chitosan with various degrees of polymerization, ranging from 3 to 9, as well as the chitosanase in an endolytic manner. Besides, the fermented SPP was recovered and displayed a better adsorption rate (up to 99.5% for the disperse dyes (red, yellow, blue, and black than the water-soluble food colorants, Allura Red AC (R40 and Tartrazine (Y4. The adsorbed R40 on the unfermented SPP and the fermented SPP was eluted by distilled water and 1 M NaOH to confirm the dye adsorption mechanism. The fermented SPP had a slightly higher adsorption capacity than the unfermented, and elution of the dye from the fermented SPP was easier than from the unfermented. The main dye adsorption mechanism of fermented SPP was physical adsorption, while the adsorption mechanism of unfermented SPP was chemical adsorption.

  18. Chitinolytic Bacteria-Assisted Conversion of Squid Pen and Its Effect on Dyes and Pigments Adsorption.

    Science.gov (United States)

    Liang, Tzu-Wen; Lo, Bo-Chang; Wang, San-Lang

    2015-07-23

    The aim of this work was to produce chitosanase by fermenting from squid pen, and recover the fermented squid pen for dye removal by adsorption. One chitosanase induced from squid pen powder (SPP)-containing medium by Bacillus cereus TKU034 was purified in high purification fold (441) and high yield of activity recovery (51%) by ammonium sulfate precipitation and combined column chromatography. The SDS-PAGE results showed its molecular mass to be around 43 kDa. The TKU034 chitosanase used for the chitooligomers preparation was studied. The enzyme products revealed that the chitosanase could degrade chitosan with various degrees of polymerization, ranging from 3 to 9, as well as the chitosanase in an endolytic manner. Besides, the fermented SPP was recovered and displayed a better adsorption rate (up to 99.5%) for the disperse dyes (red, yellow, blue, and black) than the water-soluble food colorants, Allura Red AC (R40) and Tartrazine (Y4). The adsorbed R40 on the unfermented SPP and the fermented SPP was eluted by distilled water and 1 M NaOH to confirm the dye adsorption mechanism. The fermented SPP had a slightly higher adsorption capacity than the unfermented, and elution of the dye from the fermented SPP was easier than from the unfermented. The main dye adsorption mechanism of fermented SPP was physical adsorption, while the adsorption mechanism of unfermented SPP was chemical adsorption.

  19. Greatly improved cache update times for conditions data with Frontier/Squid

    International Nuclear Information System (INIS)

    Dykstra, Dave; Lueking, Lee

    2009-01-01

    The CMS detector project loads copies of conditions data to over 100,000 computer cores worldwide by using a software subsystem called Frontier. This subsystem translates database queries into HTTP, looks up the results in a central database at CERN, and caches the results in an industry-standard HTTP proxy/caching server called Squid. One of the most challenging aspects of any cache system is coherency, that is, ensuring that changes made to the underlying data get propagated out to all clients in a timely manner. Recently, the Frontier system was enhanced to drastically reduce the time for changes to be propagated everywhere without heavily loading servers. The propagation time is now as low as 15 minutes for some kinds of data and no more than 60 minutes for the rest of the data. This was accomplished by taking advantage of an HTTP and Squid feature called If-Modified-Since. In order to use this feature, the Frontier server sends a Last-Modified timestamp, but since modification times are not normally tracked by Oracle databases, a PL/SQL program was developed to track the modification times of database tables. We discuss the details of this caching scheme and the obstacles overcome including database and Squid bugs.

  20. Growth and flagellation of Vibrio fischeri during initiation of the sepiolid squid light organ symbiosis.

    Science.gov (United States)

    Ruby, E G; Asato, L M

    1993-01-01

    A pure culture of the luminous bacterium Vibrio fischeri is maintained in the light-emitting organ of the sepiolid squid Euprymna scolopes. When the juvenile squid emerges from its egg it is symbiont-free and, because bioluminescence is part of an anti-predatory behavior, therefore must obtain a bacterial inoculum from the surrounding environment. We document here the kinetics of the process by which newly hatched juvenile squids become infected by symbiosis-competent V. fischeri. When placed in seawater containing as few as 240 colony-forming-units (CFU) per ml, the juvenile became detectably bioluminescent within a few hours. Colonization of the nascent light organ was initiated with as few as 1 to 10 bacteria, which rapidly began to grow at an exponential rate until they reached a population size of approximately 10(5) cells by 12 h after the initial infection. Subsequently, the number of bacteria in the established symbiosis was maintained essentially constant by a combination of both a > 20-fold reduction in bacterial growth rate, and an expulsion of excess bacteria into the surrounding seawater. While V. fischeri cells are normally flagellated and motile, these bacteria did not elaborate these appendages once the symbiosis was established; however, they quickly began to synthesize flagella when they were removed from the light organ environment. Thus, two important biological characteristics, growth rate and flagellation, were modulated during establishment of the association, perhaps as part of a coordinated series of symbiotic responses.

  1. Ultraviolet Laser SQUID Microscope for GaN Blue Light Emitting Diode Testing

    International Nuclear Information System (INIS)

    Daibo, M; Kamiwano, D; Kurosawa, T; Yoshizawa, M; Tayama, N

    2006-01-01

    We carried out non-contacting measurements of photocurrent distributions in GaN blue light emitting diode (LED) chips using our newly developed ultraviolet (UV) laser SQUID microscope. The UV light generates the photocurrent, and then the photocurrent induces small magnetic fields around the chip. An off-axis arranged HTS-SQUID magnetometer is employed to detect a vector magnetic field whose typical amplitude is several hundred femto-tesla. Generally, it is difficult to obtain Ohmic contacts for p-type GaN because of the low hole concentration in the p-type epitaxial layer and the lack of any available metal with a higher work function compared with the p-type GaN. Therefore, a traditional probecontacted electrical test is difficult to conduct for wide band gap semiconductors without an adequately annealed electrode. Using the UV-laser SQUID microscope, the photocurrent can be measured without any electrical contact. We show the photocurrent vector map which was reconstructed from measured magnetic fields data. We also demonstrate how we found the position of a defect of the electrical short circuits in the LED chip

  2. HTS-SQUID NDE Technique for Pipes based on Ultrasonic Guided Wave

    Science.gov (United States)

    Hatsukade, Y.; Masutani, N.; Teranishi, S.; Masamoto, K.; Kanenaga, S.; Adachi, S.; Tanabe, K.

    2017-07-01

    This article describes research on the novel high-temperature superconductor (HTS) superconducting quantum interference device (SQUID) non-destructive evaluation (NDE) technique for metallic pipes based on ultrasonic guided waves. We constructed HTS-SQUID NDE system for pipes based on ultrasonic guided waves, which were generated and received by means of the magnetostrictive effects. Using the system, we measured magnetic signals due to T (0, 1) mode ultrasonic guided waves that transmitted on aluminium pipe, and investigated influences of measurement parameters to the magnetic signals, such as direction of a HTS-SQUID gradiometer, lift-off distance, and intensity and frequency of input current fed to a magnetostrictive transmitter. With the gradiometer oriented parallel to the pipe axis, more than 10 times larger signals were measured compared with that oriented perpendicular to the pipe axis. Magnetic signals measured by the gradiometer were inverse proportional to the power of the list- off distance, and proportional to the intensity of the input current up to 1 App. Relation between the frequency of the input current and the measured signal was shown and discussed.

  3. Development of non-destructive evaluation system using an HTS-SQUID gradiometer for magnetized materials

    Science.gov (United States)

    Kawano, J.; Tsukamoto, A.; Adachi, S.; Oshikubo, Y.; Hato, T.; Tanabe, K.; Okamura, T.

    We have developed a new eddy-current non-destructive evaluation (NDE) system using an HTS SQUID gradiometer with the aim of applying it to practical materials with magnetization. The new NDE system employs a LN2-cooled external Cu pickup coil and an HTS SQUID chip placed in a magnetic shield made of HTS material. The HTS SQUID chip consists of an HTS planar gradiometer manufactured by using a ramp-edge junction technology and a multi-turn HTS thin film input coil coupled with the flip-chip configuration. The first-order coaxial gradiometric Cu pickup coil with a diameter of 16 mm and the baseline of 5.6 mm was used in the present NDE experiments. By using this NDE system, we could observe defect-induced magnetic signals without an appreciable influence of magnetization up to 10 mT. We also examined the ability of detecting deep-lying defects and compared with the results obtained using our previous NDE system.

  4. Design and Characterization of Low-noise Dewar for High-sensitivity SQUID Operation

    International Nuclear Information System (INIS)

    Yu, K. K.; Lee, Y. H.; Kim, K.; Kwon, H.; Kim, J. M.

    2010-01-01

    We have fabricated the low noise liquid helium(LHe) dewar with a different shape of thermal shield to apply the 64-channel SQUID(Superconducting Quantum Interference Device) gradiometer. The first shape of thermal shield was made of an aluminum plate with a wide width of 100 mm slit and the other shape was modified with a narrow width of 20 mm slit. The two types of dewars were estimated by comparing the thermal noise and the signal-to-noise ratio(SNR) of magnetocardiography(MCG) using the 1st order SQUID gradiometer system cooled each dewar. The white noise was different as a point of the dewar. The noise was increased as close as the edge of dewar, and also increased at the thermal shield with the more wide width slit. The white noise of the dewar with thermal shield of 100 mm slit was 6.5 fT/Hz 1/2 at the center of dewar and 25 fT/Hz 1/2 at the edge, and the white noise of the other one was 3.5 - 7 fT/Hz 1/2 . We measured the MCG using 64-channel SQUID gradiometer cooled at each LHe dewar and compared the SNR of MCG signal. The SNR was improved of 10 times at the LHe dewar with a modified thermal shield.

  5. Chitinolytic Bacteria-Assisted Conversion of Squid Pen and Its Effect on Dyes and Pigments Adsorption

    Science.gov (United States)

    Liang, Tzu-Wen; Lo, Bo-Chang; Wang, San-Lang

    2015-01-01

    The aim of this work was to produce chitosanase by fermenting from squid pen, and recover the fermented squid pen for dye removal by adsorption. One chitosanase induced from squid pen powder (SPP)-containing medium by Bacillus cereus TKU034 was purified in high purification fold (441) and high yield of activity recovery (51%) by ammonium sulfate precipitation and combined column chromatography. The SDS-PAGE results showed its molecular mass to be around 43 kDa. The TKU034 chitosanase used for the chitooligomers preparation was studied. The enzyme products revealed that the chitosanase could degrade chitosan with various degrees of polymerization, ranging from 3 to 9, as well as the chitosanase in an endolytic manner. Besides, the fermented SPP was recovered and displayed a better adsorption rate (up to 99.5%) for the disperse dyes (red, yellow, blue, and black) than the water-soluble food colorants, Allura Red AC (R40) and Tartrazine (Y4). The adsorbed R40 on the unfermented SPP and the fermented SPP was eluted by distilled water and 1 M NaOH to confirm the dye adsorption mechanism. The fermented SPP had a slightly higher adsorption capacity than the unfermented, and elution of the dye from the fermented SPP was easier than from the unfermented. The main dye adsorption mechanism of fermented SPP was physical adsorption, while the adsorption mechanism of unfermented SPP was chemical adsorption. PMID:26213948

  6. SQUID multiplexing using baseband feedback for space application of transition-edge sensor microcalorimeters

    Energy Technology Data Exchange (ETDEWEB)

    Takei, Y; Yamasaki, N Y; Hirakoso, W; Kimura, S; Mitsuda, K, E-mail: takei@astro.isas.jaxa.j [Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency, 3-1-1 Yoshinodai, Sagamihara, 229-8510 (Japan)

    2009-11-15

    A microcalorimeter array based on a transition-edge sensor (TES) thermometer is a promising imaging spectrometer for use in future x-ray astronomy missions. A TES microcalorimeter achieves {approx}<5 eV energy resolution and an array of >100 pixels also provides a moderate imaging capability. For a large format array, signal multiplexing at the low temperature stage is mandatory in order to reduce heat loads from cold stage preamplifiers and through wirings. We are developing frequency division multiplexing (FDM). In FDM, each TES is ac-biased with a different carrier frequency. Signals from several pixels are summed and then read out by one dc SQUID (superconducting quantum interference device). The maximum number of multiplexed pixels is limited by the bandwidth of a SQUID in a flux-locked loop. Assuming 1 m cable length between the room temperature and the cold stage, the bandwidth is only <1 MHz with a standard flux-locked loop, due to the delay and phase shift of wirings. We report our development of baseband feedback, a new feedback scheme that overcomes the bandwidth limitation. In baseband feedback, the signal ({approx}<10 kHz) from the TES is sent back to the SQUID after the phase of carrier frequency ({approx}1 MHz) has been adjusted. We demonstrated open-loop gain of 8 for 10 kHz signal at 5 MHz carrier frequency, which indicates the possibility of {approx}40-pixel multiplexing of the TES signal.

  7. The use of artificial neural network modeling to represent the process of concentration by molecular distillation of omega-3 from squid oil

    Directory of Open Access Journals (Sweden)

    Rossi, P.

    2014-12-01

    Full Text Available The concentration of omega-3 compounds obtained for the esterification of squid oil by molecular distillation was carried out in two stages. This operation can process these thermolabile and high molecular weight components at very low temperatures. Given the mathematical complexity of the theoretical model, artificial neural networks (ANN have provided an alternative to a classical computing analysis. The objective of this study was to create a predictive model using artificial neural network techniques to represent the concentration process of omega-3 compounds obtained from squid oil using molecular distillation. Another objective of this study was to analyze the performance of two different alternatives of ANN modeling; one of them is a model that represents all variables in the process and the other is a global model that simulates only the input and output variables of the process. The alternative of the ANN global model showed the best fit to the experimental data.La concentración de compuestos omega-3, obtenidos de la esterificación de aceite de calamar, por destilación molecular fue llevada a cabo en dos etapas. Esta operación permite procesar componentes termolábiles y de alto peso molecular a muy bajas temperaturas. Dada la alta complejidad de los modelos teóricos, las redes neuronales artificiales (RNA conforman una alternativa al análisis computacional clásico. El objetivo de este estudio fue crear un modelo predictivo usando modelos de redes neuronales artificiales para representar el proceso de concentración de compuestos omega-3 obtenidos del aceite de calamar por destilación molecular. Otro objetivo de este estudio fue analizar el desenvolvimiento de dos alternativas de modelos RNA; uno de ellos es un modelo que representa todas las variables en el proceso y otro es un modelo global que simula solo las variables de entrada y de salida del proceso. La alternativa de un modelo RNA global mostró el mejor ajuste de los

  8. Connectivity editing for quadrilateral meshes

    KAUST Repository

    Peng, Chihan; Zhang, Eugene; Kobayashi, Yoshihiro; Wonka, Peter

    2011-01-01

    We propose new connectivity editing operations for quadrilateral meshes with the unique ability to explicitly control the location, orientation, type, and number of the irregular vertices (valence not equal to four) in the mesh while preserving sharp edges. We provide theoretical analysis on what editing operations are possible and impossible and introduce three fundamental operations to move and re-orient a pair of irregular vertices. We argue that our editing operations are fundamental, because they only change the quad mesh in the smallest possible region and involve the fewest irregular vertices (i.e., two). The irregular vertex movement operations are supplemented by operations for the splitting, merging, canceling, and aligning of irregular vertices. We explain how the proposed highlevel operations are realized through graph-level editing operations such as quad collapses, edge flips, and edge splits. The utility of these mesh editing operations are demonstrated by improving the connectivity of quad meshes generated from state-of-art quadrangulation techniques. © 2011 ACM.

  9. Connectivity editing for quadrilateral meshes

    KAUST Repository

    Peng, Chihan

    2011-12-12

    We propose new connectivity editing operations for quadrilateral meshes with the unique ability to explicitly control the location, orientation, type, and number of the irregular vertices (valence not equal to four) in the mesh while preserving sharp edges. We provide theoretical analysis on what editing operations are possible and impossible and introduce three fundamental operations to move and re-orient a pair of irregular vertices. We argue that our editing operations are fundamental, because they only change the quad mesh in the smallest possible region and involve the fewest irregular vertices (i.e., two). The irregular vertex movement operations are supplemented by operations for the splitting, merging, canceling, and aligning of irregular vertices. We explain how the proposed highlevel operations are realized through graph-level editing operations such as quad collapses, edge flips, and edge splits. The utility of these mesh editing operations are demonstrated by improving the connectivity of quad meshes generated from state-of-art quadrangulation techniques. © 2011 ACM.

  10. [Genome editing of industrial microorganism].

    Science.gov (United States)

    Zhu, Linjiang; Li, Qi

    2015-03-01

    Genome editing is defined as highly-effective and precise modification of cellular genome in a large scale. In recent years, such genome-editing methods have been rapidly developed in the field of industrial strain improvement. The quickly-updating methods thoroughly change the old mode of inefficient genetic modification, which is "one modification, one selection marker, and one target site". Highly-effective modification mode in genome editing have been developed including simultaneous modification of multiplex genes, highly-effective insertion, replacement, and deletion of target genes in the genome scale, cut-paste of a large DNA fragment. These new tools for microbial genome editing will certainly be applied widely, and increase the efficiency of industrial strain improvement, and promote the revolution of traditional fermentation industry and rapid development of novel industrial biotechnology like production of biofuel and biomaterial. The technological principle of these genome-editing methods and their applications were summarized in this review, which can benefit engineering and construction of industrial microorganism.

  11. ULF-NMR system using HTS-SQUID and permanent magnet

    Energy Technology Data Exchange (ETDEWEB)

    Fukumoto, Shohei, E-mail: hatukade@ens.tut.ac.jp [Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi 441-8580 (Japan); Tsunaki, Shingo; Chigasaki, Takumi; Hatsukade, Yoshimi; Tanaka, Saburo [Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi 441-8580 (Japan)

    2013-01-15

    Highlights: ► A permanent magnet was introduced into a ULF SQUID-NMR system for polarization. ► An instrument to transfer a sample in the magnet to under a SQUID was implemented. ► An AC pulse coil was also introduced to apply a π/2 pulse to obtain an NMR signal. ► A {sup 1}H NMR signal was measured while applying a static field of 45 μT. ► The signal to noise ratio of the {sup 1}H NMR signal was about 100. -- Abstract: We have constructed an ultra-low field (ULF) nuclear magnetic resonance (NMR)/magnetic resonance imaging (MRI) system using an HTS-rf-SQUID and room-temperature electromagnets in a magnetically shielded room (MSR). In this study, in order to improve the signal to noise ratio (S/N) of the system, we introduced a permanent magnet instead of the electromagnet for pre-polarizing the sample to enhance the pre-polarizing field (B{sub p}). The cylindrical permanent magnet of 270 mT was used to magnetize a water sample for several seconds outside the MSR and about 1.5 m away from the SQUID. We constructed an instrument to transfer the magnetized sample from the permanent magnet to under the SQUID in 0.5 s. Since the non-adiabatic condition cannot be kept in such sample transfer scheme, an AC pulse coil to apply an AC pulse field B{sub AC} to rotate the magnetization moments for π/2 was introduced to measure a free induction decay (FID) signal from the sample. By this system, we obtained an NMR signal from the water sample of 10 ml while applying a static field of 45 μT and π/2 pulse after the transfer. The S/N of the NMR spectrum was about 100 by a single shot, which was 10 times larger than that obtained with the electromagnet of 32 mT. In addition, we demonstrated the measurements of the longitudinal relaxation time (T{sub 1}) and the spin echo signal of the water sample by the system.

  12. High-resolution imaging of magnetic fields using scanning superconducting quantum interference device (SQUID) microscopy

    Science.gov (United States)

    Fong de Los Santos, Luis E.

    Development of a scanning superconducting quantum interference device (SQUID) microscope system with interchangeable sensor configurations for imaging magnetic fields of room-temperature (RT) samples with sub-millimeter resolution. The low-critical-temperature (Tc) niobium-based monolithic SQUID sensor is mounted in the tip of a sapphire rod and thermally anchored to the cryostat helium reservoir. A 25 mum sapphire window separates the vacuum space from the RT sample. A positioning mechanism allows adjusting the sample-to-sensor spacing from the top of the Dewar. I have achieved a sensor-to-sample spacing of 100 mum, which could be maintained for periods of up to 4 weeks. Different SQUID sensor configurations are necessary to achieve the best combination of spatial resolution and field sensitivity for a given magnetic source. For imaging thin sections of geological samples, I used a custom-designed monolithic low-Tc niobium bare SQUID sensor, with an effective diameter of 80 mum, and achieved a field sensitivity of 1.5 pT/Hz1/2 and a magnetic moment sensitivity of 5.4 x 10-18 Am2/Hz1/2 at a sensor-to-sample spacing of 100 mum in the white noise region for frequencies above 100 Hz. Imaging action currents in cardiac tissue requires higher field sensitivity, which can only be achieved by compromising spatial resolution. I developed a monolithic low-Tc niobium multiloop SQUID sensor, with sensor sizes ranging from 250 mum to 1 mm, and achieved sensitivities of 480 - 180 fT/Hz1/2 in the white noise region for frequencies above 100 Hz, respectively. For all sensor configurations, the spatial resolution was comparable to the effective diameter and limited by the sensor-to-sample spacing. Spatial registration allowed us to compare high-resolution images of magnetic fields associated with action currents and optical recordings of transmembrane potentials to study the bidomain nature of cardiac tissue or to match petrography to magnetic field maps in thin sections of

  13. Plan for SQUID microscope at ASRC: Vision, purposes and the present status

    International Nuclear Information System (INIS)

    Kadowaki, K.; Kakeya, I.; Suzuki, J.; Hata, Y.; Hojyo, K

    2001-01-01

    A new research plan to develop SQUID microscope and apply it to advanced science and technology research was started in the year of 2000 at the Advanced Science Research Center (ASRC) of JAERI (Japan Atomic Energy Research Institute). This plan was made to develop 'research of ultrafine magnetic structures with magnetic microscope' and is scheduled to continue five years. Principle of SQUID magnetic microscope is to observe changes of magnetic field in microscopic space using SQUID element as the magnetic probe. At present this type of instrument is fabricated by Seiko Instruments Inc. in Japan and is commercially available. Therefore, this plan is being promoted in collaboration with Seiko Instruments Inc. One of the main issues of the present plan is to raise the spatial resolution to the extremity. As of magnetic microscopes, 'magnetic force microscope' and 'scanning Hall probe microscope' also exist. They have different characteristics of their own. The present plan needs challenging technical developments in various fields. Supposed the spatial resolution be made very high, for example, by making very fine SQUID loop with ultrafine processing, critical technologies like sensitivity, electronics, quantum size effect and so on are to be solved at the same time. Characteristics of the existing instrument are being examined from various aspects. At present, the following three issues are taken up and being studied. (1) High resolution and related technical developments. (2) High sensitivity. (3) High performance of cooling system. Among them, the high resolution is the most serious problem. Completely new design of the SQUID system may be needed. By using the existing instrument, magnetic fluxes trapped on YBCO films are observed and the image quality is being examined. Some of the issues which are considered to be taken up now are listed as follows. (1) Magnetic domain structures on thin film magnetic materials. (2) Observation of structures of Josephson magnetic

  14. Emulsifying and gelling properties of weakfish myofibrillar proteins as affected by squid mantle myofibrillar proteins in a model system

    Directory of Open Access Journals (Sweden)

    Daniela Mariel Suarez

    2014-03-01

    Full Text Available The aim of the present work was to investigate the physicochemical, biochemical and functional characteristics of both the myofibrils (MF and actomyosin (AM of squid mantle (Illex argentinus and weakfish (Cynoscion guatucupa muscles, and evaluate the influence of the addition of myofibrilar proteins from the squid mantle on the physicochemical and functional properties of those of the weakfish. After extraction, purification and characterization of the MF and AM of both species, emulsions of each protein fraction from each muscle were formulated. Mixtures of the MF or AM of both species were also analyzed. The emulsifying properties were monitoring using the Emulsifying Activity Index (EAI and Emulsion Stability (ES. In addition, gel pastes were formulated from the squid mantle, weakfish muscle and the mixture of both species, and the following functional properties of the gels assessed: water holding capacity, colour, textural profile analysis (TPA (hardness, elasticity, cohesiveness, gumminess and gel strength. The EAI values of emulsions formulated with the MF of the mantle were significantly (p<0.05 higher than those formulated from those of weakfish. The incorporation of squid MF in the mixture increased the EAI values. Conversely, the highest ES values were obtained with weakfish MF, and the incorporation of MF weakfish in the mixture increased the ES values. Similar EAI and ES behaviours were observed for the AM of the corresponding species. Irrespective of the thermal treatment, the gel strength of the gelled paste of squid muscle was significantly (p<0.05 lower than that of weakfish muscle and of those obtained with the different mixtures. The behaviours of the expressible moisture (EM from the gelled pastes were similar to those of gel strength. Irrespective of the thermal treatment, the pastes formulated with a high weakfish: mantle ratio showed less water loss. The gelled pastes of squid mantle showed the highest values for whiteness

  15. Boneless Pose Editing and Animation

    DEFF Research Database (Denmark)

    Bærentzen, Jakob Andreas; Hansen, Kristian Evers; Erleben, Kenny

    2007-01-01

    In this paper, we propose a pose editing and animation method for triangulated surfaces based on a user controlled partitioning of the model into deformable parts and rigid parts which are denoted handles. In our pose editing system, the user can sculpt a set of poses simply by transforming...... the handles for each pose. Using Laplacian editing, the deformable parts are deformed to match the handles. In our animation system the user can constrain one or several handles in order to define a new pose. New poses are interpolated from the examples poses, by solving a small non-linear optimization...... problem in order to obtain the interpolation weights. While the system can be used simply for building poses, it is also an animation system. The user can specify a path for a given constraint and the model is animated correspondingly....

  16. CRISPR-Cas9 Toolkit for Actinomycete Genome Editing

    DEFF Research Database (Denmark)

    Tong, Yaojun; Robertsen, Helene Lunde; Blin, Kai

    2018-01-01

    engineering approaches for boosting known and discovering novel natural products. In order to facilitate the genome editing for actinomycetes, we developed a CRISPR-Cas9 toolkit with high efficiency for actinomyces genome editing. This basic toolkit includes a software for spacer (sgRNA) identification......, a system for in-frame gene/gene cluster knockout, a system for gene loss-of-function study, a system for generating a random size deletion library, and a system for gene knockdown. For the latter, a uracil-specific excision reagent (USER) cloning technology was adapted to simplify the CRISPR vector...... construction process. The application of this toolkit was successfully demonstrated by perturbation of genomes of Streptomyces coelicolor A3(2) and Streptomyces collinus Tü 365. The CRISPR-Cas9 toolkit and related protocol described here can be widely used for metabolic engineering of actinomycetes....

  17. Editörden

    Directory of Open Access Journals (Sweden)

    Nadir Arıcan

    2007-04-01

    Full Text Available Değerli Adli Bilimci’ler, Dergimizin ilk baskısının yapıldığı 1996 yılından 2006 yılı sonuna kadar 11 ciltten oluşan dizisini ara vermeden kesintisiz olarak yayınlanma başarısını gösteren Adli Tıp Bülteni Yayın Kurulu adına saygı ile selamlıyoruz. Dergimizin 12. cildinin ilk sayısı, yayın kurulundaki görev değişikliği ile elinize ulaşıyor. “Adli Tıp Bülteni”ni tüm olumsuz koşullara karşın, siz alana emek veren adli bilimcilerin de büyük desteği ile yayın hayatım başarı ile sürdürdü. Bu başarıda başta editörlerimiz sayın Prof. Dr. Serpil Salaçin ve sayın Prof. Dr. Şebnem Korur Fincancı ile yayın kurulunda görev almış meslektaşlarımıza teşekkür ediyor ve desteklerinin artarak devam edeceğini ümit ediyoruz. Adli Tıp Bülteni, ilk editörü sayın Prof. Dr. Serpil Salaçin’in bültenin 1. sayısında belirttiği amaca uygun olarak, her geçen gün daha da güçlenerek yayın hayatını sürdürmektedir. Yayın akışında zaman zaman kesintiler olsa da, amacı doğrultusunda “alanındaki bilgi akışını sağlama ve bilimsel gelişmelerin önemli bir parçası olma özelliğini” Adli Tıp Uzmanları Derneği’nin resmi bilimsel yayın organı kimliği ile devam ettirmektedir. Hedefleri doğrultusunda uluslararası indekslerce taranan bir dergi olma yolunda ilk adımını atan dergimizin bu alandaki çalışmaları sayın Prof. Dr. Şebnem Korur Fincancı tarafından yürütülmektedir. Görevini genç meslektaşına devretmiş olsa da alanımızdaki uluslar arası deneyimi ile Adli Tıp Bülteni’ni çok farklı noktalara taşıyacağı inancındayım. Bu alanda yapacağı katkılardan dolayı sayın hocama biz kez daha teşekkür etmek istiyorum. Bundan böyle Adli Tıp Bülteni’ne yayınlanmak üzere gönderdiğiniz çalışmalarınızın değerlendirmesini daha hızlı yapabilmek ve baskı aşamasına getirmek amacı ile iletişimi elektronik ortamda yapmaya

  18. Tokamaks - Third Edition

    International Nuclear Information System (INIS)

    Rogister, A L

    2004-01-01

    John Wesson's well known book, now re-edited for the third time, provides an excellent introduction to fusion oriented plasma physics in tokamaks. The author's task was a very challenging one, for a confined plasma is a complex system characterised by a variety of dimensionless parameters and its properties change qualitatively when certain threshold values are reached in this multi-parameter space. As a consequence, theoretical description is required at different levels, which are complementary: particle orbits, kinetic and fluid descriptions, but also intuitive and empirical approaches. Theory must be carried out on many fronts: equilibrium, instabilities, heating, transport etc. Since the properties of the confined plasma depend on the boundary conditions, the physics of plasmas along open magnetic field lines and plasma surface interaction processes must also be accounted for. Those subjects (and others) are discussed in depth in chapters 2-9. Chapter 1 mostly deals with ignition requirements and the tokamak concept, while chapter 14 provides a list of useful relations: differential operators, collision times, characteristic lengths and frequencies, expressions for the neoclassical resistivity and heat conduction, the bootstrap current etc. The presentation is sufficiently broad and thorough that specialists within tokamak research can either pick useful and up-to-date information or find an authoritative introduction into other areas of the subject. It is also clear and concise so that it should provide an attractive and accurate initiation for those wishing to enter the field and for outsiders who would like to understand the concepts and be informed about the goals and challenges on the horizon. Validation of theoretical models requires adequately resolved experimental data for the various equilibrium profiles (clearly a challenge in the vicinity of transport barriers) and the fluctuations to which instabilities give rise. Chapter 10 is therefore devoted to

  19. Transcripts of the NADH-dehydrogenase subunit 3 gene are differentially edited in Oenothera mitochondria.

    Science.gov (United States)

    Schuster, W; Wissinger, B; Unseld, M; Brennicke, A

    1990-01-01

    A number of cytosines are altered to be recognized as uridines in transcripts of the nad3 locus in mitochondria of the higher plant Oenothera. Such nucleotide modifications can be found at 16 different sites within the nad3 coding region. Most of these alterations in the mRNA sequence change codon identities to specify amino acids better conserved in evolution. Individual cDNA clones differ in their degree of editing at five nucleotide positions, three of which are silent, while two lead to codon alterations specifying different amino acids. None of the cDNA clones analysed is maximally edited at all possible sites, suggesting slow processing or lowered stringency of editing at these nucleotides. Differentially edited transcripts could be editing intermediates or could code for differing polypeptides. Two edited nucleotides in an open reading frame located upstream of nad3 change two amino acids in the deduced polypeptide. Part of the well-conserved ribosomal protein gene rps12 also encoded downstream of nad3 in other plants, is lost in Oenothera mitochondria by recombination events. The functional rps12 protein must be imported from the cytoplasm since the deleted sequences of this gene are not found in the Oenothera mitochondrial genome. The pseudogene sequence is not edited at any nucleotide position. Images Fig. 3. Fig. 4. Fig. 7. PMID:1688531

  20. Understanding Editing Behaviors in Multilingual Wikipedia.

    Directory of Open Access Journals (Sweden)

    Suin Kim

    Full Text Available Multilingualism is common offline, but we have a more limited understanding of the ways multilingualism is displayed online and the roles that multilinguals play in the spread of content between speakers of different languages. We take a computational approach to studying multilingualism using one of the largest user-generated content platforms, Wikipedia. We study multilingualism by collecting and analyzing a large dataset of the content written by multilingual editors of the English, German, and Spanish editions of Wikipedia. This dataset contains over two million paragraphs edited by over 15,000 multilingual users from July 8 to August 9, 2013. We analyze these multilingual editors in terms of their engagement, interests, and language proficiency in their primary and non-primary (secondary languages and find that the English edition of Wikipedia displays different dynamics from the Spanish and German editions. Users primarily editing the Spanish and German editions make more complex edits than users who edit these editions as a second language. In contrast, users editing the English edition as a second language make edits that are just as complex as the edits by users who primarily edit the English edition. In this way, English serves a special role bringing together content written by multilinguals from many language editions. Nonetheless, language remains a formidable hurdle to the spread of content: we find evidence for a complexity barrier whereby editors are less likely to edit complex content in a second language. In addition, we find that multilinguals are less engaged and show lower levels of language proficiency in their second languages. We also examine the topical interests of multilingual editors and find that there is no significant difference between primary and non-primary editors in each language.