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...

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.

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

Directory of Open Access Journals (Sweden)

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.

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....

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

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.

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.

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.

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

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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.

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...

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

Science.gov (United States)

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.

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

Directory of Open Access Journals (Sweden)

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.

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.

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

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.

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...

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.

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

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

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

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.

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.

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

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.

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.

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

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

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

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.

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...

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.

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.

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...

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.

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.

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.

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.

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.

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

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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.

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.

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.

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

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.

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

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

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.

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.

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

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.)

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.

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

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.

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.

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.

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.

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.

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

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.

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.

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

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

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

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

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

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

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.

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.

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.

RNA editing in Drosophila melanogaster: new targets and functionalconsequences

Energy Technology Data Exchange (ETDEWEB)

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.

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.

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)

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

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.

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.

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

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.

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.

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.

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.)

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.

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.

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

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...

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.

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

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

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

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

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...

Trade-off between Transcriptome Plasticity and Genome Evolution in Cephalopods.

Science.gov (United States)

Liscovitch-Brauer, Noa; Alon, Shahar; Porath, Hagit T; Elstein, Boaz; Unger, Ron; Ziv, Tamar; Admon, Arie; Levanon, Erez Y; Rosenthal, Joshua J C; Eisenberg, Eli

2017-04-06

RNA editing, a post-transcriptional process, allows the diversification of proteomes beyond the genomic blueprint; however it is infrequently used among animals for this purpose. Recent reports suggesting increased levels of RNA editing in squids thus raise the question of the nature and effects of these events. We here show that RNA editing is particularly common in behaviorally sophisticated coleoid cephalopods, with tens of thousands of evolutionarily conserved sites. Editing is enriched in the nervous system, affecting molecules pertinent for excitability and neuronal morphology. The genomic sequence flanking editing sites is highly conserved, suggesting that the process confers a selective advantage. Due to the large number of sites, the surrounding conservation greatly reduces the number of mutations and genomic polymorphisms in protein-coding regions. This trade-off between genome evolution and transcriptome plasticity highlights the importance of RNA recoding as a strategy for diversifying proteins, particularly those associated with neural function. PAPERCLIP. Copyright © 2017 Elsevier Inc. All rights reserved.

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.

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.

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.

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

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.

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.

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.

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

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.

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

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

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

[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.

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 YBa₂Cu₃O_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-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.

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.

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...

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.

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.

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

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.).

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

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.

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.

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.

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.)

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.

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

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

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.

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.

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.

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.

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

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.

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

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.

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.

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.

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.

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

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.

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.

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.

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)

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

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.

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.

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.

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

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

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.

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.

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....

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...

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.

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

High-T_c 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 (T_c ) 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-T_c 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 YBa₂Cu₃O_7-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

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.

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.

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.

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

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.

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

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

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)

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

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.

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

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...

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

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/

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.

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

Energy Technology Data Exchange (ETDEWEB)

Chesca, Boris, E-mail: B.Chesca@lboro.ac.uk; John, Daniel [Department of Physics, Loughborough University, Loughborough LE11 3TU (United Kingdom); Mellor, Christopher J. [School of Physics and Astronomy, Nottingham University, Nottingham NG7 2RD (United Kingdom)

2015-10-19

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{sub Φ}{sup 1/2} decreases as 1/N{sup 1/2}. Here, we report the realization of both these improvements in an advanced layout of very large SQUID arrays made of YBa{sub 2}Cu{sub 3}O{sub 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{sub Φ}{sup 1/2} between (0.25 and 0.44) μΦ{sub 0}/Hz{sup 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.

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

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

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

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

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 ...

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.

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.

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.

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.

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

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

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.

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.

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.

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

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...

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

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.

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

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

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.)

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.

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

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)

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.

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)

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

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

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

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.

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.

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

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.

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.

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

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%)

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

Development and testing of high temperature-vector-SQUID conductor-magnetometers for the electro-magnetic exploration of our deposits. Final report; SQUID-Anwendungen - Entwicklung und Erprobung von Hochtemperatur-Vektor-Supraleiter SQUID-Magnetometern fuer die elektromagnetische Exploration von Lagerstaetten. Abschlussbericht

Energy Technology Data Exchange (ETDEWEB)

Matzander, U.; Friedrichs, B.

2000-03-01

Aim of the was the development of a prototype of a 3 axis HTc SQUID magnetometer for the geophysical exploration. The prototype was tested during the project in Germany and in China. Metronix task was the supervision of the development with the direction that the sensor can be used for field measurements and that the manufacturing costs will be acceptable. For magnetotelluric measurements (MT/CSAMT) further development is required to enhance the drift and noise properties of the sensor. The advantages in the geophysical TEM exploration are: greater sounding depth and good conductors (ore bodies) can be penetrated completely; the thickness of the resource can be estimated this way. At the same time the measuring time can be reduced tremendously because of the better signal to noise ratio. The productivity of the measuring campaign increases. If due to further developments coils systems can be replaced in total by the SQUID, SQUID systems will dominate the TEM market. (orig.) [German] Ziel des Projektes war es, einen Prototyp eines 3-achsigen HTc SQUIDS zur Verfuegung zu haben, welcher die Anforderungen fuer geophysikalische Messungen erfuellt. Dieser Prototyp wurde im Laufe des Projektes in Deutschland und China getestet. Die Rolle der Firma Metronix in diesem Projekt war die Einflussnahme auf die Entwicklung in der Form, dass zum einen die aus der Feldmesstechnik resultierenden Anforderungen beruecksichtigt werden, zum anderen auf eine spaetere kostenguenstige Herstellung geachtet wird. Bei magnetotellurischen Messungen (MT/CSAMT) besteht weiterer Bedarf an Verbesserungen hinsichtlich der Drift- und Rauscheigenschaften des Sensors. Fuer die geophysikalische Exploration in der TEM ergeben sich folgende Vorteile: die Erkundungstiefe ist groesser und gute Leiter (Erzkoerper) koennen vollstaendig durchteuft werden; damit kann die Maechtigkeit des Vorkommens bestimmt werden. Gleichzeitig kann auf Grund des besseren Signal / Rauschverhaeltnisses die Messzeit deutlich

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...

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)

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.

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.

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.

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.

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.

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.

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

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

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.

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.

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.

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/.

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/

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

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...

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

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

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.

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

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

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/.

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.

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.

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.

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

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.

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.

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.

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)

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

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.

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

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.

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.

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)

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.

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

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.

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...

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.

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

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

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.

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

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.

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.

[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.

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.

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.

Development of a CRISPR/Cas9 genome editing toolbox for Corynebacterium glutamicum.

Science.gov (United States)

Liu, Jiao; Wang, Yu; Lu, Yujiao; Zheng, Ping; Sun, Jibin; Ma, Yanhe

2017-11-16

Corynebacterium glutamicum is an important industrial workhorse and advanced genetic engineering tools are urgently demanded. Recently, the clustered regularly interspaced short palindromic repeats (CRISPR) and their CRISPR-associated proteins (Cas) have revolutionized the field of genome engineering. The CRISPR/Cas9 system that utilizes NGG as protospacer adjacent motif (PAM) and has good targeting specificity can be developed into a powerful tool for efficient and precise genome editing of C. glutamicum. Herein, we developed a versatile CRISPR/Cas9 genome editing toolbox for C. glutamicum. Cas9 and gRNA expression cassettes were reconstituted to combat Cas9 toxicity and facilitate effective termination of gRNA transcription. Co-transformation of Cas9 and gRNA expression plasmids was exploited to overcome high-frequency mutation of cas9, allowing not only highly efficient gene deletion and insertion with plasmid-borne editing templates (efficiencies up to 60.0 and 62.5%, respectively) but also simple and time-saving operation. Furthermore, CRISPR/Cas9-mediated ssDNA recombineering was developed to precisely introduce small modifications and single-nucleotide changes into the genome of C. glutamicum with efficiencies over 80.0%. Notably, double-locus editing was also achieved in C. glutamicum. This toolbox works well in several C. glutamicum strains including the widely-used strains ATCC 13032 and ATCC 13869. In this study, we developed a CRISPR/Cas9 toolbox that could facilitate markerless gene deletion, gene insertion, precise base editing, and double-locus editing in C. glutamicum. The CRISPR/Cas9 toolbox holds promise for accelerating the engineering of C. glutamicum and advancing its application in the production of biochemicals and biofuels.

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

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.

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.

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.

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.

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.))

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.

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...

Editing plants for virus resistance using CRISPR-Cas.

Science.gov (United States)

Green, J C; Hu, J S

This minireview summarizes recent advancements using the clustered regularly interspaced palindromic repeats-associated nuclease systems (CRISPR-Cas) derived from prokaryotes to breed plants resistant to DNA and RNA viruses. The CRISPR-Cas system represents a powerful tool able to edit and insert novel traits into plants precisely at chosen loci offering enormous advantages to classical breeding. Approaches to engineering plant virus resistance in both transgenic and non-transgenic plants are discussed. Iterations of the CRISPR-Cas system, FnCas9 and C2c2 capable of editing RNA in eukaryotic cells offer a particular advantage for providing resistance to RNA viruses which represent the great majority of known plant viruses. Scientists have obtained conflicting results using gene silencing technology to produce transgenic plants resistant to geminiviruses. CRISPR-Cas systems engineered in plants to target geminiviruses have consistently reduced virus accumulation providing increased resistance to virus infection. CRISPR-Cas may provide novel and reliable approaches to control geminiviruses and other ssDNA viruses such as Banana bunchy top virus (BBTV).

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

Targeted viral-mediated plant genome editing using crispr/cas9

KAUST Repository

Mahfouz, Magdy M.; Ali, Zahir

2015-01-01

The present disclosure provides a viral-mediated genome-editing platform that facilitates multiplexing, obviates stable transformation, and is applicable across plant species. The RNA2 genome of the tobacco rattle virus (TRV) was engineered to carry and systemically deliver a guide RNA molecules into plants overexpressing Cas9 endonuclease. High genomic modification frequencies were observed in inoculated as well as systemic leaves including the plant growing points. This system facilitates multiplexing and can lead to germinal transmission of the genomic modifications in the progeny, thereby obviating the requirements of repeated transformations and tissue culture. The editing platform of the disclosure is useful in plant genome engineering and applicable across plant species amenable to viral infections for agricultural biotechnology applications.

Targeted viral-mediated plant genome editing using crispr/cas9

KAUST Repository

Mahfouz, Magdy M.

2015-12-17

The present disclosure provides a viral-mediated genome-editing platform that facilitates multiplexing, obviates stable transformation, and is applicable across plant species. The RNA2 genome of the tobacco rattle virus (TRV) was engineered to carry and systemically deliver a guide RNA molecules into plants overexpressing Cas9 endonuclease. High genomic modification frequencies were observed in inoculated as well as systemic leaves including the plant growing points. This system facilitates multiplexing and can lead to germinal transmission of the genomic modifications in the progeny, thereby obviating the requirements of repeated transformations and tissue culture. The editing platform of the disclosure is useful in plant genome engineering and applicable across plant species amenable to viral infections for agricultural biotechnology applications.

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...

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.

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.

CRISPR-RT: A web service for designing CRISPR-C2c2 crRNA with improved target specificity

OpenAIRE

Zhu, Houxiang; Richmond, Emily; Liang, Chun

2017-01-01

CRISPR-Cas systems have been successfully applied in genome editing. Recently, the CRISPR-C2c2 system has been reported as a tool for RNA editing. Here we describe CRISPR-RT (CRISPR RNA-Targeting), the first web service to help biologists design the crRNA with improved target specificity for the CRISPR-C2c2 system. CRISPR-RT allows users to set up a wide range of parameters, making it highly flexible for current and future research in CRISPR-based RNA editing. CRISPR-RT covers major model org...

Kinetoplastid guide RNA biogenesis is dependent on subunits of the mitochondrial RNA binding complex 1 and mitochondrial RNA polymerase

Czech Academy of Sciences Publication Activity Database

Hashimi, Hassan; Číčová, Zdeňka; Novotná, Lucie; Wen, Y.-Z.; Lukeš, Julius

2009-01-01

Roč. 15, č. 4 (2009), s. 588-599 ISSN 1355-8382 R&D Projects: GA ČR GA204/09/1667; GA AV ČR IAA500960705; GA MŠk LC07032; GA MŠk 2B06129; GA ČR GD524/03/H133 Institutional research plan: CEZ:AV0Z60220518 Keywords : RNA editing * guide RNA * mitochondrion * trypanosome Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.198, year: 2009

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.

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

[sgRNA design for the CRISPR/Cas9 system and evaluation of its off-target effects].

Science.gov (United States)

Xie, Sheng-song; Zhang, Yi; Zhang, Li-sheng; Li, Guang-lei; Zhao, Chang-zhi; Ni, Pan; Zhao, Shu-hong

2015-11-01

The third generation of CRISPR/Cas9-mediated genome editing technology has been successfully applied to genome modification of various species including animals, plants and microorganisms. How to improve the efficiency of CRISPR/Cas9 genome editing and reduce its off-target effects has been extensively explored in this field. Using sgRNA (Small guide RNA) with high efficiency and specificity is one of the critical factors for successful genome editing. Several software have been developed for sgRNA design and/or off-target evaluation, which have advantages and disadvantages respectively. In this review, we summarize characters of 16 kinds online and standalone software for sgRNA design and/or off-target evaluation and conduct a comparative analysis of these different kinds of software through developing 38 evaluation indexes. We also summarize 11 experimental approaches for testing genome editing efficiency and off-target effects as well as how to screen highly efficient and specific sgRNA.

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

Chronic Treatment with Squid Phosphatidylserine Activates Glucose Uptake and Ameliorates TMT-Induced Cognitive Deficit in Rats via Activation of Cholinergic Systems

Directory of Open Access Journals (Sweden)

Hyun-Jung Park

2012-01-01

Full Text Available The present study examined the effects of squid phosphatidylserine (Squid-PS on the learning and memory function and the neural activity in rats with TMT-induced memory deficits. The rats were administered saline or squid derived Squid-PS (Squid-PS 50 mg kg−1, p.o. daily for 21 days. The cognitive improving efficacy of Squid-PS on the amnesic rats, which was induced by TMT, was investigated by assessing the passive avoidance task and by performing choline acetyltransferase (ChAT and acetylcholinesterase (AchE immunohistochemistry. 18F-Fluorodeoxyglucose and performed a positron emission tomography (PET scan was also performed. In the passive avoidance test, the control group which were injected with TMT showed a markedly lower latency time than the non-treated normal group (P<0.05. However, treatment of Squid-PS significantly recovered the impairment of memory compared to the control group (P<0.05. Consistent with the behavioral data, Squid-PS significantly alleviated the loss of ChAT immunoreactive neurons in the hippocampal CA3 compared to that of the control group (P<0.01. Also, Squid-PS significantly increased the AchE positive neurons in the hippocampal CA1 and CA3. In the PET analysis, Squid-PS treatment increased the glucose uptake more than twofold in the frontal lobe and the hippocampus (P<0.05, resp.. These results suggest that Squid-PS may be useful for improving the cognitive function via regulation of cholinergic enzyme activity and neural activity.

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)

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.

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.

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.

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

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

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.

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.

Cas9 versus Cas12a/Cpf1: Structure-function comparisons and implications for genome editing.

Science.gov (United States)

Swarts, Daan C; Jinek, Martin

2018-05-22

Cas9 and Cas12a are multidomain CRISPR-associated nucleases that can be programmed with a guide RNA to bind and cleave complementary DNA targets. The guide RNA sequence can be varied, making these effector enzymes versatile tools for genome editing and gene regulation applications. While Cas9 is currently the best-characterized and most widely used nuclease for such purposes, Cas12a (previously named Cpf1) has recently emerged as an alternative for Cas9. Cas9 and Cas12a have distinct evolutionary origins and exhibit different structural architectures, resulting in distinct molecular mechanisms. Here we compare the structural and mechanistic features that distinguish Cas9 and Cas12a, and describe how these features modulate their activity. We discuss implications for genome editing, and how they may influence the choice of Cas9 or Cas12a for specific applications. Finally, we review recent studies in which Cas12a has been utilized as a genome editing tool. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes. © 2018 Wiley Periodicals, Inc.

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)

Efficient, footprint-free human iPSC genome editing by consolidation of Cas9/CRISPR and piggyBac technologies.

Science.gov (United States)

Wang, Gang; Yang, Luhan; Grishin, Dennis; Rios, Xavier; Ye, Lillian Y; Hu, Yong; Li, Kai; Zhang, Donghui; Church, George M; Pu, William T

2017-01-01

Genome editing of human induced pluripotent stem cells (hiPSCs) offers unprecedented opportunities for in vitro disease modeling and personalized cell replacement therapy. The introduction of Cas9-directed genome editing has expanded adoption of this approach. However, marker-free genome editing using standard protocols remains inefficient, yielding desired targeted alleles at a rate of ∼1-5%. We developed a protocol based on a doxycycline-inducible Cas9 transgene carried on a piggyBac transposon to enable robust and highly efficient Cas9-directed genome editing, so that a parental line can be expeditiously engineered to harbor many separate mutations. Treatment with doxycycline and transfection with guide RNA (gRNA), donor DNA and piggyBac transposase resulted in efficient, targeted genome editing and concurrent scarless transgene excision. Using this approach, in 7 weeks it is possible to efficiently obtain genome-edited clones with minimal off-target mutagenesis and with indel mutation frequencies of 40-50% and homology-directed repair (HDR) frequencies of 10-20%.

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.

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.

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.

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.

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.

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

CRISPR/Cas9 in Genome Editing and Beyond.

Science.gov (United States)

Wang, Haifeng; La Russa, Marie; Qi, Lei S

2016-06-02

The Cas9 protein (CRISPR-associated protein 9), derived from type II CRISPR (clustered regularly interspaced short palindromic repeats) bacterial immune systems, is emerging as a powerful tool for engineering the genome in diverse organisms. As an RNA-guided DNA endonuclease, Cas9 can be easily programmed to target new sites by altering its guide RNA sequence, and its development as a tool has made sequence-specific gene editing several magnitudes easier. The nuclease-deactivated form of Cas9 further provides a versatile RNA-guided DNA-targeting platform for regulating and imaging the genome, as well as for rewriting the epigenetic status, all in a sequence-specific manner. With all of these advances, we have just begun to explore the possible applications of Cas9 in biomedical research and therapeutics. In this review, we describe the current models of Cas9 function and the structural and biochemical studies that support it. We focus on the applications of Cas9 for genome editing, regulation, and imaging, discuss other possible applications and some technical considerations, and highlight the many advantages that CRISPR/Cas9 technology offers.

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.

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.

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)

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.

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

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.

[Advances in CRISPR-Cas-mediated genome editing system in plants].

Science.gov (United States)

Wang, Chun; Wang, Kejian

2017-10-25

Targeted genome editing technology is an important tool to study the function of genes and to modify organisms at the genetic level. Recently, CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins) system has emerged as an efficient tool for specific genome editing in animals and plants. CRISPR-Cas system uses CRISPR-associated endonuclease and a guide RNA to generate double-strand breaks at the target DNA site, subsequently leading to genetic modifications. CRISPR-Cas system has received widespread attention for manipulating the genomes with simple, easy and high specificity. This review summarizes recent advances of diverse applications of the CRISPR-Cas toolkit in plant research and crop breeding, including expanding the range of genome editing, precise editing of a target base, and efficient DNA-free genome editing technology. This review also discusses the potential challenges and application prospect in the future, and provides a useful reference for researchers who are interested in this field.

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.

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

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.

Two Distinct Approaches for CRISPR-Cas9-Mediated Gene Editing in Cryptococcus neoformans and Related Species.

Science.gov (United States)

Wang, Ping

2018-06-27

Cryptococcus neoformans and related species are encapsulated basidiomycetous fungi that cause meningoencephalitis in individuals with immune deficiency. This pathogen has a tractable genetic system; however, gene disruption via electroporation remains difficult, while biolistic transformation is often limited by lack of multiple genetic markers and the high initial cost of equipment. The approach using clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) has become the technology of choice for gene editing in many organisms due to its simplicity, efficiency, and versatility. The technique has been successfully demonstrated in C. neoformans and Cryptococcus deneoformans in which two DNA plasmids expressing either the Streptococcus pyogenes CAS9 gene or the guide RNA (gRNA) were employed. However, potential adverse effects due to constitutive expression and the time-consuming process of constructing vectors to express each gRNA remain as a primary barrier for wide adaptation. This report describes the delivery of preassembled CRISPR-Cas9-gRNA ribonucleoproteins (RNPs) via electroporation that is able to generate edited mutant alleles. RNP-mediated CRISPR-Cas9 was used to replace the wild-type GIB2 gene encoding a Gβ-like/RACK1 Gib2 protein with a gib2 :: NAT allele via homologous recombination in both C. neoformans and C. deneoformans In addition, a DNA plasmid (pCnCas9:U6-gRNA) that expresses both Cas9 and gRNA, allowing for convenient yet low-cost DNA-mediated gene editing, is described. pCnCas9:U6-gRNA contains an endogenous U6 promoter for gRNA expression and restriction sites for one-step insertion of a gRNA. These approaches and resources provide new opportunities to accelerate genetic studies of Cryptococcus species. IMPORTANCE For genetic studies of the Cryptococcus genus, generation of mutant strains is often hampered by a limited number of selectable genetic markers, the tedious process of vector

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.

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.

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

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.

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.

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.

Emerging Role of CRISPR/Cas9 Technology for MicroRNAs Editing in Cancer Research.

Science.gov (United States)

Aquino-Jarquin, Guillermo

2017-12-15

MicroRNAs (miRNA) are small, noncoding RNA molecules with a master role in the regulation of important tasks in different critical processes of cancer pathogenesis. Because there are different miRNAs implicated in all the stages of cancer, for example, functioning as oncogenes, this makes these small molecules suitable targets for cancer diagnosis and therapy. RNA-mediated interference has been one major approach for sequence-specific regulation of gene expression in eukaryotic organisms. Recently, the CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 system, first identified in bacteria and archaea as an adaptive immune response to invading genetic material, has been explored as a sequence-specific molecular tool for editing genomic sequences for basic research in life sciences and for therapeutic purposes. There is growing evidence that small noncoding RNAs, including miRNAs, can be targeted by the CRISPR/Cas9 system despite their lacking an open reading frame to evaluate functional loss. Thus, CRISPR/Cas9 technology represents a novel gene-editing strategy with compelling robustness, specificity, and stability for the modification of miRNA expression. Here, I summarize key features of current knowledge of genomic editing by CRISPR/Cas9 technology as a feasible strategy for globally interrogating miRNA gene function and miRNA-based therapeutic intervention. Alternative emerging strategies for nonviral delivery of CRISPR/Cas9 core components into human cells in a clinical context are also analyzed critically. Cancer Res; 77(24); 6812-7. ©2017 AACR . ©2017 American Association for Cancer Research.

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.

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)

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...

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

Dynamics of d-wave YBa{sub 2}Cu{sub 3}O{sub 7-x} dc SQUIDs

Energy Technology Data Exchange (ETDEWEB)

Bauch, T [Quantum Device Physics Laboratory, Department of Microtechnology and Nanoscience, MC2, Chalmers University of Technology, S-41296 Goeteborg (Sweden); Cedergren, K [Quantum Device Physics Laboratory, Department of Microtechnology and Nanoscience, MC2, Chalmers University of Technology, S-41296 Goeteborg (Sweden); Johansson, J [Quantum Device Physics Laboratory, Department of Microtechnology and Nanoscience, MC2, Chalmers University of Technology, S-41296 Goeteborg (Sweden); Rotoli, G [Dipartimento di Ingeneria Meccanica, Energetica e Gestionale, Universita of L' Aquila, Localita Moneluco, L' Aquila (Italy); Tafuri, F [Dipartimento Ingeneria dell' Informatione, INFM, Seconda Universita di Napoli, Aversa (Italy); Lombardi, F [Quantum Device Physics Laboratory, Department of Microtechnology and Nanoscience, MC2, Chalmers University of Technology, S-41296 Goeteborg (Sweden)

2007-02-15

The predominant d-wave pairing symmetry in high temperature superconductors leads to an unconventional current-phase relation in Josephson junctions. This circumstance may induce new effects in the dynamics of dc SQUIDs. In this contribution we report on the measurements of the dependence of the SQUID Josephson current on the external magnetic field taken at very low temperatures, down to 20 mK. Different grain boundaries have been fabricated by using the biepitaxial and the bicrystal technique. Some of the effects which are induced by a nonsinusoidal current-phase relation can be clearly identified in the dynamics of the SQUIDs. The experimental data are also compared with theoretical simulations taking into account the inductance of the loop. The data show that, in specific conditions, a non-negligible inductance of the loop can induce effects similar to an unconventional current-phase relation, with a pronounced second harmonic sin(2{psi}) term. This fact has to be taken into account when designing d-wave SQUIDs for quantum circuitry.

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

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...

CRISPR/Cas9:A powerful tool for crop genome editing

Institute of Scientific and Technical Information of China (English)

Gaoyuan Song; Meiling Jia; Kai Chen; Xingchen Kong; Bushra Khattak; Chuanxiao Xie; Aili Li; Long Mao

2016-01-01

The CRISPR/Cas9 technology is evolved from a type II bacterial immune system and represents a new generation of targeted genome editing technology that can be applied to nearly all organisms. Site-specific modification is achieved by a single guide RNA(usually about 20nucleotides) that is complementary to a target gene or locus and is anchored by a protospaceradjacent motif. Cas9 nuclease then cleaves the targeted DNA to generate double-strand breaks(DSBs), which are subsequently repaired by non-homologous end joining(NHEJ) or homology-directed repair(HDR) mechanisms. NHEJ may introduce indels that cause frame shift mutations and hence the disruption of gene functions. When combined with double or multiplex guide RNA design, NHEJ may also introduce targeted chromosome deletions,whereas HDR can be engineered for target gene correction, gene replacement, and gene knock-in. In this review, we briefly survey the history of the CRISPR/Cas9 system invention and its genome-editing mechanism. We also describe the most recent innovation of the CRISPR/Cas9 technology, particularly the broad applications of modified Cas9 variants, and discuss the potential of this system for targeted genome editing and modification for crop improvement.

CRISPR/Cas9:A powerful tool for crop genome editing

Institute of Scientific and Technical Information of China (English)

Gaoyuan Song; Meiling Jia; Kai Chen; Xingchen Kong; Bushra Khattak; Chuanxiao Xie; Aili Li; Long Mao

2016-01-01

The CRISPR/Cas9 technology is evolved from a type II bacterial immune system and represents a new generation of targeted genome editing technology that can be applied to nearly all organisms. Site-specific modification is achieved by a single guide RNA (usually about 20 nucleotides) that is complementary to a target gene or locus and is anchored by a protospacer-adjacent motif. Cas9 nuclease then cleaves the targeted DNA to generate double-strand breaks (DSBs), which are subsequently repaired by non-homologous end joining (NHEJ) or homology-directed repair (HDR) mechanisms. NHEJ may introduce indels that cause frame shift mutations and hence the disruption of gene functions. When combined with double or multiplex guide RNA design, NHEJ may also introduce targeted chromosome deletions, whereas HDR can be engineered for target gene correction, gene replacement, and gene knock-in. In this review, we briefly survey the history of the CRISPR/Cas9 system invention and its genome-editing mechanism. We also describe the most recent innovation of the CRISPR/Cas9 technology, particularly the broad applications of modified Cas9 variants, and discuss the potential of this system for targeted genome editing and modification for crop improvement.

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...

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)

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

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...

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

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.

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.

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.

Efficient Generation and Editing of Feeder-free IPSCs from Human Pancreatic Cells Using the CRISPR-Cas9 System.

Science.gov (United States)

Nandal, Anjali; Mallon, Barbara; Telugu, Bhanu P

2017-11-08

Embryonic and induced pluripotent stem cells can self-renew and differentiate into multiple cell types of the body. The pluripotent cells are thus coveted for research in regenerative medicine and are currently in clinical trials for eye diseases, diabetes, heart diseases, and other disorders. The potential to differentiate into specialized cell types coupled with the recent advances in genome editing technologies including the CRISPR/Cas system have provided additional opportunities for tailoring the genome of iPSC for varied applications including disease modeling, gene therapy, and biasing pathways of differentiation, to name a few. Among the available editing technologies, the CRISPR/Cas9 from Streptococcus pyogenes has emerged as a tool of choice for site-specific editing of the eukaryotic genome. The CRISPRs are easily accessible, inexpensive, and highly efficient in engineering targeted edits. The system requires a Cas9 nuclease and a guide sequence (20-mer) specific to the genomic target abutting a 3-nucleotide "NGG" protospacer-adjacent-motif (PAM) for targeting Cas9 to the desired genomic locus, alongside a universal Cas9 binding tracer RNA (together called single guide RNA or sgRNA). Here we present a step-by-step protocol for efficient generation of feeder-independent and footprint-free iPSC and describe methodologies for genome editing of iPSC using the Cas9 ribonucleoprotein (RNP) complexes. The genome editing protocol is effective and can be easily multiplexed by pre-complexing sgRNAs for more than one target with the Cas9 protein and simultaneously delivering into the cells. Finally, we describe a simplified approach for identification and characterization of iPSCs with desired edits. Taken together, the outlined strategies are expected to streamline generation and editing of iPSC for manifold applications.

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

The Conspicuity of CRISPR-Cpf1 System as a Significant Breakthrough in Genome Editing.

Science.gov (United States)

Bayat, Hadi; Modarressi, Mohammad Hossein; Rahimpour, Azam

2018-01-01

Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein (Cas) is a microbial adaptive immune system. CRISPR-Cas systems are classified into two main classes and six types. Cpf1 is a putative type V (class II) CRISPR effector, which has revolutionized the genome editing approaches through multiple distinct features such as using T-rich protospacer-adjacent motif, applying a short guide RNA lacking trans-activating crRNA, introducing a staggered double-strand break, and possessing RNA processing activity in addition to DNA nuclease activity. In the present review, we attempt to highlight most recent advances in CRISPR-Cpf1 (CRISPR-Cas12a) system in particular, considering ground expeditions of the nature and the biology of this system, introducing novel Cpf1 variants that have broadened the versatility and feasibility of CRISPR-Cpf1 system, and lastly the great impact of the CRISPR-Cpf1 system on the manipulation of the genome of prokaryotic, mammalian, and plant models is summarized. With regard to recent developments in utilizing the CRISPR-Cpf1 system in genome editing of various organisms, it can be concluded with confidence that this system is a reliable molecular toolbox of genome editing approaches.

Seasonal Habitat Patterns of Japanese Common Squid (Todarodes Pacificus Inferred from Satellite-Based Species Distribution Models

Directory of Open Access Journals (Sweden)

Irene D. Alabia

2016-11-01

Full Text Available The understanding of the spatio-temporal distributions of the species habitat in the marine environment is central to effectual resource management and conservation. Here, we examined the potential habitat distributions of Japanese common squid (Todarodes pacificus in the Sea of Japan during a four-year period. The seasonal patterns of preferential habitat were inferred from species distribution models, built using squid occurrences detected from night-time visible images and remotely-sensed environmental factors. The predicted squid habitat (i.e., areas with high habitat suitability revealed strong seasonal variability, characterized by a reduction of potential habitat, confined off of the southern part of the basin during the winter–spring period (December–May. Apparent expansion of preferential habitat occurred during summer–autumn months (June–November, concurrent with the formation of highly suitable habitat patches in certain regions of the Sea of Japan. These habitat distribution patterns were in response to changes in oceanographic conditions and synchronous with seasonal migration of squid. Moreover, the most important variables regulating the spatio-temporal patterns of suitable habitat were sea surface temperature, depth, sea surface height anomaly, and eddy kinetic energy. These variables could affect the habitat distributions through their impacts on growth and survival of squid, local nutrient transport, and the availability of favorable spawning and feeding grounds.

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.

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.

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.

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.

CRISPR/Cas9 Based Genome Editing of Penicillium chrysogenum.

Science.gov (United States)

Pohl, C; Kiel, J A K W; Driessen, A J M; Bovenberg, R A L; Nygård, Y

2016-07-15

CRISPR/Cas9 based systems have emerged as versatile platforms for precision genome editing in a wide range of organisms. Here we have developed powerful CRISPR/Cas9 tools for marker-based and marker-free genome modifications in Penicillium chrysogenum, a model filamentous fungus and industrially relevant cell factory. The developed CRISPR/Cas9 toolbox is highly flexible and allows editing of new targets with minimal cloning efforts. The Cas9 protein and the sgRNA can be either delivered during transformation, as preassembled CRISPR-Cas9 ribonucleoproteins (RNPs) or expressed from an AMA1 based plasmid within the cell. The direct delivery of the Cas9 protein with in vitro synthesized sgRNA to the cells allows for a transient method for genome engineering that may rapidly be applicable for other filamentous fungi. The expression of Cas9 from an AMA1 based vector was shown to be highly efficient for marker-free gene deletions.

Effect of Melanin Free Ink Extracted From Squid (Loligo sp.) on Proximate and Sensory Characteristics of Soft-Bone Milkfish (Chanos chanos) During Storage

Science.gov (United States)

Winarni Agustini, Tri; Hadiyanto; Wijayanti, Ima; Amalia, Ulfah; Benjakul, Soottawat

2018-02-01

Antioxidant could be extracted and isolated from squid inks. Squid ink in the form of melanin free ink (MFI) could be act as an electron donor which can stabilize free radicals in lipid oxidation. This study was carried out to assess the antioxidant activity of squid inks converted into MFI in different dilution and to optimize the extraction conditions for the application of MFI as an antioxidative agent on fish product. Three different types of MFI extracts i.e : pure squid ink, squid ink with 5 times dilution and squid ink with 10 times dilutions by using cooled ionized water (4°C). The ink was then centrifuged at 18.000 x g for 30 minutes at cooled centrifuge (4°C) followed by DPPH analysis. The results showed that the IC50 of MFI extracts were 2.84 ppm; 1.11 ppm and 0.34 ppm, respectively (p squid ink with 10 times dilution in extraction of MFI had the highest value in free radical inhibitory. Although the IC50 of three different dilutions are equally low, and are considered as very strong antioxidative agent, however, it showed that the MFI extracted from squid ink had the ability to prevent free radical

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

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 ...

Recent Advances in Genome Editing Using CRISPR/Cas9

Science.gov (United States)

Ding, Yuduan; Li, Hong; Chen, Ling-Ling; Xie, Kabin

2016-01-01

The CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 (CRISPR-associated nuclease 9) system is a versatile tool for genome engineering that uses a guide RNA (gRNA) to target Cas9 to a specific sequence. This simple RNA-guided genome-editing technology has become a revolutionary tool in biology and has many innovative applications in different fields. In this review, we briefly introduce the Cas9-mediated genome-editing method, summarize the recent advances in CRISPR/Cas9 technology, and discuss their implications for plant research. To date, targeted gene knockout using the Cas9/gRNA system has been established in many plant species, and the targeting efficiency and capacity of Cas9 has been improved by optimizing its expression and that of its gRNA. The CRISPR/Cas9 system can also be used for sequence-specific mutagenesis/integration and transcriptional control of target genes. We also discuss off-target effects and the constraint that the protospacer-adjacent motif (PAM) puts on CRISPR/Cas9 genome engineering. To address these problems, a number of bioinformatic tools are available to help design specific gRNAs, and new Cas9 variants and orthologs with high fidelity and alternative PAM specificities have been engineered. Owing to these recent efforts, the CRISPR/Cas9 system is becoming a revolutionary and flexible tool for genome engineering. Adoption of the CRISPR/Cas9 technology in plant research would enable the investigation of plant biology at an unprecedented depth and create innovative applications in precise crop breeding. PMID:27252719

TMEPAI genome editing in triple negative breast cancer cells

Directory of Open Access Journals (Sweden)

Bantari W.K. Wardhani

2017-05-01

Full Text Available Background: Clustered regularly interspaced short palindromic repeats/CRISPR-associated 9 (CRISPR/Cas9 is a powerful genome editing technique. It consists of RNA-guided DNA endonuclease Cas9 and single guide RNA (gRNA. By combining their expressions, high efficiency cleavage of the target gene can be achieved, leading to the formation of DNA double-strand break (DSB at the genomic locus of interest which will be repaired via NHEJ (non-homologous end joining or HDR (homology-directed repair and mediate DNA alteration. We aimed to apply the CRISPR/Cas9 technique to knock-out the transmembrane prostate androgen-induced protein (TMEPAI gene in the triple negative breast cancer cell line.Methods: Designed gRNA which targets the TMEPAI gene was synthesized, annealed, and cloned into gRNA expression vector. It was co-transfected into the TNBC cell line using polyethylenimine (PEI together with Cas9-GFP and puromycin resistant gene vector. At 24-hours post-transfection, cells were selected by puromycin for 3 days before they were cloned. Selected knock-out clones were subsequently checked on their protein levels by western blotting.Results: CRISPR/Cas9, a genome engineering technique successfully knocked-out TMEPAI in the Hs578T TNBC cell line. Sequencing shows a frameshift mutation in TMEPAI. Western blot shows the absence of TMEPAI band on Hs578T KO cells.Conclusion: TMEPAI gene was deleted in the TNBC cell line using the genomic editing technique CRISPR/Cas9. The deletion was confirmed by genome and protein analysis.

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.)

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.

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.

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.

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

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.

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.

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.

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

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)

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

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)

Extreme plasticity in life-history strategy allows a migratory predator (jumbo squid) to cope with a changing climate.

Science.gov (United States)

Hoving, Henk-Jan T; Gilly, William F; Markaida, Unai; Benoit-Bird, Kelly J; -Brown, Zachary W; Daniel, Patrick; Field, John C; Parassenti, Liz; Liu, Bilin; Campos, Bernardita

2013-07-01

Dosidicus gigas (jumbo or Humboldt squid) is a semelparous, major predator of the eastern Pacific that is ecologically and commercially important. In the Gulf of California, these animals mature at large size (>55 cm mantle length) in 1-1.5 years and have supported a major commercial fishery in the Guaymas Basin during the last 20 years. An El Niño event in 2009-2010, was accompanied by a collapse of this fishery, and squid in the region showed major changes in the distribution and life-history strategy. Large squid abandoned seasonal coastal-shelf habitats in 2010 and instead were found in the Salsipuedes Basin to the north, an area buffered from the effects of El Niño by tidal upwelling and a well-mixed water column. The commercial fishery also relocated to this region. Although large squid were not found in the Guaymas Basin from 2010 to 2012, small squid were abundant and matured at an unusually small mantle-length (adapt to and cope with El Niño. This ability is likely to be an important factor in conjunction with longerterm climate-change and the potential ecological impacts of this invasive predator on marine ecosystems. © 2013 Blackwell Publishing Ltd.

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}.

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.

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

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)

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.

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.

E+ subgroup PPR protein defective kernel 36 is required for multiple mitochondrial transcripts editing and seed development in maize and Arabidopsis.

Science.gov (United States)

Wang, Gang; Zhong, Mingyu; Shuai, Bilian; Song, Jiandong; Zhang, Jie; Han, Liang; Ling, Huiling; Tang, Yuanping; Wang, Guifeng; Song, Rentao

2017-06-01

Mitochondria are semi-autonomous organelles that are the powerhouse of the cells. Plant mitochondrial RNA editing guided by pentatricopeptide repeat (PPR) proteins is essential for energy production. We identify a maize defective kernel mutant dek36, which produces small and collapsed kernels, leading to embryos and/or seedlings lethality. Seed filling in dek36 is drastically impaired, in line with the defects observed in the organization of endosperm transfer tissue. Positional cloning reveals that DEK36, encoding a mitochondria-targeted E+ subgroup PPR protein, is required for mitochondrial RNA editing at atp4-59, nad7-383 and ccmF N -302, thus resulting in decreased activities of mitochondrial complex I, complex III and complex IV in dek36. Loss-of-function of its Arabidopsis ortholog At DEK36 causes arrested embryo and endosperm development, leading to embryo lethality. At_dek36 also has RNA editing defects in atp4, nad7, ccmF N 1 and ccmF N 2 , but at the nonconserved sites. Importantly, efficiency of all editing sites in ccmF N 1 , ccmF N 2 and rps12 is severely decreased in At_dek36, probably caused by the impairment of their RNA stabilization. These results suggest that the DEK36 orthologue pair are essential for embryo and endosperm development in both maize and Arabidopsis, but through divergent function in regulating RNA metabolism of their mitochondrial targets. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Y1Ba2Cu3O(7-delta) thin film dc SQUIDs (superconducting quantum interference device)

Science.gov (United States)

Racah, Daniel

1991-03-01

Direct current superconducting quantum interferometers (SQUIDs) based on HTSC thin films have been measured and characterized. The thin films used were of different quality: (1) Granular films on Sapphire substrates, prepared either by e-gun evaporation, by laser ablation or by MOCVD (metal oxide chemical vapor deposition), (2) Epitaxial films on MgO substrates. Modulations of the voltage on the SQUIDs as a function of the applied flux have been observed in a wide range of temperatures. The nature of the modulation was found to be strongly dependent on the morphology of the film and on its critical current. The SQUIDs based on granular films were relatively noisy, hysteretic and with a complicated V-phi shape. Those devices based on low quality (lowIc) granular films could be measured only at low temperatures (much lower than 77 K). While those of higher quality (granular films with high Ic) could be measured near to the superconductive transition. The SQUID based on high quality epitaxial film was measured near Tc and showed an anomalous, time dependent behavior.

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.

Endosomal Escape and Delivery of CRISPR/Cas9 Genome Editing Machinery Enabled by Nanoscale Zeolitic Imidazolate Framework

KAUST Repository

Alsaiari, Shahad K.

2017-12-22

CRISPR/Cas9 is a combined protein (Cas9) and an engineered single guide RNA (sgRNA) genome editing platform that offers revolutionary solutions to genetic diseases. It has, however, a double delivery problem owning to the large protein size and the highly charged RNA component. In this work, we report the first example of CRISPR/Cas9 encapsulated by nanoscale zeolitic imidazole frameworks (ZIFs) with a loading efficiency of 17% and enhanced endosomal escape promoted by the protonated imidazole moieties. The gene editing potential of CRISPR/Cas9 encapsulated by ZIF-8 (CC-ZIFs) is further verified by knocking down the gene expression of green fluorescent protein by 37% over 4 days employing CRISPR/Cas9 machinery. The nanoscale CC-ZIFs are biocompatible and easily scaled-up offering excellent loading capacity and controlled co-delivery of intact Cas9 protein and sgRNA.

Endosomal Escape and Delivery of CRISPR/Cas9 Genome Editing Machinery Enabled by Nanoscale Zeolitic Imidazolate Framework

KAUST Repository

Alsaiari, Shahad K.; Patil, Sachin; Alyami, Mram Z.; Alamoudi, Kholod; Aleisa, Fajr A; Merzaban, Jasmeen; Li, Mo; Khashab, Niveen M.

2017-01-01

CRISPR/Cas9 is a combined protein (Cas9) and an engineered single guide RNA (sgRNA) genome editing platform that offers revolutionary solutions to genetic diseases. It has, however, a double delivery problem owning to the large protein size and the highly charged RNA component. In this work, we report the first example of CRISPR/Cas9 encapsulated by nanoscale zeolitic imidazole frameworks (ZIFs) with a loading efficiency of 17% and enhanced endosomal escape promoted by the protonated imidazole moieties. The gene editing potential of CRISPR/Cas9 encapsulated by ZIF-8 (CC-ZIFs) is further verified by knocking down the gene expression of green fluorescent protein by 37% over 4 days employing CRISPR/Cas9 machinery. The nanoscale CC-ZIFs are biocompatible and easily scaled-up offering excellent loading capacity and controlled co-delivery of intact Cas9 protein and sgRNA.

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.

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.

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.

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

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...

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

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

A Cas9 transgenic Plasmodium yoelii parasite for efficient gene editing.

Science.gov (United States)

Qian, Pengge; Wang, Xu; Yang, Zhenke; Li, Zhenkui; Gao, Han; Su, Xin-Zhuan; Cui, Huiting; Yuan, Jing

2018-06-01

The RNA-guided endonuclease Cas9 has applied as an efficient gene-editing method in malaria parasite Plasmodium. However, the size (4.2 kb) of the commonly used Cas9 from Streptococcus pyogenes (SpCas9) limits its utility for genome editing in the parasites only introduced with cas9 plasmid. To establish the endogenous and constitutive expression of Cas9 protein in the rodent malaria parasite P. yoelii, we replaced the coding region of an endogenous gene sera1 with the intact SpCas9 coding sequence using the CRISPR/Cas9-mediated genome editing method, generating the cas9-knockin parasite (PyCas9ki) of the rodent malaria parasite P. yoelii. The resulted PyCas9ki parasite displays normal progression during the whole life cycle and possesses the Cas9 protein expression in asexual blood stage. By introducing the plasmid (pYCs) containing only sgRNA and homologous template elements, we successfully achieved both deletion and tagging modifications for different endogenous genes in the genome of PyCas9ki parasite. This cas9-knockin PyCas9ki parasite provides a new platform facilitating gene functions study in the rodent malaria parasite P. yoelii. Copyright © 2018 Elsevier B.V. All rights reserved.

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

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 ...

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, ...

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...

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

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.

Efficient Oligo nucleotide mediated CRISPR-Cas9 Gene Editing in Aspergilli

DEFF Research Database (Denmark)

Nødvig, Christina Spuur; Hoof, Jakob Blæsbjerg; Kogle, Martin Engelhard

2018-01-01

CRISPR-Cas9 technologies are revolutionizing fungal gene editing. Here we show that survival of specific Cas9/sgRNA mediated DNA double strand breaks (DSBs) depends on the non-homologous end-joining, NHEJ, DNA repair pathway and we use this observation to develop a tool to assess protospacer....... niger, and in A. oryzae indicating that this type of repair may be wide spread in filamentous fungi. Importantly, we demonstrate that by using single-stranded oligo nucleotides for CRISPR-Cas9 mediated gene editing it is possible to introduce specific point mutations as well gene deletions...

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 ...

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.

The Impact of Chromatin Dynamics on Cas9-Mediated Genome Editing in Human Cells.

Science.gov (United States)

Daer, René M; Cutts, Josh P; Brafman, David A; Haynes, Karmella A

2017-03-17

In order to efficiently edit eukaryotic genomes, it is critical to test the impact of chromatin dynamics on CRISPR/Cas9 function and develop strategies to adapt the system to eukaryotic contexts. So far, research has extensively characterized the relationship between the CRISPR endonuclease Cas9 and the composition of the RNA-DNA duplex that mediates the system's precision. Evidence suggests that chromatin modifications and DNA packaging can block eukaryotic genome editing by custom-built DNA endonucleases like Cas9; however, the underlying mechanism of Cas9 inhibition is unclear. Here, we demonstrate that closed, gene-silencing-associated chromatin is a mechanism for the interference of Cas9-mediated DNA editing. Our assays use a transgenic cell line with a drug-inducible switch to control chromatin states (open and closed) at a single genomic locus. We show that closed chromatin inhibits binding and editing at specific target sites and that artificial reversal of the silenced state restores editing efficiency. These results provide new insights to improve Cas9-mediated editing in human and other mammalian cells.

Effect of single- and two-cycle high hydrostatic pressure treatments on water properties, physicochemical and microbial qualities of minimally processed squids (todarodes pacificus).

Science.gov (United States)

Zhang, Yifeng; Jiao, Shunshan; Lian, Zixuan; Deng, Yun; Zhao, Yanyun

2015-05-01

This study investigated the effect of single- and two-cycle high hydrostatic pressure (HHP) treatments on water properties, physicochemical, and microbial qualities of squids (Todarodes pacificus) during 4 °C storage for up to 10 d. Single-cycle treatments were applied at 200, 400, or 600 MPa for 20 min (S-200, S-400, and S-600), and two-cycle treatments consisted of two 10 min cycles at 200, 400, or 600 MPa, respectively (T-200, T-400, and T-600). HHP-treated samples had higher (P pressure level caused no significant difference in water state of squids. The two-cycle HHP treatment was more effective in controlling total volatile basic nitrogen, pH, and total plate counts (TPC) of squids during storage, in which TPC of S-600 and T-600 was 2.9 and 1.8 log CFU/g at 10 d, respectively, compared with 7.5 log CFU/g in control. HHP treatments delayed browning discoloration of the squids during storage, and the higher pressure level and two-cycle HHP were more effective. Water properties highly corresponded with color and texture indices of squids. This study demonstrated that the two-cycle HHP treatment was more effective in controlling microbial growth and quality deterioration while having similar impact on the physicochemical and water properties of squids in comparison with the single-cycle treatment, thus more desirable for extending shelf-life of fresh squids. © 2015 Institute of Food Technologists®

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 ...

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.

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.

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.

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 ...

Molecular evolution of pentatricopeptide repeat genes reveals truncation in species lacking an editing target and structural domains under distinct selective pressures

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Hayes Michael L

2012-05-01

Full Text Available Abstract Background Pentatricopeptide repeat (PPR proteins are required for numerous RNA processing events in plant organelles including C-to-U editing, splicing, stabilization, and cleavage. Fifteen PPR proteins are known to be required for RNA editing at 21 sites in Arabidopsis chloroplasts, and belong to the PLS class of PPR proteins. In this study, we investigate the co-evolution of four PPR genes (CRR4, CRR21, CLB19, and OTP82 and their six editing targets in Brassicaceae species. PPR genes are composed of approximately 10 to 20 tandem repeats and each repeat has two α-helical regions, helix A and helix B, that are separated by short coil regions. Each repeat and structural feature was examined to determine the selective pressures on these regions. Results All of the PPR genes examined are under strong negative selection. Multiple independent losses of editing site targets are observed for both CRR21 and OTP82. In several species lacking the known editing target for CRR21, PPR genes are truncated near the 17th PPR repeat. The coding sequences of the truncated CRR21 genes are maintained under strong negative selection; however, the 3’ UTR sequences beyond the truncation site have substantially diverged. Phylogenetic analyses of four PPR genes show that sequences corresponding to helix A are high compared to helix B sequences. Differential evolutionary selection of helix A versus helix B is observed in both plant and mammalian PPR genes. Conclusion PPR genes and their cognate editing sites are mutually constrained in evolution. Editing sites are frequently lost by replacement of an edited C with a genomic T. After the loss of an editing site, the PPR genes are observed with three outcomes: first, few changes are detected in some cases; second, the PPR gene is present as a pseudogene; and third, the PPR gene is present but truncated in the C-terminal region. The retention of truncated forms of CRR21 that are maintained under strong negative

Molecular evolution of pentatricopeptide repeat genes reveals truncation in species lacking an editing target and structural domains under distinct selective pressures.

Science.gov (United States)

Hayes, Michael L; Giang, Karolyn; Mulligan, R Michael

2012-05-14

Pentatricopeptide repeat (PPR) proteins are required for numerous RNA processing events in plant organelles including C-to-U editing, splicing, stabilization, and cleavage. Fifteen PPR proteins are known to be required for RNA editing at 21 sites in Arabidopsis chloroplasts, and belong to the PLS class of PPR proteins. In this study, we investigate the co-evolution of four PPR genes (CRR4, CRR21, CLB19, and OTP82) and their six editing targets in Brassicaceae species. PPR genes are composed of approximately 10 to 20 tandem repeats and each repeat has two α-helical regions, helix A and helix B, that are separated by short coil regions. Each repeat and structural feature was examined to determine the selective pressures on these regions. All of the PPR genes examined are under strong negative selection. Multiple independent losses of editing site targets are observed for both CRR21 and OTP82. In several species lacking the known editing target for CRR21, PPR genes are truncated near the 17th PPR repeat. The coding sequences of the truncated CRR21 genes are maintained under strong negative selection; however, the 3' UTR sequences beyond the truncation site have substantially diverged. Phylogenetic analyses of four PPR genes show that sequences corresponding to helix A are high compared to helix B sequences. Differential evolutionary selection of helix A versus helix B is observed in both plant and mammalian PPR genes. PPR genes and their cognate editing sites are mutually constrained in evolution. Editing sites are frequently lost by replacement of an edited C with a genomic T. After the loss of an editing site, the PPR genes are observed with three outcomes: first, few changes are detected in some cases; second, the PPR gene is present as a pseudogene; and third, the PPR gene is present but truncated in the C-terminal region. The retention of truncated forms of CRR21 that are maintained under strong negative selection even in the absence of an editing site target

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.

Age, maturation, and population structure of the Humboldt squid Dosidicus gigas off the Peruvian Exclusive Economic Zones

Institute of Scientific and Technical Information of China (English)

LIU Bilin; CHEN Xinjun; CHEN Yong; TIAN Siquan; LI Jianhua; FANG Zhou; YANG Mingxia

2013-01-01

Age,maturation and population structure of the Humboldt squid Dosidicus gigas were studied based on random sampling of the Chinese jigging fishery off the Peruvian Exclusive Economic Zones (EEZ) during 2008-2010.Estimated ages ranged from 144 to 633 days,confirming that the squid is a short-lived species with longevity no longer than 2 years.Occurrence of mature females and hatching in each month indicated that Humboldt squid spawned year-round.Back-calculated hatching dates for the samples were from January 22nd,2008 to April 22nd,2010 with a peak between January and March.Two size-based and two hatching date-based populations could be defined from mantle length (ML) at maturity and back-calculated hatching dates,respectively.Females matured at a larger size than males,and there was a significant difference in ML at maturity between the two hatching groups (P＜0.05).The waters adjacent to 11°S off the Peruvian EEZ may be a potential spawning ground.This study shows the complexity of the population structure and large variability in key life history parameters in the Humboldt squid off the Peruvian EEZ,which should be considered in the assessment and management of this important resource.

Heat Increases the Editing Efficiency of Human Papillomavirus E2 Gene by Inducing Upregulation of APOBEC3A and 3G.

Science.gov (United States)

Yang, Yang; Wang, Hexiao; Zhang, Xinrui; Huo, Wei; Qi, Ruiqun; Gao, Yali; Zhang, Gaofeng; Song, Bing; Chen, Hongduo; Gao, Xinghua

2017-04-01

Apolipoprotein B mRNA-editing catalytic polypeptide (APOBEC) 3 proteins have been identified as potent viral DNA mutators and have broad antiviral activity. In this study, we demonstrated that apolipoprotein B mRNA-editing catalytic polypeptide 3A (A3A) and A3G expression levels were significantly upregulated in human papillomavirus (HPV)-infected cell lines and tissues. Heat treatment resulted in elevated expression of A3A and A3G in a temperature-dependent manner in HPV-infected cells. Correspondingly, HPV-infected cells heat-treated at 44 °C showed accumulated G-to-A or C-to-T mutation in HPV E2 gene. Knockdown of A3A or A3G could promote cell viability, along with the lower frequency of A/T in HPV E2 gene. In addition, regressing genital viral warts also harbored high G-to-A or C-to-T mutation in HPV E2 gene. Taken together, we demonstrate that apolipoprotein B mRNA-editing catalytic polypeptide 3 expression and editing function was heat sensitive to a certain degree, partly explaining the mechanism of action of local hyperthermia to treat viral warts. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

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.

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.

Genome Editing with Crispr-Cas9 Systems: Basic Research and Clinical Applications

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Anna Meiliana

2017-04-01

Full Text Available BACKGROUND: Recently established genome editing technologies will open new avenues for biological research and development. Human genome editing is a powerful tool which offers great scientific and therapeutic potential. CONTENT: Genome editing using the clustered regularly interspaced short palindromic repeats (CRISPR/CRISPRassociated protein 9 (Cas9 technology is revolutionizing the gene function studies and possibly will give rise to an entirely new degree of therapeutics for a large range of diseases. Prompt advances in the CRISPR/Cas9 technology, as well as delivery modalities for gene therapy applications, are dismissing the barriers to the clinical translation of this technology. Many studies conducted showed promising results, but as current available technologies for evaluating off-target gene modification, several elements must be addressed to validate the safety of the CRISPR/Cas9 platform for clinical application, as the ethical implication as well. SUMMARY: The CRISPR/Cas9 system is a powerful genome editing technology with the potential to create a variety of novel therapeutics for a range of diseases, many of which are currently untreatable. KEYWORDS: genome editing, CRISPR-Cas, guideRNA, DSB, ZFNs, TALEN

Short RNA guides cleavage by eukaryotic RNase III.

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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.

Advances in the delivery of RNA therapeutics: from concept to clinical reality.

Science.gov (United States)

Kaczmarek, James C; Kowalski, Piotr S; Anderson, Daniel G

2017-06-27

The rapid expansion of the available genomic data continues to greatly impact biomedical science and medicine. Fulfilling the clinical potential of genetic discoveries requires the development of therapeutics that can specifically modulate the expression of disease-relevant genes. RNA-based drugs, including short interfering RNAs and antisense oligonucleotides, are particularly promising examples of this newer class of biologics. For over two decades, researchers have been trying to overcome major challenges for utilizing such RNAs in a therapeutic context, including intracellular delivery, stability, and immune response activation. This research is finally beginning to bear fruit as the first RNA drugs gain FDA approval and more advance to the final phases of clinical trials. Furthermore, the recent advent of CRISPR, an RNA-guided gene-editing technology, as well as new strides in the delivery of messenger RNA transcribed in vitro, have triggered a major expansion of the RNA-therapeutics field. In this review, we discuss the challenges for clinical translation of RNA-based therapeutics, with an emphasis on recent advances in delivery technologies, and present an overview of the applications of RNA-based drugs for modulation of gene/protein expression and genome editing that are currently being investigated both in the laboratory as well as in the clinic.

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...

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

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

Magnetorelaxometry of few Fe3O4 nanoparticles at 77 K employing a self-compensated SQUID magnetometer

International Nuclear Information System (INIS)

Guillaume, Alexander; Scholtyssek, Jan M.; Lak, Aidin; Kassner, Alexander; Ludwig, Frank; Schilling, Meinhard

2016-01-01

Magnetic nanoparticles (MNPs) are of great interest for industrial and medical applications. Therefore, the properties of the particles have to be well controlled. Several magnetic measurement schemes have been developed in order to determine particle parameters such as size distribution and structural properties. In general, systems are designed either for the analysis of large amounts of MNP (≫1000) or for single particle investigation. Up to now, the region in between has been less studied. However, small and well defined amounts of MNPs are of high interest, e.g. for the systematic investigation of particle–particle interactions. In this paper, we present a method using electron beam lithographic preparation of small amounts of MNPs directly on a self-compensating high-temperature superconducting quantum interference device (SQUID) with micrometer dimensions which is insensitive to homogeneous fields and first order gradients but very sensitive to internal magnetic dipole fields. Magnetorelaxometry (MRX) measurements were carried out at 77 K sample temperature in a magnetically shielded room in order to analyze the dynamic behavior of MNP samples and to evaluate the detection limit of our SQUID sensors. Calculations based on the magnetic moment superposition model (MSM) and finite element simulations (FEM) indicate that the MNP samples can be fabricated in a well-defined way by the presented method. Based on MRX measurements of a sample with 200 single-core magnetite MNPs with core diameters of 12 nm, we estimate the detection limit of our SQUID MRX setup as 70 MNPs. - Highlights: • Novel self-compensated superconducting quantum interference device (SQUID). • Electron-beam lithographical patterning of magnetic nanoparticles directly on SQUID. • Magnetorelaxometric detection of 200 nanoparticles with diameter of 12 nm at 77 K. • FEM simulations provide detection limit of less than 100 nanoparticles.

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....

Squids old and young: Scale-free design for a simple billboard

Science.gov (United States)

Packard, Andrew

2011-03-01

Squids employ a large range of brightness-contrast spatial frequencies in their camouflage and signalling displays. The 'billboard' of coloured elements ('spots'=chromatophore organs) in the skin is built autopoietically-probably by lateral inhibitory processes-and enlarges as much as 10,000-fold during development. The resulting two-dimensional array is a fractal-like colour/size hierarchy lying in several layers of a multilayered network. Dynamic control of the array by muscles and nerves produces patterns that recall 'half-tone' processing (cf. ink-jet printer). In the more sophisticated (loliginid) squids, patterns also combine 'continuous tones' (cf. dye-sublimation printer). Physiologists and engineers can exploit the natural colour-coding of the integument to understand nerve and muscle system dynamics, examined here at the level of the ensemble. Integrative functions of the whole (H) are analysed in terms of the power spectrum within and between ensembles and of spontaneous waves travelling through the billboard. Video material may be obtained from the author at the above address.

Postnatal Cardiac Gene Editing Using CRISPR/Cas9 With AAV9-Mediated Delivery of Short Guide RNAs Results in Mosaic Gene Disruption.

Science.gov (United States)

Johansen, Anne Katrine; Molenaar, Bas; Versteeg, Danielle; Leitoguinho, Ana Rita; Demkes, Charlotte; Spanjaard, Bastiaan; de Ruiter, Hesther; Akbari Moqadam, Farhad; Kooijman, Lieneke; Zentilin, Lorena; Giacca, Mauro; van Rooij, Eva

2017-10-27

CRISPR/Cas9 (clustered regularly interspaced palindromic repeats/CRISPR-associated protein 9)-based DNA editing has rapidly evolved as an attractive tool to modify the genome. Although CRISPR/Cas9 has been extensively used to manipulate the germline in zygotes, its application in postnatal gene editing remains incompletely characterized. To evaluate the feasibility of CRISPR/Cas9-based cardiac genome editing in vivo in postnatal mice. We generated cardiomyocyte-specific Cas9 mice and demonstrated that Cas9 expression does not affect cardiac function or gene expression. As a proof-of-concept, we delivered short guide RNAs targeting 3 genes critical for cardiac physiology, Myh6 , Sav1 , and Tbx20 , using a cardiotropic adeno-associated viral vector 9. Despite a similar degree of DNA disruption and subsequent mRNA downregulation, only disruption of Myh6 was sufficient to induce a cardiac phenotype, irrespective of short guide RNA exposure or the level of Cas9 expression. DNA sequencing analysis revealed target-dependent mutations that were highly reproducible across mice resulting in differential rates of in- and out-of-frame mutations. Finally, we applied a dual short guide RNA approach to effectively delete an important coding region of Sav1 , which increased the editing efficiency. Our results indicate that the effect of postnatal CRISPR/Cas9-based cardiac gene editing using adeno-associated virus serotype 9 to deliver a single short guide RNA is target dependent. We demonstrate a mosaic pattern of gene disruption, which hinders the application of the technology to study gene function. Further studies are required to expand the versatility of CRISPR/Cas9 as a robust tool to study novel cardiac gene functions in vivo. © 2017 American Heart Association, Inc.

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.

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.

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

CRISPR-Cas9-Mediated Genome Editing and Transcriptional Control in Yarrowia lipolytica.

Science.gov (United States)

Schwartz, Cory; Wheeldon, Ian

2018-01-01

The discovery and adaptation of RNA-guided nucleases has resulted in the rapid development of efficient, scalable, and easily accessible synthetic biology tools for targeted genome editing and transcriptional control. In these systems, for example CRISPR-Cas9 from Streptococcus pyogenes, a protein with nuclease activity is targeted to a specific nucleotide sequence by a short RNA molecule, whereupon binding it cleaves the targeted nucleotide strand. To extend this genome-editing ability to the industrially important oleaginous yeast Yarrowia lipolytica, we developed a set of easily usable and effective CRISPR-Cas9 episomal vectors. In this protocols chapter, we first present a method by which arbitrary protein-coding genes can be disrupted via indel formation after CRISPR-Cas9 targeting. A second method demonstrates how the same CRISPR-Cas9 system can be used to induce markerless gene cassette integration into the genome by inducing homologous recombination after DNA cleavage by Cas9. Finally, we describe how a catalytically inactive form of Cas9 fused to a transcriptional repressor can be used to control transcription of native genes in Y. lipolytica. The CRISPR-Cas9 tools and strategies described here greatly increase the types of genome editing and transcriptional control that can be achieved in Y. lipolytica, and promise to facilitate more advanced engineering of this important oleaginous host.

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

Computational Insights into the High-Fidelity Catalysis of Aminoacyl-tRNA Synthetases

Science.gov (United States)

Aboelnga, Mohamed M.

Obtaining insights into the catalytic function of enzymes is an important area of research due to their widespread applications in the biotechnology and pharmaceutical industries. Among these enzymes, the aminoacyl-tRNA synthetases (aaRSs) are known for their remarkable fidelity in catalyzing the aminoacylation reactions of tRNA in protein biosynthesis. Despite the exceptional execution of this critical function, mechanistic details of the reactions catalyzed by aminoacyl-tRNA synthetases remain elusive demonstrating the obvious need to explore their remarkable chemistry. During the PhD studies reported in this thesis the mechanism of aminoacylation, pre?transfer editing and post?transfer editing catalyzed by different aaRS have been established using multi-scale computational enzymology. In the first two chapters a detailed information about aaRS and the addressed questions was given in addition to an overview of the used computational methodology currently used to investigate the enzymatic mechanisms. The aminoacylation mechanism of threonine by Threonyl-tRNA synthetases, glutamine by Glutaminyl-tRNA synthetases and glutamate by Glutamyl-tRNA synthetases have been clearly unveiled in chapter 3 and 4. Also, valuable information regarding the role of cofactors and active site residues has been obtained. While investigating the post-transfer editing mechanisms, which proceed in a remote and distinct active site, two different scenarios were experimentally suggested for two types of threonyl-tRNA synthetase species to correct the misacylation of the structurally related serine. We explored these two mechanisms as in chapters 5 and 6. Moreover, the synthetic site in which the aminoacylation reaction is catalyzed, is also responsible for a second type of proofreading reaction called pre-transfer editing mechanism. In chapter 7, this latter mechanism has been elucidated for both Seryl-tRNA synthetases and Isoleucyl-tRNA synthetases against their non-cognate substrates

Peptide/Cas9 nanostructures for ribonucleoprotein cell membrane transport and gene edition.

Science.gov (United States)

Lostalé-Seijo, Irene; Louzao, Iria; Juanes, Marisa; Montenegro, Javier

2017-12-01

The discovery of RNA guided endonucleases has emerged as one of the most important tools for gene edition and biotechnology. The selectivity and simplicity of the CRISPR/Cas9 strategy allows the straightforward targeting and editing of particular loci in the cell genome without the requirement of protein engineering. However, the transfection of plasmids encoding the Cas9 and the guide RNA could lead to undesired permanent recombination and immunogenic responses. Therefore, the direct delivery of transient Cas9 ribonucleoprotein constitutes an advantageous strategy for gene edition and other potential therapeutic applications of the CRISPR/Cas9 system. The covalent fusion of Cas9 with penetrating peptides requires multiple incubation steps with the target cells to achieve efficient levels of gene edition. These and other recent reports suggested that covalent conjugation of the anionic Cas9 ribonucleoprotein to cationic peptides would be associated with a hindered nuclease activity due to undesired electrostatic interactions. We here report a supramolecular strategy for the direct delivery of Cas9 by an amphiphilic penetrating peptide that was prepared by a hydrazone bond formation between a cationic peptide scaffold and a hydrophobic aldehyde tail. The peptide/protein non-covalent nanoparticles performed with similar efficiency and less toxicity than one of the best methods described to date. To the best of our knowledge this report constitutes the first supramolecular strategy for the direct delivery of Cas9 using a penetrating peptide vehicle. The results reported here confirmed that peptide amphiphilic vectors can deliver Cas9 in a single incubation step, with good efficiency and low toxicity. This work will encourage the search and development of conceptually new synthetic systems for transitory endonucleases direct delivery.

mRNA Transcript Diversity Creates New Opportunities for Pharmacological Intervention