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Sample records for stem loop sequences

  1. Stem loop sequences specific to transposable element IS605 are found linked to lipoprotein genes in Borrelia plasmids.

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    Nicholas Delihas

    Full Text Available BACKGROUND: Plasmids of Borrelia species are dynamic structures that contain a large number of repetitive genes, gene fragments, and gene fusions. In addition, the transposable element IS605/200 family, as well as degenerate forms of this IS element, are prevalent. In Helicobacter pylori, flanking regions of the IS605 transposase gene contain sequences that fold into identical small stem loops. These function in transposition at the single-stranded DNA level. METHODOLOGY/PRINCIPAL FINDINGS: In work reported here, bioinformatics techniques were used to scan Borrelia plasmid genomes for IS605 transposable element specific stem loop sequences. Two variant stem loop motifs are found in the left and right flanking regions of the transposase gene. Both motifs appear to have dispersed in plasmid genomes and are found "free-standing" and phylogenetically conserved without the associated IS605 transposase gene or the adjacent flanking sequence. Importantly, IS605 specific stem loop sequences are also found at the 3' ends of lipoprotein genes (PFam12 and PFam60, however the left and right sequences appear to develop their own evolutionary patterns. The lipoprotein gene-linked left stem loop sequences maintain the IS605 stem loop motif in orthologs but only at the RNA level. These show mutations whereby variants fold into phylogenetically conserved RNA-type stem loops that contain the wobble non-Watson-Crick G-U base-pairing. The right flanking sequence is associated with the family lipoprotein-1 genes. A comparison of homologs shows that the IS605 stem loop motif rapidly dissipates, but a more elaborate secondary structure appears to develop in its place. CONCLUSIONS/SIGNIFICANCE: Stem loop sequences specific to the transposable element IS605 are present in plasmid regions devoid of a transposase gene and significantly, are found linked to lipoprotein genes in Borrelia plasmids. These sequences are evolutionarily conserved and/or structurally developed in

  2. The analysis of novel microRNA mimic sequences in cancer cells reveals lack of specificity in stem-loop RT-qPCR-based microRNA detection.

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    Winata, Patrick; Williams, Marissa; McGowan, Eileen; Nassif, Najah; van Zandwijk, Nico; Reid, Glen

    2017-11-17

    MicroRNAs are frequently downregulated in cancer, and restoring expression has tumour suppressive activity in tumour cells. Our recent phase I clinical trial investigated microRNA-based therapy in patients with malignant pleural mesothelioma. Treatment with TargomiRs, microRNA mimics with novel sequence packaged in EGFR antibody-targeted bacterial minicells, revealed clear signs of clinical activity. In order to detect delivery of microRNA mimics to tumour cells in future clinical trials, we tested hydrolysis probe-based assays specific for the sequence of the novel mimics in transfected mesothelioma cell lines using RT-qPCR. The custom assays efficiently and specifically amplified the consensus mimics. However, we found that these assays gave a signal when total RNA from untransfected and control mimic-transfected cells were used as templates. Further investigation revealed that the reverse transcription step using stem-loop primers appeared to introduce substantial non-specific amplification with either total RNA or synthetic RNA templates. This suggests that reverse transcription using stem-loop primers suffers from an intrinsic lack of specificity for the detection of highly similar microRNAs in the same family, especially when analysing total RNA. These results suggest that RT-qPCR is unlikely to be an effective means to detect delivery of microRNA mimic-based drugs to tumour cells in patients.

  3. Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling.

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    Schudoma, Christian; May, Patrick; Nikiforova, Viktoria; Walther, Dirk

    2010-01-01

    The specific function of RNA molecules frequently resides in their seemingly unstructured loop regions. We performed a systematic analysis of RNA loops extracted from experimentally determined three-dimensional structures of RNA molecules. A comprehensive loop-structure data set was created and organized into distinct clusters based on structural and sequence similarity. We detected clear evidence of the hallmark of homology present in the sequence-structure relationships in loops. Loops differing by structures. Thus, our results support the application of homology modeling for RNA loop model building. We established a threshold that may guide the sequence divergence-based selection of template structures for RNA loop homology modeling. Of all possible sequences that are, under the assumption of isosteric relationships, theoretically compatible with actual sequences observed in RNA structures, only a small fraction is contained in the Rfam database of RNA sequences and classes implying that the actual RNA loop space may consist of a limited number of unique loop structures and conserved sequences. The loop-structure data sets are made available via an online database, RLooM. RLooM also offers functionalities for the modeling of RNA loop structures in support of RNA engineering and design efforts.

  4. Unusual loop-sequence flexibility of the proximal RNA replication element in EMCV.

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    Jan Zoll

    Full Text Available Picornaviruses contain stable RNA structures at the 5' and 3' ends of the RNA genome, OriL and OriR involved in viral RNA replication. The OriL RNA element found at the 5' end of the enterovirus genome folds into a cloverleaf-like configuration. In vivo SELEX experiments revealed that functioning of the poliovirus cloverleaf depends on a specific structure in this RNA element. Little is known about the OriL of cardioviruses. Here, we investigated structural aspects and requirements of the apical loop of proximal stem-loop SL-A of mengovirus, a strain of EMCV. Using NMR spectroscopy, we showed that the mengovirus SL-A apical loop consists of an octaloop. In vivo SELEX experiments demonstrated that a large number of random sequences are tolerated in the apical octaloop that support virus replication. Mutants in which the SL-A loop size and the length of the upper part of the stem were varied showed that both stem-length and stability of the octaloop are important determinants for viral RNA replication and virus reproduction. Together, these data show that stem-loop A plays an important role in virus replication. The high degree of sequence flexibility and the lack of selective pressure on the octaloop argue against a role in sequence specific RNA-protein or RNA-RNA interactions in which octaloop nucleotides are involved.

  5. Detection of siRNA Mediated Target mRNA Cleavage Activities in Human Cells by a Novel Stem-Loop Array RT-PCR Analysis

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    2016-09-07

    sequences of the target mRNA, and a double stranded stem at the 5′ end that forms a stem -loop to function as a forceps to stabilize the secondary...E-mjournal homepage: www.elsevier.com/locate/bbrepDetection of siRNA-mediated target mRNA cleavage activities in human cells by a novel stem -loop...challenges for the accurate and efficient detection and verification of cleavage sites on target mRNAs. Here we used a sensitive stem -loop array reverse

  6. Mutations of the kissing-loop dimerization sequence influence the site specificity of murine leukemia virus recombination in vivo

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    Mikkelsen, J G; Lund, Anders Henrik; Duch, M

    2000-01-01

    synthesis in newly infected cells. We have previously shown that template shifts within the 5' leader of murine leukemia viruses occur preferentially within the kissing stem-loop motif, a cis element crucial for in vitro RNA dimer formation. By use of a forced recombination approach based on single......-cycle transfer of Akv murine leukemia virus-based vectors harboring defective primer binding site sequences, we now report that modifications of the kissing-loop structure, ranging from a deletion of the entire sequence to introduction of a single point mutation in the loop motif, significantly disturb site...... specificity of recombination within the highly structured 5' leader region. In addition, we find that an intact kissing-loop sequence favors optimal RNA encapsidation and vector transduction. Our data are consistent with the kissing-loop dimerization model and suggest that a direct intermolecular RNA...

  7. Mitochondrial D-loop sequence variation among Italian horse breeds

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    Zanotti Marta

    2004-11-01

    Full Text Available Abstract The genetic variability of the mitochondrial D-loop DNA sequence in seven horse breeds bred in Italy (Giara, Haflinger, Italian trotter, Lipizzan, Maremmano, Thoroughbred and Sarcidano was analysed. Five unrelated horses were chosen in each breed and twenty-two haplotypes were identified. The sequences obtained were aligned and compared with a reference sequence and with 27 mtDNA D-loop sequences selected in the GenBank database, representing Spanish, Portuguese, North African, wild horses and an Equus asinus sequence as the outgroup. Kimura two-parameter distances were calculated and a cluster analysis using the Neighbour-joining method was performed to obtain phylogenetic trees among breeds bred in Italy and among Italian and foreign breeds. The cluster analysis indicates that all the breeds but Giara are divided in the two trees, and no clear relationships were revealed between Italian populations and the other breeds. These results could be interpreted as showing the mixed origin of breeds bred in Italy and probably indicate the presence of many ancient maternal lineages with high diversity in mtDNA sequences.

  8. Arbitrary digital pulse sequence generator with delay-loop timing

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    Hošák, Radim; Ježek, Miroslav

    2018-04-01

    We propose an idea of an electronic multi-channel arbitrary digital sequence generator with temporal granularity equal to two clock cycles. We implement the generator with 32 channels using a low-cost ARM microcontroller and demonstrate its capability to produce temporal delays ranging from tens of nanoseconds to hundreds of seconds, with 24 ns timing granularity and linear scaling of delay with respect to the number of delay loop iterations. The generator is optionally synchronized with an external clock source to provide 100 ps jitter and overall sequence repeatability within the whole temporal range. The generator is fully programmable and able to produce digital sequences of high complexity. The concept of the generator can be implemented using different microcontrollers and applied for controlling of various optical, atomic, and nuclear physics measurement setups.

  9. Single-cell sequencing in stem cell biology.

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    Wen, Lu; Tang, Fuchou

    2016-04-15

    Cell-to-cell variation and heterogeneity are fundamental and intrinsic characteristics of stem cell populations, but these differences are masked when bulk cells are used for omic analysis. Single-cell sequencing technologies serve as powerful tools to dissect cellular heterogeneity comprehensively and to identify distinct phenotypic cell types, even within a 'homogeneous' stem cell population. These technologies, including single-cell genome, epigenome, and transcriptome sequencing technologies, have been developing rapidly in recent years. The application of these methods to different types of stem cells, including pluripotent stem cells and tissue-specific stem cells, has led to exciting new findings in the stem cell field. In this review, we discuss the recent progress as well as future perspectives in the methodologies and applications of single-cell omic sequencing technologies.

  10. Recombination in the 5' leader of murine leukemia virus is accurate and influenced by sequence identity with a strong bias toward the kissing-loop dimerization region

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    Mikkelsen, J G; Lund, Anders Henrik; Duch, M

    1998-01-01

    during minus-strand DNA synthesis occurred within defined areas of the genome and did not lead to misincorporations at the crossover site. The nonrandom distribution of recombination sites did not reflect a bias for specific sites due to selection at the level of marker gene expression. We address...... whether template switching is affected by the length of sequence identity, by palindromic sequences, and/or by putative stem-loop structures. Sixteen of 24 sites of recombination colocalized with the kissing-loop dimerization region, and we propose that RNA-RNA interactions between palindromic sequences...

  11. Functional analysis of the stem-loop structures at the 5' end of the Aichi virus genome

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    Nagashima, Shigeo; Sasaki, Jun; Taniguchi, Koki

    2003-01-01

    Aichi virus is a member of the family Picornaviridae. Computer-assisted secondary structure prediction suggested the formation of three stem-loop structures (SL-A, SL-B, and SL-C from the 5' end) within the 5'-end 120 nucleotides of the genome. We have already shown that the most 5'-end stem-loop, SL-A, is critical for viral RNA replication. Here, using an infectious cDNA clone and a replicon harboring a luciferase gene, we revealed that formation of SL-B and SL-C on the positive strand is essential for viral RNA replication. In addition, the specific nucleotide sequence of the loop segment of SL-B was also shown to be critical for viral RNA replication. Mutations of the upper and lower stems of SL-C that do not disrupt the base-pairings hardly affected RNA replication, but decreased the yields of viable viruses significantly compared with for the wild-type. This suggests that SL-C plays a role at some step besides RNA replication during virus infection

  12. Whole-loop mitochondrial DNA D-loop sequence variability in Egyptian Arabian equine matrilines

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    Hudson, William

    2017-01-01

    Background Egyptian Arabian horses have been maintained in a state of genetic isolation for over a hundred years. There is only limited genetic proof that the studbook records of female lines of Egyptian Arabian pedigrees are reliable. This study characterized the mitochondrial DNA (mtDNA) signatures of 126 horses representing 14 matrilines in the Egyptian Agricultural Organization (EAO) horse-breeding program. Findings Analysis of the whole D-loop sequence yielded additional information compared to hypervariable region-1 (HVR1) analysis alone, with 42 polymorphic sites representing ten haplotypes compared to 16 polymorphic sites representing nine haplotypes, respectively. Most EAO haplotypes belonged to ancient haplogroups, suggesting origin from a wide geographical area over many thousands of years, although one haplotype was novel. Conclusions Historical families share haplotypes and some individuals from different strains belonged to the same haplogroup: the classical EAO strain designation is not equivalent to modern monophyletic matrilineal groups. Phylogenetic inference showed that the foundation mares of the historical haplotypes were highly likely to have the same haplotypes as the animals studied (p > 0.998 in all cases), confirming the reliability of EAO studbook records and providing the opportunity for breeders to confirm the ancestry of their horses. PMID:28859174

  13. The cellular RNA-binding protein EAP recognizes a conserved stem-loop in the Epstein-Barr virus small RNA EBER 1.

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    Toczyski, D P; Steitz, J A

    1993-01-01

    EAP (EBER-associated protein) is an abundant, 15-kDa cellular RNA-binding protein which associates with certain herpesvirus small RNAs. We have raised polyclonal anti-EAP antibodies against a glutathione S-transferase-EAP fusion protein. Analysis of the RNA precipitated by these antibodies from Epstein-Barr virus (EBV)- or herpesvirus papio (HVP)-infected cells shows that > 95% of EBER 1 (EBV-encoded RNA 1) and the majority of HVP 1 (an HVP small RNA homologous to EBER 1) are associated with EAP. RNase protection experiments performed on native EBER 1 particles with affinity-purified anti-EAP antibodies demonstrate that EAP binds a stem-loop structure (stem-loop 3) of EBER 1. Since bacterially expressed glutathione S-transferase-EAP fusion protein binds EBER 1, we conclude that EAP binding is independent of any other cellular or viral protein. Detailed mutational analyses of stem-loop 3 suggest that EAP recognizes the majority of the nucleotides in this hairpin, interacting with both single-stranded and double-stranded regions in a sequence-specific manner. Binding studies utilizing EBER 1 deletion mutants suggest that there may also be a second, weaker EAP-binding site on stem-loop 4 of EBER 1. These data and the fact that stem-loop 3 represents the most highly conserved region between EBER 1 and HVP 1 suggest that EAP binding is a critical aspect of EBER 1 and HVP 1 function. Images PMID:8380232

  14. Optical and electrochemical detection of a verotoxigenic E. coli gene using DNAzyme-labeled stem-loops

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    Gloria Longinotti

    2017-12-01

    Full Text Available The activity of a peroxidase-mimicking DNAzyme was optimized to be used as a catalytic label in a stem-loop genosensor construction for quantifying the gene sequence Shiga-like toxin I of verotoxigenic E. coli. Experimental conditions such as pH, buffer composition, potassium ion concentration, and hemin-to-oligonucleotides ratio, were analyzed to maximize optical and electrochemical responses using microvolumes. Different stem-loop constructions were evaluated to obtain the optimum response against the target concentration. Linear ranges of 0.05-0.5 µM and limits of detection of 174 nM and 144 nM were estimated for the optical and electrochemical measurements, respectively. Selectivity was proved by assaying other verotoxigenic, enterotoxigenic and enteroinvasive sequences. The results show that, if a combination of small-volume electrochemical cells and low-cost untreated screen-printed electrodes with a relatively high geometric area is used, electrochemical measurements present similar sensitivity and limits of detection to the more usual optical ones, allowing the development of low-cost electrochemical biosensors based on the use of soluble DNAzymes as labels.

  15. Small interfering RNA targeted to stem-loop II of the 5' untranslated region effectively inhibits expression of six HCV genotypes

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    Dash Srikanta

    2006-11-01

    Full Text Available Abstract Background The antiviral action of interferon alpha targets the 5' untranslated region (UTR used by hepatitis C virus (HCV to translate protein by an internal ribosome entry site (IRES mechanism. Although this sequence is highly conserved among different clinical strains, approximately half of chronically infected hepatitis C patients do not respond to interferon therapy. Therefore, development of small interfering RNA (siRNA targeted to the 5'UTR to inhibit IRES mediated translation may represent an alternative approach that could circumvent the problem of interferon resistance. Results Four different plasmid constructs were prepared for intracellular delivery of siRNAs targeting the stem loop II-III of HCV 5' UTR. The effect of siRNA production on IRES mediated translation was investigated using chimeric clones between the gene for green fluorescence protein (GFP and IRES sequences of six different HCV genotypes. The siRNA targeted to stem loop II effectively mediated degradation of HCV IRES mRNA and inhibited GFP expression in the case of six different HCV genotypes, where as siRNAs targeted to stem loop III did not. Furthermore, intracytoplasmic expression of siRNA into transfected Huh-7 cells efficiently degraded HCV genomic RNA and inhibited core protein expression from infectious full-length infectious clones HCV 1a and HCV 1b strains. Conclusion These in vitro studies suggest that siRNA targeted to stem-loop II is highly effective inhibiting IRES mediated translation of the major genotypes of HCV. Stem-loop II siRNA may be a good target for developing an intracellular immunization strategy based antiviral therapy to inhibit hepatitis C virus strains that are not inhibited by interferon.

  16. Placental fetal stem segmentation in a sequence of histology images

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    Athavale, Prashant; Vese, Luminita A.

    2012-02-01

    Recent research in perinatal pathology argues that analyzing properties of the placenta may reveal important information on how certain diseases progress. One important property is the structure of the placental fetal stems. Analysis of the fetal stems in a placenta could be useful in the study and diagnosis of some diseases like autism. To study the fetal stem structure effectively, we need to automatically and accurately track fetal stems through a sequence of digitized hematoxylin and eosin (H&E) stained histology slides. There are many problems in successfully achieving this goal. A few of the problems are: large size of images, misalignment of the consecutive H&E slides, unpredictable inaccuracies of manual tracing, very complicated texture patterns of various tissue types without clear characteristics, just to name a few. In this paper we propose a novel algorithm to achieve automatic tracing of the fetal stem in a sequence of H&E images, based on an inaccurate manual segmentation of a fetal stem in one of the images. This algorithm combines global affine registration, local non-affine registration and a novel 'dynamic' version of the active contours model without edges. We first use global affine image registration of all the images based on displacement, scaling and rotation. This gives us approximate location of the corresponding fetal stem in the image that needs to be traced. We then use the affine registration algorithm "locally" near this location. At this point, we use a fast non-affine registration based on L2-similarity measure and diffusion regularization to get a better location of the fetal stem. Finally, we have to take into account inaccuracies in the initial tracing. This is achieved through a novel dynamic version of the active contours model without edges where the coefficients of the fitting terms are computed iteratively to ensure that we obtain a unique stem in the segmentation. The segmentation thus obtained can then be used as an

  17. Mitochondrial D-loop sequence of domesticated waterfowl in Central Java: goose and muscovy duck

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    Susanti, R.; Iswari, R. S.

    2018-03-01

    This study aims to determine the genetic characterization of domesticated waterfowl (goose and Muscovy duck) in Central Java based on a D-loop mtDNA gene. The D-loop gene was amplified using PCR technique by specific primer and sequenced using dideoxy termination method. Multiple alignments of D-loop gene obtained were 710 nucleotides at position 74 to 783 at the 5’ end (for goose) and 712 nucleotides at position 48 to 759 at the 5’ end (for Muscovy duck). The results of the polymorphism analysis on D-loop sequences of muscovy duck produced 3 haplotypes. In the D-loop gene of goose does not show polymorphism, with substitution at G117A. Phylogenetic trees reconstructions of goose and Muscovy duck, which was collected during this research compared with another species from Anser, Chairina and Anas was generated 2 forms of clusters. The first group consists of all kind of Muscovy duck together with Chairina moschata and Anas, while the second group consists of all geese and Anser cygnoides the other. The determination of Muscovy duck and geese identity can be distinguished from the genetic marker information. Based on the phylogenetic analysis, it can be concluded that the Muscovy duck is closely related to Chairina moschata, while geese is closely related to Anser cygnoides.

  18. A regulatory transcriptional loop controls proliferation and differentiation in Drosophila neural stem cells.

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    Tetsuo Yasugi

    Full Text Available Neurogenesis is initiated by a set of basic Helix-Loop-Helix (bHLH transcription factors that specify neural progenitors and allow them to generate neurons in multiple rounds of asymmetric cell division. The Drosophila Daughterless (Da protein and its mammalian counterparts (E12/E47 act as heterodimerization factors for proneural genes and are therefore critically required for neurogenesis. Here, we demonstrate that Da can also be an inhibitor of the neural progenitor fate whose absence leads to stem cell overproliferation and tumor formation. We explain this paradox by demonstrating that Da induces the differentiation factor Prospero (Pros whose asymmetric segregation is essential for differentiation in one of the two daughter cells. Da co-operates with the bHLH transcription factor Asense, whereas the other proneural genes are dispensible. After mitosis, Pros terminates Asense expression in one of the two daughter cells. In da mutants, pros is not expressed, leading to the formation of lethal transplantable brain tumors. Our results define a transcriptional feedback loop that regulates the balance between self-renewal and differentiation in Drosophila optic lobe neuroblasts. They indicate that initiation of a neural differentiation program in stem cells is essential to prevent tumorigenesis.

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

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    Giovanna Sattin

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

  20. HER2 in Breast Cancer Stemness: A Negative Feedback Loop towards Trastuzumab Resistance

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    Babak Nami

    2017-04-01

    Full Text Available HER2 receptor tyrosine kinase that is overexpressed in approximately 20% of all breast cancers (BCs is a poor prognosis factor and a precious target for BC therapy. Trastuzumab is approved by FDA to specifically target HER2 for treating HER2+ BC. However, about 60% of patients with HER2+ breast tumor develop de novo resistance to trastuzumab, partially due to the loss of expression of HER2 extracellular domain on their tumor cells. This is due to shedding/cleavage of HER2 by metalloproteinases (ADAMs and MMPs. HER2 shedding results in the accumulation of intracellular carboxyl-terminal HER2 (p95HER2, which is a common phenomenon in trastuzumab-resistant tumors and is suggested as a predictive marker for trastuzumab resistance. Up-regulation of the metalloproteinases is a poor prognosis factor and is commonly seen in mesenchymal-like cancer stem cells that are risen during epithelial to mesenchymal transition (EMT of tumor cells. HER2 cleavage during EMT can explain why secondary metastatic tumors with high percentage of mesenchymal-like cancer stem cells are mostly resistant to trastuzumab but still sensitive to lapatinib. Importantly, many studies report HER2 interaction with oncogenic/stemness signaling pathways including TGF-β/Smad, Wnt/β-catenin, Notch, JAK/STAT and Hedgehog. HER2 overexpression promotes EMT and the emergence of cancer stem cell properties in BC. Increased expression and activation of metalloproteinases during EMT leads to proteolytic cleavage and shedding of HER2 receptor, which downregulates HER2 extracellular domain and eventually increases trastuzumab resistance. Here, we review the hypothesis that a negative feedback loop between HER2 and stemness signaling drives resistance of BC to trastuzumab.

  1. RNA-dependent RNA polymerase of hepatitis C virus binds to its coding region RNA stem-loop structure, 5BSL3.2, and its negative strand.

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    Kanamori, Hiroshi; Yuhashi, Kazuhito; Ohnishi, Shin; Koike, Kazuhiko; Kodama, Tatsuhiko

    2010-05-01

    The hepatitis C virus NS5B RNA-dependent RNA polymerase (RdRp) is a key enzyme involved in viral replication. Interaction between NS5B RdRp and the viral RNA sequence is likely to be an important step in viral RNA replication. The C-terminal half of the NS5B-coding sequence, which contains the important cis-acting replication element, has been identified as an NS5B-binding sequence. In the present study, we confirm the specific binding of NS5B to one of the RNA stem-loop structures in the region, 5BSL3.2. In addition, we show that NS5B binds to the complementary strand of 5BSL3.2 (5BSL3.2N). The bulge structure of 5BSL3.2N was shown to be indispensable for tight binding to NS5B. In vitro RdRp activity was inhibited by 5BSL3.2N, indicating the importance of the RNA element in the polymerization by RdRp. These results suggest the involvement of the RNA stem-loop structure of the negative strand in the replication process.

  2. Genetic diversity of mtDNA D-loop sequences in four native Chinese chicken breeds.

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    Guo, H W; Li, C; Wang, X N; Li, Z J; Sun, G R; Li, G X; Liu, X J; Kang, X T; Han, R L

    2017-10-01

    1. To explore the genetic diversity of Chinese indigenous chicken breeds, a 585 bp fragment of the mitochondrial DNA (mtDNA) region was sequenced in 102 birds from the Xichuan black-bone chicken, Yunyang black-bone chicken and Lushi chicken. In addition, 30 mtDNA D-loop sequences of Silkie fowls were downloaded from NCBI. The mtDNA D-loop sequence polymorphism and maternal origin of 4 chicken breeds were analysed in this study. 2. The results showed that a total of 33 mutation sites and 28 haplotypes were detected in the 4 chicken breeds. The haplotype diversity and nucleotide diversity of these 4 native breeds were 0.916 ± 0.014 and 0.012 ± 0.002, respectively. Three clusters were formed in 4 Chinese native chickens and 12 reference breeds. Both the Xichuan black-bone chicken and Yunyang black-bone chicken were grouped into one cluster. Four haplogroups (A, B, C and E) emerged in the median-joining network in these breeds. 3. It was concluded that these 4 Chinese chicken breeds had high genetic diversity. The phylogenetic tree and median network profiles showed that Chinese native chickens and its neighbouring countries had at least two maternal origins, one from Yunnan, China and another from Southeast Asia or its surrounding area.

  3. Stem-Loop RT-qPCR as an Efficient Tool for the Detection and Quantification of Small RNAs in Giardia lamblia

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    Marcial-Quino, Jaime; Gómez-Manzo, Saúl; Fierro, Francisco; Vanoye-Carlo, America; Rufino-González, Yadira; Sierra-Palacios, Edgar; Castillo-Villanueva, Adriana; Castillo-Rodríguez, Rosa Angélica; Rodríguez-Bustamante, Eduardo; Arreguin-Espinosa, Roberto; Reyes-Vivas, Horacio

    2016-01-01

    Stem-loop quantitative reverse transcription PCR (RT-qPCR) is a molecular technique used for identification and quantification of individual small RNAs in cells. In this work, we used a Universal ProbeLibrary (UPL)-based design to detect—in a rapid, sensitive, specific, and reproducible way—the small nucleolar RNA (snoRNA) GlsR17 and its derived miRNA (miR2) of Giardia lamblia using a stem-loop RT-qPCR approach. Both small RNAs could be isolated from both total RNA and small RNA samples. Identification of the two small RNAs was carried out by sequencing the PCR-amplified small RNA products upon ligation into the pJET1.2/blunt vector. GlsR17 is constitutively expressed during the 72 h cultures of trophozoites, while the mature miR2 is present in 2-fold higher abundance during the first 48 h than at 72 h. Because it has been suggested that miRNAs in G. lamblia have an important role in the regulation of gene expression, the use of the stem-loop RT-qPCR method could be valuable for the study of miRNAs of G. lamblia. This methodology will be a powerful tool for studying gene regulation in G. lamblia, and will help to better understand the features and functions of these regulatory molecules and how they work within the RNA interference (RNAi) pathway in G. lamblia. PMID:27999395

  4. Stem-Loop RT-qPCR as an Efficient Tool for the Detection and Quantification of Small RNAs in Giardia lamblia

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    Jaime Marcial-Quino

    2016-12-01

    Full Text Available Stem-loop quantitative reverse transcription PCR (RT-qPCR is a molecular technique used for identification and quantification of individual small RNAs in cells. In this work, we used a Universal ProbeLibrary (UPL-based design to detect—in a rapid, sensitive, specific, and reproducible way—the small nucleolar RNA (snoRNA GlsR17 and its derived miRNA (miR2 of Giardia lamblia using a stem-loop RT-qPCR approach. Both small RNAs could be isolated from both total RNA and small RNA samples. Identification of the two small RNAs was carried out by sequencing the PCR-amplified small RNA products upon ligation into the pJET1.2/blunt vector. GlsR17 is constitutively expressed during the 72 h cultures of trophozoites, while the mature miR2 is present in 2-fold higher abundance during the first 48 h than at 72 h. Because it has been suggested that miRNAs in G. lamblia have an important role in the regulation of gene expression, the use of the stem-loop RT-qPCR method could be valuable for the study of miRNAs of G. lamblia. This methodology will be a powerful tool for studying gene regulation in G. lamblia, and will help to better understand the features and functions of these regulatory molecules and how they work within the RNA interference (RNAi pathway in G. lamblia.

  5. Transcript Lifetime Is Balanced between Stabilizing Stem-Loop Structures and Degradation-Promoting Polyadenylation in Plant Mitochondria

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    Kuhn, Josef; Tengler, Ulrike; Binder, Stefan

    2001-01-01

    To determine the influence of posttranscriptional modifications on 3′ end processing and RNA stability in plant mitochondria, pea atp9 and Oenothera atp1 transcripts were investigated for the presence and function of 3′ nonencoded nucleotides. A 3′ rapid amplification of cDNA ends approach initiated at oligo(dT)-adapter primers finds the expected poly(A) tails predominantly attached within the second stem or downstream of the double stem-loop structures at sites of previously mapped 3′ ends. Functional studies in a pea mitochondrial in vitro processing system reveal a rapid removal of the poly(A) tails up to termini at the stem-loop structure but little if any influence on further degradation of the RNA. In contrast 3′ poly(A) tracts at RNAs without such stem-loop structures significantly promote total degradation in vitro. To determine the in vivo identity of 3′ nonencoded nucleotides more accurately, pea atp9 transcripts were analyzed by a direct anchor primer ligation-reverse transcriptase PCR approach. This analysis identified maximally 3-nucleotide-long nonencoded extensions most frequently of adenosines combined with cytidines. Processing assays with substrates containing homopolymer stretches of different lengths showed that 10 or more adenosines accelerate RNA processivity, while 3 adenosines have no impact on RNA life span. Thus polyadenylation can generally stimulate the decay of RNAs, but processivity of degradation is almost annihilated by the stabilizing effect of the stem-loop structures. These antagonistic actions thus result in the efficient formation of 3′ processed and stable transcripts. PMID:11154261

  6. The monoclonal S9.6 antibody exhibits highly variable binding affinities towards different R-loop sequences.

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    Fabian König

    Full Text Available The monoclonal antibody S9.6 is a widely-used tool to purify, analyse and quantify R-loop structures in cells. A previous study using the surface plasmon resonance technology and a single-chain variable fragment (scFv of S9.6 showed high affinity (0.6 nM for DNA-RNA and also a high affinity (2.7 nM for RNA-RNA hybrids. We used the microscale thermophoresis method allowing surface independent interaction studies and electromobility shift assays to evaluate additional RNA-DNA hybrid sequences and to quantify the binding affinities of the S9.6 antibody with respect to distinct sequences and their GC-content. Our results confirm high affinity binding to previously analysed sequences, but reveals that binding affinities are highly sequence specific. Our study presents R-loop sequences that independent of GC-content and in different sequence variations exhibit either no binding, binding affinities in the micromolar range and as well high affinity binding in the nanomolar range. Our study questions the usefulness of the S9.6 antibody in the quantitative analysis of R-loop sequences in vivo.

  7. Label-free logic modules and two-layer cascade based on stem-loop probes containing a G-quadruplex domain.

    Science.gov (United States)

    Guo, Yahui; Cheng, Junjie; Wang, Jine; Zhou, Xiaodong; Hu, Jiming; Pei, Renjun

    2014-09-01

    A simple, versatile, and label-free DNA computing strategy was designed by using toehold-mediated strand displacement and stem-loop probes. A full set of logic gates (YES, NOT, OR, NAND, AND, INHIBIT, NOR, XOR, XNOR) and a two-layer logic cascade were constructed. The probes contain a G-quadruplex domain, which was blocked or unfolded through inputs initiating strand displacement and the obviously distinguishable light-up fluorescent signal of G-quadruplex/NMM complex was used as the output readout. The inputs are the disease-specific nucleotide sequences with potential for clinic diagnosis. The developed versatile computing system based on our label-free and modular strategy might be adapted in multi-target diagnosis through DNA hybridization and aptamer-target interaction. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. A feedback regulatory loop involving microRNA-9 and nuclear receptor TLX in neural stem cell fate determination.

    Science.gov (United States)

    Zhao, Chunnian; Sun, GuoQiang; Li, Shengxiu; Shi, Yanhong

    2009-04-01

    MicroRNAs have been implicated as having important roles in stem cell biology. MicroRNA-9 (miR-9) is expressed specifically in neurogenic areas of the brain and may be involved in neural stem cell self-renewal and differentiation. We showed previously that the nuclear receptor TLX is an essential regulator of neural stem cell self-renewal. Here we show that miR-9 suppresses TLX expression to negatively regulate neural stem cell proliferation and accelerate neural differentiation. Introducing a TLX expression vector that is not prone to miR-9 regulation rescued miR-9-induced proliferation deficiency and inhibited precocious differentiation. In utero electroporation of miR-9 in embryonic brains led to premature differentiation and outward migration of the transfected neural stem cells. Moreover, TLX represses expression of the miR-9 pri-miRNA. By forming a negative regulatory loop with TLX, miR-9 provides a model for controlling the balance between neural stem cell proliferation and differentiation.

  9. Detection of Ultra-Rare Mitochondrial Mutations in Breast Stem Cells by Duplex Sequencing.

    Directory of Open Access Journals (Sweden)

    Eun Hyun Ahn

    Full Text Available Long-lived adult stem cells could accumulate non-repaired DNA damage or mutations that increase the risk of tumor formation. To date, studies on mutations in stem cells have concentrated on clonal (homoplasmic mutations and have not focused on rarely occurring stochastic mutations that may accumulate during stem cell dormancy. A major challenge in investigating these rare mutations is that conventional next generation sequencing (NGS methods have high error rates. We have established a new method termed Duplex Sequencing (DS, which detects mutations with unprecedented accuracy. We present a comprehensive analysis of mitochondrial DNA mutations in human breast normal stem cells and non-stem cells using DS. The vast majority of mutations occur at low frequency and are not detectable by NGS. The most prevalent point mutation types are the C>T/G>A and A>G/T>C transitions. The mutations exhibit a strand bias with higher prevalence of G>A, T>C, and A>C mutations on the light strand of the mitochondrial genome. The overall rare mutation frequency is significantly lower in stem cells than in the corresponding non-stem cells. We have identified common and unique non-homoplasmic mutations between non-stem and stem cells that include new mutations which have not been reported previously. Four mutations found within the MT-ND5 gene (m.12684G>A, m.12705C>T, m.13095T>C, m.13105A>G are present in all groups of stem and non-stem cells. Two mutations (m.8567T>C, m.10547C>G are found only in non-stem cells. This first genome-wide analysis of mitochondrial DNA mutations may aid in characterizing human breast normal epithelial cells and serve as a reference for cancer stem cell mutation profiles.

  10. Genetic analysis of the Hungarian draft horse population using partial mitochondrial DNA D-loop sequencing

    Science.gov (United States)

    2018-01-01

    Background The Hungarian draft is a horse breed with a recent mixed ancestry created in the 1920s by crossing local mares with draught horses imported from France and Belgium. The interest in its conservation and characterization has increased over the last few years. The aim of this work is to contribute to the characterization of the endangered Hungarian heavy draft horse populations in order to obtain useful information to implement conservation strategies for these genetic stocks. Methods To genetically characterize the breed and to set up the basis for a conservation program, in the present study a hypervariable region of the mitochrondial DNA (D-loop) was used to assess genetic diversity in Hungarian draft horses. Two hundred and eighty five sequences obtained in our laboratory and 419 downloaded sequences available from Genbank were analyzed. Results One hundred and sixty-four haplotypes and thirty-six polymorphic sites were observed. High haplotype and nucleotide diversity values (Hd = 0.954 ± 0.004; π = 0.028 ± 0.0004) were identified in Hungarian population, although they were higher within than among the different populations (Hd = 0.972 ± 0.002; π = 0.03097 ± 0.002). Fourteen of the previously observed seventeen haplogroups were detected. Discussion Our samples showed a large intra- and interbreed variation. There was no clear clustering on the median joining network figure. The overall information collected in this work led us to consider that the genetic scenario observed for Hungarian draft breed is more likely the result of contributions from ‘ancestrally’ different genetic backgrounds. This study could contribute to the development of a breeding plan for Hungarian draft horses and help to formulate a genetic conservation plan, avoiding inbreeding while. PMID:29404201

  11. Combined sequencing of mRNA and DNA from human embryonic stem cells

    Directory of Open Access Journals (Sweden)

    Florian Mertes

    2016-06-01

    Full Text Available Combined transcriptome and whole genome sequencing of the same ultra-low input sample down to single cells is a rapidly evolving approach for the analysis of rare cells. Besides stem cells, rare cells originating from tissues like tumor or biopsies, circulating tumor cells and cells from early embryonic development are under investigation. Herein we describe a universal method applicable for the analysis of minute amounts of sample material (150 to 200 cells derived from sub-colony structures from human embryonic stem cells. The protocol comprises the combined isolation and separate amplification of poly(A mRNA and whole genome DNA followed by next generation sequencing. Here we present a detailed description of the method developed and an overview of the results obtained for RNA and whole genome sequencing of human embryonic stem cells, sequencing data is available in the Gene Expression Omnibus (GEO database under accession number GSE69471.

  12. MRI of the brain stem using fluid attenuated inversion recivery pulse sequences

    International Nuclear Information System (INIS)

    De Coene, B.; Hajnal, J.V.; Pennock, J.M.; Bydder, G.M.

    1993-01-01

    Heavily T2-weighted fluid-attenuated inversion recovery (FLAIR) sequences with inversion times of 2000-2500 ms and echo times of 130-200 ms were used to image the brain stem of a normal adult and five patients. These sequences produce high signal from many white matter tracts and display high lesion contrast. The corticospinal and parietopontine tracts, lateral and medial lemnisci, superior and inferior cerebellar peduncles, medial longitudinal fasciculi, thalamo-olivary tracts the cuneate and gracile fasiculi gave high signal and were directly visualised. The oculomotor and trigeminal nerves were demonstrated within the brain stem. Lesions not seen with conventional T2-weighted spin echo sequences were seen with high contrast in patients with infarction, multiple sclerosis, sarcoidosis, chunt obstruction and metastatic tumour. The anatomical detail and high lesion contrast given by the FLAIR pulse sequence appear likely to be of value in diagnosis of disease in the brain stem. (orig.)

  13. Universal Quantum Computing with Measurement-Induced Continuous-Variable Gate Sequence in a Loop-Based Architecture.

    Science.gov (United States)

    Takeda, Shuntaro; Furusawa, Akira

    2017-09-22

    We propose a scalable scheme for optical quantum computing using measurement-induced continuous-variable quantum gates in a loop-based architecture. Here, time-bin-encoded quantum information in a single spatial mode is deterministically processed in a nested loop by an electrically programmable gate sequence. This architecture can process any input state and an arbitrary number of modes with almost minimum resources, and offers a universal gate set for both qubits and continuous variables. Furthermore, quantum computing can be performed fault tolerantly by a known scheme for encoding a qubit in an infinite-dimensional Hilbert space of a single light mode.

  14. Detection of negative and positive RNA strand of poliovirus Sabin 1 and echovirus E19 by a stem-loop reverse transcription PCR.

    Science.gov (United States)

    Fikatas, A; Dimitriou, T G; Kyriakopoulou, Z; Moschonas, G D; Amoutzias, G D; Mossialos, D; Gartzonika, C; Levidiotou-Stefanou, S; Markoulatos, P

    2017-09-01

    In this report a strand specific RT-PCR was established for the detection of the replicative negative RNA strand of poliovirus sabin 1 (Sabin1) and Echovirus 19 (E19) strains. The key for the successful conduction of the assay was the use of a specific reverse transcription primer targeting the 5'-UTR of enteroviruses that consisted of a stem-loop structure at the 5'-end and an enteroviral-specific sequence at the 3'-end. The stem loop RT-PCR was found to be an accurate and sensitive method, detecting even 10 -2 CCID 50 of poliovirus sabin 1 (Sabin1) and E19 strains 6 h postinfection (p.i.), while CPE appeared 3 days later. This assay was also validated in SiHa and Caski cell lines that are not used for the detection of enteroviruses. The negative RNA strand was detected 6 h and 12 h p.i. in SiHa and Caski cells, when these cell lines were inoculated with 10 5 and 1 CCID 50 respectively, whereas CPE was observed 5 days p.i for SiHa cells and 8 days p.i for Caski cells and that only at 10 5 CCID 50 . The results show that this approach may be used for replacing the time-consuming cell cultures in order to detect the active replication of enteroviruses. Enteroviruses are positive stranded RNA viruses that may cause severe diseases. The conventional method for detection of active viral replication involves virus isolation in sensitive cell cultures followed by titration and seroneutralization. In this report, we describe the use of a stem-loop secondary structured oligonucleotide in RT-PCR assay for the detection of the replicative negative strand of the positive-stranded RNA of poliovirus sabin 1 and E19 strains. This approach proved to be a useful tool that may be used for replacing the time-consuming cell culture assays in order to detect the active replication of enteroviruses. © 2017 The Society for Applied Microbiology.

  15. Genetic distance of Malaysian mousedeer based on mitochondrial DNA cytochrome oxidase I (COI) and D-loop region sequences

    Science.gov (United States)

    Bakar, Mohamad-Azam Akmal Abu; Rovie-Ryan, Jeffrine Japning; Ampeng, Ahmad; Yaakop, Salmah; Nor, Shukor Md; Md-Zain, Badrul Munir

    2018-04-01

    Mousedeer is one of the primitive mammals that can be found mainly in Southeast-Asia region. There are two species of mousedeer in Malaysia which are Tragulus kanchil and Tragulus napu. Both species can be distinguish by size, coat coloration, and throat pattern but clear diagnosis still cannot be found. The objective of the study is to show the genetic distance relationship between T. kanchil and T. napu and their population based on mitochondrial DNA (mtDNA) cytochrome oxidase I (COI) and D-loop region. There are 42 sample of mousedeer were used in this study collected by PERHILITAN from different locality. Another 29 D-loop sequence were retrieved from Genbank for comparative analysis. All sample were amplified using universal primer and species-specific primer for COI and D-loop genes via PCR process. The amplified sequences were analyzed to determine genetic distance of T. kanchil and T. napu. From the analysis, the average genetic distance between T. kanchil and T. napu based on locus COI and D-loop were 0.145 and 0.128 respectively. The genetic distance between populations of T. kanchil based on locus COI was between 0.003-0.013. For locus D-loop, genetic distance analysis showed distance in relationship between west-coast populations to east-coast population of T. kanchil. COI and D-loop mtDNA region provided a clear picture on the relationship within the mousedeer species. Last but not least, conservation effort toward protecting this species can be done by study the molecular genetics and prevent the extinction of this species.

  16. miR-137 forms a regulatory loop with nuclear receptor TLX and LSD1 in neural stem cells.

    Science.gov (United States)

    Sun, GuoQiang; Ye, Peng; Murai, Kiyohito; Lang, Ming-Fei; Li, Shengxiu; Zhang, Heying; Li, Wendong; Fu, Chelsea; Yin, Jason; Wang, Allen; Ma, Xiaoxiao; Shi, Yanhong

    2011-11-08

    miR-137 is a brain-enriched microRNA. Its role in neural development remains unknown. Here we show that miR-137 has an essential role in controlling embryonic neural stem cell fate determination. miR-137 negatively regulates cell proliferation and accelerates neural differentiation of embryonic neural stem cells. In addition, we show that the histone lysine-specific demethylase 1 (LSD1), a transcriptional co-repressor of nuclear receptor TLX, is a downstream target of miR-137. In utero electroporation of miR-137 in embryonic mouse brains led to premature differentiation and outward migration of the transfected cells. Introducing a LSD1 expression vector lacking the miR-137 recognition site rescued miR-137-induced precocious differentiation. Furthermore, we demonstrate that TLX, an essential regulator of neural stem cell self-renewal, represses the expression of miR-137 by recruiting LSD1 to the genomic regions of miR-137. Thus, miR-137 forms a feedback regulatory loop with TLX and LSD1 to control the dynamics between neural stem cell proliferation and differentiation during neural development.

  17. Giardia telomeric sequence d(TAGGG)4 forms two intramolecular G-quadruplexes in K+ solution: effect of loop length and sequence on the folding topology.

    Science.gov (United States)

    Hu, Lanying; Lim, Kah Wai; Bouaziz, Serge; Phan, Anh Tuân

    2009-11-25

    Recently, it has been shown that in K(+) solution the human telomeric sequence d[TAGGG(TTAGGG)(3)] forms a (3 + 1) intramolecular G-quadruplex, while the Bombyx mori telomeric sequence d[TAGG(TTAGG)(3)], which differs from the human counterpart only by one G deletion in each repeat, forms a chair-type intramolecular G-quadruplex, indicating an effect of G-tract length on the folding topology of G-quadruplexes. To explore the effect of loop length and sequence on the folding topology of G-quadruplexes, here we examine the structure of the four-repeat Giardia telomeric sequence d[TAGGG(TAGGG)(3)], which differs from the human counterpart only by one T deletion within the non-G linker in each repeat. We show by NMR that this sequence forms two different intramolecular G-quadruplexes in K(+) solution. The first one is a novel basket-type antiparallel-stranded G-quadruplex containing two G-tetrads, a G x (A-G) triad, and two A x T base pairs; the three loops are consecutively edgewise-diagonal-edgewise. The second one is a propeller-type parallel-stranded G-quadruplex involving three G-tetrads; the three loops are all double-chain-reversal. Recurrence of several structural elements in the observed structures suggests a "cut and paste" principle for the design and prediction of G-quadruplex topologies, for which different elements could be extracted from one G-quadruplex and inserted into another.

  18. diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data.

    Science.gov (United States)

    Lareau, Caleb A; Aryee, Martin J; Berger, Bonnie

    2018-02-15

    The 3D architecture of DNA within the nucleus is a key determinant of interactions between genes, regulatory elements, and transcriptional machinery. As a result, differences in DNA looping structure are associated with variation in gene expression and cell state. To systematically assess changes in DNA looping architecture between samples, we introduce diffloop, an R/Bioconductor package that provides a suite of functions for the quality control, statistical testing, annotation, and visualization of DNA loops. We demonstrate this functionality by detecting differences between ENCODE ChIA-PET samples and relate looping to variability in epigenetic state. Diffloop is implemented as an R/Bioconductor package available at https://bioconductor.org/packages/release/bioc/html/diffloop.html. aryee.martin@mgh.harvard.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  19. In vitro synthesis of minus-strand RNA by an isolated cereal yellow dwarf virus RNA-dependent RNA polymerase requires VPg and a stem-loop structure at the 3' end of the virus RNA.

    Science.gov (United States)

    Osman, Toba A M; Coutts, Robert H A; Buck, Kenneth W

    2006-11-01

    Cereal yellow dwarf virus (CYDV) RNA has a 5'-terminal genome-linked protein (VPg). We have expressed the VPg region of the CYDV genome in bacteria and used the purified protein (bVPg) to raise an antiserum which was able to detect free VPg in extracts of CYDV-infected oat plants. A template-dependent RNA-dependent RNA polymerase (RdRp) has been produced from a CYDV membrane-bound RNA polymerase by treatment with BAL 31 nuclease. The RdRp was template specific, being able to utilize templates from CYDV plus- and minus-strand RNAs but not those of three unrelated viruses, Red clover necrotic mosaic virus, Cucumber mosaic virus, and Tobacco mosaic virus. RNA synthesis catalyzed by the RdRp required a 3'-terminal GU sequence and the presence of bVPg. Additionally, synthesis of minus-strand RNA on a plus-strand RNA template required the presence of a putative stem-loop structure near the 3' terminus of CYDV RNA. The base-paired stem, a single-nucleotide (A) bulge in the stem, and the sequence of a tetraloop were all required for the template activity. Evidence was produced showing that minus-strand synthesis in vitro was initiated by priming by bVPg at the 3' end of the template. The data are consistent with a model in which the RdRp binds to the stem-loop structure which positions the active site to recognize the 3'-terminal GU sequence for initiation of RNA synthesis by the addition of an A residue to VPg.

  20. A “four-ferrocene” modified stem-loop structure as a probe for sensitive detection and single-base mismatch discrimination of DNA

    International Nuclear Information System (INIS)

    Chatelain, Grégory; Ripert, Micaël; Farre, Carole; Ansanay-Alex, Salomé; Chaix, Carole

    2012-01-01

    We report the use of a four-ferrocene modified oligonucleotide as a probe for DNA detection with a gold electrode microsystem. This oligonucleotide is synthesized by automated solid-phase synthesis with four successive ferrocene moieties at the 5′-end and a C6-thiol modifier group at the 3′-end. The grafting of this 4Fc-DNA probe on a gold electrode microsystem results in the appearance of the ferrocene redox couple in cyclic voltammetry. The probe sequence is a stem-loop structure that folds efficiently on the electrode, thus optimizing electron transfer. Such architecture serves as sensor for DNA detection which is based on hybridization. The resulting disposable voltammetric sensor allowed direct, reagentless DNA detection in a small volume (20 μL). Electrochemical response upon hybridization with complementary short sequence (30-base length) and long sequence (50-base length) strands was observed by differential pulse voltammetry. Current variations were compared. The longer the sequence, the greater the decrease in current. The system's detection limit was estimated at 3.5 pM (0.07 fmol in 20 μL) with the 50-base length target and provided a dynamic detection range between 3.5 pM and 5 nM. Single mismatch detection showed a good level of sensitivity. The system was regenerated twice with no significant loss of Fc signal. Finally, 1 pM sensitivity was reached with a long chain analog of DNA PCR products of Influenza virus.

  1. A Small Stem Loop Structure Of The Ebola Virus Trailer Is Essential For Replication And Interacts With Heat Shock Protein A8

    Science.gov (United States)

    2016-12-02

    Nucleic Acids Research , 2016 1–15 doi: 10.1093/nar/gkw825 A small stem -loop structure of the Ebola virus trailer is essential for replication and...is a single- stranded RNA that is linked to a stem -loop, as found in the region of the replication promoter element of the EBOV genomic leader (18...Kuhn4, Gustavo Palacios3, Sheli R. Radoshitzky3, Stuart F. J. Le Grice1,* and Reed F. Johnson2,* 1RT Biochemistry Section, Basic Research Laboratory

  2. Phylogenetic relationships of Malaysia's pig-tailed macaque Macaca nemestrina based on D-loop region sequences

    Science.gov (United States)

    Abdul-Latiff M. A., B.; Ampeng, A.; Yaakop, S.; Md-Zain B., M.

    2014-09-01

    Phylogenetic relationships among Malaysian pig-tailed macaques have never been established even though the data are crucial in aiding conservation plan for the species. The aims of this study is to establish the phylogenetic relationships of Macaca nemestrina in Malaysia. A total of 21 genetic samples of M. nemestrina yielding 458 bp of D-loop sequences were used in phylogenetic analyses, in addition to one sample of M. fascicularis which was used as an outgroup. Sequence character analysis revealed that D-loop locus contains 23% parsimony informative character detected among the ingroups. Further analysis indicated a clear separation between populations originating from different regions; the Malay Peninsula populations are separated from Borneo Insular population; and Perak population formed a distinctive clade within Peninsular Malaysia populations. Phylogenetic trees (NJ, MP and Bayesian) portray a consistent clustering paradigm as Borneo population was distinguished from Peninsula population (100% bootstrap value in the NJ, MP, 1.00 posterior probability in Bayesian trees). Perak's population was separated from other Peninsula populations (100% in NJ, 99% in MP and 1.00 in Bayesian). D-loop region of mtDNA is proven to be a suitable locus in studying the separation of M. nemestrina at population level. These findings are crucial in aiding the conservation management and translocation process of M. fascicularis populations in Malaysia.

  3. Maternal phylogenetic relationships and genetic variation among Arabian horse populations using whole mitochondrial DNA D-loop sequencing.

    Science.gov (United States)

    Khanshour, Anas M; Cothran, Ernest Gus

    2013-09-13

    Maternal inheritance is an essential point in Arabian horse population genetics and strains classification. The mitochondrial DNA (mtDNA) sequencing is a highly informative tool to investigate maternal lineages. We sequenced the whole mtDNA D-loop of 251 Arabian horses to study the genetic diversity and phylogenetic relationships of Arabian populations and to examine the traditional strain classification system that depends on maternal family lines using native Arabian horses from the Middle East. The variability in the upstream region of the D-loop revealed additional differences among the haplotypes that had identical sequences in the hypervariable region 1 (HVR1). While the American-Arabians showed relatively low diversity, the Syrian population was the most variable and contained a very rare and old haplogroup. The Middle Eastern horses had major genetic contributions to the Western horses and there was no clear pattern of differentiation among all tested populations. Our results also showed that several individuals from different strains shared a single haplotype, and individuals from a single strain were represented in clearly separated haplogroups. The whole mtDNA D-loop sequence was more powerful for analysis of the maternal genetic diversity in the Arabian horses than using just the HVR1. Native populations from the Middle East, such as Syrians, could be suggested as a hot spot of genetic diversity and may help in understanding the evolution history of the Arabian horse breed. Most importantly, there was no evidence that the Arabian horse breed has clear subdivisions depending on the traditional maternal based strain classification system.

  4. Intraspecific variations in Cyt b and D-loop sequences of Testudine species, Lissemys punctata from south Karnataka

    Directory of Open Access Journals (Sweden)

    R. Lalitha

    2018-01-01

    Full Text Available The freshwater Testudine species have gained importance in recent years, as most of their population is threatened due to exploitation for delicacy and pet trade. In this regard, Lissemys punctata, a freshwater terrapin, predominantly distributed in Asian countries has gained its significance for the study. A pilot study report on mitochondrial markers (Cyt b and D-loop conducted on L. punctata species from southern Karnataka, India was presented in this investigation. A complete region spanning 1.14 kb and ∼1 kb was amplified by HotStart PCR and sequenced by Sanger sequencing. The Cyt b sequence revealed 85 substitution sites, no indels and 17 parsimony informative sites, whereas D-loop showed 189 variable sites, 51 parsimony informative sites with 5′ functional domains TAS, CSB-F, CSBs (1, 2, 3 preceding tandem repeat at 3′ end. Current data highlights the intraspecific variations in these target regions and variations validated using suitable evolutionary models points out that the overall point mutations observed in the region are transitions leading to no structural and functional alterations. The mitochondrial data generated uncover the genetic diversity within species and conservationist can utilize the data to estimate the effective population size or for forensic identification of animal or its seizures during unlawful trade activities.

  5. Sequence typing of adenovirus from samples from hematological stem cell transplant recipients.

    Science.gov (United States)

    Al Qurashi, Yasir Mohammed A; Guiver, Malcolm; Cooper, Robert J

    2011-11-01

    Adenovirus infections are usually mild or even asymptomatic, but infections with the virus are being recognized increasingly as a major cause of mortality and morbidity in the immunocompromised, particularly hematological stem cell transplant patients where infections can be life threatening and mortality may reach 60%. Typing by sequencing the HVR7 region of the hexon was established and validated using 60 isolates of different serotypes from the six of the seven species which had been typed previously by serum neutralization. Analysis of nucleotide sequences was used to type 227 samples from 41 hematological stem cell transplant recipients. Types from six species were detected but species C types were detected in 51.4% and species A in 34.3% of patients. Seven patients were infected with different adenovirus types sequentially and a further six patients had evidence of simultaneous multiple infections. Many of the sequences had several differences from the prototype strains which will allow tracing of outbreaks and provide evidence for cross-infection in a hospital setting. In this study, the phylogenetic analysis of adenovirus sequences from hematological stem cell transplant patients' samples showed evidence of two possible cross-infection incidents involving three and five patients, respectively. Copyright © 2011 Wiley-Liss, Inc.

  6. Molecular mechanisms for the regulation of histone mRNA stem-loop-binding protein by phosphorylation

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Jun; Tan, Dazhi; DeRose, Eugene F.; Perera, Lalith; Dominski, Zbigniew; Marzluff, William F.; Tong, Liang; Tanaka Hall, Traci M. [NIH; (UNC); (Columbia)

    2014-08-06

    Replication-dependent histone mRNAs end with a conserved stem loop that is recognized by stem-loop–binding protein (SLBP). The minimal RNA-processing domain of SLBP is phosphorylated at an internal threonine, and Drosophila SLBP (dSLBP) also is phosphorylated at four serines in its 18-aa C-terminal tail. We show that phosphorylation of dSLBP increases RNA-binding affinity dramatically, and we use structural and biophysical analyses of dSLBP and a crystal structure of human SLBP phosphorylated on the internal threonine to understand the striking improvement in RNA binding. Together these results suggest that, although the C-terminal tail of dSLBP does not contact the RNA, phosphorylation of the tail promotes SLBP conformations competent for RNA binding and thereby appears to reduce the entropic penalty for the association. Increased negative charge in this C-terminal tail balances positively charged residues, allowing a more compact ensemble of structures in the absence of RNA.

  7. Small, synthetic, GC-rich mRNA stem-loop modules 5' proximal to the AUG start-codon predictably tune gene expression in yeast.

    Science.gov (United States)

    Lamping, Erwin; Niimi, Masakazu; Cannon, Richard D

    2013-07-29

    A large range of genetic tools has been developed for the optimal design and regulation of complex metabolic pathways in bacteria. However, fewer tools exist in yeast that can precisely tune the expression of individual enzymes in novel metabolic pathways suitable for industrial-scale production of non-natural compounds. Tuning expression levels is critical for reducing the metabolic burden of over-expressed proteins, the accumulation of toxic intermediates, and for redirecting metabolic flux from native pathways involving essential enzymes without negatively affecting the viability of the host. We have developed a yeast membrane protein hyper-expression system with critical advantages over conventional, plasmid-based, expression systems. However, expression levels are sometimes so high that they adversely affect protein targeting/folding or the growth and/or phenotype of the host. Here we describe the use of small synthetic mRNA control modules that allowed us to predictably tune protein expression levels to any desired level. Down-regulation of expression was achieved by engineering small GC-rich mRNA stem-loops into the 5' UTR that inhibited translation initiation of the yeast ribosomal 43S preinitiation complex (PIC). Exploiting the fact that the yeast 43S PIC has great difficulty scanning through GC-rich mRNA stem-loops, we created yeast strains containing 17 different RNA stem-loop modules in the 5' UTR that expressed varying amounts of the fungal multidrug efflux pump reporter Cdr1p from Candida albicans. Increasing the length of mRNA stem-loops (that contained only GC-pairs) near the AUG start-codon led to a surprisingly large decrease in Cdr1p expression; ~2.7-fold for every additional GC-pair added to the stem, while the mRNA levels remained largely unaffected. An mRNA stem-loop of seven GC-pairs (∆G = -15.8 kcal/mol) reduced Cdr1p expression levels by >99%, and even the smallest possible stem-loop of only three GC-pairs (∆G = -4.4 kcal/mol) inhibited

  8. Small, synthetic, GC-rich mRNA stem-loop modules 5′ proximal to the AUG start-codon predictably tune gene expression in yeast

    Science.gov (United States)

    2013-01-01

    Background A large range of genetic tools has been developed for the optimal design and regulation of complex metabolic pathways in bacteria. However, fewer tools exist in yeast that can precisely tune the expression of individual enzymes in novel metabolic pathways suitable for industrial-scale production of non-natural compounds. Tuning expression levels is critical for reducing the metabolic burden of over-expressed proteins, the accumulation of toxic intermediates, and for redirecting metabolic flux from native pathways involving essential enzymes without negatively affecting the viability of the host. We have developed a yeast membrane protein hyper-expression system with critical advantages over conventional, plasmid-based, expression systems. However, expression levels are sometimes so high that they adversely affect protein targeting/folding or the growth and/or phenotype of the host. Here we describe the use of small synthetic mRNA control modules that allowed us to predictably tune protein expression levels to any desired level. Down-regulation of expression was achieved by engineering small GC-rich mRNA stem-loops into the 5′ UTR that inhibited translation initiation of the yeast ribosomal 43S preinitiation complex (PIC). Results Exploiting the fact that the yeast 43S PIC has great difficulty scanning through GC-rich mRNA stem-loops, we created yeast strains containing 17 different RNA stem-loop modules in the 5′ UTR that expressed varying amounts of the fungal multidrug efflux pump reporter Cdr1p from Candida albicans. Increasing the length of mRNA stem-loops (that contained only GC-pairs) near the AUG start-codon led to a surprisingly large decrease in Cdr1p expression; ~2.7-fold for every additional GC-pair added to the stem, while the mRNA levels remained largely unaffected. An mRNA stem-loop of seven GC-pairs (∆G = −15.8 kcal/mol) reduced Cdr1p expression levels by >99%, and even the smallest possible stem-loop of only three GC-pairs (

  9. Mitochondrial DNA D-loop sequence variation among 5 maternal lines of the Zemaitukai horse breed

    Directory of Open Access Journals (Sweden)

    E. Gus Cothran

    2005-12-01

    Full Text Available Genetic variation in Zemaitukai horses was investigated using mitochondrial DNA (mtDNA sequencing. The study was performed on 421 bp of the mitochondrial DNA control region, which is known to be more variable than other sections of the mitochondrial genome. Samples from each of the remaining maternal family lines of Zemaitukai horses and three random samples for other Lithuanian (Lithuanian Heavy Draught, Zemaitukai large type and ten European horse breeds were sequenced. Five distinct haplotypes were obtained for the five Zemaitukai maternal families supporting the pedigree data. The minimal difference between two different sequence haplotypes was 6 and the maximal 11 nucleotides in Zemaitukai horse breed. A total of 20 nucleotide differences compared to the reference sequence were found in Lithuanian horse breeds. Genetic cluster analysis did not shown any clear pattern of relationship among breeds of different type.

  10. Risk of Breast Cancer with CXCR4-using HIV Defined by V3-Loop Sequencing

    Science.gov (United States)

    Goedert, James J.; Swenson, Luke C.; Napolitano, Laura A.; Haddad, Mojgan; Anastos, Kathryn; Minkoff, Howard; Young, Mary; Levine, Alexandra; Adeyemi, Oluwatoyin; Seaberg, Eric C.; Aouizerat, Bradley; Rabkin, Charles S.; Harrigan, P. Richard; Hessol, Nancy A.

    2014-01-01

    Objective Evaluate the risk of female breast cancer associated with HIV-CXCR4 (X4) tropism as determined by various genotypic measures. Methods A breast cancer case-control study, with pairwise comparisons of tropism determination methods, was conducted. From the Women's Interagency HIV Study repository, one stored plasma specimen was selected from 25 HIV-infected cases near the breast cancer diagnosis date and 75 HIV-infected control women matched for age and calendar date. HIVgp120-V3 sequences were derived by Sanger population sequencing (PS) and 454-pyro deep sequencing (DS). Sequencing-based HIV-X4 tropism was defined using the geno2pheno algorithm, with both high-stringency DS [False-Positive-Rate (FPR 3.5) and 2% X4 cutoff], and lower stringency DS (FPR 5.75, 15% X4 cut-off). Concordance of tropism results by PS, DS, and previously performed phenotyping was assessed with kappa (κ) statistics. Case-control comparisons used exact P-values and conditional logistic regression. Results In 74 women (19 cases, 55 controls) with complete results, prevalence of HIV-X4 by PS was 5% in cases vs 29% in controls (P=0.06, odds ratio 0.14, confidence interval 0.003-1.03). Smaller case-control prevalence differences were found with high-stringency DS (21% vs 36%, P=0.32), lower-stringency DS (16% vs 35%, P=0.18), and phenotyping (11% vs 31%, P=0.10). HIV-X4-tropism concordance was best between PS and lower-stringency DS (93%, κ=0.83). Other pairwise concordances were 82%-92% (κ=0.56-0.81). Concordance was similar among cases and controls. Conclusions HIV-X4 defined by population sequencing (PS) had good agreement with lower stringency deep sequencing and was significantly associated with lower odds of breast cancer. PMID:25321183

  11. Visualization and correction of automated segmentation, tracking and lineaging from 5-D stem cell image sequences.

    Science.gov (United States)

    Wait, Eric; Winter, Mark; Bjornsson, Chris; Kokovay, Erzsebet; Wang, Yue; Goderie, Susan; Temple, Sally; Cohen, Andrew R

    2014-10-03

    Neural stem cells are motile and proliferative cells that undergo mitosis, dividing to produce daughter cells and ultimately generating differentiated neurons and glia. Understanding the mechanisms controlling neural stem cell proliferation and differentiation will play a key role in the emerging fields of regenerative medicine and cancer therapeutics. Stem cell studies in vitro from 2-D image data are well established. Visualizing and analyzing large three dimensional images of intact tissue is a challenging task. It becomes more difficult as the dimensionality of the image data increases to include time and additional fluorescence channels. There is a pressing need for 5-D image analysis and visualization tools to study cellular dynamics in the intact niche and to quantify the role that environmental factors play in determining cell fate. We present an application that integrates visualization and quantitative analysis of 5-D (x,y,z,t,channel) and large montage confocal fluorescence microscopy images. The image sequences show stem cells together with blood vessels, enabling quantification of the dynamic behaviors of stem cells in relation to their vascular niche, with applications in developmental and cancer biology. Our application automatically segments, tracks, and lineages the image sequence data and then allows the user to view and edit the results of automated algorithms in a stereoscopic 3-D window while simultaneously viewing the stem cell lineage tree in a 2-D window. Using the GPU to store and render the image sequence data enables a hybrid computational approach. An inference-based approach utilizing user-provided edits to automatically correct related mistakes executes interactively on the system CPU while the GPU handles 3-D visualization tasks. By exploiting commodity computer gaming hardware, we have developed an application that can be run in the laboratory to facilitate rapid iteration through biological experiments. We combine unsupervised image

  12. Estrogen Repression of MicroRNAs Is Associated with High Guanine Content in the Terminal Loop Sequences of Their Precursors

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    Amit Cohen

    2017-08-01

    Full Text Available Widespread microRNA (miRNA repression is a phenomenon observed in mammals after exposure to cigarette smoke and in many types of cancer. A comprehensive reduction in miRNA expression after treatment with the hormone estrogen has also previously been described. Here, we reveal a conserved association of miRNA downregulation after estrogen exposure in zebrafish, mouse, and human breast cancer cell line, with a high guanine content in the terminal loop sequences of their precursors, and offer a possible link between estrogen-related miRNA-adducts formation and carcinogenesis. We also show common gene expression patterns shared by breast cancer tumors and estrogen-treated zebrafish, suggesting that this organism can be used as a powerful model system for the study of human breast cancer.

  13. A single nucleotide in stem loop II of 5'-untranslated region contributes to virulence of enterovirus 71 in mice.

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    Ming-Te Yeh

    Full Text Available BACKGROUND: Enterovirus 71 (EV71 has emerged as a neuroinvasive virus responsible for several large outbreaks in the Asia-Pacific region while virulence determinant remains unexplored. PRINCIPAL FINDINGS: In this report, we investigated increased virulence of unadapted EV71 clinical isolate 237 as compared with isolate 4643 in mice. A fragment 12 nucleotides in length in stem loop (SL II of 237 5'-untranslated region (UTR visibly reduced survival time and rate in mice was identified by constructing a series of infectious clones harboring chimeric 5'-UTR. In cells transfected with bicistronic plasmids, and replicon RNAs, the 12-nt fragment of isolate 237 enhanced translational activities and accelerated replication of subgenomic EV71. Finally, single nucleotide change from cytosine to uridine at base 158 in this short fragment of 5'-UTR was proven to reduce viral translation and EV71 virulence in mice. Results collectively indicated a pivotal role of novel virulence determinant C158 on virus translation in vitro and EV71 virulence in vivo. CONCLUSIONS: These results presented the first reported virulence determinant in EV71 5'-UTR and first position discovered from unadapted isolates.

  14. Mitochondrial D-loop sequences reveal a mixture of endemism and immigration in Egyptian goat populations.

    Science.gov (United States)

    Ahmed, Sahar; Grobler, Paul; Madisha, Thabang; Kotze, Antionette

    2017-09-01

    The mitochondrial D-loop region was used to investigate genetic diversity within and between populations of Egyptian goats, to elucidate processes that explain present patterns of diversity and differentiation and to characterize Egyptian goats relative to international breeds. A total of 120 animals from six populations were sampled. Results confirm the main trend from previous studies of mtDNA diversity in goats, with high levels of diversity within populations, but with a comparative lack of genetic structure supporting geographic distribution. Haplotype diversity varied in a narrow range whereas nucleotide diversity values were more informative in showing differences between populations. The majority of goats analyzed (93.2%) displayed haplotypes that group with Haplogroup A, the most common type found in global goat populations. The remaining animals grouped with the less common Haplogroup G. Population differentiation analysis showed some uniqueness in the Aswan and Sharkawi populations from the South and East of Egypt. Overall, the structure of the Egyptian goat population is characterized by a high degree of homogeneity among populations from the north-western coastal region, the Nile Delta and the upper and middle regions of the Nile valley, but with possible introgression of rarer haplotypes into populations at the southern and eastern extremities of the country.

  15. Amino acid substitutions in subunit 9 of the mitochondrial ATPase complex of Saccharomyces cerevisiae. Sequence analysis of a series of revertants of an oli1 mit- mutant carrying an amino acid substitution in the hydrophilic loop of subunit 9.

    Science.gov (United States)

    Willson, T A; Nagley, P

    1987-09-01

    This work concerns a biochemical genetic study of subunit 9 of the mitochondrial ATPase complex of Saccharomyces cerevisiae. Subunit 9, encoded by the mitochondrial oli1 gene, contains a hydrophilic loop connecting two transmembrane stems. In one particular oli1 mit- mutant 2422, the substitution of a positively charged amino acid in this loop (Arg39----Met) renders the ATPase complex non-functional. A series of 20 revertants, selected for their ability to grow on nonfermentable substrates, has been isolated from mutant 2422. The results of DNA sequence analysis of the oli1 gene in each revertant have led to the recognition of three groups of revertants. Class I revertants have undergone a same-site reversion event: the mutant Met39 is replaced either by arginine (as in wild-type) or lysine. Class II revertants maintain the mutant Met39 residue, but have undergone a second-site reversion event (Asn35----Lys). Two revertants showing an oligomycin-resistant phenotype carry this same second-site reversion in the loop region together with a further amino acid substitution in either of the two membrane-spanning segments of subunit 9 (either Gly23----Ser or Leu53----Phe). Class III revertants contain subunit 9 with the original mutant 2422 sequence, and additionally carry a recessive nuclear suppressor, demonstrated to represent a single gene. The results on the revertants in classes I and II indicate that there is a strict requirement for a positively charged residue in the hydrophilic loop close to the boundary of the lipid bilayer. The precise location of this positive charge is less stringent; in functional ATPase complexes it can be found at either residue 39 or 35. This charged residue is possibly required to interact with some other component of the mitochondrial ATPase complex. These findings, together with hydropathy plots of subunit 9 polypeptides from normal, mutant and revertant strains, led to the conclusion that the hydrophilic loop in normal subunit 9

  16. Mutation of mapped TIA-1/TIAR binding sites in the 3' terminal stem-loop of West Nile virus minus-strand RNA in an infectious clone negatively affects genomic RNA amplification.

    Science.gov (United States)

    Emara, Mohamed M; Liu, Hsuan; Davis, William G; Brinton, Margo A

    2008-11-01

    Previous data showed that the cellular proteins TIA-1 and TIAR bound specifically to the West Nile virus 3' minus-strand stem-loop [WNV3'(-)SL] RNA (37) and colocalized with flavivirus replication complexes in WNV- and dengue virus-infected cells (21). In the present study, the sites on the WNV3'(-)SL RNA required for efficient in vitro T-cell intracellular antigen-related (TIAR) and T-cell intracellular antigen-1 (TIA-1) protein binding were mapped to short AU sequences (UAAUU) located in two internal loops of the WNV3'(-)SL RNA structure. Infectious clone RNAs with all or most of the binding site nucleotides in one of the 3' (-)SL loops deleted or substituted did not produce detectable virus after transfection or subsequent passage. With one exception, deletion/mutation of a single terminal nucleotide in one of the binding sequences had little effect on the efficiency of protein binding or virus production, but mutation of a nucleotide in the middle of a binding sequence reduced both the in vitro protein binding efficiency and virus production. Plaque size, intracellular genomic RNA levels, and virus production progressively decreased with decreasing in vitro TIAR/TIA-1 binding activity, but the translation efficiency of the various mutant RNAs was similar to that of the parental RNA. Several of the mutant RNAs that inefficiently interacted with TIAR/TIA-1 in vitro rapidly reverted in vivo, indicating that they could replicate at a low level and suggesting that an interaction between TIAR/TIA-1 and the viral 3'(-)SL RNA is not required for initial low-level symmetric RNA replication but instead facilitates the subsequent asymmetric amplification of genome RNA from the minus-strand template.

  17. Draft Genome Sequence of the Phytopathogenic Fungus Ganoderma boninense, the Causal Agent of Basal Stem Rot Disease on Oil Palm.

    Science.gov (United States)

    Utomo, Condro; Tanjung, Zulfikar Achmad; Aditama, Redi; Buana, Rika Fithri Nurani; Pratomo, Antonius Dony Madu; Tryono, Reno; Liwang, Tony

    2018-04-26

    Ganoderma boninense is the dominant fungal pathogen of basal stem rot (BSR) disease on Elaeis guineensis We sequenced the nuclear genome of mycelia using both Illumina and Pacific Biosciences platforms for assembly of scaffolds. The draft genome comprised 79.24 Mb, 495 scaffolds, and 26,226 predicted coding sequences. Copyright © 2018 Utomo et al.

  18. Genetic Diversity and Phylogenetic Evolution of Tibetan Sheep Based on mtDNA D-Loop Sequences.

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    Jianbin Liu

    Full Text Available The molecular and population genetic evidence of the phylogenetic status of the Tibetan sheep (Ovis aries is not well understood, and little is known about this species' genetic diversity. This knowledge gap is partly due to the difficulty of sample collection. This is the first work to address this question. Here, the genetic diversity and phylogenetic relationship of 636 individual Tibetan sheep from fifteen populations were assessed using 642 complete sequences of the mitochondrial DNA D-loop. Samples were collected from the Qinghai-Tibetan Plateau area in China, and reference data were obtained from the six reference breed sequences available in GenBank. The length of the sequences varied considerably, between 1031 and 1259 bp. The haplotype diversity and nucleotide diversity were 0.992±0.010 and 0.019±0.001, respectively. The average number of nucleotide differences was 19.635. The mean nucleotide composition of the 350 haplotypes was 32.961% A, 29.708% T, 22.892% C, 14.439% G, 62.669% A+T, and 37.331% G+C. Phylogenetic analysis showed that all four previously defined haplogroups (A, B, C, and D were found in the 636 individuals of the fifteen Tibetan sheep populations but that only the D haplogroup was found in Linzhou sheep. Further, the clustering analysis divided the fifteen Tibetan sheep populations into at least two clusters. The estimation of the demographic parameters from the mismatch analyses showed that haplogroups A, B, and C had at least one demographic expansion in Tibetan sheep. These results contribute to the knowledge of Tibetan sheep populations and will help inform future conservation programs about the Tibetan sheep native to the Qinghai-Tibetan Plateau.

  19. The nematode eukaryotic translation initiation factor 4E/G complex works with a trans-spliced leader stem-loop to enable efficient translation of trimethylguanosine-capped RNAs.

    Science.gov (United States)

    Wallace, Adam; Filbin, Megan E; Veo, Bethany; McFarland, Craig; Stepinski, Janusz; Jankowska-Anyszka, Marzena; Darzynkiewicz, Edward; Davis, Richard E

    2010-04-01

    Eukaryotic mRNA translation begins with recruitment of the 40S ribosome complex to the mRNA 5' end through the eIF4F initiation complex binding to the 5' m(7)G-mRNA cap. Spliced leader (SL) RNA trans splicing adds a trimethylguanosine (TMG) cap and a sequence, the SL, to the 5' end of mRNAs. Efficient translation of TMG-capped mRNAs in nematodes requires the SL sequence. Here we define a core set of nucleotides and a stem-loop within the 22-nucleotide nematode SL that stimulate translation of mRNAs with a TMG cap. The structure and core nucleotides are conserved in other nematode SLs and correspond to regions of SL1 required for early Caenorhabditis elegans development. These SL elements do not facilitate translation of m(7)G-capped RNAs in nematodes or TMG-capped mRNAs in mammalian or plant translation systems. Similar stem-loop structures in phylogenetically diverse SLs are predicted. We show that the nematode eukaryotic translation initiation factor 4E/G (eIF4E/G) complex enables efficient translation of the TMG-SL RNAs in diverse in vitro translation systems. TMG-capped mRNA translation is determined by eIF4E/G interaction with the cap and the SL RNA, although the SL does not increase the affinity of eIF4E/G for capped RNA. These results suggest that the mRNA 5' untranslated region (UTR) can play a positive and novel role in translation initiation through interaction with the eIF4E/G complex in nematodes and raise the issue of whether eIF4E/G-RNA interactions play a role in the translation of other eukaryotic mRNAs.

  20. The Nematode Eukaryotic Translation Initiation Factor 4E/G Complex Works with a trans-Spliced Leader Stem-Loop To Enable Efficient Translation of Trimethylguanosine-Capped RNAs ▿ †

    Science.gov (United States)

    Wallace, Adam; Filbin, Megan E.; Veo, Bethany; McFarland, Craig; Stepinski, Janusz; Jankowska-Anyszka, Marzena; Darzynkiewicz, Edward; Davis, Richard E.

    2010-01-01

    Eukaryotic mRNA translation begins with recruitment of the 40S ribosome complex to the mRNA 5′ end through the eIF4F initiation complex binding to the 5′ m7G-mRNA cap. Spliced leader (SL) RNA trans splicing adds a trimethylguanosine (TMG) cap and a sequence, the SL, to the 5′ end of mRNAs. Efficient translation of TMG-capped mRNAs in nematodes requires the SL sequence. Here we define a core set of nucleotides and a stem-loop within the 22-nucleotide nematode SL that stimulate translation of mRNAs with a TMG cap. The structure and core nucleotides are conserved in other nematode SLs and correspond to regions of SL1 required for early Caenorhabditis elegans development. These SL elements do not facilitate translation of m7G-capped RNAs in nematodes or TMG-capped mRNAs in mammalian or plant translation systems. Similar stem-loop structures in phylogenetically diverse SLs are predicted. We show that the nematode eukaryotic translation initiation factor 4E/G (eIF4E/G) complex enables efficient translation of the TMG-SL RNAs in diverse in vitro translation systems. TMG-capped mRNA translation is determined by eIF4E/G interaction with the cap and the SL RNA, although the SL does not increase the affinity of eIF4E/G for capped RNA. These results suggest that the mRNA 5′ untranslated region (UTR) can play a positive and novel role in translation initiation through interaction with the eIF4E/G complex in nematodes and raise the issue of whether eIF4E/G-RNA interactions play a role in the translation of other eukaryotic mRNAs. PMID:20154140

  1. Hepatitis B virus nuclear export elements: RNA stem-loop α and β, key parts of the HBV post-transcriptional regulatory element.

    Science.gov (United States)

    Lim, Chun Shen; Brown, Chris M

    2016-09-01

    Many viruses contain RNA elements that modulate splicing and/or promote nuclear export of their RNAs. The RNAs of the major human pathogen, hepatitis B virus (HBV) contain a large (~600 bases) composite cis-acting 'post-transcriptional regulatory element' (PRE). This element promotes expression from these naturally intronless transcripts. Indeed, the related woodchuck hepadnavirus PRE (WPRE) is used to enhance expression in gene therapy and other expression vectors. These PRE are likely to act through a combination of mechanisms, including promotion of RNA nuclear export. Functional components of both the HBV PRE and WPRE are 2 conserved RNA cis-acting stem-loop (SL) structures, SLα and SLβ. They are within the coding regions of polymerase (P) gene, and both P and X genes, respectively. Based on previous studies using mutagenesis and/or nuclear magnetic resonance (NMR), here we propose 2 covariance models for SLα and SLβ. The model for the 30-nucleotide SLα contains a G-bulge and a CNGG(U) apical loop of which the first and the fourth loop residues form a CG pair and the fifth loop residue is bulged out, as observed in the NMR structure. The model for the 23-nucleotide SLβ contains a 7-base-pair stem and a 9-nucleotide loop. Comparison of the models with other RNA structural elements, as well as similarity searches of human transcriptome and viral genomes demonstrate that SLα and SLβ are specific to HBV transcripts. However, they are well conserved among the hepadnaviruses of non-human primates, the woodchuck and ground squirrel.

  2. Phylogenetic relationships of Scomberomorus commerson using sequence analysis of the mtDNA D-loop region in the Persian Gulf, Oman Sea and Arabian Sea

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    Ana Mansourkiaei

    2016-04-01

    Full Text Available Abstract Narrow-barred Spanish mackerel, Scomberomorus commerson, is an epipelagic and migratory species of family Scombridae which have a significant role in terms of ecology and fishery. 100 samples were collected from the Persian Gulf, Oman Sea and Arabian Sea. Part of their dorsal fins was snipped and transferred to micro-tubes containing ethanol; then, DNAs were extracted and HRM-Real Time PCR was performed to designate representative specimens for sequencing. Phylogenetic relationships of S. commerson from Persian Gulf, Oman Sea and Arabian Sea were investigated using sequence data of mitochondrial DNA D-loop region. None clustered Neighbor Joining tree indicated the proximity amid S. commerson in four sites. As numbers demonstrated in sequence analyses of mitochondrial DNA D-Loop region a sublimely high degree of genetic similarity among S. commerson from the Persian Gulf and Oman Sea were perceived, thereafter, having one stock structure of S. commerson in four regions were proved, and this approximation can be merely justified by their migration process along the coasts of Oman Sea and Persian Gulf. Therefore, the assessment of distribution patterns of 20 haplotypes in the constructed phylogenetic tree using mtDNA D-Loop sequences ascertained that no significant clustering according to the sampling sites was concluded.

  3. The helix-loop-helix protein id1 controls stem cell proliferation during regenerative neurogenesis in the adult zebrafish telencephalon.

    Science.gov (United States)

    Rodriguez Viales, Rebecca; Diotel, Nicolas; Ferg, Marco; Armant, Olivier; Eich, Julia; Alunni, Alessandro; März, Martin; Bally-Cuif, Laure; Rastegar, Sepand; Strähle, Uwe

    2015-03-01

    The teleost brain has the remarkable ability to generate new neurons and to repair injuries during adult life stages. Maintaining life-long neurogenesis requires careful management of neural stem cell pools. In a genome-wide expression screen for transcription regulators, the id1 gene, encoding a negative regulator of E-proteins, was found to be upregulated in response to injury. id1 expression was mapped to quiescent type I neural stem cells in the adult telencephalic stem cell niche. Gain and loss of id1 function in vivo demonstrated that Id1 promotes stem cell quiescence. The increased id1 expression observed in neural stem cells in response to injury appeared independent of inflammatory signals, suggesting multiple antagonistic pathways in the regulation of reactive neurogenesis. Together, we propose that Id1 acts to maintain the neural stem cell pool by counteracting neurogenesis-promoting signals. © 2014 AlphaMed Press.

  4. Systematic identification of cis-regulatory sequences active in mouse and human embryonic stem cells.

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    Marica Grskovic

    2007-08-01

    Full Text Available Understanding the transcriptional regulation of pluripotent cells is of fundamental interest and will greatly inform efforts aimed at directing differentiation of embryonic stem (ES cells or reprogramming somatic cells. We first analyzed the transcriptional profiles of mouse ES cells and primordial germ cells and identified genes upregulated in pluripotent cells both in vitro and in vivo. These genes are enriched for roles in transcription, chromatin remodeling, cell cycle, and DNA repair. We developed a novel computational algorithm, CompMoby, which combines analyses of sequences both aligned and non-aligned between different genomes with a probabilistic segmentation model to systematically predict short DNA motifs that regulate gene expression. CompMoby was used to identify conserved overrepresented motifs in genes upregulated in pluripotent cells. We show that the motifs are preferentially active in undifferentiated mouse ES and embryonic germ cells in a sequence-specific manner, and that they can act as enhancers in the context of an endogenous promoter. Importantly, the activity of the motifs is conserved in human ES cells. We further show that the transcription factor NF-Y specifically binds to one of the motifs, is differentially expressed during ES cell differentiation, and is required for ES cell proliferation. This study provides novel insights into the transcriptional regulatory networks of pluripotent cells. Our results suggest that this systematic approach can be broadly applied to understanding transcriptional networks in mammalian species.

  5. Population genetic structure of skipjack tuna Katsuwonus pelamis from the Indian coast using sequence analysis of the mitochondrial DNA D-loop region

    Digital Repository Service at National Institute of Oceanography (India)

    Menezes, M.R.; Kumar, G.; Kunal, S.P.

    Biology (2012) 80, 2198–2212 doi:10.1111/j.1095-8649.2012.03270.x, available online at wileyonlinelibrary.com Population genetic structure of skipjack tuna Katsuwonus pelamis from the Indian coast using sequence analysis of the mitochondrial DNA D...-loop region M. R. Menezes*, G. Kumar and S. P. Kunal Biological Oceanography Division, National Institute of Oceanography (CSIR), Dona Paula, Goa 403 004, India (Received 26 May 2011, Accepted 14 February 2012) Genetic structure of skipjack tuna Katsuwonus...

  6. Three genetic stocks of frigate tuna Auxis thazard thazard (Lacepede, 1800) along the Indian coast revealed from sequence analyses of mitochondrial DNA D-loop region

    Digital Repository Service at National Institute of Oceanography (India)

    GirishKumar; Kunal, S.P.; Menezes, M.R.; Meena, R.M.

    revealed from sequence analyses of mitochondrial DNA D-loop region Name of authors: 1. Girish Kumar* Biological Oceanography Division (BOD) National Institute of Oceanography (NIO) Dona Paula, Goa 403004, India. Email: girishkumar....nio@gmail.com Tel: +919766548060 2. Swaraj Priyaranjan Kunal Biological Oceanography Division (BOD) National Institute of Oceanography (NIO) Dona Paula, Goa 403004, India. Email: swar.mbt@gmail.com 3. Maria Rosalia Menezes Biological Oceanography...

  7. A small stem-loop structure of the Ebola virus trailer is essential for replication and interacts with heat-shock protein A8.

    Science.gov (United States)

    Sztuba-Solinska, Joanna; Diaz, Larissa; Kumar, Mia R; Kolb, Gaëlle; Wiley, Michael R; Jozwick, Lucas; Kuhn, Jens H; Palacios, Gustavo; Radoshitzky, Sheli R; J Le Grice, Stuart F; Johnson, Reed F

    2016-11-16

    Ebola virus (EBOV) is a single-stranded negative-sense RNA virus belonging to the Filoviridae family. The leader and trailer non-coding regions of the EBOV genome likely regulate its transcription, replication, and progeny genome packaging. We investigated the cis-acting RNA signals involved in RNA-RNA and RNA-protein interactions that regulate replication of eGFP-encoding EBOV minigenomic RNA and identified heat shock cognate protein family A (HSC70) member 8 (HSPA8) as an EBOV trailer-interacting host protein. Mutational analysis of the trailer HSPA8 binding motif revealed that this interaction is essential for EBOV minigenome replication. Selective 2'-hydroxyl acylation analyzed by primer extension analysis of the secondary structure of the EBOV minigenomic RNA indicates formation of a small stem-loop composed of the HSPA8 motif, a 3' stem-loop (nucleotides 1868-1890) that is similar to a previously identified structure in the replicative intermediate (RI) RNA and a panhandle domain involving a trailer-to-leader interaction. Results of minigenome assays and an EBOV reverse genetic system rescue support a role for both the panhandle domain and HSPA8 motif 1 in virus replication. Published by Oxford University Press on behalf of Nucleic Acids Research 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

  8. Alternative Mode of E-Site tRNA Binding in the Presence of a Downstream mRNA Stem Loop at the Entrance Channel.

    Science.gov (United States)

    Zhang, Yan; Hong, Samuel; Ruangprasert, Ajchareeya; Skiniotis, Georgios; Dunham, Christine M

    2018-03-06

    Structured mRNAs positioned downstream of the ribosomal decoding center alter gene expression by slowing protein synthesis. Here, we solved the cryo-EM structure of the bacterial ribosome bound to an mRNA containing a 3' stem loop that regulates translation. Unexpectedly, the E-site tRNA adopts two distinct orientations. In the first structure, normal interactions with the 50S and 30S E site are observed. However, in the second structure, although the E-site tRNA makes normal interactions with the 50S E site, its anticodon stem loop moves ∼54 Å away from the 30S E site to interact with the 30S head domain and 50S uL5. This position of the E-site tRNA causes the uL1 stalk to adopt a more open conformation that likely represents an intermediate state during E-site tRNA dissociation. These results suggest that structured mRNAs at the entrance channel restrict 30S subunit movement required during translation to slow E-site tRNA dissociation. Copyright © 2018 Elsevier Ltd. All rights reserved.

  9. Identification of sequence polymorphisms in the D-Loop region of mitochondrial DNA as a risk factor for colon cancer.

    Science.gov (United States)

    Guo, Zhanjun; Zhao, Shengnan; Fan, Haiyan; Du, Yanming; Zhao, Yufei; Wang, Guiying

    2016-11-01

    The accumulation of single nucleotide polymorphisms (SNPs) in the displacement loop (D-Loop) of mitochondrial DNA (mtDNA) has been identified for their association with cancer risk in a number of cancers. We investigated the colon cancer risk profile of D-Loop SNPs in a case-control study. The frequent alleles of nucleotides 73G/A, 146T/C, 195T/C, 324C/G, 16261C/T, and 16304T/C as well as the minor allele of 309C/C insert were significantly associated with an increased risk for colon cancer. In conclusion, SNPs in the mtDNA D-Loop were found to be valuable markers for colon cancer risk evaluation.

  10. Gene expression profiling of liver cancer stem cells by RNA-sequencing.

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    David W Y Ho

    Full Text Available BACKGROUND: Accumulating evidence supports that tumor growth and cancer relapse are driven by cancer stem cells. Our previous work has demonstrated the existence of CD90(+ liver cancer stem cells (CSCs in hepatocellular carcinoma (HCC. Nevertheless, the characteristics of these cells are still poorly understood. In this study, we employed a more sensitive RNA-sequencing (RNA-Seq to compare the gene expression profiling of CD90(+ cells sorted from tumor (CD90(+CSCs with parallel non-tumorous liver tissues (CD90(+NTSCs and elucidate the roles of putative target genes in hepatocarcinogenesis. METHODOLOGY/PRINCIPAL FINDINGS: CD90(+ cells were sorted respectively from tumor and adjacent non-tumorous human liver tissues using fluorescence-activated cell sorting. The amplified RNAs of CD90(+ cells from 3 HCC patients were subjected to RNA-Seq analysis. A differential gene expression profile was established between CD90(+CSCs and CD90(+NTSCs, and validated by quantitative real-time PCR (qRT-PCR on the same set of amplified RNAs, and further confirmed in an independent cohort of 12 HCC patients. Five hundred genes were differentially expressed (119 up-regulated and 381 down-regulated genes between CD90(+CSCs and CD90(+NTSCs. Gene ontology analysis indicated that the over-expressed genes in CD90(+CSCs were associated with inflammation, drug resistance and lipid metabolism. Among the differentially expressed genes, glypican-3 (GPC3, a member of glypican family, was markedly elevated in CD90(+CSCs compared to CD90(+NTSCs. Immunohistochemistry demonstrated that GPC3 was highly expressed in forty-two human liver tumor tissues but absent in adjacent non-tumorous liver tissues. Flow cytometry indicated that GPC3 was highly expressed in liver CD90(+CSCs and mature cancer cells in liver cancer cell lines and human liver tumor tissues. Furthermore, GPC3 expression was positively correlated with the number of CD90(+CSCs in liver tumor tissues. CONCLUSIONS

  11. Gene Expression Profiling of Liver Cancer Stem Cells by RNA-Sequencing

    Science.gov (United States)

    Lam, Chi Tat; Ng, Michael N. P.; Yu, Wan Ching; Lau, Joyce; Wan, Timothy; Wang, Xiaoqi; Yan, Zhixiang; Liu, Hang; Fan, Sheung Tat

    2012-01-01

    Background Accumulating evidence supports that tumor growth and cancer relapse are driven by cancer stem cells. Our previous work has demonstrated the existence of CD90+ liver cancer stem cells (CSCs) in hepatocellular carcinoma (HCC). Nevertheless, the characteristics of these cells are still poorly understood. In this study, we employed a more sensitive RNA-sequencing (RNA-Seq) to compare the gene expression profiling of CD90+ cells sorted from tumor (CD90+CSCs) with parallel non-tumorous liver tissues (CD90+NTSCs) and elucidate the roles of putative target genes in hepatocarcinogenesis. Methodology/Principal Findings CD90+ cells were sorted respectively from tumor and adjacent non-tumorous human liver tissues using fluorescence-activated cell sorting. The amplified RNAs of CD90+ cells from 3 HCC patients were subjected to RNA-Seq analysis. A differential gene expression profile was established between CD90+CSCs and CD90+NTSCs, and validated by quantitative real-time PCR (qRT-PCR) on the same set of amplified RNAs, and further confirmed in an independent cohort of 12 HCC patients. Five hundred genes were differentially expressed (119 up-regulated and 381 down-regulated genes) between CD90+CSCs and CD90+NTSCs. Gene ontology analysis indicated that the over-expressed genes in CD90+CSCs were associated with inflammation, drug resistance and lipid metabolism. Among the differentially expressed genes, glypican-3 (GPC3), a member of glypican family, was markedly elevated in CD90+CSCs compared to CD90+NTSCs. Immunohistochemistry demonstrated that GPC3 was highly expressed in forty-two human liver tumor tissues but absent in adjacent non-tumorous liver tissues. Flow cytometry indicated that GPC3 was highly expressed in liver CD90+CSCs and mature cancer cells in liver cancer cell lines and human liver tumor tissues. Furthermore, GPC3 expression was positively correlated with the number of CD90+CSCs in liver tumor tissues. Conclusions/Significance The identified genes

  12. Hybrid Sequencing of Full-Length cDNA Transcripts of Stems and Leaves in Dendrobium officinale

    Directory of Open Access Journals (Sweden)

    Liu He

    2017-10-01

    Full Text Available Dendrobium officinale is an extremely valuable orchid used in traditional Chinese medicine, so sought after that it has a higher market value than gold. Although the expression profiles of some genes involved in the polysaccharide synthesis have previously been investigated, little research has been carried out on their alternatively spliced isoforms in D. officinale. In addition, information regarding the translocation of sugars from leaves to stems in D. officinale also remains limited. We analyzed the polysaccharide content of D. officinale leaves and stems, and completed in-depth transcriptome sequencing of these two diverse tissue types using second-generation sequencing (SGS and single-molecule real-time (SMRT sequencing technology. The results of this study yielded a digital inventory of gene and mRNA isoform expressions. A comparative analysis of both transcriptomes uncovered a total of 1414 differentially expressed genes, including 844 that were up-regulated and 570 that were down-regulated in stems. Of these genes, one sugars will eventually be exported transporter (SWEET and one sucrose transporter (SUT are expressed to a greater extent in D. officinale stems than in leaves. Two glycosyltransferase (GT and four cellulose synthase (Ces genes undergo a distinct degree of alternative splicing. In the stems, the content of polysaccharides is twice as much as that in the leaves. The differentially expressed GT and transcription factor (TF genes will be the focus of further study. The genes DoSWEET4 and DoSUT1 are significantly expressed in the stem, and are likely to be involved in sugar loading in the phloem.

  13. A Positive Regulatory Loop between a Wnt-Regulated Non-coding RNA and ASCL2 Controls Intestinal Stem Cell Fate.

    Science.gov (United States)

    Giakountis, Antonis; Moulos, Panagiotis; Zarkou, Vasiliki; Oikonomou, Christina; Harokopos, Vaggelis; Hatzigeorgiou, Artemis G; Reczko, Martin; Hatzis, Pantelis

    2016-06-21

    The canonical Wnt pathway plays a central role in stem cell maintenance, differentiation, and proliferation in the intestinal epithelium. Constitutive, aberrant activity of the TCF4/β-catenin transcriptional complex is the primary transforming factor in colorectal cancer. We identify a nuclear long non-coding RNA, termed WiNTRLINC1, as a direct target of TCF4/β-catenin in colorectal cancer cells. WiNTRLINC1 positively regulates the expression of its genomic neighbor ASCL2, a transcription factor that controls intestinal stem cell fate. WiNTRLINC1 interacts with TCF4/β-catenin to mediate the juxtaposition of its promoter with the regulatory regions of ASCL2. ASCL2, in turn, regulates WiNTRLINC1 transcriptionally, closing a feedforward regulatory loop that controls stem cell-related gene expression. This regulatory circuitry is highly amplified in colorectal cancer and correlates with increased metastatic potential and decreased patient survival. Our results uncover the interplay between non-coding RNA-mediated regulation and Wnt signaling and point to the diagnostic and therapeutic potential of WiNTRLINC1. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

  14. Intraspecific variations in Cyt b and D-loop sequences of Testudine species, Lissemys punctata from south Karnataka

    OpenAIRE

    R. Lalitha; V.R. Chandavar

    2018-01-01

    The freshwater Testudine species have gained importance in recent years, as most of their population is threatened due to exploitation for delicacy and pet trade. In this regard, Lissemys punctata, a freshwater terrapin, predominantly distributed in Asian countries has gained its significance for the study. A pilot study report on mitochondrial markers (Cyt b and D-loop) conducted on L. punctata species from southern Karnataka, India was presented in this investigation. A complete region span...

  15. Establishment and in-house validation of stem-loop RT PCR method for MicroRNA398 expression analysis

    Directory of Open Access Journals (Sweden)

    Timotijević Gordana S.

    2015-01-01

    Full Text Available MicroRNAs (miRNAs belong to the class of small non-coding RNAs which have important roles throughout development as well as in plant response to diverse environmental stresses. Some of plant miRNAs are essential for regulation and maintenance of nutritive homeostasis when nutrients are in excess or shortage comparing to optimal concentration for certain plant species. Better understanding of miRNAs functions implies development of efficient technology for profiling their gene expression. We set out to establish validate the methodology for miRNA gene expression analysis in cucumber grown under suboptimal mineral nutrient regimes, including iron deficiency. Reverse transcription by “stem-loop” primers in combination with Real time PCR method is one of potential approaches for quantification of miRNA gene expression. In this paper we presented a method for “stem loop” primer design specific for miR398, as well as reaction optimization and determination of Real time PCR efficiency. Proving the accuracy of this method was imperative as “stem loop” RT which consider separate transcription of target and endogenous control. The method was verified by comparison of the obtained data with results of miR398 expression achieved using a commercial kit based on simultaneous conversion of all RNAs in cDNAs. [Projekat Ministarstva nauke Republike Srbije, br. 173005 i br. ON-173028

  16. Strong transcription blockage mediated by R-loop formation within a G-rich homopurine-homopyrimidine sequence localized in the vicinity of the promoter.

    Science.gov (United States)

    Belotserkovskii, Boris P; Soo Shin, Jane Hae; Hanawalt, Philip C

    2017-06-20

    Guanine-rich (G-rich) homopurine-homopyrimidine nucleotide sequences can block transcription with an efficiency that depends upon their orientation, composition and length, as well as the presence of negative supercoiling or breaks in the non-template DNA strand. We report that a G-rich sequence in the non-template strand reduces the yield of T7 RNA polymerase transcription by more than an order of magnitude when positioned close (9 bp) to the promoter, in comparison to that for a distal (∼250 bp) location of the same sequence. This transcription blockage is much less pronounced for a C-rich sequence, and is not significant for an A-rich sequence. Remarkably, the blockage is not pronounced if transcription is performed in the presence of RNase H, which specifically digests the RNA strands within RNA-DNA hybrids. The blockage also becomes less pronounced upon reduced RNA polymerase concentration. Based upon these observations and those from control experiments, we conclude that the blockage is primarily due to the formation of stable RNA-DNA hybrids (R-loops), which inhibit successive rounds of transcription. Our results could be relevant to transcription dynamics in vivo (e.g. transcription 'bursting') and may also have practical implications for the design of expression vectors. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  17. Loop kinematics

    International Nuclear Information System (INIS)

    Migdal, A.A.

    1982-01-01

    Basic operators acting in the loop space are introduced. The topology of this space and properties of the Stokes type loop functionals are discussed. The parametrically invariant loop calculus developed here is used in the loop dynamics

  18. A Versatile Method to Design Stem-Loop Primer-Based Quantitative PCR Assays for Detecting Small Regulatory RNA Molecules

    OpenAIRE

    Czimmerer, Zsolt; Hulvely, Julianna; Simandi, Zoltan; Varallyay, Eva; Havelda, Zoltan; Szabo, Erzsebet; Varga, Attila; Dezso, Balazs; Balogh, Maria; Horvath, Attila; Domokos, Balint; Torok, Zsolt; Nagy, Laszlo; Balint, Balint L.

    2013-01-01

    Short regulatory RNA-s have been identified as key regulators of gene expression in eukaryotes. They have been involved in the regulation of both physiological and pathological processes such as embryonal development, immunoregulation and cancer. One of their relevant characteristics is their high stability, which makes them excellent candidates for use as biomarkers. Their number is constantly increasing as next generation sequencing methods reveal more and more details of their synthesis. T...

  19. MicroRNA sequence motifs reveal asymmetry between the stem arms

    DEFF Research Database (Denmark)

    Gorodkin, Jan; Havgaard, Jakob Hull; Ensterö, M.

    2006-01-01

    The processing of micro RNAs (miRNAs) from their stemloop precursor have revealed asymmetry in the processing of the mature and its star sequence. Furthermore, the miRNA processing system between organism differ. To assess this at the sequence level we have investigated mature miRNAs in their gen......The processing of micro RNAs (miRNAs) from their stemloop precursor have revealed asymmetry in the processing of the mature and its star sequence. Furthermore, the miRNA processing system between organism differ. To assess this at the sequence level we have investigated mature mi...

  20. Real-time sequence-validated loop-mediated isothermal amplification assays for detection of Middle East respiratory syndrome coronavirus (MERS-CoV.

    Directory of Open Access Journals (Sweden)

    Sanchita Bhadra

    Full Text Available The Middle East respiratory syndrome coronavirus (MERS-CoV, an emerging human coronavirus, causes severe acute respiratory illness with a 35% mortality rate. In light of the recent surge in reported infections we have developed asymmetric five-primer reverse transcription loop-mediated isothermal amplification (RT-LAMP assays for detection of MERS-CoV. Isothermal amplification assays will facilitate the development of portable point-of-care diagnostics that are crucial for management of emerging infections. The RT-LAMP assays are designed to amplify MERS-CoV genomic loci located within the open reading frame (ORF1a and ORF1b genes and upstream of the E gene. Additionally we applied one-step strand displacement probes (OSD for real-time sequence-specific verification of LAMP amplicons. Asymmetric amplification effected by incorporating a single loop primer in each assay accelerated the time-to-result of the OSD-RT-LAMP assays. The resulting assays could detect 0.02 to 0.2 plaque forming units (PFU (5 to 50 PFU/ml of MERS-CoV in infected cell culture supernatants within 30 to 50 min and did not cross-react with common human respiratory pathogens.

  1. Survival of hypoxic human mesenchymal stem cells is enhanced by a positive feedback loop involving miR-210 and hypoxia-inducible factor 1.

    Science.gov (United States)

    Chang, Woochul; Lee, Chang Youn; Park, Jun-Hee; Park, Moon-Seo; Maeng, Lee-So; Yoon, Chee Soon; Lee, Min Young; Hwang, Ki-Chul; Chung, Yong-An

    2013-01-01

    The use of mesenchymal stem cells (MSCs) has emerged as a potential new treatment for myocardial infarction. However, the poor viability of MSCs after transplantation critically limits the efficacy of this new strategy. The expression of microRNA-210 (miR-210) is induced by hypoxia and is important for cell survival under hypoxic conditions. Hypoxia increases the levels of hypoxia inducible factor-1 (HIF-1) protein and miR-210 in human MSCs (hMSCs). miR-210 positively regulates HIF-1α activity. Furthermore, miR-210 expression is also induced by hypoxia through the regulation of HIF-1α. To investigate the effect of miR-210 on hMSC survival under hypoxic conditions, survival rates along with signaling related to cell survival were evaluated in hMSCs over-expressing miR-210 or ones that lacked HIF-1α expression. Elevated miR-210 expression increased survival rates along with Akt and ERK activity in hMSCs with hypoxia. These data demonstrated that a positive feedback loop involving miR-210 and HIF-1α was important for MSC survival under hypoxic conditions.

  2. Development of a Low-Cost Stem-Loop Real-Time Quantification PCR Technique for EBV miRNA Expression Analysis.

    Science.gov (United States)

    Bergallo, Massimiliano; Merlino, Chiara; Montin, Davide; Galliano, Ilaria; Gambarino, Stefano; Mareschi, Katia; Fagioli, Franca; Montanari, Paola; Martino, Silvana; Tovo, Pier-Angelo

    2016-09-01

    MicroRNAs (miRNAs) are short, single stranded, non-coding RNA molecules. They are produced by many different species and are key regulators of several physiological processes. miRNAs are also encoded by the genomes of multiple virus families, such as herpesvirus family. In particular, miRNAs from Epstein Barr virus were found at high concentrations in different associated pathologies, such as Burkitt's lymphoma, Hodgkin disease, and nasopharyngeal carcinoma. Thanks to their stability, these molecules could possibly serve as biomarkers for EBV-associated diseases. In this study, a stem-loop real-time PCR for miR-BART2-5p, miR-BART15, and miR-BART22 EBV miRNAs detection and quantification has been developed. Evaluation of these miRNAs in 31 serum samples (12 from patients affected by primary immunodeficiency, 9 from X-linked agammaglobulinemia and 10 from healthy subjects) has been carried out. The amplification performance showed a wide dynamic range (10(8)-10(2) copies/reaction) and sensibility equal to 10(2) copies/reaction for all the target tested. Serum samples analysis, on the other hand, showed a statistical significant higher level of miR-BART22 in primary immunodeficiency patients (P = 0.0001) compared to other groups and targets. The results confirmed the potential use of this assay as a tool for monitoring EBV-associated disease and for miRNAs expression profile analysis.

  3. Phylogenetic and Genetic Analysis of D-loop and Cyt-b Region of mtDNA Sequence in Iranian Sistani, Sarabi and Brown Swiss Cows

    Directory of Open Access Journals (Sweden)

    reza valizadeh

    2016-06-01

    Full Text Available Cattle have an important role in primary human civilization, so molecular studies for more accurate recognition of their origin are effective to identify unknown historical aspects. Cattle can be divided in to 2 main groups including Bos Tuarus and Bos Indicus. Both types of cattle can be found in Iran; therefore study of their origin has particular importance. The aim of this study was to investigate the nucleotide sequences of Cytochrome-b (Cyt-b and HVR1&2 loci of D-loop gene region in mitochondrial DNA of Sistani, Sarabi and Brown Swiss breeds of cattle. Twenty blood samples of each breed, from non-relative individuals were obtained from blood bank of animal science department of Faculty of Agriculture, Ferdowsi University of Mashhad. The DNA content of sample was extracted based on the guanidinium thiocianate-silicagel method. Polymerase Chain Reaction with specific designed primers was performed to amplify Cyt-b and HVR 1&2 loci with 751 and 701 bp lengths, respectively. Sequencing of amplified Cyt-b and HVR 1&2 loci were done based on Sanger method by automatic sequencer machine (ABI 3130. Nucleotide diversity in Brown Swiss, Sarabi and Sistani breeds were estimated 0.0037, 0.0024 and 0.0029, respectively. Sequences of Cyt-b and HVR 1&2 were register in National Center for Biotechnology Institute due to nucleotide differences. Results of phylogenetic test using UPGMA for both loci showed that Sarabi and Sistani breeds are belonging to first group and Brown Swiss breed to other group.

  4. Sequence typing of human adenoviruses isolated from Polish patients subjected to allogeneic hematopoietic stem cell transplantation - a single center experience.

    Science.gov (United States)

    Przybylski, Maciej; Rynans, Sylwia; Waszczuk-Gajda, Anna; Bilinski, Jarosław; Basak, Grzegorz W; Jędrzejczak, Wiesław W; Wróblewska, Marta; Młynarczyk, Grażyna; Dzieciątkowski, Tomasz

    2018-03-28

    Human adenoviruses (HAdV) from species A, B and C are commonly recognized as pathogens causing severe morbidity and mortality in hematopoietic stem cell transplant (HSCT) recipients. The purpose of the present study was to determine HAdV types responsible for viremia in HSCT recipients at a large tertiary hospital in Poland. Analysis of partial nucleotide sequences of HAdV hexon gene was used to type 40 clinical isolates of HAdV obtained from 40 HSCT recipients. We identified six different HAdV serotypes belonging to species B, C and E. We demonstrated high variability in sequences of detected HAdV types, and patients infected with the same HAdV types were not hospitalized at the same time, which suggests the low possibility of cross-infection. In almost all patients, anti-HAdV antibodies in IgG class were detected, which indicates a history of HAdV infection in the past. Clinical symptoms accompanying HAdV viremia were in 89%, and in 61.5% of individuals, HAdV was a sole pathogen detected. There were no cases with high-level HAdV viremia and severe systemic or organ infections. Graft-versus-host disease (GvHD) was present in patients infected with species B and C, but grade II of GvHD was observed only in patients infected with HAdV-B. The predominance of HAdV-C and common presence of anti-HAdV antibodies in IgG class may strongly suggest that most infections in the present study were reactivations of HAdV persisting into the patient's mucosa-associated lymphoid tissues. Variability of HAdV sequences suggests that cross-infections between patients were very rare. GvHD: graft-versus-host disease; HAdV: human adenoviruses; HSCT: hematopoietic stem cell transplantation.

  5. A versatile method to design stem-loop primer-based quantitative PCR assays for detecting small regulatory RNA molecules.

    Directory of Open Access Journals (Sweden)

    Zsolt Czimmerer

    Full Text Available Short regulatory RNA-s have been identified as key regulators of gene expression in eukaryotes. They have been involved in the regulation of both physiological and pathological processes such as embryonal development, immunoregulation and cancer. One of their relevant characteristics is their high stability, which makes them excellent candidates for use as biomarkers. Their number is constantly increasing as next generation sequencing methods reveal more and more details of their synthesis. These novel findings aim for new detection methods for the individual short regulatory RNA-s in order to be able to confirm the primary data and characterize newly identified subtypes in different biological conditions. We have developed a flexible method to design RT-qPCR assays that are very sensitive and robust. The newly designed assays were tested extensively in samples from plant, mouse and even human formalin fixed paraffin embedded tissues. Moreover, we have shown that these assays are able to quantify endogenously generated shRNA molecules. The assay design method is freely available for anyone who wishes to use a robust and flexible system for the quantitative analysis of matured regulatory RNA-s.

  6. Current status of low power/shutdown PSA and accident sequence analysis for loss of RHR during mid-loop operation

    International Nuclear Information System (INIS)

    Park, Chang Kyu; Choi, Young; Kim, Tae Woon; Jin, Young Ho

    1994-07-01

    Probabilistic safety assessment (PSA) has been applied to only full-power operation of nuclear power plant (NPP), but some events which were recently occurred could reach severe plant damage state. Thus, various countries around the world have focused their interests on the evaluation for low power/shutdown (LP/S) operation. This report covers the main stream of LP/S PSA methodology, current status of LP/S PSA practices and results, and accident sequence analysis for loss of RHR during mid-loop operation. Therefore this report would be helpful for us to practice LP/S PSA for YGN 5,6 NPP which will be built in the near future. Also the results of accident sequence analysis show that operator's mis-diagnosis and failure of recovery action would initiate core damage during LP/S operation. In summary, overall environmental improvements (equipments, procedures, Tech Spec, etc, ...) and operating support system will be very useful to reduce risk during LP/S operation. (Author) 5 figs., 9 tabs

  7. Sequence comparison of the rDNA introns from six different species of Tetrahymena

    DEFF Research Database (Denmark)

    Nielsen, Henrik; Engberg, J

    1985-01-01

    model for the intron RNA of Cech et al. (Proc. Natl. Acad. Sci. U.S.A. 80, 3903 (83)). Most of the sequence variation in the four new sequences reported here is found in single stranded loops in the model. However, in four cases we found nucleotide substitutions in duplex stem regions, two of them...

  8. A sequence predicted to form a stem–loop is proposed to be required for formation of an RNA–protein complex involving the 3'UTR of beta-subunit F0F1-ATPase mRNA

    Czech Academy of Sciences Publication Activity Database

    Kramarova, T. V.; Antonická, Hana; Houštěk, Josef; Cannon, B.; Nedergaard, J.

    2008-01-01

    Roč. 1777, 7-8 (2008), s. 747-757 ISSN 0005-2728 R&D Projects: GA MZd(CZ) NR7790; GA MŠk(CZ) 1M0520 Grant - others:Univerzita Karlova(CZ) 97807 Institutional research plan: CEZ:AV0Z50110509 Keywords : ATPase * RNA-protein komplex * stem-loop secondary structure Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.447, year: 2008

  9. Evidence for an RNA pseudoknot loop-helix interaction essential for efficient -1 ribosomal frameshifting.

    Science.gov (United States)

    Liphardt, J; Napthine, S; Kontos, H; Brierley, I

    1999-05-07

    RNA pseudoknots are structural elements that participate in a variety of biological processes. At -1 ribosomal frameshifting sites, several types of pseudoknot have been identified which differ in their organisation and functionality. The pseudoknot found in infectious bronchitis virus (IBV) is typical of those that possess a long stem 1 of 11-12 bp and a long loop 2 (30-164 nt). A second group of pseudoknots are distinguishable that contain stems of only 5 to 7 bp and shorter loops. The NMR structure of one such pseudoknot, that of mouse mammary tumor virus (MMTV), has revealed that it is kinked at the stem 1-stem 2 junction, and that this kinked conformation is essential for efficient frameshifting. We recently investigated the effect on frameshifting of modulating stem 1 length and stability in IBV-based pseudoknots, and found that a stem 1 with at least 11 bp was needed for efficient frameshifting. Here, we describe the sequence manipulations that are necessary to bypass the requirement for an 11 bp stem 1 and to convert a short non-functional IBV-derived pseudoknot into a highly efficient, kinked frameshifter pseudoknot. Simple insertion of an adenine residue at the stem 1-stem 2 junction (an essential feature of a kinked pseudoknot) was not sufficient to create a functional pseudoknot. An additional change was needed: efficient frameshifting was recovered only when the last nucleotide of loop 2 was changed from a G to an A. The requirement for an A at the end of loop 2 is consistent with a loop-helix contact similar to those described in other RNA tertiary structures. A mutational analysis of both partners of the proposed interaction, the loop 2 terminal adenine residue and two G.C pairs near the top of stem 1, revealed that the interaction was essential for efficient frameshifting. The specific requirement for a 3'-terminal A residue was lost when loop 2 was increased from 8 to 14 nt, suggesting that the loop-helix contact may be required only in those

  10. Comparative analysis of transcriptomes in aerial stems and roots of Ephedra sinica based on high-throughput mRNA sequencing

    Directory of Open Access Journals (Sweden)

    Taketo Okada

    2016-12-01

    Full Text Available Ephedra plants are taxonomically classified as gymnosperms, and are medicinally important as the botanical origin of crude drugs and as bioresources that contain pharmacologically active chemicals. Here we show a comparative analysis of the transcriptomes of aerial stems and roots of Ephedra sinica based on high-throughput mRNA sequencing by RNA-Seq. De novo assembly of short cDNA sequence reads generated 23,358, 13,373, and 28,579 contigs longer than 200 bases from aerial stems, roots, or both aerial stems and roots, respectively. The presumed functions encoded by these contig sequences were annotated by BLAST (blastx. Subsequently, these contigs were classified based on gene ontology slims, Enzyme Commission numbers, and the InterPro database. Furthermore, comparative gene expression analysis was performed between aerial stems and roots. These transcriptome analyses revealed differences and similarities between the transcriptomes of aerial stems and roots in E. sinica. Deep transcriptome sequencing of Ephedra should open the door to molecular biological studies based on the entire transcriptome, tissue- or organ-specific transcriptomes, or targeted genes of interest.

  11. Cascade detection for the extraction of localized sequence features; specificity results for HIV-1 protease and structure-function results for the Schellman loop.

    Science.gov (United States)

    Newell, Nicholas E

    2011-12-15

    The extraction of the set of features most relevant to function from classified biological sequence sets is still a challenging problem. A central issue is the determination of expected counts for higher order features so that artifact features may be screened. Cascade detection (CD), a new algorithm for the extraction of localized features from sequence sets, is introduced. CD is a natural extension of the proportional modeling techniques used in contingency table analysis into the domain of feature detection. The algorithm is successfully tested on synthetic data and then applied to feature detection problems from two different domains to demonstrate its broad utility. An analysis of HIV-1 protease specificity reveals patterns of strong first-order features that group hydrophobic residues by side chain geometry and exhibit substantial symmetry about the cleavage site. Higher order results suggest that favorable cooperativity is weak by comparison and broadly distributed, but indicate possible synergies between negative charge and hydrophobicity in the substrate. Structure-function results for the Schellman loop, a helix-capping motif in proteins, contain strong first-order features and also show statistically significant cooperativities that provide new insights into the design of the motif. These include a new 'hydrophobic staple' and multiple amphipathic and electrostatic pair features. CD should prove useful not only for sequence analysis, but also for the detection of multifactor synergies in cross-classified data from clinical studies or other sources. Windows XP/7 application and data files available at: https://sites.google.com/site/cascadedetect/home. nacnewell@comcast.net Supplementary information is available at Bioinformatics online.

  12. a Sensor Aided H.264/AVC Video Encoder for Aerial Video Sequences with in the Loop Metadata Correction

    Science.gov (United States)

    Cicala, L.; Angelino, C. V.; Ruatta, G.; Baccaglini, E.; Raimondo, N.

    2015-08-01

    Unmanned Aerial Vehicles (UAVs) are often employed to collect high resolution images in order to perform image mosaicking and/or 3D reconstruction. Images are usually stored on board and then processed with on-ground desktop software. In such a way the computational load, and hence the power consumption, is moved on ground, leaving on board only the task of storing data. Such an approach is important in the case of small multi-rotorcraft UAVs because of their low endurance due to the short battery life. Images can be stored on board with either still image or video data compression. Still image system are preferred when low frame rates are involved, because video coding systems are based on motion estimation and compensation algorithms which fail when the motion vectors are significantly long and when the overlapping between subsequent frames is very small. In this scenario, UAVs attitude and position metadata from the Inertial Navigation System (INS) can be employed to estimate global motion parameters without video analysis. A low complexity image analysis can be still performed in order to refine the motion field estimated using only the metadata. In this work, we propose to use this refinement step in order to improve the position and attitude estimation produced by the navigation system in order to maximize the encoder performance. Experiments are performed on both simulated and real world video sequences.

  13. Romidepsin Used as Monotherapy in Sequence with Allogeneic Stem Cell Transplant in a Patient with Peripheral T-Cell Lymphoma

    Directory of Open Access Journals (Sweden)

    Nicholas Finn

    2014-01-01

    Full Text Available Despite advances in the field, a clear treatment algorithm for most peripheral T-cell lymphoma (PTCL subtypes remains to be defined. Generating reliable randomized data for this type of pathology remains a challenge because of the relative rarity of the disease and the heterogeneity of subtypes. Newer agents, such as the class-I selective histone deacetylase inhibitor romidepsin, have demonstrated efficacy and manageable toxicity in the relapsed and refractory setting. Whether novel agents should be used in conjunction with more conventional cytotoxic therapies or in sequence with a transplant strategy is unknown at this time. Here we report the successful use of romidepsin monotherapy as a bridge to allogeneic stem cell transplantation in a patient who had previously relapsed after several lines of conventional cytotoxic therapy for PTCL. Romidepsin provided the patient with sufficient disease control to proceed to transplantation while remaining in complete remission.

  14. LoopIng: a template-based tool for predicting the structure of protein loops.

    KAUST Repository

    Messih, Mario Abdel; Lepore, Rosalba; Tramontano, Anna

    2015-01-01

    ) and significant enhancements for long loops (11-20 residues). The quality of the predictions is robust to errors that unavoidably affect the stem regions when these are modeled. The method returns a confidence score for the predicted template loops and has

  15. Draft whole genome sequence of groundnut stem rot fungus Athelia rolfsii revealing genetic architect of its pathogenicity and virulence.

    Science.gov (United States)

    Iquebal, M A; Tomar, Rukam S; Parakhia, M V; Singla, Deepak; Jaiswal, Sarika; Rathod, V M; Padhiyar, S M; Kumar, Neeraj; Rai, Anil; Kumar, Dinesh

    2017-07-13

    Groundnut (Arachis hypogaea L.) is an important oil seed crop having major biotic constraint in production due to stem rot disease caused by fungus, Athelia rolfsii causing 25-80% loss in productivity. As chemical and biological combating strategies of this fungus are not very effective, thus genome sequencing can reveal virulence and pathogenicity related genes for better understanding of the host-parasite interaction. We report draft assembly of Athelia rolfsii genome of ~73 Mb having 8919 contigs. Annotation analysis revealed 16830 genes which are involved in fungicide resistance, virulence and pathogenicity along with putative effector and lethal genes. Secretome analysis revealed CAZY genes representing 1085 enzymatic genes, glycoside hydrolases, carbohydrate esterases, carbohydrate-binding modules, auxillary activities, glycosyl transferases and polysaccharide lyases. Repeat analysis revealed 11171 SSRs, LTR, GYPSY and COPIA elements. Comparative analysis with other existing ascomycotina genome predicted conserved domain family of WD40, CYP450, Pkinase and ABC transporter revealing insight of evolution of pathogenicity and virulence. This study would help in understanding pathogenicity and virulence at molecular level and development of new combating strategies. Such approach is imperative in endeavour of genome based solution in stem rot disease management leading to better productivity of groundnut crop in tropical region of world.

  16. Rapid authentication of the precious herb saffron by loop-mediated isothermal amplification (LAMP) based on internal transcribed spacer 2 (ITS2) sequence.

    Science.gov (United States)

    Zhao, Mingming; Shi, Yuhua; Wu, Lan; Guo, Licheng; Liu, Wei; Xiong, Chao; Yan, Song; Sun, Wei; Chen, Shilin

    2016-05-05

    Saffron is one of the most expensive species of Chinese herbs and has been subjected to various types of adulteration because of its high price and limited production. The present study introduces a loop-mediated isothermal amplification (LAMP) technique for the differentiation of saffron from its adulterants. This novel technique is sensitive, efficient and simple. Six specific LAMP primers were designed on the basis of the nucleotide sequence of the internal transcribed spacer 2 (ITS2) nuclear ribosomal DNA of Crocus sativus. All LAMP amplifications were performed successfully, and visual detection occurred within 60 min at isothermal conditions of 65 °C. The results indicated that the LAMP primers are accurate and highly specific for the discrimination of saffron from its adulterants. In particular, 10 fg of genomic DNA was determined to be the limit for template accuracy of LAMP in saffron. Thus, the proposed novel, simple, and sensitive LAMP assay is well suited for immediate on-site discrimination of herbal materials. Based on the study, a practical standard operating procedure (SOP) for utilizing the LAMP protocol for herbal authentication is provided.

  17. Polymerase chain reaction assay for verifying the labeling of meat and commercial meat products from game birds targeting specific sequences from the mitochondrial D-loop region.

    Science.gov (United States)

    Rojas, M; González, I; Pavón, M A; Pegels, N; Hernández, P E; García, T; Martín, R

    2010-05-01

    A PCR assay was developed for the identification of meats and commercial meat products from quail (Coturnix coturnix), pheasant (Phasianus colchicus), partridge (Alectoris spp.), guinea fowl (Numida meleagris), pigeon (Columba spp.), Eurasian woodcock (Scolopax rusticola), and song thrush (Turdus philomelos) based on oligonucleotide primers targeting specific sequences from the mitochondrial D-loop region. The primers designed generated specific fragments of 96, 100, 104, 106, 147, 127, and 154 bp in length for quail, pheasant, partridge, guinea fowl, pigeon, Eurasian woodcock, and song thrush tissues, respectively. The specificity of each primer pair was tested against DNA from various game and domestic species. In this work, satisfactory amplification was accomplished in the analysis of experimentally pasteurized (72 degrees C for 30 min) and sterilized (121 degrees C for 20 min) meats, as well as in commercial meat products from the target species. The technique was also applied to raw and sterilized muscular binary mixtures, with a detection limit of 0.1% (wt/wt) for each of the targeted species. The proposed PCR assay represents a rapid and straightforward method for the detection of possible mislabeling in game bird meat products.

  18. A Sequence in the loop domain of hepatitis C virus E2 protein identified in silico as crucial for the selective binding to human CD81.

    Directory of Open Access Journals (Sweden)

    Chun-Chun Chang

    Full Text Available Hepatitis C virus (HCV is a species-specific pathogenic virus that infects only humans and chimpanzees. Previous studies have indicated that interactions between the HCV E2 protein and CD81 on host cells are required for HCV infection. To determine the crucial factors for species-specific interactions at the molecular level, this study employed in silico molecular docking involving molecular dynamic simulations of the binding of HCV E2 onto human and rat CD81s. In vitro experiments including surface plasmon resonance measurements and cellular binding assays were applied for simple validations of the in silico results. The in silico studies identified two binding regions on the HCV E2 loop domain, namely E2-site1 and E2-site2, as being crucial for the interactions with CD81s, with the E2-site2 as the determinant factor for human-specific binding. Free energy calculations indicated that the E2/CD81 binding process might follow a two-step model involving (i the electrostatic interaction-driven initial binding of human-specific E2-site2, followed by (ii changes in the E2 orientation to facilitate the hydrophobic and van der Waals interaction-driven binding of E2-site1. The sequence of the human-specific, stronger-binding E2-site2 could serve as a candidate template for the future development of HCV-inhibiting peptide drugs.

  19. Preparing Historically Underserved Students for STEM Careers: The Role of an Inquiry-based High School Science Sequence Beginning with Physics

    Science.gov (United States)

    Bridges, Jon P.

    Improving the STEM readiness of students from historically underserved groups is a moral and economic imperative requiring greater attention and effort than has been shown to date. The current literature suggests a high school science sequence beginning with physics and centered on developing conceptual understanding, using inquiry labs and modeling to allow students to explore new ideas, and addressing and correcting student misconceptions can increase student interest in and preparation for STEM careers. The purpose of this study was to determine if the science college readiness of historically underserved students can be improved by implementing an inquiry-based high school science sequence comprised of coursework in physics, chemistry, and biology for every student. The study used a retrospective cohort observational design to address the primary research question: are there differences between historically underserved students completing a Physics First science sequence and their peers completing a traditional science sequence in 1) science college-readiness test scores, 2) rates of science college-and career-readiness, and 3) interest in STEM? Small positive effects were found for all three outcomes for historically underserved students in the Physics First sequence.

  20. LoopIng: a template-based tool for predicting the structure of protein loops.

    KAUST Repository

    Messih, Mario Abdel

    2015-08-06

    Predicting the structure of protein loops is very challenging, mainly because they are not necessarily subject to strong evolutionary pressure. This implies that, unlike the rest of the protein, standard homology modeling techniques are not very effective in modeling their structure. However, loops are often involved in protein function, hence inferring their structure is important for predicting protein structure as well as function.We describe a method, LoopIng, based on the Random Forest automated learning technique, which, given a target loop, selects a structural template for it from a database of loop candidates. Compared to the most recently available methods, LoopIng is able to achieve similar accuracy for short loops (4-10 residues) and significant enhancements for long loops (11-20 residues). The quality of the predictions is robust to errors that unavoidably affect the stem regions when these are modeled. The method returns a confidence score for the predicted template loops and has the advantage of being very fast (on average: 1 min/loop).www.biocomputing.it/loopinganna.tramontano@uniroma1.itSupplementary data are available at Bioinformatics online.

  1. Next-generation sequencing-based detection of circulating tumour DNA After allogeneic stem cell transplantation for lymphoma.

    Science.gov (United States)

    Herrera, Alex F; Kim, Haesook T; Kong, Katherine A; Faham, Malek; Sun, Heather; Sohani, Aliyah R; Alyea, Edwin P; Carlton, Victoria E; Chen, Yi-Bin; Cutler, Corey S; Ho, Vincent T; Koreth, John; Kotwaliwale, Chitra; Nikiforow, Sarah; Ritz, Jerome; Rodig, Scott J; Soiffer, Robert J; Antin, Joseph H; Armand, Philippe

    2016-12-01

    Next-generation sequencing (NGS)-based circulating tumour DNA (ctDNA) detection is a promising monitoring tool for lymphoid malignancies. We evaluated whether the presence of ctDNA was associated with outcome after allogeneic haematopoietic stem cell transplantation (HSCT) in lymphoma patients. We studied 88 patients drawn from a phase 3 clinical trial of reduced-intensity conditioning HSCT in lymphoma. Conventional restaging and collection of peripheral blood samples occurred at pre-specified time points before and after HSCT and were assayed for ctDNA by sequencing of the immunoglobulin or T-cell receptor genes. Tumour clonotypes were identified in 87% of patients with adequate tumour samples. Sixteen of 19 (84%) patients with disease progression after HSCT had detectable ctDNA prior to progression at a median of 3·7 months prior to relapse/progression. Patients with detectable ctDNA 3 months after HSCT had inferior progression-free survival (PFS) (2-year PFS 58% vs. 84% in ctDNA-negative patients, P = 0·033). In multivariate models, detectable ctDNA was associated with increased risk of progression/death (Hazard ratio 3·9, P = 0·003) and increased risk of relapse/progression (Hazard ratio 10·8, P = 0·0006). Detectable ctDNA is associated with an increased risk of relapse/progression, but further validation studies are necessary to confirm these findings and determine the clinical utility of NGS-based minimal residual disease monitoring in lymphoma patients after HSCT. © 2016 John Wiley & Sons Ltd.

  2. Evaluation of a Stenotrophomonas maltophilia bacteremia cluster in hematopoietic stem cell transplantation recipients using whole genome sequencing

    Directory of Open Access Journals (Sweden)

    Stefanie Kampmeier

    2017-11-01

    Full Text Available Abstract Background Stenotrophomonas maltophilia ubiquitously occurs in the hospital environment. This opportunistic pathogen can cause severe infections in immunocompromised hosts such as hematopoietic stem cell transplantation (HSCT recipients. Between February and July 2016, a cluster of four patients on the HSCT unit suffered from S. maltophilia bloodstream infections (BSI. Methods For epidemiological investigation we retrospectively identified the colonization status of patients admitted to the ward during this time period and performed environmental monitoring of shower heads, shower outlets, washbasins and toilets in patient rooms. We tested antibiotic susceptibility of detected S. maltophilia isolates. Environmental and blood culture samples were subjected to whole genome sequence (WGS-based typing. Results Of four patients with S. maltophlilia BSI, three were found to be colonized previously. In addition, retrospective investigations revealed two patients being colonized in anal swab samples but not infected. Environmental monitoring revealed one shower outlet contaminated with S. maltophilia. Antibiotic susceptibility testing of seven S. maltophlia strains resulted in two trimethoprim/sulfamethoxazole resistant and five susceptible isolates, however, not excluding an outbreak scenario. WGS-based typing did not result in any close genotypic relationship among the patients’ isolates. In contrast, one environmental isolate from a shower outlet was closely related to a single patient’s isolate. Conclusion WGS-based typing successfully refuted an outbreak of S. maltophilia on a HSCT ward but uncoverd that sanitary installations can be an actual source of S. maltophilia transmissions.

  3. Biochemical characterisation of the chlamydial MurF ligase, and possible sequence of the chlamydial peptidoglycan pentapeptide stem.

    Science.gov (United States)

    Patin, Delphine; Bostock, Julieanne; Chopra, Ian; Mengin-Lecreulx, Dominique; Blanot, Didier

    2012-06-01

    Chlamydiaceae are obligate intracellular bacteria that do not synthesise detectable peptidoglycan although they possess an almost complete arsenal of genes encoding peptidoglycan biosynthetic activities. In this paper, the murF gene from Chlamydia trachomatis was shown to be capable of complementing a conditional Escherichia coli mutant impaired in UDP-MurNAc-tripeptide:D-Ala-D-Ala ligase activity. Recombinant MurF from C. trachomatis was overproduced and purified from E. coli. It exhibited ATP-dependent UDP-MurNAc-X-γ-D-Glu-meso-A(2)pm:D-Ala-D-Ala ligase activity in vitro. No significant difference of kinetic parameters was seen when X was L-Ala, L-Ser or Gly. The L-Lys-containing UDP-MurNAc-tripeptide was a poorer substrate as compared to the meso-A(2)pm-containing one. Based on the respective substrate specificities of the chlamydial MurC, MurE, MurF and Ddl enzymes, a sequence L-Ala/L-Ser/Gly-γ-D-Glu-meso-A(2)pm-D-Ala-D-Ala is expected for the chlamydial pentapeptide stem, with Gly at position 1 being less likely.

  4. Predictive lethal proarrhythmic risk evaluation using a closed-loop-circuit cell network with human induced pluripotent stem cells derived cardiomyocytes

    Science.gov (United States)

    Nomura, Fumimasa; Hattori, Akihiro; Terazono, Hideyuki; Kim, Hyonchol; Odaka, Masao; Sugio, Yoshihiro; Yasuda, Kenji

    2016-06-01

    For the prediction of lethal arrhythmia occurrence caused by abnormality of cell-to-cell conduction, we have developed a next-generation in vitro cell-to-cell conduction assay, i.e., a quasi in vivo assay, in which the change in spatial cell-to-cell conduction is quantitatively evaluated from the change in waveforms of the convoluted electrophysiological signals from lined-up cardiomyocytes on a single closed loop of a microelectrode of 1 mm diameter and 20 µm width in a cultivation chip. To evaluate the importance of the closed-loop arrangement of cardiomyocytes for prediction, we compared the change in waveforms of convoluted signals of the responses in the closed-loop circuit arrangement with that of the response of cardiomyocyte clusters using a typical human ether a go-go related gene (hERG) ion channel blocker, E-4031. The results showed that (1) waveform prolongation and fluctuation both in the closed loops and clusters increased depending on the E-4031 concentration increase. However, (2) only the waveform signals in closed loops showed an apparent temporal change in waveforms from ventricular tachycardia (VT) to ventricular fibrillation (VF), which is similar to the most typical cell-to-cell conductance abnormality. The results indicated the usefulness of convoluted waveform signals of a closed-loop cell network for acquiring reproducible results acquisition and more detailed temporal information on cell-to-cell conduction.

  5. Sequence similarity between the erythrocyte binding domain 1 of the Plasmodium vivax Duffy binding protein and the V3 loop of HIV-1 strain MN reveals binding residues for the Duffy Antigen Receptor for Chemokines

    OpenAIRE

    Bolton, Michael J; Garry, Robert F

    2011-01-01

    Abstract Background The surface glycoprotein (SU, gp120) of the human immunodeficiency virus (HIV) must bind to a chemokine receptor, CCR5 or CXCR4, to invade CD4+ cells. Plasmodium vivax uses the Duffy Binding Protein (DBP) to bind the Duffy Antigen Receptor for Chemokines (DARC) and invade reticulocytes. Results Variable loop 3 (V3) of HIV-1 SU and domain 1 of the Plasmodium vivax DBP share a sequence similarity. The site of amino acid sequence similarity was necessary, but not sufficient, ...

  6. Length and amino acid sequence of peptides substituted for the 5-HT3A receptor M3M4 loop may affect channel expression and desensitization.

    Directory of Open Access Journals (Sweden)

    Nicole K McKinnon

    Full Text Available 5-HT3A receptors are pentameric neurotransmitter-gated ion channels in the Cys-loop receptor family. Each subunit contains an extracellular domain, four transmembrane segments (M1, M2, M3, M4 and a 115 residue intracellular loop between M3 and M4. In contrast, the M3M4 loop in prokaryotic homologues is <15 residues. To investigate the limits of M3M4 loop length and composition on channel function we replaced the 5-HT3A M3M4 loop with two to seven alanine residues (5-HT3A-A(n = 2-7. Mutants were expressed in Xenopus laevis oocytes and characterized using two electrode voltage clamp recording. All mutants were functional. The 5-HT EC(50's were at most 5-fold greater than wild-type (WT. The desensitization rate differed significantly among the mutants. Desensitization rates for 5-HT3A-A(2, 5-HT3A-A(4, 5-HT3A-A(6, and 5-HT3A-A(7 were similar to WT. In contrast, 5-HT3A-A(3 and 5-HT3A-A(5 had desensitization rates at least an order of magnitude faster than WT. The one Ala loop construct, 5-HT3A-A(1, entered a non-functional state from which it did not recover after the first 5-HT application. These results suggest that the large M3M4 loop of eukaryotic Cys-loop channels is not required for receptor assembly or function. However, loop length and amino acid composition can effect channel expression and desensitization. We infer that the cytoplasmic ends of the M3 and M4 segments may undergo conformational changes during channel gating and desensitization and/or the loop may influence the position and mobility of these segments as they undergo gating-induced conformational changes. Altering structure or conformational mobility of the cytoplasmic ends of M3 and M4 may be the basis by which phosphorylation or protein binding to the cytoplasmic loop alters channel function.

  7. Structure-Function Model for Kissing Loop Interactions That Initiate Dimerization of Ty1 RNA

    Directory of Open Access Journals (Sweden)

    Eric R. Gamache

    2017-04-01

    Full Text Available The genomic RNA of the retrotransposon Ty1 is packaged as a dimer into virus-like particles. The 5′ terminus of Ty1 RNA harbors cis-acting sequences required for translation initiation, packaging and initiation of reverse transcription (TIPIRT. To identify RNA motifs involved in dimerization and packaging, a structural model of the TIPIRT domain in vitro was developed from single-nucleotide resolution RNA structural data. In general agreement with previous models, the first 326 nucleotides of Ty1 RNA form a pseudoknot with a 7-bp stem (S1, a 1-nucleotide interhelical loop and an 8-bp stem (S2 that delineate two long, structured loops. Nucleotide substitutions that disrupt either pseudoknot stem greatly reduced helper-Ty1-mediated retrotransposition of a mini-Ty1, but only mutations in S2 destabilized mini-Ty1 RNA in cis and helper-Ty1 RNA in trans. Nested in different loops of the pseudoknot are two hairpins with complementary 7-nucleotide motifs at their apices. Nucleotide substitutions in either motif also reduced retrotransposition and destabilized mini- and helper-Ty1 RNA. Compensatory mutations that restore base-pairing in the S2 stem or between the hairpins rescued retrotransposition and RNA stability in cis and trans. These data inform a model whereby a Ty1 RNA kissing complex with two intermolecular kissing-loop interactions initiates dimerization and packaging.

  8. Sequencing Analysis of Mutant Allele $cdc$28-$srm$ of Protein Kinase CDC28 and Molecular Dynamics Study of Glycine-Rich Loop in Wild-Type and Mutant Allele G16S of CDK2 as Model

    CERN Document Server

    Koltovaya, N A; Kholmurodov, Kh T; Kretov, D A

    2005-01-01

    The central role that cyclin-dependent kinases play in the timing of cell division and the high incidence of genetic alteration of CDKs or deregulation of CDK inhibitors in a number of cancers make CDC28 of the yeast \\textit{Saccharomyces cerevisiae }very attractive model for studies of mechanisms of CDK regulation. Earlier it was found that certain gene mutations including \\textit{cdc28-srm} affect cell cycle progression, maintenance of different genetic structures and increase cell sensitivity to ionizing radiation. A~\\textit{cdc28-srm} mutation is not temperature-sensitive mutation and differs from the known \\textit{cdc28-ts }mutations because it has the evident phenotypic manifestations at 30 $^{\\circ}$C. Sequencing analysis of \\textit{cdc28-srm} revealed a single nucleotide substitution G20S. This is a third glycine in a conserved sequence GxGxxG in the G-rich loop positioned opposite the activation T-loop. Despite its demonstrated importance, the role of the G-loop has remained unclear. The crystal stru...

  9. The kissing-loop motif is a preferred site of 5' leader recombination during replication of SL3-3 murine leukemia viruses in mice

    DEFF Research Database (Denmark)

    Lund, Anders Henrik; Mikkelsen, J G; Schmidt, J

    1999-01-01

    , and the upstream part of the 5' untranslated region, enabled us to map recombination sites, guided by distinct scattered nucleotide differences. In 30 of 44 analyzed sequences, recombination was mapped to a 33-nucleotide similarity window coinciding with the kissing-loop stem-loop motif implicated in dimerization...... of the diploid genome. Interestingly, the recombination pattern preference found in replication-competent viruses from T-cell tumors is very similar to the pattern previously reported for retroviral vectors in cell culture experiments. The data therefore sustain the hypothesis that the kissing loop, presumably...

  10. The subgenomic promoter of brome mosaic virus folds into a stem-loop structure capped by a pseudo-triloop that is structurally similar to the triloop of the genomic promoter

    DEFF Research Database (Denmark)

    Skov, J.; Gaudin, M.; Podbevsek, P.

    2012-01-01

    In brome mosaic virus, both the replication of the genomic (+)-RNA strands and the transcription of the subgenomic RNA are carried out by the viral replicase. The production of (-)-RNA strands is dependent on the formation of an AUA triloop in the stem-loop C (SLC) hairpin in the 3'-untranslated...... region of the (+)-RNA strands. Two alternate hypotheses have been put forward for the mechanism of subgenomic RNA transcription. One posits that transcription commences by recognition of at least four key nucleotides in the subgenomic promoter by the replicase. The other posits that subgenomic...... transcription starts by binding of the replicase to a hairpin formed by the subgenomic promoter that resembles the minus strand promoter hairpin SLC. In this study, we have determined the three-dimensional structure of the subgenomic promoter hairpin using NMR spectroscopy. The data show that the hairpin...

  11. Sequence similarity between the erythrocyte binding domain of the Plasmodium vivax Duffy binding protein and the V3 loop of HIV-1 strain MN reveals a functional heparin binding motif involved in binding to the Duffy antigen receptor for chemokines

    OpenAIRE

    Bolton, Michael J; Garry, Robert F

    2011-01-01

    Abstract Background The HIV surface glycoprotein gp120 (SU, gp120) and the Plasmodium vivax Duffy binding protein (PvDBP) bind to chemokine receptors during infection and have a site of amino acid sequence similarity in their binding domains that often includes a heparin binding motif (HBM). Infection by either pathogen has been found to be inhibited by polyanions. Results Specific polyanions that inhibit HIV infection and bind to the V3 loop of X4 strains also inhibited DBP-mediated infectio...

  12. Discovery of the rare HLA-B*39:77 allele in an unrelated Taiwanese bone marrow stem cell donor using the sequence-based typing method.

    Science.gov (United States)

    Yang, K L; Lee, S K; Lin, P Y

    2013-08-01

    We detected a rare HLA-B locus allele, B*39:77, in a Taiwanese unrelated marrow stem cell donor in our routine HLA sequence-based typing (SBT) exercise for a possible haematopoietic stem cell donation. In exons 2, 3 and 4, the DNA sequence of B*39:77 is identical to the sequence of B*39:01:01:01 except one nucleotide at nucleotide position 733 (G->A) in exon 4. The nucleotide variation caused one amino acid alteration at residue 221 (Gly->Ser). B*39:77 was probably derived from a nucleotide substitution event involving B*39:01:01:01. The probable HLA-A, -B, -C, -DRB1 and -DQB1 haplotype in association with B*39:77 may be deduced as A*02:01-B*39:77-C*07:02-DRB1*08:03-DQB1*06:01. Our discovery of B*39:77 in Taiwanese adds further polymorphism of B*39 variants in Taiwanese population. © 2013 John Wiley & Sons Ltd.

  13. Quantitative analysis by next generation sequencing of hematopoietic stem and progenitor cells (LSK and of splenic B cells transcriptomes from wild-type and Usp3-knockout mice

    Directory of Open Access Journals (Sweden)

    Cesare Lancini

    2016-03-01

    Full Text Available The data described here provide genome-wide expression profiles of murine primitive hematopoietic stem and progenitor cells (LSK and of B cell populations, obtained by high throughput sequencing. Cells are derived from wild-type mice and from mice deficient for the ubiquitin-specific protease 3 (USP3; Usp3Δ/Δ. Modification of histone proteins by ubiquitin plays a crucial role in the cellular response to DNA damage (DDR (Jackson and Durocher, 2013 [1]. USP3 is a histone H2A deubiquitinating enzyme (DUB that regulates ubiquitin-dependent DDR in response to DNA double-strand breaks (Nicassio et al., 2007; Doil et al., 2008 [2,3]. Deletion of USP3 in mice increases the incidence of spontaneous tumors and affects hematopoiesis [4]. In particular, Usp3-knockout mice show progressive loss of B and T cells and decreased functional potential of hematopoietic stem cells (HSCs during aging. USP3-deficient cells, including HSCs, display enhanced histone ubiquitination, accumulate spontaneous DNA damage and are hypersensitive to ionizing radiation (Lancini et al., 2014 [4]. To address whether USP3 loss leads to deregulation of specific molecular pathways relevant to HSC homeostasis and/or B cell development, we have employed the RNA-sequencing technology and investigated transcriptional differences between wild-type and Usp3Δ/Δ LSK, naïve B cells or in vitro activated B cells. The data relate to the research article “Tight regulation of ubiquitin-mediated DNA damage response by USP3 preserves the functional integrity of hematopoietic stem cells” (Lancini et al., 2014 [4]. The RNA-sequencing and analysis data sets have been deposited in NCBI׳s Gene Expression Omnibus (Edgar et al., 2002 [5] and are accessible through GEO Series accession number GSE58495 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58495. With this article, we present validation of the RNA-seq data set through quantitative real-time PCR and comparative analysis. Keywords: B

  14. Sequence similarity between the erythrocyte binding domain of the Plasmodium vivax Duffy binding protein and the V3 loop of HIV-1 strain MN reveals a functional heparin binding motif involved in binding to the Duffy antigen receptor for chemokines

    Directory of Open Access Journals (Sweden)

    Bolton Michael J

    2011-11-01

    Full Text Available Abstract Background The HIV surface glycoprotein gp120 (SU, gp120 and the Plasmodium vivax Duffy binding protein (PvDBP bind to chemokine receptors during infection and have a site of amino acid sequence similarity in their binding domains that often includes a heparin binding motif (HBM. Infection by either pathogen has been found to be inhibited by polyanions. Results Specific polyanions that inhibit HIV infection and bind to the V3 loop of X4 strains also inhibited DBP-mediated infection of erythrocytes and DBP binding to the Duffy Antigen Receptor for Chemokines (DARC. A peptide including the HBM of PvDBP had similar affinity for heparin as RANTES and V3 loop peptides, and could be specifically inhibited from heparin binding by the same polyanions that inhibit DBP binding to DARC. However, some V3 peptides can competitively inhibit RANTES binding to heparin, but not the PvDBP HBM peptide. Three other members of the DBP family have an HBM sequence that is necessary for erythrocyte binding, however only the protein which binds to DARC, the P. knowlesi alpha protein, is inhibited by heparin from binding to erythrocytes. Heparitinase digestion does not affect the binding of DBP to erythrocytes. Conclusion The HBMs of DBPs that bind to DARC have similar heparin binding affinities as some V3 loop peptides and chemokines, are responsible for specific sulfated polysaccharide inhibition of parasite binding and invasion of red blood cells, and are more likely to bind to negative charges on the receptor than cell surface glycosaminoglycans.

  15. A Quasi-Experimental Examination: Cognitive Sequencing of Instruction Using Experiential Learning Theory for STEM Concepts in Agricultural Education

    Science.gov (United States)

    Smith, Kasee L.; Rayfield, John

    2017-01-01

    Understanding methods for effectively instructing STEM education concepts is essential in the current climate of education (Freeman, Marginson, & Tyler 2014). Kolb's experiential learning theory (ELT) outlines four specific modes of learning, based on preferences for grasping and transforming information. This quasi-experimental study was…

  16. Comparison of DNA Microarray, Loop-Mediated Isothermal Amplification (LAMP) and Real-Time PCR with DNA Sequencing for Identification of Fusarium spp. Obtained from Patients with Hematologic Malignancies.

    Science.gov (United States)

    de Souza, Marcela; Matsuzawa, Tetsuhiro; Sakai, Kanae; Muraosa, Yasunori; Lyra, Luzia; Busso-Lopes, Ariane Fidelis; Levin, Anna Sara Shafferman; Schreiber, Angélica Zaninelli; Mikami, Yuzuru; Gonoi, Tohoru; Kamei, Katsuhiko; Moretti, Maria Luiza; Trabasso, Plínio

    2017-08-01

    The performance of three molecular biology techniques, i.e., DNA microarray, loop-mediated isothermal amplification (LAMP), and real-time PCR were compared with DNA sequencing for properly identification of 20 isolates of Fusarium spp. obtained from blood stream as etiologic agent of invasive infections in patients with hematologic malignancies. DNA microarray, LAMP and real-time PCR identified 16 (80%) out of 20 samples as Fusarium solani species complex (FSSC) and four (20%) as Fusarium spp. The agreement among the techniques was 100%. LAMP exhibited 100% specificity, while DNA microarray, LAMP and real-time PCR showed 100% sensitivity. The three techniques had 100% agreement with DNA sequencing. Sixteen isolates were identified as FSSC by sequencing, being five Fusarium keratoplasticum, nine Fusarium petroliphilum and two Fusarium solani. On the other hand, sequencing identified four isolates as Fusarium non-solani species complex (FNSSC), being three isolates as Fusarium napiforme and one isolate as Fusarium oxysporum. Finally, LAMP proved to be faster and more accessible than DNA microarray and real-time PCR, since it does not require a thermocycler. Therefore, LAMP signalizes as emerging and promising methodology to be used in routine identification of Fusarium spp. among cases of invasive fungal infections.

  17. The Activity of Escherichia coli Dihydroorotate Dehydrogenase Is Dependent on a Conserved Loop Identified by Sequence Homology, Mutagenesis, and Limited Proteolysis

    DEFF Research Database (Denmark)

    Björnberg, Olof; Grüner, Anne Charlotte; Roepstorff, Peter

    1999-01-01

    of dihydroorotate dehydrogenases, but sedimentation in sucrose gradients suggests a dimeric structure also of the E. coli enzyme. Product inhibition showed that the E. coli enzyme, in contrast to the L. lactis enzyme, has separate binding sites for dihydroorotate and the electron acceptor. Trypsin readily cleaved...... the E. coli enzyme into two fragments of 182 and 154 residues, respectively. Cleavage reduced the activity more than 100-fold but left other molecular properties, including the heat stability, intact. The trypsin cleavage site, at R182, is positioned in a conserved region that, in the L. lactis enzyme......, forms a loop where a cysteine residue is very critical for activity. In the corresponding position, the enzyme from E. coli has a serine residue. Mutagenesis of this residue (S175) to alanine or cysteine reduced the activities 10000- and 500-fold, respectively. The S175C mutant was also defective...

  18. Algorithm for counting large directed loops

    Energy Technology Data Exchange (ETDEWEB)

    Bianconi, Ginestra [Abdus Salam International Center for Theoretical Physics, Strada Costiera 11, 34014 Trieste (Italy); Gulbahce, Natali [Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, NM 87545 (United States)

    2008-06-06

    We derive a Belief-Propagation algorithm for counting large loops in a directed network. We evaluate the distribution of the number of small loops in a directed random network with given degree sequence. We apply the algorithm to a few characteristic directed networks of various network sizes and loop structures and compare the algorithm with exhaustive counting results when possible. The algorithm is adequate in estimating loop counts for large directed networks and can be used to compare the loop structure of directed networks and their randomized counterparts.

  19. IGF-1R Promotes Symmetric Self-Renewal and Migration of Alkaline Phosphatase+ Germ Stem Cells through HIF-2α-OCT4/CXCR4 Loop under Hypoxia

    Directory of Open Access Journals (Sweden)

    Yung-Che Kuo

    2018-02-01

    Full Text Available Summary: Hypoxia cooperates with endocrine signaling to maintain the symmetric self-renewal proliferation and migration of embryonic germline stem cells (GSCs. However, the lack of an appropriate in vitro cell model has dramatically hindered the understanding of the mechanism underlying this cooperation. Here, using a serum-free system, we demonstrated that hypoxia significantly induced the GSC mesenchymal transition, increased the expression levels of the pluripotent transcription factor OCT4 and migration-associated proteins (SDF-1, CXCR4, IGF-1, and IGF-1R, and activated the cellular expression and translocalization of the CXCR4-downstream proteins ARP3/pFAK. The underlying mechanism involved significant IGF-1/IGF-1R activation of OCT4/CXCR4 expression through HIF-2α regulation. Picropodophyllin-induced inhibition of IGF-1R phosphorylation significantly suppressed hypoxia-induced SDF-1/CXCR4 expression and cell migration. Furthermore, transactivation between IGF-1R and CXCR4 was involved. In summary, we demonstrated that niche hypoxia synergistically cooperates with its associated IGF-1R signaling to regulate the symmetric division (self-renewal proliferation and cell migration of alkaline phosphatase-positive GSCs through HIF-2α-OCT4/CXCR4 during embryogenesis. : In this article, Huang and colleagues demonstrate that niche hypoxia promotes symmetric self-renewal proliferation and migration of PGC-like CD49f+AP+GSCs through IGF-IR regulation. Using a serum-free culture system, the crosstalk between IGF-1R and CXCR4 signaling was discovered. This work demonstrated that embryonic hypoxia synergistically cooperated with IGF-1R signaling to regulate the symmetric self-renewal and migration of PGC-like GSCs through a HIF-2α–OCT4/CXCR4 loop. Keywords: hypoxia, niche, germline stem cells, self-renewal, migration, IGF-1R, HIF-2α, OCT4, SDF-1, CXCR4

  20. Quantitative analysis by next generation sequencing of hematopoietic stem and progenitor cells (LSK) and of splenic B cells transcriptomes from wild-type and Usp3-knockout mice.

    Science.gov (United States)

    Lancini, Cesare; Gargiulo, Gaetano; van den Berk, Paul C M; Citterio, Elisabetta

    2016-03-01

    The data described here provide genome-wide expression profiles of murine primitive hematopoietic stem and progenitor cells (LSK) and of B cell populations, obtained by high throughput sequencing. Cells are derived from wild-type mice and from mice deficient for the ubiquitin-specific protease 3 (USP3; Usp3Δ/Δ). Modification of histone proteins by ubiquitin plays a crucial role in the cellular response to DNA damage (DDR) (Jackson and Durocher, 2013) [1]. USP3 is a histone H2A deubiquitinating enzyme (DUB) that regulates ubiquitin-dependent DDR in response to DNA double-strand breaks (Nicassio et al., 2007; Doil et al., 2008) [2], [3]. Deletion of USP3 in mice increases the incidence of spontaneous tumors and affects hematopoiesis [4]. In particular, Usp3-knockout mice show progressive loss of B and T cells and decreased functional potential of hematopoietic stem cells (HSCs) during aging. USP3-deficient cells, including HSCs, display enhanced histone ubiquitination, accumulate spontaneous DNA damage and are hypersensitive to ionizing radiation (Lancini et al., 2014) [4]. To address whether USP3 loss leads to deregulation of specific molecular pathways relevant to HSC homeostasis and/or B cell development, we have employed the RNA-sequencing technology and investigated transcriptional differences between wild-type and Usp3Δ/Δ LSK, naïve B cells or in vitro activated B cells. The data relate to the research article "Tight regulation of ubiquitin-mediated DNA damage response by USP3 preserves the functional integrity of hematopoietic stem cells" (Lancini et al., 2014) [4]. The RNA-sequencing and analysis data sets have been deposited in NCBI׳s Gene Expression Omnibus (Edgar et al., 2002) [5] and are accessible through GEO Series accession number GSE58495 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58495). With this article, we present validation of the RNA-seq data set through quantitative real-time PCR and comparative analysis.

  1. In Silico Derivation of HLA-Specific Alloreactivity Potential from Whole Exome Sequencing of Stem Cell Transplant Donors and Recipients: Understanding the Quantitative Immunobiology of Allogeneic Transplantation

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    Max eJameson-Lee

    2014-11-01

    Full Text Available Donor T cell mediated graft versus host effects (GVH may result from the aggregate alloreactivity to minor histocompatibility antigens (mHA presented by the HLA molecules in each donor-recipient pair undergoing stem cell transplantation (SCT. Whole exome sequencing has previously demonstrated a large number of nonsynonymous single nucleotide polymorphisms (SNP present in HLA-matched recipients of SCT donors (GVH direction. The nucleotide sequence flanking each of these SNPs was obtained and the amino acid sequence determined. All the possible nonameric-peptides incorporating the variant amino acid resulting from these SNPs were interrogated in-silico for their likelihood to be presented by the HLA class I molecules using the Immune Epitope Database stabilized matrix method (SMM and NetMHCpan algorithms. The SMM algorithm predicted that a median of 18,396 peptides weakly bound HLA class I molecules in individual SCT recipients, and 2,254 peptides displayed strong binding. A similar library of presented peptides was identified when the data was interrogated using the NetMHCpan algorithm. The bioinformatic algorithm presented here demonstrates that there may be a high level of mHA variation in HLA-matched individuals, constituting an HLA-specific alloreactivity potential.

  2. Exploring the correlation between the sequence composition of the nucleotide binding G5 loop of the FeoB GTPase domain (NFeoB) and intrinsic rate of GDP release.

    Science.gov (United States)

    Guilfoyle, Amy P; Deshpande, Chandrika N; Schenk, Gerhard; Maher, Megan J; Jormakka, Mika

    2014-12-12

    GDP release from GTPases is usually extremely slow and is in general assisted by external factors, such as association with guanine exchange factors or membrane-embedded GPCRs (G protein-coupled receptors), which accelerate the release of GDP by several orders of magnitude. Intrinsic factors can also play a significant role; a single amino acid substitution in one of the guanine nucleotide recognition motifs, G5, results in a drastically altered GDP release rate, indicating that the sequence composition of this motif plays an important role in spontaneous GDP release. In the present study, we used the GTPase domain from EcNFeoB (Escherichia coli FeoB) as a model and applied biochemical and structural approaches to evaluate the role of all the individual residues in the G5 loop. Our study confirms that several of the residues in the G5 motif have an important role in the intrinsic affinity and release of GDP. In particular, a T151A mutant (third residue of the G5 loop) leads to a reduced nucleotide affinity and provokes a drastically accelerated dissociation of GDP.

  3. Inhibition of CXCL12/CXCR4 autocrine/paracrine loop reduces viability of human glioblastoma stem-like cells affecting self-renewal activity

    International Nuclear Information System (INIS)

    Gatti, Monica; Pattarozzi, Alessandra; Bajetto, Adriana; Würth, Roberto; Daga, Antonio; Fiaschi, Pietro; Zona, Gianluigi; Florio, Tullio; Barbieri, Federica

    2013-01-01

    Cancer stem cells (CSCs) or tumor initiating cells (TICs) drive glioblastoma (GBM) development, invasiveness and drug resistance. Distinct molecular pathways might regulate CSC biology as compared to cells in the bulk tumor mass, representing potential therapeutic targets. Chemokine CXCL12 and its receptor CXCR4 control proliferation, invasion and angiogenesis in GBM cell lines and primary cultures, but little is known about their activity in GBM CSCs. We demonstrate that CSCs, isolated from five human GBMs, express CXCR4 and release CXCL12 in vitro, although different levels of expression and secretion were observed in individual cultures, as expected for the heterogeneity of GBMs. CXCL12 treatment induced Akt-mediated significant pro-survival and self-renewal activities, while proliferation was induced at low extent. The role of CXCR4 signaling in CSC survival and self-renewal was further demonstrated using the CXCR4 antagonist AMD3100 that reduced self-renewal and survival with greater efficacy in the cultures that released higher CXCL12 amounts. The specificity of CXCL12 in sustaining CSC survival was demonstrated by the lack of AMD3100-dependent inhibition of viability in differentiated cells derived from the same GBMs. These findings, although performed on a limited number of tumor samples, suggest that the CXCL12/CXCR4 interaction mediates survival and self-renewal in GBM CSCs with high selectivity, thus emerging as a candidate system responsible for maintenance of cancer progenitors, and providing survival benefits to the tumor

  4. Interaction of the host protein NbDnaJ with Potato virus X minus-strand stem-loop 1 RNA and capsid protein affects viral replication and movement.

    Science.gov (United States)

    Cho, Sang-Yun; Cho, Won Kyong; Sohn, Seong-Han; Kim, Kook-Hyung

    2012-01-06

    Plant viruses must interact with host cellular components to replicate and move from cell to cell. In the case of Potato virus X (PVX), it carries stem-loop 1 (SL1) RNA essential for viral replication and movement. Using two-dimensional electrophoresis northwestern blot analysis, we previously identified several host proteins that bind to SL1 RNA. Of those, we further characterized a DnaJ-like protein from Nicotiana benthamiana named NbDnaJ. An electrophoretic mobility shift assay confirmed that NbDnaJ binds only to SL1 minus-strand RNA, and bimolecular fluorescence complementation (BiFC) indicated that NbDnaJ interacts with PVX capsid protein (CP). Using a series of deletion mutants, the C-terminal region of NbDnaJ was found to be essential for the interaction with PVX CP. The expression of NbDnaJ significantly changed upon infection with different plant viruses such as PVX, Tobacco mosaic virus, and Cucumber mosaic virus, but varied depending on the viral species. In transient experiments, both PVX replication and movement were inhibited in plants that over-expressed NbDnaJ but accelerated in plants in which NbDnaJ was silenced. In summary, we suggest that the newly identified NbDnaJ plays a role in PVX replication and movement by interacting with SL1(-) RNA and PVX CP. Copyright © 2011 Elsevier Inc. All rights reserved.

  5. Modification of a loop sequence between α-helices 6 and 7 of virus capsid (CA protein in a human immunodeficiency virus type 1 (HIV-1 derivative that has simian immunodeficiency virus (SIVmac239 vif and CA α-helices 4 and 5 loop improves replication in cynomolgus monkey cells

    Directory of Open Access Journals (Sweden)

    Adachi Akio

    2009-08-01

    Full Text Available Abstract Background Human immunodeficiency virus type 1 (HIV-1 productively infects only humans and chimpanzees but not cynomolgus or rhesus monkeys while simian immunodeficiency virus isolated from macaque (SIVmac readily establishes infection in those monkeys. Several HIV-1 and SIVmac chimeric viruses have been constructed in order to develop an animal model for HIV-1 infection. Construction of an HIV-1 derivative which contains sequences of a SIVmac239 loop between α-helices 4 and 5 (L4/5 of capsid protein (CA and the entire SIVmac239 vif gene was previously reported. Although this chimeric virus could grow in cynomolgus monkey cells, it did so much more slowly than did SIVmac. It was also reported that intrinsic TRIM5α restricts the post-entry step of HIV-1 replication in rhesus and cynomolgus monkey cells, and we previously demonstrated that a single amino acid in a loop between α-helices 6 and 7 (L6/7 of HIV type 2 (HIV-2 CA determines the susceptibility of HIV-2 to cynomolgus monkey TRIM5α. Results In the study presented here, we replaced L6/7 of HIV-1 CA in addition to L4/5 and vif with the corresponding segments of SIVmac. The resultant HIV-1 derivatives showed enhanced replication capability in established T cell lines as well as in CD8+ cell-depleted primary peripheral blood mononuclear cells from cynomolgus monkey. Compared with the wild type HIV-1 particles, the viral particles produced from a chimeric HIV-1 genome with those two SIVmac loops were less able to saturate the intrinsic restriction in rhesus monkey cells. Conclusion We have succeeded in making the replication of simian-tropic HIV-1 in cynomolgus monkey cells more efficient by introducing into HIV-1 the L6/7 CA loop from SIVmac. It would be of interest to determine whether HIV-1 derivatives with SIVmac CA L4/5 and L6/7 can establish infection of cynomolgus monkeys in vivo.

  6. Sequence similarity between the erythrocyte binding domain 1 of the Plasmodium vivax Duffy binding protein and the V3 loop of HIV-1 strain MN reveals binding residues for the Duffy Antigen Receptor for Chemokines

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    Garry Robert F

    2011-01-01

    Full Text Available Abstract Background The surface glycoprotein (SU, gp120 of the human immunodeficiency virus (HIV must bind to a chemokine receptor, CCR5 or CXCR4, to invade CD4+ cells. Plasmodium vivax uses the Duffy Binding Protein (DBP to bind the Duffy Antigen Receptor for Chemokines (DARC and invade reticulocytes. Results Variable loop 3 (V3 of HIV-1 SU and domain 1 of the Plasmodium vivax DBP share a sequence similarity. The site of amino acid sequence similarity was necessary, but not sufficient, for DARC binding and contained a consensus heparin binding site essential for DARC binding. Both HIV-1 and P. vivax can be blocked from binding to their chemokine receptors by the chemokine, RANTES and its analog AOP-RANTES. Site directed mutagenesis of the heparin binding motif in members of the DBP family, the P. knowlesi alpha, beta and gamma proteins abrogated their binding to erythrocytes. Positively charged residues within domain 1 are required for binding of P. vivax and P. knowlesi erythrocyte binding proteins. Conclusion A heparin binding site motif in members of the DBP family may form part of a conserved erythrocyte receptor binding pocket.

  7. Remarkable sequence conservation of the last intron in the PKD1 gene.

    Science.gov (United States)

    Rodova, Marianna; Islam, M Rafiq; Peterson, Kenneth R; Calvet, James P

    2003-10-01

    The last intron of the PKD1 gene (intron 45) was found to have exceptionally high sequence conservation across four mammalian species: human, mouse, rat, and dog. This conservation did not extend to the comparable intron in pufferfish. Pairwise comparisons for intron 45 showed 91% identity (human vs. dog) to 100% identity (mouse vs. rat) for an average for all four species of 94% identity. In contrast, introns 43 and 44 of the PKD1 gene had average pairwise identities of 57% and 54%, and exons 43, 44, and 45 and the coding region of exon 46 had average pairwise identities of 80%, 84%, 82%, and 80%. Intron 45 is 90 to 95 bp in length, with the major region of sequence divergence being in a central 4-bp to 9-bp variable region. RNA secondary structure analysis of intron 45 predicts a branching stem-loop structure in which the central variable region lies in one loop and the putative branch point sequence lies in another loop, suggesting that the intron adopts a specific stem-loop structure that may be important for its removal. Although intron 45 appears to conform to the class of small, G-triplet-containing introns that are spliced by a mechanism utilizing intron definition, its high sequence conservation may be a reflection of constraints imposed by a unique mechanism that coordinates splicing of this last PKD1 intron with polyadenylation.

  8. Morpholino spin-labeling for base-pair sequencing of a 3'-terminal RNA stem by proton homonuclear Overhauser enhancements: yeast ribosomal 5S RNA

    International Nuclear Information System (INIS)

    Lee, K.M.; Marshall, A.G.

    1987-01-01

    Base-pair sequences for 5S and 5.8S RNAs are not readily extracted from proton homonuclear nuclear Overhauser enhancement (NOE) connectivity experiments alone, due to extensive peak overlap in the downfield (11-15 ppm) proton NMR spectrum. In this paper, we introduce a new method for base-pair proton peak assignment for ribosomal RNAs, based upon the distance-dependent broadening of the resonances of base-pair protons spatially proximal to a paramagnetic group. Introduction of a nitroxide spin-label covalently attached to the 3'-terminal ribose provides an unequivocal starting point for base-pair hydrogen-bond proton NMR assignment. Subsequent NOE connectivities then establish the base-pair sequence for the terminal stem of a 5S RNA. Periodate oxidation of yeast 5S RNA, followed by reaction with 4-amino-2,2,6,6-tetramethylpiperidinyl-1-oxy (TEMPO-NH2) and sodium borohydride reduction, produces yeast 5S RNA specifically labeled with a paramagnetic nitroxide group at the 3'-terminal ribose. Comparison of the 500-MHz 1H NMR spectra of native and 3'-terminal spin-labeled yeast 5S RNA serves to identify the terminal base pair (G1 . C120) and its adjacent base pair (G2 . U119) on the basis of their proximity to the 3'-terminal spin-label. From that starting point, we have then identified (G . C, A . U, or G . U) and sequenced eight of the nine base pairs in the terminal helix via primary and secondary NOE's

  9. Treatment of low-strength wastewater using immobilized biomass in a sequencing batch external loop reactor: influence of the medium superficial velocity on the stability and performance

    Directory of Open Access Journals (Sweden)

    Camargo E.F.M.

    2002-01-01

    Full Text Available An anaerobic sequencing batch bioreactor with external circulation of the liquid phase wherein the biomass was immobilized on a polyurethane foam matrix was analyzed, focussing on the influence of the liquid superficial velocity on the reactor's stability and efficiency. Eight-hour cycles were carried out at 30ºC treating glucose-based synthetic wastewater around 500 mgDQO/L. The performance of the reactor was assessed without circulation and with circulating liquid superficial velocity between 0.034 and 0.188 cm/s. The reactor attained operating stability and a high organic matter removal was achieved when liquid was circulated. A first order model was used to evaluate the influence of the liquid superficial velocity (vS, resulting in an increase in the apparent first order parameter when vS increased from 0.034 to 0.094 cm/s. The parameter value remained unchangeable when 0.188 cm/s was applied, indicating that beyond this value no improvement on liquid mass transfer was observed. Moreover, the necessary time to reach the final removal efficiency decreased when liquid circulation was applied, indicating that a 3-hour cycle could be enough.

  10. Interaction between the cellular protein eEF1A and the 3'-terminal stem-loop of West Nile virus genomic RNA facilitates viral minus-strand RNA synthesis.

    Science.gov (United States)

    Davis, William G; Blackwell, Jerry L; Shi, Pei-Yong; Brinton, Margo A

    2007-09-01

    RNase footprinting and nitrocellulose filter binding assays were previously used to map one major and two minor binding sites for the cell protein eEF1A on the 3'(+) stem-loop (SL) RNA of West Nile virus (WNV) (3). Base substitutions in the major eEF1A binding site or adjacent areas of the 3'(+) SL were engineered into a WNV infectious clone. Mutations that decreased, as well as ones that increased, eEF1A binding in in vitro assays had a negative effect on viral growth. None of these mutations affected the efficiency of translation of the viral polyprotein from the genomic RNA, but all of the mutations that decreased in vitro eEF1A binding to the 3' SL RNA also decreased viral minus-strand RNA synthesis in transfected cells. Also, a mutation that increased the efficiency of eEF1A binding to the 3' SL RNA increased minus-strand RNA synthesis in transfected cells, which resulted in decreased synthesis of genomic RNA. These results strongly suggest that the interaction between eEF1A and the WNV 3' SL facilitates viral minus-strand synthesis. eEF1A colocalized with viral replication complexes (RC) in infected cells and antibody to eEF1A coimmunoprecipitated viral RC proteins, suggesting that eEF1A facilitates an interaction between the 3' end of the genome and the RC. eEF1A bound with similar efficiencies to the 3'-terminal SL RNAs of four divergent flaviviruses, including a tick-borne flavivirus, and colocalized with dengue virus RC in infected cells. These results suggest that eEF1A plays a similar role in RNA replication for all flaviviruses.

  11. Draft genome sequence of an endophytic bacterium, Paenibacillus tyrfis strain SUK123, isolated from Santiria apiculata stem

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    Emmanuel Haruna

    2017-12-01

    Full Text Available Here we report the draft genome sequence of an endophytic Paenibacillus tyrfis strain isolated from the Universiti Kebangsaan Malaysia reserve forest, Malaysia. The genome size was approximately 8.04 Mb, and the assembly consisted of 107 scaffolds with 168 contigs, and had a G + C content of 53%. Phylogenetic analysis of strain SUK123 using the 16S rRNA gene revealed that it belonged to the family Paenibacillaceae with the highest similarity to Paenibacillus elgii SDT (99%. Whole genome comparison of SUK123 with related species using average nucleotide identity (ANI analysis revealed a similarity of 98% to Paenibacillus tyrfis Mst1T, 94% to Paenibacillus elgii B69T, 91% to Paenibacillus ehimensis A2T, 68% to Paenibacillus polymyxa SC2T and 69% to Paenibacillus alvei DMS29T. The draft genome was deposited at the European Nucleotide Archive (PRJEB21373.

  12. Characterization of a Large Panel of Rabbit Monoclonal Antibodies against HIV-1 gp120 and Isolation of Novel Neutralizing Antibodies against the V3 Loop.

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    Yali Qin

    Full Text Available We recently reported the induction of potent, cross-clade neutralizing antibodies (nAbs against Human Immunodeficiency Virus type-1 (HIV-1 in rabbits using gp120 based on an M-group consensus sequence. To better characterize these antibodies, 93 hybridomas were generated, which represent the largest panel of monoclonal antibodies (mAbs ever generated from a vaccinated rabbit. The single most frequently recognized epitope of the isolated mAbs was at the very C-terminal end of the protein (APTKAKRRVVEREKR, followed by the V3 loop. A total of seven anti-V3 loop mAbs were isolated, two of which (10A3 and 10A37 exhibited neutralizing activity. In contrast to 10A3 and most other anti-V3 loop nAbs, 10A37 was atypical with its epitope positioned more towards the C-terminal half of the loop. To our knowledge, 10A37 is the most potent and broadly neutralizing anti-V3 loop mAb induced by vaccination. Interestingly, all seven anti-V3 loop mAbs competed with PGT121, suggesting a possibility that early induction of potent anti-V3 loop antibodies could prevent induction of more broadly neutralizing PGT121-like antibodies that target the conserved base of the V3 loop stem.

  13. Residues 39-56 of Stem Cell Factor Protein Sequence Are Capable of Stimulating the Expansion of Cord Blood CD34+ Cells.

    Science.gov (United States)

    Shen, Bin; Jiang, Wenhong; Fan, Jie; Dai, Wei; Ding, Xinxin; Jiang, Yongping

    2015-01-01

    Stem cell factor (SCF) can stimulate hematopoietic stem cell (HSC) expansion; however, the specific structural region(s) of SCF protein that are critical for this function are still unknown. A novel monoclonal antibody (named 23C8) against recombinant human SCF (rhSCF) was previously found to inhibit the ability of rhSCF to enhance HSC expansion, making it possible to identify the relevant active region to HSC. Eleven polypeptides were synthesized, which were designed to cover the full-length of rhSCF, with overlaps that are at least 3 amino acids long. ELISA was used to identify the polypeptide(s) that specifically react with the anti-SCF. The effects of the synthetic polypeptides on human HSC expansion, or on the ability of the full-length rhSCF to stimulate cell proliferation, were evaluated ex vivo. Total cell number was monitored using hemocytometer whereas CD34+ cell number was calculated based on the proportion determined via flow cytometry on day 6 of culture. Of all polypeptides analyzed, only one, named P0, corresponding to the SCF protein sequence at residues 39-56, was recognized by 23C8 mAb during ELISA. P0 stimulated the expansion of CD34+ cells derived from human umbilical cord blood (UCB). Addition of P0 increased the numbers of total mononucleated cells and CD34+ cells, by ~2 fold on day 6. P0 also showed partial competition against full-length rhSCF in the ex vivo cell expansion assay. Residues 39-56 of rhSCF comprise a critical functional region for its ability to enhance expansion of human UCB CD34+ cells. The peptide P0 is a potential candidate for further development as a synthetic substitute for rhSCF in laboratory and clinical applications.

  14. A short autocomplementary sequence plays an essential role in avian sarcoma-leukosis virus RNA dimerization.

    Science.gov (United States)

    Fossé, P; Motté, N; Roumier, A; Gabus, C; Muriaux, D; Darlix, J L; Paoletti, J

    1996-12-24

    Retroviral genomes consist of two identical RNA molecules joined noncovalently near their 5'-ends. Recently, two models have been proposed for RNA dimer formation on the basis of results obtained in vitro with human immunodeficiency virus type 1 RNA and Moloney murine leukemia virus RNA. It was first proposed that viral RNA dimerizes by forming an interstrand quadruple helix with purine tetrads. The second model postulates that RNA dimerization is initiated by a loop-loop interaction between the two RNA molecules. In order to better characterize the dimerization process of retroviral genomic RNA, we analyzed the in vitro dimerization of avian sarcoma-leukosis virus (ASLV) RNA using different transcripts. We determined the requirements for heterodimer formation, the thermal dissociation of RNA dimers, and the influence of antisense DNA oligonucleotides on dimer formation. Our results strongly suggest that purine tetrads are not involved in dimer formation. Data show that an autocomplementary sequence located upstream from the splice donor site and within a major packaging signal plays a crucial role in ASLV RNA dimer formation in vitro. This sequence is able to form a stem-loop structure, and phylogenetic analysis reveals that it is conserved in 28 different avian sarcoma and leukosis viruses. These results suggest that dimerization of ASLV RNA is initiated by a loop-loop interaction between two RNA molecules and provide an additional argument for the ubiquity of the dimerization process via loop-loop interaction.

  15. Alternative loop rings

    CERN Document Server

    Goodaire, EG; Polcino Milies, C

    1996-01-01

    For the past ten years, alternative loop rings have intrigued mathematicians from a wide cross-section of modern algebra. As a consequence, the theory of alternative loop rings has grown tremendously. One of the main developments is the complete characterization of loops which have an alternative but not associative, loop ring. Furthermore, there is a very close relationship between the algebraic structures of loop rings and of group rings over 2-groups. Another major topic of research is the study of the unit loop of the integral loop ring. Here the interaction between loop rings and group ri

  16. Quantitative assessment of hematopoietic chimerism by quantitative real-time polymerase chain reaction of sequence polymorphism systems after hematopoietic stem cell transplantation.

    Science.gov (United States)

    Qin, Xiao-ying; Li, Guo-xuan; Qin, Ya-zhen; Wang, Yu; Wang, Feng-rong; Liu, Dai-hong; Xu, Lan-ping; Chen, Huan; Han, Wei; Wang, Jing-zhi; Zhang, Xiao-hui; Li, Jin-lan; Li, Ling-di; Liu, Kai-yan; Huang, Xiao-jun

    2011-08-01

    Analysis of changes in recipient and donor hematopoietic cell origin is extremely useful to monitor the effect of hematopoietic stem cell transplantation (HSCT) and sequential adoptive immunotherapy by donor lymphocyte infusions. We developed a sensitive, reliable and rapid real-time PCR method based on sequence polymorphism systems to quantitatively assess the hematopoietic chimerism after HSCT. A panel of 29 selected sequence polymorphism (SP) markers was screened by real-time PCR in 101 HSCT patients with leukemia and other hematological diseases. The chimerism kinetics of bone marrow samples of 8 HSCT patients in remission and relapse situations were followed longitudinally. Recipient genotype discrimination was possible in 97.0% (98 of 101) with a mean number of 2.5 (1-7) informative markers per recipient/donor pair. Using serial dilutions of plasmids containing specific SP markers, the linear correlation (r) of 0.99, the slope between -3.2 and -3.7 and the sensitivity of 0.1% were proved reproducible. By this method, it was possible to very accurately detect autologous signals in the range from 0.1% to 30%. The accuracy of the method in the very important range of autologous signals below 5% was extraordinarily high (standard deviation real-time PCR method over short tandem repeat PCR chimerism assays is the absence of PCR competition and plateau biases, with demonstrated greater sensitivity and linearity. Finally, we prospectively analyzed bone marrow samples of 8 patients who received allografts and presented the chimerism kinetics of remission and relapse situations that illustrated the sensitivity level and the promising clinical application of this method. This SP-based real-time PCR assay provides a rapid, sensitive, and accurate quantitative assessment of mixed chimerism that can be useful in predicting graft rejection and early relapse.

  17. Re-analysis of RNA-Sequencing Data on Apple Stem Grooving Virus infected Apple reveals more significant differentially expressed genes

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    Bipin Balan

    2017-12-01

    Full Text Available RNA sequencing (RNA-Seq technology has enabled the researchers to investigate the host global gene expression changes in plant-virus interactions which helped to understand the molecular basis of virus diseases. The re-analysis of RNA-Seq studies using most updated genome version and the available best analysis pipeline will produce most accurate results. In this study, we re-analysed the Apple stem grooving virus (ASGV infected apple shoots in comparison with that of virus-free in vitro shoots [1] using the most updated Malus x domestica genome downloaded from Phytozome database. The re-analysis was done by using HISAT2 software and Cufflinks program was used to mine the differentially expressed genes. We found that ~20% more reads was mapped to the latest genome using the updated pipeline, which proved the significance of such re-analysis. The comparison of the updated results with that of previous was done. In addition, we performed protein-protein interaction (PPI to investigate the proteins affected by ASGV infection.

  18. Conformal anomaly of super Wilson loop

    Energy Technology Data Exchange (ETDEWEB)

    Belitsky, A.V., E-mail: andrei.belitsky@asu.edu [Department of Physics, Arizona State University, Tempe, AZ 85287-1504 (United States)

    2012-09-11

    Classically supersymmetric Wilson loop on a null polygonal contour possesses all symmetries required to match it onto non-MHV amplitudes in maximally supersymmetric Yang-Mills theory. However, to define it quantum mechanically, one is forced to regularize it since perturbative loop diagrams are not well defined due to presence of ultraviolet divergences stemming from integration in the vicinity of the cusps. A regularization that is adopted by practitioners by allowing one to use spinor helicity formalism, on the one hand, and systematically go to higher orders of perturbation theory is based on a version of dimensional regularization, known as Four-Dimensional Helicity scheme. Recently it was demonstrated that its use for the super Wilson loop at one loop breaks both conformal symmetry and Poincare supersymmetry. Presently, we exhibit the origin for these effects and demonstrate how one can undo this breaking. The phenomenon is alike the one emerging in renormalization group mixing of conformal operators in conformal theories when one uses dimensional regularization. The rotation matrix to the diagonal basis is found by means of computing the anomaly in the Ward identity for the conformal boost. Presently, we apply this ideology to the super Wilson loop. We compute the one-loop conformal anomaly for the super Wilson loop and find that the anomaly depends on its Grassmann coordinates. By subtracting this anomalous contribution from the super Wilson loop we restore its interpretation as a dual description for reduced non-MHV amplitudes which are expressed in terms of superconformal invariants.

  19. Comparison of energy expenditure and closed-loop performance of thermal and reactive distillation sequences coupled for biodiesel production; Comparacion de gasto energetico y desempeno a lazo cerrado de secuencias de destilacion reactiva y termicamente acopladas para produccion de biodiesel

    Energy Technology Data Exchange (ETDEWEB)

    Cornejo-Jacob, J.L [Universidad Michoacana de San Nicolas de Hidalgo, Morelia, Michoacan (Mexico); Vazquez-Ojeda, M; Segovia-Hernandez, J.G; Hernandez, S [Universidad de Guanajuato, Guanajuato, Guanajuato (Mexico); Maya-Yescas, R. [Universidad Michoacana de San Nicolas de Hidalgo, Morelia, Michoacan (Mexico)]. E-mail: rmayay@umich.mx

    2013-03-15

    Biodiesel is the common name for fatty acid methyl esters, obtained by esterification (basic catalysis) or trans-esterification (acid catalysis) of vegetable or animal oils with alcohols, and used as liquid fuel. Production involves the reaction, under mild conditions, between the oil and, typically, excess of methanol. Traditional production of biodiesel exhibits some handicaps, such as the shift of equilibrium to fatty acids by using excess of alcohol that must be separated and recycled. As alternative, it is possible to integrate reaction/separation operations into a single intensified unit, a reactive distillation column, followed by a second separation unit. These configurations exhibit several advantages such as shifting equilibrium in the reactive region and, because of the thermal integration with the second unit, energy savings during products separation. In order to design these production sequences taking advantage of steady state knowledge (energy savings) and considering dynamic performance, this work performs a controllability analysis for six possible configurations; open-loop control properties, evaluated by single value decomposition, are probed by implementing PI controllers to the system. The reactive distillation column coupled to a stripper, without reboilers, shows to be the best option in terms of closed-loop performance and energy savings. [Spanish] Biodiesel es el nombre comun dado a metil esteres de acidos grasos obtenidos por esterificacion (catalisis basica) o trans-esterificacion (catalisis acida) de aceites animales o vegetales con alcoholes, y usados como combustibles liquidos. Su produccion involucra la reaccion entre el aceite y, tipicamente, exceso de metanol a condiciones moderadas. La produccion tradicional de biodiesel exhibe algunas desventajas como el desplazamiento del equilibrio hacia acidos grasos debido al exceso de alcohol, que debe ser separado y reciclado. Alternativamente, es posible integrar las operaciones reaccion

  20. Inhibition of HIV Replication by Cyclic and Hairpin PNAs Targeting the HIV-1 TAR RNA Loop

    Science.gov (United States)

    Upert, Gregory; Di Giorgio, Audrey; Upadhyay, Alok; Manvar, Dinesh; Pandey, Nootan; Pandey, Virendra N.; Patino, Nadia

    2012-01-01

    Human immunodeficiency virus-1 (HIV-1) replication and gene expression entails specific interaction of the viral protein Tat with its transactivation responsive element (TAR), to form a highly stable stem-bulge-loop structure. Previously, we described triphenylphosphonium (TPP) cation-based vectors that efficiently deliver nucleotide analogs (PNAs) into the cytoplasm of cells. In particular, we showed that the TPP conjugate of a linear 16-mer PNA targeting the apical stem-loop region of TAR impedes Tat-mediated transactivation of the HIV-1 LTR in vitro and also in cell culture systems. In this communication, we conjugated TPP to cyclic and hairpin PNAs targeting the loop region of HIV-1 TAR and evaluated their antiviral efficacy in a cell culture system. We found that TPP-cyclic PNAs containing only 8 residues, showed higher antiviral potency compared to hairpin PNAs of 12 or 16 residues. We further noted that the TPP-conjugates of the 8-mer cyclic PNA as well as the 16-mer linear PNA displayed similar antiviral efficacy. However, cyclic PNAs were shown to be highly specific to their target sequences. This communication emphasizes on the importance of small constrained cyclic PNAs over both linear and hairpin structures for targeting biologically relevant RNA hairpins. PMID:23029603

  1. Inhibition of HIV Replication by Cyclic and Hairpin PNAs Targeting the HIV-1 TAR RNA Loop

    Directory of Open Access Journals (Sweden)

    Gregory Upert

    2012-01-01

    Full Text Available Human immunodeficiency virus-1 (HIV-1 replication and gene expression entails specific interaction of the viral protein Tat with its transactivation responsive element (TAR, to form a highly stable stem-bulge-loop structure. Previously, we described triphenylphosphonium (TPP cation-based vectors that efficiently deliver nucleotide analogs (PNAs into the cytoplasm of cells. In particular, we showed that the TPP conjugate of a linear 16-mer PNA targeting the apical stem-loop region of TAR impedes Tat-mediated transactivation of the HIV-1 LTR in vitro and also in cell culture systems. In this communication, we conjugated TPP to cyclic and hairpin PNAs targeting the loop region of HIV-1 TAR and evaluated their antiviral efficacy in a cell culture system. We found that TPP-cyclic PNAs containing only 8 residues, showed higher antiviral potency compared to hairpin PNAs of 12 or 16 residues. We further noted that the TPP-conjugates of the 8-mer cyclic PNA as well as the 16-mer linear PNA displayed similar antiviral efficacy. However, cyclic PNAs were shown to be highly specific to their target sequences. This communication emphasizes on the importance of small constrained cyclic PNAs over both linear and hairpin structures for targeting biologically relevant RNA hairpins.

  2. Loop Transfer Matrix and Loop Quantum Mechanics

    International Nuclear Information System (INIS)

    Savvidy, George K.

    2000-01-01

    The gonihedric model of random surfaces on a 3d Euclidean lattice has equivalent representation in terms of transfer matrix K(Q i ,Q f ), which describes the propagation of loops Q. We extend the previous construction of the loop transfer matrix to the case of nonzero self-intersection coupling constant κ. We introduce the loop generalization of Fourier transformation which allows to diagonalize transfer matrices, that depend on symmetric difference of loops only and express all eigenvalues of 3d loop transfer matrix through the correlation functions of the corresponding 2d statistical system. The loop Fourier transformation allows to carry out the analogy with quantum mechanics of point particles, to introduce conjugate loop momentum P and to define loop quantum mechanics. We also consider transfer matrix on 4d lattice which describes propagation of memebranes. This transfer matrix can also be diagonalized by using the generalized Fourier transformation, and all its eigenvalues are equal to the correlation functions of the corresponding 3d statistical system. In particular the free energy of the 4d membrane system is equal to the free energy of 3d gonihedric system of loops and is equal to the free energy of 2d Ising model. (author)

  3. Stem Cells

    Science.gov (United States)

    Stem cells are cells with the potential to develop into many different types of cells in the body. ... the body. There are two main types of stem cells: embryonic stem cells and adult stem cells. Stem ...

  4. Dynamical system modeling to simulate donor T cell response to whole exome sequencing-derived recipient peptides: Understanding randomness in alloreactivity incidence following stem cell transplantation.

    Directory of Open Access Journals (Sweden)

    Vishal Koparde

    Full Text Available Quantitative relationship between the magnitude of variation in minor histocompatibility antigens (mHA and graft versus host disease (GVHD pathophysiology in stem cell transplant (SCT donor-recipient pairs (DRP is not established. In order to elucidate this relationship, whole exome sequencing (WES was performed on 27 HLA matched related (MRD, & 50 unrelated donors (URD, to identify nonsynonymous single nucleotide polymorphisms (SNPs. An average 2,463 SNPs were identified in MRD, and 4,287 in URD DRP (p<0.01; resulting peptide antigens that may be presented on HLA class I molecules in each DRP were derived in silico (NetMHCpan ver2.0 and the tissue expression of proteins these were derived from determined (GTex. MRD DRP had an average 3,670 HLA-binding-alloreactive peptides, putative mHA (pmHA with an IC50 of <500 nM, and URD, had 5,386 (p<0.01. To simulate an alloreactive donor cytotoxic T cell response, the array of pmHA in each patient was considered as an operator matrix modifying a hypothetical cytotoxic T cell clonal vector matrix; each responding T cell clone's proliferation was determined by the logistic equation of growth, accounting for HLA binding affinity and tissue expression of each alloreactive peptide. The resulting simulated organ-specific alloreactive T cell clonal growth revealed marked variability, with the T cell count differences spanning orders of magnitude between different DRP. Despite an estimated, uniform set of constants used in the model for all DRP, and a heterogeneously treated group of patients, higher total and organ-specific T cell counts were associated with cumulative incidence of moderate to severe GVHD in recipients. In conclusion, exome wide sequence differences and the variable alloreactive peptide binding to HLA in each DRP yields a large range of possible alloreactive donor T cell responses. Our findings also help understand the apparent randomness observed in the development of alloimmune responses.

  5. Next-generation sequencing technology a new tool for killer cell immunoglobulin-like receptor allele typing in hematopoietic stem cell transplantation.

    Science.gov (United States)

    Maniangou, B; Retière, C; Gagne, K

    2018-02-01

    Killer cell Immunoglobulin-like Receptor (KIR) genes are a family of genes located together within the leukocyte receptor cluster on human chromosome 19q13.4. To date, 17 KIR genes have been identified including nine inhibitory genes (2DL1/L2/L3/L4/L5A/L5B, 3DL1/L2/L3), six activating genes (2DS1/S2/S3/S4/S5, 3DS1) and two pseudogenes (2DP1, 3DP1) classified into group A (KIR A) and group B (KIR B) haplotypes. The number and the nature of KIR genes vary between the individuals. In addition, these KIR genes are known to be polymorphic at allelic level (907 alleles described in July 2017). KIR genes encode for receptors which are predominantly expressed by Natural Killer (NK) cells. KIR receptors recognize HLA class I molecules and are able to kill residual recipient leukemia cells, and thus reduce the likelihood of relapse. KIR alleles of Hematopoietic Stem Cell (HSC) donor would require to be known (Alicata et al. Eur J Immunol 2016) because the KIR allele polymorphism may affect both the KIR + NK cell phenotype and function (Gagne et al. Eur J Immunol 2013; Bari R, et al. Sci Rep 2016) as well as HSCT outcome (Boudreau et al. JCO 2017). The introduction of the Next Generation Sequencing (NGS) has overcome current conventional DNA sequencing method limitations, known to be time consuming. Recently, a novel NGS KIR allele typing approach of all KIR genes was developed by our team in Nantes from 30 reference DNAs (Maniangou et al. Front in Immunol 2017). This NGS KIR allele typing approach is simple, fast, reliable, specific and showed a concordance rate of 95% for centromeric and telomeric KIR genes in comparison with high-resolution KIR typing obtained to those published data using exome capture (Norman PJ et al. Am J Hum Genet 2016). This NGS KIR allele typing approach may also be used in reproduction and to better study KIR + NK cell implication in the control of viral infections. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  6. Sequence Classification: 894064 [

    Lifescience Database Archive (English)

    Full Text Available al protein; intron of RPL18A pre-mRNA forms stem-loop structures that are a target for Rnt1p cleavage leading to degradation; Rpl18ap || http://www.ncbi.nlm.nih.gov/protein/6324452 ...

  7. The Brownian loop soup

    OpenAIRE

    Lawler, Gregory F.; Werner, Wendelin

    2003-01-01

    We define a natural conformally invariant measure on unrooted Brownian loops in the plane and study some of its properties. We relate this measure to a measure on loops rooted at a boundary point of a domain and show how this relation gives a way to ``chronologically add Brownian loops'' to simple curves in the plane.

  8. Genetic instability associated with loop or stem–loop structures within transcription units can be independent of nucleotide excision repair

    Science.gov (United States)

    Burns, John A; Chowdhury, Moinuddin A; Cartularo, Laura; Berens, Christian; Scicchitano, David A

    2018-01-01

    Abstract Simple sequence repeats (SSRs) are found throughout the genome, and under some conditions can change in length over time. Germline and somatic expansions of trinucleotide repeats are associated with a series of severely disabling illnesses, including Huntington's disease. The underlying mechanisms that effect SSR expansions and contractions have been experimentally elusive, but models suggesting a role for DNA repair have been proposed, in particular the involvement of transcription-coupled nucleotide excision repair (TCNER) that removes transcription-blocking DNA damage from the transcribed strand of actively expressed genes. If the formation of secondary DNA structures that are associated with SSRs were to block RNA polymerase progression, TCNER could be activated, resulting in the removal of the aberrant structure and a concomitant change in the region's length. To test this, TCNER activity in primary human fibroblasts was assessed on defined DNA substrates containing extrahelical DNA loops that lack discernible internal base pairs or DNA stem–loops that contain base pairs within the stem. The results show that both structures impede transcription elongation, but there is no corresponding evidence that nucleotide excision repair (NER) or TCNER operates to remove them. PMID:29474673

  9. LoopX: A Graphical User Interface-Based Database for Comprehensive Analysis and Comparative Evaluation of Loops from Protein Structures.

    Science.gov (United States)

    Kadumuri, Rajashekar Varma; Vadrevu, Ramakrishna

    2017-10-01

    Due to their crucial role in function, folding, and stability, protein loops are being targeted for grafting/designing to create novel or alter existing functionality and improve stability and foldability. With a view to facilitate a thorough analysis and effectual search options for extracting and comparing loops for sequence and structural compatibility, we developed, LoopX a comprehensively compiled library of sequence and conformational features of ∼700,000 loops from protein structures. The database equipped with a graphical user interface is empowered with diverse query tools and search algorithms, with various rendering options to visualize the sequence- and structural-level information along with hydrogen bonding patterns, backbone φ, ψ dihedral angles of both the target and candidate loops. Two new features (i) conservation of the polar/nonpolar environment and (ii) conservation of sequence and conformation of specific residues within the loops have also been incorporated in the search and retrieval of compatible loops for a chosen target loop. Thus, the LoopX server not only serves as a database and visualization tool for sequence and structural analysis of protein loops but also aids in extracting and comparing candidate loops for a given target loop based on user-defined search options.

  10. Renormalization of loop functions for all loops

    International Nuclear Information System (INIS)

    Brandt, R.A.; Neri, F.; Sato, M.

    1981-01-01

    It is shown that the vacuum expectation values W(C 1 ,xxx, C/sub n/) of products of the traces of the path-ordered phase factors P exp[igcontour-integral/sub C/iA/sub μ/(x)dx/sup μ/] are multiplicatively renormalizable in all orders of perturbation theory. Here A/sub μ/(x) are the vector gauge field matrices in the non-Abelian gauge theory with gauge group U(N) or SU(N), and C/sub i/ are loops (closed paths). When the loops are smooth (i.e., differentiable) and simple (i.e., non-self-intersecting), it has been shown that the generally divergent loop functions W become finite functions W when expressed in terms of the renormalized coupling constant and multiplied by the factors e/sup -K/L(C/sub i/), where K is linearly divergent and L(C/sub i/) is the length of C/sub i/. It is proved here that the loop functions remain multiplicatively renormalizable even if the curves have any finite number of cusps (points of nondifferentiability) or cross points (points of self-intersection). If C/sub γ/ is a loop which is smooth and simple except for a single cusp of angle γ, then W/sub R/(C/sub γ/) = Z(γ)W(C/sub γ/) is finite for a suitable renormalization factor Z(γ) which depends on γ but on no other characteristic of C/sub γ/. This statement is made precise by introducing a regularization, or via a loop-integrand subtraction scheme specified by a normalization condition W/sub R/(C-bar/sub γ/) = 1 for an arbitrary but fixed loop C-bar/sub γ/. Next, if C/sub β/ is a loop which is smooth and simple except for a cross point of angles β, then W(C/sub β/) must be renormalized together with the loop functions of associated sets S/sup i//sub β/ = ]C/sup i/ 1 ,xxx, C/sup i//sub p/i] (i = 2,xxx,I) of loops C/sup i//sub q/ which coincide with certain parts of C/sub β/equivalentC 1 1 . Then W/sub R/(S/sup i//sub β/) = Z/sup i/j(β)W(S/sup j//sub β/) is finite for a suitable matrix Z/sup i/j

  11. Random walk loop soup

    OpenAIRE

    Lawler, Gregory F.; Ferreras, José A. Trujillo

    2004-01-01

    The Brownian loop soup introduced in Lawler and Werner (2004) is a Poissonian realization from a sigma-finite measure on unrooted loops. This measure satisfies both conformal invariance and a restriction property. In this paper, we define a random walk loop soup and show that it converges to the Brownian loop soup. In fact, we give a strong approximation result making use of the strong approximation result of Koml\\'os, Major, and Tusn\\'ady. To make the paper self-contained, we include a proof...

  12. Primary structure and promoter analysis of leghemoglobin genes of the stem-nodulated tropical legume Sesbania rostrata: conserved coding sequences, cis-elements and trans-acting factors

    DEFF Research Database (Denmark)

    Metz, B A; Welters, P; Hoffmann, H J

    1988-01-01

    The primary structure of a leghemoglobin (lb) gene from the stem-nodulated, tropical legume Sesbania rostrata and two lb gene promoter regions was analysed. The S. rostrata lb gene structure and Lb amino acid composition were found to be highly conserved with previously described lb genes and Lb ...

  13. Design of a PWR emergency core cooling simulator loop

    International Nuclear Information System (INIS)

    Melo, C.A. de.

    1982-12-01

    The preliminary design of a PWR Emergency Core Cooling Simulator Loop for investigations of the phenomena involved in a postulated Loss-of-Coolant Accident, during the Reflooding Phase, is presented. The functions of each component of the loop, the design methods and calculations, the specification of the instrumentation, the system operation sequence, the materials list and a cost assessment are included. (Author) [pt

  14. On loop extensions and cohomology of loops

    OpenAIRE

    Benítez, Rolando Jiménez; Meléndez, Quitzeh Morales

    2015-01-01

    In this paper are defined cohomology-like groups that classify loop extensions satisfying a given identity in three variables for association identities, and in two variables for the case of commutativity. It is considered a large amount of identities. This groups generalize those defined in works of Nishigori [2] and of Jhonson and Leedham-Green [4]. It is computed the number of metacyclic extensions for trivial action of the quotient on the kernel in one particular case for left Bol loops a...

  15. Neutron transport in irradiation loops (IRENE loop)

    International Nuclear Information System (INIS)

    Sarsam, Maher.

    1980-09-01

    This thesis is composed of two parts with different aspects. Part one is a technical description of the loop and its main ancillary facilities as well as of the safety and operational regulations. The measurement methods on the model of the ISIS reactor and on the loop in the OSIRIS reactor are described. Part two deals with the possibility of calculating the powers dissipated by each rod of the fuel cluster, using appropriate computer codes, not only in the reflector but also in the core and to suggest a method of calculation [fr

  16. Expression profiles of cancer stem cell markers: CD133, CD44, Musashi-1 and EpCAM in the cardiac mucosa-Barrett's esophagus-early esophageal adenocarcinoma-advanced esophageal adenocarcinoma sequence.

    Science.gov (United States)

    Mokrowiecka, Anna; Veits, Lothar; Falkeis, Christina; Musial, Jacek; Kordek, Radzislaw; Lochowski, Mariusz; Kozak, Jozef; Wierzchniewska-Lawska, Agnieszka; Vieth, Michael; Malecka-Panas, Ewa

    2017-03-01

    Barrett's esophagus (BE), which develops as a result of gastroesophageal reflux disease, is a preneoplastic condition for esophageal adenocarcinoma (EAC). A new hypothesis suggests that cancer is a disease of stem cells, however, their expression and pathways in BE - EAC sequence are not fully elucidated yet. We used a panel of putative cancer stem cells markers to identify stem cells in consecutive steps of BE-related cancer progression. Immunohistochemistry was performed on formalin-fixed, paraffin-embedded blocks from 58 patients with normal cardiac mucosa (n=5), BE (n=14), early EAC (pT1) from mucosal resection (n=17) and advanced EAC (pT1-T4) from postoperative specimens (n=22). Expression of the CD133, CD44, Musashi-1 and EpCAM was analyzed using respective monoclonal antibodies. All markers showed a heterogeneous expression pattern, mainly at the base of the crypts of Barrett's epithelium and EAC, with positive stromal cells in metaplastic and dysplastic lesions. Immuno-expression of EpCAM, CD44 and CD133 in cardiac mucosa was significantly lower (mean immunoreactivity score (IRS)=1.2; 0.0; 0.4; respectively) compared to their expression in Barrett's metaplasia (mean IRS=4.3; 0.14; 0.7; respectively), in early adenocarcinoma (mean IRS=4.4; 0.29; 1.3; respectively) and in advanced adenocarcinoma (mean IRS=6.6; 0.7; 2.7; respectively) (p<0.05). On the contrary, Musashi-1 expression was higher in BE and early ADC compared to GM and advanced ADC (NS). Our results suggest that the stem cells could be present in premalignant lesions. EpCAM, CD44 and CD133 expression could be candidate markers for BE progression, whereas Musashi-1 may be a marker of the small intestinal features of Barrett's mucosa. Copyright © 2016 Elsevier GmbH. All rights reserved.

  17. Saturating representation of loop conformational fragments in structure databanks

    Directory of Open Access Journals (Sweden)

    Fiser András

    2006-07-01

    Full Text Available Abstract Background Short fragments of proteins are fundamental starting points in various structure prediction applications, such as in fragment based loop modeling methods but also in various full structure build-up procedures. The applicability and performance of these approaches depend on the availability of short fragments in structure databanks. Results We studied the representation of protein loop fragments up to 14 residues in length. All possible query fragments found in sequence databases (Sequence Space were clustered and cross referenced with available structural fragments in Protein Data Bank (Structure Space. We found that the expansion of PDB in the last few years resulted in a dense coverage of loop conformational fragments. For each loops of length 8 in the current Sequence Space there is at least one loop in Structure Space with 50% or higher sequence identity. By correlating sequence and structure clusters of loops we found that a 50% sequence identity generally guarantees structural similarity. These percentages of coverage at 50% sequence cutoff drop to 96, 94, 68, 53, 33 and 13% for loops of length 9, 10, 11, 12, 13, and 14, respectively. There is not a single loop in the current Sequence Space at any length up to 14 residues that is not matched with a conformational segment that shares at least 20% sequence identity. This minimum observed identity is 40% for loops of 12 residues or shorter and is as high as 50% for 10 residue or shorter loops. We also assessed the impact of rapidly growing sequence databanks on the estimated number of new loop conformations and found that while the number of sequentially unique sequence segments increased about six folds during the last five years there are almost no unique conformational segments among these up to 12 residues long fragments. Conclusion The results suggest that fragment based prediction approaches are not limited any more by the completeness of fragments in databanks but

  18. Water loop for training

    International Nuclear Information System (INIS)

    Moeller, S.V.

    1983-02-01

    The procedures used to operate the water loop of the Institute of Nuclear Enginering (IEN) in Brazil are presented. The aim is to help future operators of the training water loop in the operation technique and in a better comprehension of the phenomena occured during the execution of an experience. (E.G.) [pt

  19. Ciliate telomerase RNA loop IV nucleotides promote hierarchical RNP assembly and holoenzyme stability.

    Science.gov (United States)

    Robart, Aaron R; O'Connor, Catherine M; Collins, Kathleen

    2010-03-01

    Telomerase adds simple-sequence repeats to chromosome 3' ends to compensate for the loss of repeats with each round of genome replication. To accomplish this de novo DNA synthesis, telomerase uses a template within its integral RNA component. In addition to providing the template, the telomerase RNA subunit (TER) also harbors nontemplate motifs that contribute to the specialized telomerase catalytic cycle of reiterative repeat synthesis. Most nontemplate TER motifs function through linkage with the template, but in ciliate and vertebrate telomerases, a stem-loop motif binds telomerase reverse transcriptase (TERT) and reconstitutes full activity of the minimal recombinant TERT+TER RNP, even when physically separated from the template. Here, we resolve the functional requirements for this motif of ciliate TER in physiological RNP context using the Tetrahymena thermophila p65-TER-TERT core RNP reconstituted in vitro and the holoenzyme reconstituted in vivo. Contrary to expectation based on assays of the minimal recombinant RNP, we find that none of a panel of individual loop IV nucleotide substitutions impacts the profile of telomerase product synthesis when reconstituted as physiological core RNP or holoenzyme RNP. However, loop IV nucleotide substitutions do variably reduce assembly of TERT with the p65-TER complex in vitro and reduce the accumulation and stability of telomerase RNP in endogenous holoenzyme context. Our results point to a unifying model of a conformational activation role for this TER motif in the telomerase RNP enzyme.

  20. R-loops: targets for nuclease cleavage and repeat instability.

    Science.gov (United States)

    Freudenreich, Catherine H

    2018-01-11

    R-loops form when transcribed RNA remains bound to its DNA template to form a stable RNA:DNA hybrid. Stable R-loops form when the RNA is purine-rich, and are further stabilized by DNA secondary structures on the non-template strand. Interestingly, many expandable and disease-causing repeat sequences form stable R-loops, and R-loops can contribute to repeat instability. Repeat expansions are responsible for multiple neurodegenerative diseases, including Huntington's disease, myotonic dystrophy, and several types of ataxias. Recently, it was found that R-loops at an expanded CAG/CTG repeat tract cause DNA breaks as well as repeat instability (Su and Freudenreich, Proc Natl Acad Sci USA 114, E8392-E8401, 2017). Two factors were identified as causing R-loop-dependent breaks at CAG/CTG tracts: deamination of cytosines and the MutLγ (Mlh1-Mlh3) endonuclease, defining two new mechanisms for how R-loops can generate DNA breaks (Su and Freudenreich, Proc Natl Acad Sci USA 114, E8392-E8401, 2017). Following R-loop-dependent nicking, base excision repair resulted in repeat instability. These results have implications for human repeat expansion diseases and provide a paradigm for how RNA:DNA hybrids can cause genome instability at structure-forming DNA sequences. This perspective summarizes mechanisms of R-loop-induced fragility at G-rich repeats and new links between DNA breaks and repeat instability.

  1. Large lithium loop experience

    International Nuclear Information System (INIS)

    Kolowith, R.; Owen, T.J.; Berg, J.D.; Atwood, J.M.

    1981-10-01

    An engineering design and operating experience of a large, isothermal, lithium-coolant test loop are presented. This liquid metal coolant loop is called the Experimental Lithium System (ELS) and has operated safely and reliably for over 6500 hours through September 1981. The loop is used for full-scale testing of components for the Fusion Materials Irradiation Test (FMIT) Facility. Main system parameters include coolant temperatures to 430 0 C and flow to 0.038 m 3 /s (600 gal/min). Performance of the main pump, vacuum system, and control system is discussed. Unique test capabilities of the ELS are also discussed

  2. Natively unstructured loops differ from other loops.

    Directory of Open Access Journals (Sweden)

    Avner Schlessinger

    2007-07-01

    Full Text Available Natively unstructured or disordered protein regions may increase the functional complexity of an organism; they are particularly abundant in eukaryotes and often evade structure determination. Many computational methods predict unstructured regions by training on outliers in otherwise well-ordered structures. Here, we introduce an approach that uses a neural network in a very different and novel way. We hypothesize that very long contiguous segments with nonregular secondary structure (NORS regions differ significantly from regular, well-structured loops, and that a method detecting such features could predict natively unstructured regions. Training our new method, NORSnet, on predicted information rather than on experimental data yielded three major advantages: it removed the overlap between testing and training, it systematically covered entire proteomes, and it explicitly focused on one particular aspect of unstructured regions with a simple structural interpretation, namely that they are loops. Our hypothesis was correct: well-structured and unstructured loops differ so substantially that NORSnet succeeded in their distinction. Benchmarks on previously used and new experimental data of unstructured regions revealed that NORSnet performed very well. Although it was not the best single prediction method, NORSnet was sufficiently accurate to flag unstructured regions in proteins that were previously not annotated. In one application, NORSnet revealed previously undetected unstructured regions in putative targets for structural genomics and may thereby contribute to increasing structural coverage of large eukaryotic families. NORSnet found unstructured regions more often in domain boundaries than expected at random. In another application, we estimated that 50%-70% of all worm proteins observed to have more than seven protein-protein interaction partners have unstructured regions. The comparative analysis between NORSnet and DISOPRED2 suggested

  3. Introduction to Loop Heat Pipes

    Science.gov (United States)

    Ku, Jentung

    2015-01-01

    This is the presentation file for the short course Introduction to Loop Heat Pipes, to be conducted at the 2015 Thermal Fluids and Analysis Workshop, August 3-7, 2015, Silver Spring, Maryland. This course will discuss operating principles and performance characteristics of a loop heat pipe. Topics include: 1) pressure profiles in the loop; 2) loop operating temperature; 3) operating temperature control; 4) loop startup; 4) loop shutdown; 5) loop transient behaviors; 6) sizing of loop components and determination of fluid inventory; 7) analytical modeling; 8) examples of flight applications; and 9) recent LHP developments.

  4. Diffusion of Wilson loops

    International Nuclear Information System (INIS)

    Brzoska, A.M.; Lenz, F.; Thies, M.; Negele, J.W.

    2005-01-01

    A phenomenological analysis of the distribution of Wilson loops in SU(2) Yang-Mills theory is presented in which Wilson loop distributions are described as the result of a diffusion process on the group manifold. It is shown that, in the absence of forces, diffusion implies Casimir scaling and, conversely, exact Casimir scaling implies free diffusion. Screening processes occur if diffusion takes place in a potential. The crucial distinction between screening of fundamental and adjoint loops is formulated as a symmetry property related to the center symmetry of the underlying gauge theory. The results are expressed in terms of an effective Wilson loop action and compared with various limits of SU(2) Yang-Mills theory

  5. Blind loop syndrome

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/article/001146.htm Blind loop syndrome To use the sharing features on ... Clinical Professor of Medicine, The George Washington University School of Medicine, Washington, DC. Also reviewed by David ...

  6. Mashup the OODA Loop

    National Research Council Canada - National Science Library

    Heier, Jeffrey E

    2008-01-01

    ...) processes via the Observe, Orient, Decide, and Act (OODA) Loop concept. As defined by Wikipedia, a mashup is a Website or application that combines the content from more than one source into an integrated presentation...

  7. Reactor loops at Chalk River

    International Nuclear Information System (INIS)

    Sochaski, R.O.

    1962-07-01

    This report describes broadly the nine in-reactor loops, and their components, located in and around the NRX and NRU reactors at Chalk River. First an introduction and general description is given of the loops and their function, supplemented with a table outlining some loop specifications and nine simplified flow sheets, one for each individual loop. The report then proceeds to classify each loop into two categories, the 'main loop circuit' and the 'auxiliary circuit', and descriptions are given of each circuit's components in turn. These components, in part, are comprised of the main loop pumps, the test section, loop heaters, loop coolers, delayed-neutron monitors, surge tank, Dowtherm coolers, loop piping. Here again photographs, drawings and tables are included to provide a clearer understanding of the descriptive literature and to include, in tables, some specifications of the more important components in each loop. (author)

  8. Dechanneling by dislocation loops

    International Nuclear Information System (INIS)

    Chalant, Gerard.

    1976-09-01

    Ion implantation always induces the creation of dislocation loops. When the damage profile is determined by a backscattering technique, the dechanneling by these loops is implicitely at the origin of these measurements. The dechanneling of alpha particles by dislocation loops produced by the coalescence of quenched-in vacancies in aluminium is studied. The dechanneling and the concentration of loops were determined simultaneously. The dechanneling width around dislocation was found equal to lambda=6A, both for perfect and imperfect loops having a mean diameter d=250A. In the latter case, a dechanneling probability chi=0.34 was determined for the stacking fault, in good agreement with previous determination in gold. A general formula is proposed which takes into account the variation of lambda with the curvature (or the diameter d) of the loops. Finally, by a series of isothermal anneals, the self-diffusion energy ΔH of aluminium was measured. The value obtained ΔH=1.32+-0.10eV is in good agreement with the values obtained by other methods [fr

  9. Investigating core genetic-and-epigenetic cell cycle networks for stemness and carcinogenic mechanisms, and cancer drug design using big database mining and genome-wide next-generation sequencing data.

    Science.gov (United States)

    Li, Cheng-Wei; Chen, Bor-Sen

    2016-10-01

    Recent studies have demonstrated that cell cycle plays a central role in development and carcinogenesis. Thus, the use of big databases and genome-wide high-throughput data to unravel the genetic and epigenetic mechanisms underlying cell cycle progression in stem cells and cancer cells is a matter of considerable interest. Real genetic-and-epigenetic cell cycle networks (GECNs) of embryonic stem cells (ESCs) and HeLa cancer cells were constructed by applying system modeling, system identification, and big database mining to genome-wide next-generation sequencing data. Real GECNs were then reduced to core GECNs of HeLa cells and ESCs by applying principal genome-wide network projection. In this study, we investigated potential carcinogenic and stemness mechanisms for systems cancer drug design by identifying common core and specific GECNs between HeLa cells and ESCs. Integrating drug database information with the specific GECNs of HeLa cells could lead to identification of multiple drugs for cervical cancer treatment with minimal side-effects on the genes in the common core. We found that dysregulation of miR-29C, miR-34A, miR-98, and miR-215; and methylation of ANKRD1, ARID5B, CDCA2, PIF1, STAMBPL1, TROAP, ZNF165, and HIST1H2AJ in HeLa cells could result in cell proliferation and anti-apoptosis through NFκB, TGF-β, and PI3K pathways. We also identified 3 drugs, methotrexate, quercetin, and mimosine, which repressed the activated cell cycle genes, ARID5B, STK17B, and CCL2, in HeLa cells with minimal side-effects.

  10. Epigenetic Loss of MLH1 Expression in Normal Human Hematopoietic Stem Cell Clones is Defined by the Promoter CpG Methylation Pattern Observed by High-Throughput Methylation Specific Sequencing.

    Science.gov (United States)

    Kenyon, Jonathan; Nickel-Meester, Gabrielle; Qing, Yulan; Santos-Guasch, Gabriela; Drake, Ellen; PingfuFu; Sun, Shuying; Bai, Xiaodong; Wald, David; Arts, Eric; Gerson, Stanton L

    Normal human hematopoietic stem and progenitor cells (HPC) lose expression of MLH1 , an important mismatch repair (MMR) pathway gene, with age. Loss of MMR leads to replication dependent mutational events and microsatellite instability observed in secondary acute myelogenous leukemia and other hematologic malignancies. Epigenetic CpG methylation upstream of the MLH1 promoter is a contributing factor to acquired loss of MLH1 expression in tumors of the epithelia and proximal mucosa. Using single molecule high-throughput bisulfite sequencing we have characterized the CpG methylation landscape from -938 to -337 bp upstream of the MLH1 transcriptional start site (position +0), from 30 hematopoietic colony forming cell clones (CFC) either expressing or not expressing MLH1 . We identify a correlation between MLH1 promoter methylation and loss of MLH1 expression. Additionally, using the CpG site methylation frequencies obtained in this study we were able to generate a classification algorithm capable of sorting the expressing and non-expressing CFC. Thus, as has been previously described for many tumor cell types, we report for the first time a correlation between the loss of MLH1 expression and increased MLH1 promoter methylation in CFC derived from CD34 + selected hematopoietic stem and progenitor cells.

  11. Logical inference techniques for loop parallelization

    KAUST Repository

    Oancea, Cosmin E.

    2012-01-01

    This paper presents a fully automatic approach to loop parallelization that integrates the use of static and run-time analysis and thus overcomes many known difficulties such as nonlinear and indirect array indexing and complex control flow. Our hybrid analysis framework validates the parallelization transformation by verifying the independence of the loop\\'s memory references. To this end it represents array references using the USR (uniform set representation) language and expresses the independence condition as an equation, S = Ø, where S is a set expression representing array indexes. Using a language instead of an array-abstraction representation for S results in a smaller number of conservative approximations but exhibits a potentially-high runtime cost. To alleviate this cost we introduce a language translation F from the USR set-expression language to an equally rich language of predicates (F(S) ⇒ S = Ø). Loop parallelization is then validated using a novel logic inference algorithm that factorizes the obtained complex predicates (F(S)) into a sequence of sufficient-independence conditions that are evaluated first statically and, when needed, dynamically, in increasing order of their estimated complexities. We evaluate our automated solution on 26 benchmarks from PERFECTCLUB and SPEC suites and show that our approach is effective in parallelizing large, complex loops and obtains much better full program speedups than the Intel and IBM Fortran compilers. Copyright © 2012 ACM.

  12. The interaction between the iron-responsive element binding protein and its cognate RNA is highly dependent upon both RNA sequence and structure.

    Science.gov (United States)

    Jaffrey, S R; Haile, D J; Klausner, R D; Harford, J B

    1993-09-25

    To assess the influence of RNA sequence/structure on the interaction RNAs with the iron-responsive element binding protein (IRE-BP), twenty eight altered RNAs were tested as competitors for an RNA corresponding to the ferritin H chain IRE. All changes in the loop of the predicted IRE hairpin and in the unpaired cytosine residue characteristically found in IRE stems significantly decreased the apparent affinity of the RNA for the IRE-BP. Similarly, alteration in the spacing and/or orientation of the loop and the unpaired cytosine of the stem by either increasing or decreasing the number of base pairs separating them significantly reduced efficacy as a competitor. It is inferred that the IRE-BP forms multiple contacts with its cognate RNA, and that these contacts, acting in concert, provide the basis for the high affinity of this interaction.

  13. Types of Stem Cells

    Science.gov (United States)

    ... Stem Cell Glossary Search Toggle Nav Types of Stem Cells Stem cells are the foundation from which all ... Learn About Stem Cells > Types of Stem Cells Stem cells Stem cells are the foundation for every organ ...

  14. Conformal boundary loop models

    International Nuclear Information System (INIS)

    Jacobsen, Jesper Lykke; Saleur, Hubert

    2008-01-01

    We study a model of densely packed self-avoiding loops on the annulus, related to the Temperley-Lieb algebra with an extra idempotent boundary generator. Four different weights are given to the loops, depending on their homotopy class and whether they touch the outer rim of the annulus. When the weight of a contractible bulk loop x≡q+q -1 element of (-2,2], this model is conformally invariant for any real weight of the remaining three parameters. We classify the conformal boundary conditions and give exact expressions for the corresponding boundary scaling dimensions. The amplitudes with which the sectors with any prescribed number and types of non-contractible loops appear in the full partition function Z are computed rigorously. Based on this, we write a number of identities involving Z which hold true for any finite size. When the weight of a contractible boundary loop y takes certain discrete values, y r ≡([r+1] q )/([r] q ) with r integer, other identities involving the standard characters K r,s of the Virasoro algebra are established. The connection with Dirichlet and Neumann boundary conditions in the O(n) model is discussed in detail, and new scaling dimensions are derived. When q is a root of unity and y=y r , exact connections with the A m type RSOS model are made. These involve precise relations between the spectra of the loop and RSOS model transfer matrices, valid in finite size. Finally, the results where y=y r are related to the theory of Temperley-Lieb cabling

  15. IGF-1R Promotes Symmetric Self-Renewal and Migration of Alkaline Phosphatase+ Germ Stem Cells through HIF-2α-OCT4/CXCR4 Loop under Hypoxia.

    Science.gov (United States)

    Kuo, Yung-Che; Au, Heng-Kien; Hsu, Jue-Liang; Wang, Hsiao-Feng; Lee, Chiung-Ju; Peng, Syue-Wei; Lai, Ssu-Chuan; Wu, Yu-Chih; Ho, Hong-Nerng; Huang, Yen-Hua

    2018-02-13

    Hypoxia cooperates with endocrine signaling to maintain the symmetric self-renewal proliferation and migration of embryonic germline stem cells (GSCs). However, the lack of an appropriate in vitro cell model has dramatically hindered the understanding of the mechanism underlying this cooperation. Here, using a serum-free system, we demonstrated that hypoxia significantly induced the GSC mesenchymal transition, increased the expression levels of the pluripotent transcription factor OCT4 and migration-associated proteins (SDF-1, CXCR4, IGF-1, and IGF-1R), and activated the cellular expression and translocalization of the CXCR4-downstream proteins ARP3/pFAK. The underlying mechanism involved significant IGF-1/IGF-1R activation of OCT4/CXCR4 expression through HIF-2α regulation. Picropodophyllin-induced inhibition of IGF-1R phosphorylation significantly suppressed hypoxia-induced SDF-1/CXCR4 expression and cell migration. Furthermore, transactivation between IGF-1R and CXCR4 was involved. In summary, we demonstrated that niche hypoxia synergistically cooperates with its associated IGF-1R signaling to regulate the symmetric division (self-renewal proliferation) and cell migration of alkaline phosphatase-positive GSCs through HIF-2α-OCT4/CXCR4 during embryogenesis. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  16. The complete mitochondrial genome sequence of the spider habronattus oregonensis reveals rearranged and extremely truncated tRNAs

    International Nuclear Information System (INIS)

    Masta, Susan E.; Boore, Jeffrey L.

    2004-01-01

    We sequenced the entire mitochondrial genome of the jumping spider Habronattus oregonensis of the arachnid order Araneae (Arthropoda: Chelicerata). A number of unusual features distinguish this genome from other chelicerate and arthropod mitochondrial genomes. Most of the transfer RNA gene sequences are greatly reduced in size and cannot be folded into typical cloverleaf-shaped secondary structures. At least nine of the tRNA sequences lack the potential to form TYC arm stem pairings, and instead are inferred to have TV-replacement loops. Furthermore, sequences that could encode the 3' aminoacyl acceptor stems in at least 10 tRNAs appear to be lacking, because fully paired acceptor stems are not possible and because the downstream sequences instead encode adjacent genes. Hence, these appear to be among the smallest known tRNA genes. We postulate that an RNA editing mechanism must exist to restore the 3' aminoacyl acceptor stems in order to allow the tRNAs to function. At least seven tRN As are rearranged with respect to the chelicerate Limulus polyphemus, although the arrangement of the protein-coding genes is identical. Most mitochondrial protein-coding genes of H. oregonensis have ATN as initiation codons, as commonly found in arthropod mtDNAs, but cytochrome oxidase subunit 2 and 3 genes apparently use UUG as an initiation codon. Finally, many of the gene sequences overlap one another and are truncated. This 14,381 bp genome, the first mitochondrial genome of a spider yet sequenced, is one of the smallest arthropod mitochondrial genomes known. We suggest that post transcriptional RNA editing can likely maintain function of the tRNAs while permitting the accumulation of mutations that would otherwise be deleterious. Such mechanisms may have allowed for the minimization of the spider mitochondrial genome

  17. Loop quantum gravity

    International Nuclear Information System (INIS)

    Pullin, J.

    2015-01-01

    Loop quantum gravity is one of the approaches that are being studied to apply the rules of quantum mechanics to the gravitational field described by the theory of General Relativity . We present an introductory summary of the main ideas and recent results. (Author)

  18. Blind Loop Syndrome

    Science.gov (United States)

    ... or scleroderma involving the small intestine History of radiation therapy to the abdomen Diabetes Diverticulosis of the small intestine Complications A blind loop can cause escalating problems, including: Poor absorption of fats. Bacteria in your small intestine break down the bile ...

  19. Improving Loop Dependence Analysis

    DEFF Research Database (Denmark)

    Jensen, Nicklas Bo; Karlsson, Sven

    2017-01-01

    Programmers can no longer depend on new processors to have significantly improved single-thread performance. Instead, gains have to come from other sources such as the compiler and its optimization passes. Advanced passes make use of information on the dependencies related to loops. We improve th...

  20. Cytokine loops driving senescence

    Czech Academy of Sciences Publication Activity Database

    Bartek, Jiří; Hodný, Zdeněk; Lukáš, Jan

    2008-01-01

    Roč. 10, č. 8 (2008), s. 887-889 ISSN 1465-7392 Institutional research plan: CEZ:AV0Z50520514 Keywords : cellular senescence * cytokines * autocrine feedback loop Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 17.774, year: 2008

  1. Loop Quantum Gravity

    Directory of Open Access Journals (Sweden)

    Rovelli Carlo

    1998-01-01

    Full Text Available The problem of finding the quantum theory of the gravitational field, and thus understanding what is quantum spacetime, is still open. One of the most active of the current approaches is loop quantum gravity. Loop quantum gravity is a mathematically well-defined, non-perturbative and background independent quantization of general relativity, with its conventional matter couplings. Research in loop quantum gravity today forms a vast area, ranging from mathematical foundations to physical applications. Among the most significant results obtained are: (i The computation of the physical spectra of geometrical quantities such as area and volume, which yields quantitative predictions on Planck-scale physics. (ii A derivation of the Bekenstein-Hawking black hole entropy formula. (iii An intriguing physical picture of the microstructure of quantum physical space, characterized by a polymer-like Planck scale discreteness. This discreteness emerges naturally from the quantum theory and provides a mathematically well-defined realization of Wheeler's intuition of a spacetime ``foam''. Long standing open problems within the approach (lack of a scalar product, over-completeness of the loop basis, implementation of reality conditions have been fully solved. The weak part of the approach is the treatment of the dynamics: at present there exist several proposals, which are intensely debated. Here, I provide a general overview of ideas, techniques, results and open problems of this candidate theory of quantum gravity, and a guide to the relevant literature.

  2. Stem cells

    NARCIS (Netherlands)

    Jukes, Jojanneke; Both, Sanne; Post, Janine; van Blitterswijk, Clemens; Karperien, Marcel; de Boer, Jan; van Blitterswijk, Clemens A.

    2008-01-01

    This chapter defines stem cells and their properties. It identifies the major differences between embryonic and adult stem cells. Stem cells can be defined by two properties: the ability to make identical copies of themselves and the ability to form other cell types of the body. These properties are

  3. Random walk loop soups and conformal loop ensembles

    NARCIS (Netherlands)

    van de Brug, T.; Camia, F.; Lis, M.

    2016-01-01

    The random walk loop soup is a Poissonian ensemble of lattice loops; it has been extensively studied because of its connections to the discrete Gaussian free field, but was originally introduced by Lawler and Trujillo Ferreras as a discrete version of the Brownian loop soup of Lawler and Werner, a

  4. Mining protein loops using a structural alphabet and statistical exceptionality

    Directory of Open Access Journals (Sweden)

    Martin Juliette

    2010-02-01

    Full Text Available Abstract Background Protein loops encompass 50% of protein residues in available three-dimensional structures. These regions are often involved in protein functions, e.g. binding site, catalytic pocket... However, the description of protein loops with conventional tools is an uneasy task. Regular secondary structures, helices and strands, have been widely studied whereas loops, because they are highly variable in terms of sequence and structure, are difficult to analyze. Due to data sparsity, long loops have rarely been systematically studied. Results We developed a simple and accurate method that allows the description and analysis of the structures of short and long loops using structural motifs without restriction on loop length. This method is based on the structural alphabet HMM-SA. HMM-SA allows the simplification of a three-dimensional protein structure into a one-dimensional string of states, where each state is a four-residue prototype fragment, called structural letter. The difficult task of the structural grouping of huge data sets is thus easily accomplished by handling structural letter strings as in conventional protein sequence analysis. We systematically extracted all seven-residue fragments in a bank of 93000 protein loops and grouped them according to the structural-letter sequence, named structural word. This approach permits a systematic analysis of loops of all sizes since we consider the structural motifs of seven residues rather than complete loops. We focused the analysis on highly recurrent words of loops (observed more than 30 times. Our study reveals that 73% of loop-lengths are covered by only 3310 highly recurrent structural words out of 28274 observed words. These structural words have low structural variability (mean RMSd of 0.85 Å. As expected, half of these motifs display a flanking-region preference but interestingly, two thirds are shared by short (less than 12 residues and long loops. Moreover, half of

  5. Mining protein loops using a structural alphabet and statistical exceptionality.

    Science.gov (United States)

    Regad, Leslie; Martin, Juliette; Nuel, Gregory; Camproux, Anne-Claude

    2010-02-04

    Protein loops encompass 50% of protein residues in available three-dimensional structures. These regions are often involved in protein functions, e.g. binding site, catalytic pocket... However, the description of protein loops with conventional tools is an uneasy task. Regular secondary structures, helices and strands, have been widely studied whereas loops, because they are highly variable in terms of sequence and structure, are difficult to analyze. Due to data sparsity, long loops have rarely been systematically studied. We developed a simple and accurate method that allows the description and analysis of the structures of short and long loops using structural motifs without restriction on loop length. This method is based on the structural alphabet HMM-SA. HMM-SA allows the simplification of a three-dimensional protein structure into a one-dimensional string of states, where each state is a four-residue prototype fragment, called structural letter. The difficult task of the structural grouping of huge data sets is thus easily accomplished by handling structural letter strings as in conventional protein sequence analysis. We systematically extracted all seven-residue fragments in a bank of 93000 protein loops and grouped them according to the structural-letter sequence, named structural word. This approach permits a systematic analysis of loops of all sizes since we consider the structural motifs of seven residues rather than complete loops. We focused the analysis on highly recurrent words of loops (observed more than 30 times). Our study reveals that 73% of loop-lengths are covered by only 3310 highly recurrent structural words out of 28274 observed words). These structural words have low structural variability (mean RMSd of 0.85 A). As expected, half of these motifs display a flanking-region preference but interestingly, two thirds are shared by short (less than 12 residues) and long loops. Moreover, half of recurrent motifs exhibit a significant level of

  6. Massively Parallel Interrogation of Aptamer Sequence, Structure and Function

    Energy Technology Data Exchange (ETDEWEB)

    Fischer, N O; Tok, J B; Tarasow, T M

    2008-02-08

    Optimization of high affinity reagents is a significant bottleneck in medicine and the life sciences. The ability to synthetically create thousands of permutations of a lead high-affinity reagent and survey the properties of individual permutations in parallel could potentially relieve this bottleneck. Aptamers are single stranded oligonucleotides affinity reagents isolated by in vitro selection processes and as a class have been shown to bind a wide variety of target molecules. Methodology/Principal Findings. High density DNA microarray technology was used to synthesize, in situ, arrays of approximately 3,900 aptamer sequence permutations in triplicate. These sequences were interrogated on-chip for their ability to bind the fluorescently-labeled cognate target, immunoglobulin E, resulting in the parallel execution of thousands of experiments. Fluorescence intensity at each array feature was well resolved and shown to be a function of the sequence present. The data demonstrated high intra- and interchip correlation between the same features as well as among the sequence triplicates within a single array. Consistent with aptamer mediated IgE binding, fluorescence intensity correlated strongly with specific aptamer sequences and the concentration of IgE applied to the array. The massively parallel sequence-function analyses provided by this approach confirmed the importance of a consensus sequence found in all 21 of the original IgE aptamer sequences and support a common stem:loop structure as being the secondary structure underlying IgE binding. The microarray application, data and results presented illustrate an efficient, high information content approach to optimizing aptamer function. It also provides a foundation from which to better understand and manipulate this important class of high affinity biomolecules.

  7. Massively parallel interrogation of aptamer sequence, structure and function.

    Directory of Open Access Journals (Sweden)

    Nicholas O Fischer

    Full Text Available BACKGROUND: Optimization of high affinity reagents is a significant bottleneck in medicine and the life sciences. The ability to synthetically create thousands of permutations of a lead high-affinity reagent and survey the properties of individual permutations in parallel could potentially relieve this bottleneck. Aptamers are single stranded oligonucleotides affinity reagents isolated by in vitro selection processes and as a class have been shown to bind a wide variety of target molecules. METHODOLOGY/PRINCIPAL FINDINGS: High density DNA microarray technology was used to synthesize, in situ, arrays of approximately 3,900 aptamer sequence permutations in triplicate. These sequences were interrogated on-chip for their ability to bind the fluorescently-labeled cognate target, immunoglobulin E, resulting in the parallel execution of thousands of experiments. Fluorescence intensity at each array feature was well resolved and shown to be a function of the sequence present. The data demonstrated high intra- and inter-chip correlation between the same features as well as among the sequence triplicates within a single array. Consistent with aptamer mediated IgE binding, fluorescence intensity correlated strongly with specific aptamer sequences and the concentration of IgE applied to the array. CONCLUSION AND SIGNIFICANCE: The massively parallel sequence-function analyses provided by this approach confirmed the importance of a consensus sequence found in all 21 of the original IgE aptamer sequences and support a common stem:loop structure as being the secondary structure underlying IgE binding. The microarray application, data and results presented illustrate an efficient, high information content approach to optimizing aptamer function. It also provides a foundation from which to better understand and manipulate this important class of high affinity biomolecules.

  8. Logical inference techniques for loop parallelization

    KAUST Repository

    Oancea, Cosmin E.; Rauchwerger, Lawrence

    2012-01-01

    This paper presents a fully automatic approach to loop parallelization that integrates the use of static and run-time analysis and thus overcomes many known difficulties such as nonlinear and indirect array indexing and complex control flow. Our hybrid analysis framework validates the parallelization transformation by verifying the independence of the loop's memory references. To this end it represents array references using the USR (uniform set representation) language and expresses the independence condition as an equation, S = Ø, where S is a set expression representing array indexes. Using a language instead of an array-abstraction representation for S results in a smaller number of conservative approximations but exhibits a potentially-high runtime cost. To alleviate this cost we introduce a language translation F from the USR set-expression language to an equally rich language of predicates (F(S) ⇒ S = Ø). Loop parallelization is then validated using a novel logic inference algorithm that factorizes the obtained complex predicates (F(S)) into a sequence of sufficient-independence conditions that are evaluated first statically and, when needed, dynamically, in increasing order of their estimated complexities. We evaluate our automated solution on 26 benchmarks from PERFECTCLUB and SPEC suites and show that our approach is effective in parallelizing large, complex loops and obtains much better full program speedups than the Intel and IBM Fortran compilers. Copyright © 2012 ACM.

  9. Amino-acid composition after loop deletion drives domain swapping.

    Science.gov (United States)

    Nandwani, Neha; Surana, Parag; Udgaonkar, Jayant B; Das, Ranabir; Gosavi, Shachi

    2017-10-01

    Rational engineering of a protein to enable domain swapping requires an understanding of the sequence, structural and energetic factors that favor the domain-swapped oligomer over the monomer. While it is known that the deletion of loops between β-strands can promote domain swapping, the spliced sequence at the position of the loop deletion is thought to have a minimal role to play in such domain swapping. Here, two loop-deletion mutants of the non-domain-swapping protein monellin, frame-shifted by a single residue, were designed. Although the spliced sequence in the two mutants differed by only one residue at the site of the deletion, only one of them (YEIKG) promoted domain swapping. The mutant containing the spliced sequence YENKG was entirely monomeric. This new understanding that the domain swapping propensity after loop deletion may depend critically on the chemical composition of the shortened loop will facilitate the rational design of domain swapping. © 2017 The Protein Society.

  10. Closing the loop.

    Science.gov (United States)

    Dassau, E; Atlas, E; Phillip, M

    2010-02-01

    The dream of closing the loop is actually the dream of creating an artificial pancreas and freeing the patients from being involved with the care of their own diabetes. Insulin-dependent diabetes (type 1) is a chronic incurable disease which requires constant therapy without the possibility of any 'holidays' or insulin-free days. It means that patients have to inject insulin every day of their life, several times per day, and in order to do it safely they also have to measure their blood glucose levels several times per day. Patients need to plan their meals, their physical activities and their insulin regime - there is only very small room for spontaneous activities. This is why the desire for an artificial pancreas is so strong despite the fact that it will not cure the diabetic patients. Attempts to develop a closed-loop system started in the 1960s but never got to a clinical practical stage of development. In recent years the availability of continuous glucose sensors revived those efforts and stimulated the clinician and researchers to believe that closing the loop might be possible nowadays. Many papers have been published over the years describing several different ideas on how to close the loop. Most of the suggested systems have a sensing arm that measures the blood glucose repeatedly or continuously, an insulin delivery arm that injects insulin upon command and a computer that makes the decisions of when and how much insulin to deliver. The differences between the various published systems in the literature are mainly in their control algorithms. However, there are also differences related to the method and site of glucose measurement and insulin delivery. SC glucose measurements and insulin delivery are the most studied option but other combinations of insulin measurements and glucose delivery including intravascular and intraperitoneal (IP) are explored. We tried to select recent publications that we believe had influenced and inspired people interested

  11. Loop Quantum Cosmology.

    Science.gov (United States)

    Bojowald, Martin

    2008-01-01

    Quantum gravity is expected to be necessary in order to understand situations in which classical general relativity breaks down. In particular in cosmology one has to deal with initial singularities, i.e., the fact that the backward evolution of a classical spacetime inevitably comes to an end after a finite amount of proper time. This presents a breakdown of the classical picture and requires an extended theory for a meaningful description. Since small length scales and high curvatures are involved, quantum effects must play a role. Not only the singularity itself but also the surrounding spacetime is then modified. One particular theory is loop quantum cosmology, an application of loop quantum gravity to homogeneous systems, which removes classical singularities. Its implications can be studied at different levels. The main effects are introduced into effective classical equations, which allow one to avoid the interpretational problems of quantum theory. They give rise to new kinds of early-universe phenomenology with applications to inflation and cyclic models. To resolve classical singularities and to understand the structure of geometry around them, the quantum description is necessary. Classical evolution is then replaced by a difference equation for a wave function, which allows an extension of quantum spacetime beyond classical singularities. One main question is how these homogeneous scenarios are related to full loop quantum gravity, which can be dealt with at the level of distributional symmetric states. Finally, the new structure of spacetime arising in loop quantum gravity and its application to cosmology sheds light on more general issues, such as the nature of time. Supplementary material is available for this article at 10.12942/lrr-2008-4.

  12. Loop Quantum Cosmology

    Directory of Open Access Journals (Sweden)

    Bojowald Martin

    2008-07-01

    Full Text Available Quantum gravity is expected to be necessary in order to understand situations in which classical general relativity breaks down. In particular in cosmology one has to deal with initial singularities, i.e., the fact that the backward evolution of a classical spacetime inevitably comes to an end after a finite amount of proper time. This presents a breakdown of the classical picture and requires an extended theory for a meaningful description. Since small length scales and high curvatures are involved, quantum effects must play a role. Not only the singularity itself but also the surrounding spacetime is then modified. One particular theory is loop quantum cosmology, an application of loop quantum gravity to homogeneous systems, which removes classical singularities. Its implications can be studied at different levels. The main effects are introduced into effective classical equations, which allow one to avoid the interpretational problems of quantum theory. They give rise to new kinds of early-universe phenomenology with applications to inflation and cyclic models. To resolve classical singularities and to understand the structure of geometry around them, the quantum description is necessary. Classical evolution is then replaced by a difference equation for a wave function, which allows an extension of quantum spacetime beyond classical singularities. One main question is how these homogeneous scenarios are related to full loop quantum gravity, which can be dealt with at the level of distributional symmetric states. Finally, the new structure of spacetime arising in loop quantum gravity and its application to cosmology sheds light on more general issues, such as the nature of time.

  13. Loop Quantum Cosmology

    Directory of Open Access Journals (Sweden)

    Bojowald Martin

    2005-12-01

    Full Text Available Quantum gravity is expected to be necessary in order to understand situations where classical general relativity breaks down. In particular in cosmology one has to deal with initial singularities, i.e., the fact that the backward evolution of a classical space-time inevitably comes to an end after a finite amount of proper time. This presents a breakdown of the classical picture and requires an extended theory for a meaningful description. Since small length scales and high curvatures are involved, quantum effects must play a role. Not only the singularity itself but also the surrounding space-time is then modified. One particular realization is loop quantum cosmology, an application of loop quantum gravity to homogeneous systems, which removes classical singularities. Its implications can be studied at different levels. Main effects are introduced into effective classical equations which allow to avoid interpretational problems of quantum theory. They give rise to new kinds of early universe phenomenology with applications to inflation and cyclic models. To resolve classical singularities and to understand the structure of geometry around them, the quantum description is necessary. Classical evolution is then replaced by a difference equation for a wave function which allows to extend space-time beyond classical singularities. One main question is how these homogeneous scenarios are related to full loop quantum gravity, which can be dealt with at the level of distributional symmetric states. Finally, the new structure of space-time arising in loop quantum gravity and its application to cosmology sheds new light on more general issues such as time.

  14. Role of an Absolutely Conserved Tryptophan Pair in the Extracellular Domain of Cys-Loop Receptors

    DEFF Research Database (Denmark)

    Braun, Nina; Lynagh, Timothy; Yu, Rilei

    2016-01-01

    Cys-loop receptors mediate fast synaptic transmission in the nervous system, and their dysfunction is associated with a number of diseases. While some sequence variability is essential to ensure specific recognition of a chemically diverse set of ligands, other parts of the underlying amino acid...... sequences show a high degree of conservation, possibly to preserve the overall structural fold across the protein family. In this study, we focus on the only two absolutely conserved residues across the Cys-loop receptor family, two Trp side chains in the WXD motif of Loop D and in the WXPD motif of Loop A...

  15. First cytoplasmic loop of glucagon-like peptide-1 receptor can function at the third cytoplasmic loop position of rhodopsin.

    Science.gov (United States)

    Yamashita, Takahiro; Tose, Koji; Shichida, Yoshinori

    2008-01-01

    G protein-coupled receptors (GPCRs) are classified into several families based on their amino acid sequences. In family 1, GPCRs such as rhodopsin and adrenergic receptor, the structure-function relationship has been extensively investigated to demonstrate that exposure of the third cytoplasmic loop is essential for selective G protein activation. In contrast, much less is known about other families. Here we prepared chimeric mutants between Gt-coupled rhodopsin and Gi/Go- and Gs-coupled glucagon-like peptide-1 (GLP-1) receptor of family 2 and tried to identify the loop region that functions at the third cytoplasmic loop position of rhodopsin. We succeeded in expressing a mutant having the first cytoplasmic loop of GLP-1 receptor and found that this mutant activated Gi and Go efficiently but did not activate Gt. Moreover, the rhodopsin mutant having the first loop of Gs-coupled secretin receptor of family 2 decreased the Gi and Go activation efficiencies. Therefore, the first loop of GLP-1 receptor would share a similar role to the third loop of rhodopsin in G protein activation. This result strongly suggested that different families of GPCRs have maintained molecular architectures of their ancestral types to generate a common mechanism, namely exposure of the cytoplasmic loop, to activate peripheral G protein.

  16. Metschnikowia Species Share a Pool of Diverse rRNA Genes Differing in Regions That Determine Hairpin-Loop Structures and Evolve by Reticulation.

    Directory of Open Access Journals (Sweden)

    Matthias Sipiczki

    Full Text Available Modern taxonomy of yeasts is mainly based on phylogenetic analysis of conserved DNA and protein sequences. By far the most frequently used sequences are those of the repeats of the chromosomal rDNA array. It is generally accepted that the rDNA repeats of a genome have identical sequences due to the phenomenon of sequence homogenisation and can thus be used for identification and barcoding of species. Here we show that the rDNA arrays of the type strains of Metschnikowia andauensis and M. fructicola are not homogenised. Both have arrays consisting of diverse repeats that differ from each other in the D1/D2 domains by up to 18 and 25 substitutions. The variable sites are concentrated in two regions that correspond to back-folding stretches of hairpin loops in the predicted secondary structure of the RNA molecules. The substitutions do not alter significantly the overall hairpin-loop structure due to wobble base pairing at sites of C-T transitions and compensatory mutations in the complementary strand of the hairpin stem. The phylogenetic and network analyses of the cloned sequences revealed that the repeats had not evolved in a vertical tree-like way but reticulation might have shaped the rDNA arrays of both strains. The neighbour-net analysis of all cloned sequences of the type strains and the database sequences of different strains further showed that these species share a continuous pool of diverse repeats that appear to evolve by reticulate evolution.

  17. Wilson loops in minimal surfaces

    International Nuclear Information System (INIS)

    Drukker, Nadav; Gross, David J.; Ooguri, Hirosi

    1999-01-01

    The AdS/CFT correspondence suggests that the Wilson loop of the large N gauge theory with N = 4 supersymmetry in 4 dimensions is described by a minimal surface in AdS 5 x S 5 . The authors examine various aspects of this proposal, comparing gauge theory expectations with computations of minimal surfaces. There is a distinguished class of loops, which the authors call BPS loops, whose expectation values are free from ultra-violet divergence. They formulate the loop equation for such loops. To the extent that they have checked, the minimal surface in AdS 5 x S 5 gives a solution of the equation. The authors also discuss the zig-zag symmetry of the loop operator. In the N = 4 gauge theory, they expect the zig-zag symmetry to hold when the loop does not couple the scalar fields in the supermultiplet. They will show how this is realized for the minimal surface

  18. Wilson loops and minimal surfaces

    International Nuclear Information System (INIS)

    Drukker, Nadav; Gross, David J.; Ooguri, Hirosi

    1999-01-01

    The AdS-CFT correspondence suggests that the Wilson loop of the large N gauge theory with N=4 supersymmetry in four dimensions is described by a minimal surface in AdS 5 xS 5 . We examine various aspects of this proposal, comparing gauge theory expectations with computations of minimal surfaces. There is a distinguished class of loops, which we call BPS loops, whose expectation values are free from ultraviolet divergence. We formulate the loop equation for such loops. To the extent that we have checked, the minimal surface in AdS 5 xS 5 gives a solution of the equation. We also discuss the zigzag symmetry of the loop operator. In the N=4 gauge theory, we expect the zigzag symmetry to hold when the loop does not couple the scalar fields in the supermultiplet. We will show how this is realized for the minimal surface. (c) 1999 The American Physical Society

  19. Structural and mutational analyses of cis-acting sequences in the 5'-untranslated region of satellite RNA of bamboo mosaic potexvirus

    International Nuclear Information System (INIS)

    Annamalai, Padmanaban; Hsu, Y.-H.; Liu, Y.-P.; Tsai, C.-H.; Lin, N.-S.

    2003-01-01

    The satellite RNA of Bamboo mosaic virus (satBaMV) contains on open reading frame for a 20-kDa protein that is flanked by a 5'-untranslated region (UTR) of 159 nucleotides (nt) and a 3'-UTR of 129 nt. A secondary structure was predicted for the 5'-UTR of satBaMV RNA, which folds into a large stem-loop (LSL) and a small stem-loop. Enzymatic probing confirmed the existence of LSL (nt 8-138) in the 5'-UTR. The essential cis-acting sequences in the 5'-UTR required for satBaMV RNA replication were determined by deletion and substitution mutagenesis. Their replication efficiencies were analyzed in Nicotiana benthamiana protoplasts and Chenopodium quinoa plants coinoculated with helper BaMV RNA. All deletion mutants abolished the replication of satBaMV RNA, whereas mutations introduced in most of the loop regions and stems showed either no replication or a decreased replication efficiency. Mutations that affected the positive-strand satBaMV RNA accumulation also affected the accumulation of negative-strand RNA; however, the accumulation of genomic and subgenomic RNAs of BaMV were not affected. Moreover, covariation analyses of natural satBaMV variants provide substantial evidence that the secondary structure in the 5'-UTR of satBaMV is necessary for efficient replication

  20. On some properties of conjugacy closed loops

    International Nuclear Information System (INIS)

    Adeniran, John Olusola

    2002-07-01

    It is shown that central loops are not conjugacy closed loops but instead are loops of units in their loop algebras that are conjugacy closed. It is also shown that certain inner mappings of a conjugacy closed loop are nuclear. Some invariants of left conjugacy closed loops are obtained. (author)

  1. Two-loop polygon Wilson loops in N = 4 SYM

    International Nuclear Information System (INIS)

    Anastasiou, C.; Brandhuber, A.; Heslop, P.; Spence, B.; Travaglini, G.; Khoze, V.V.

    2009-01-01

    We compute for the first time the two-loop corrections to arbitrary n-gon lightlike Wilson loops in N = 4 supersymmetric Yang-Mills theory, using efficient numerical methods. The calculation is motivated by the remarkable agreement between the finite part of planar six-point MHV amplitudes and hexagon Wilson loops which has been observed at two loops. At n = 6 we confirm that the ABDK/BDS ansatz must be corrected by adding a remainder function, which depends only on conformally invariant ratios of kinematic variables. We numerically compute remainder functions for n = 7,8 and verify dual conformal invariance. Furthermore, we study simple and multiple collinear limits of the Wilson loop remainder functions and demonstrate that they have precisely the form required by the collinear factorisation of the corresponding two-loop n-point amplitudes. The number of distinct diagram topologies contributing to the n-gon Wilson loops does not increase with n, and there is a fixed number of 'master integrals', which we have computed. Thus we have essentially computed general polygon Wilson loops, and if the correspondence with amplitudes continues to hold, all planar n-point two-loop MHV amplitudes in the N = 4 theory.

  2. High temperature storage loop :

    Energy Technology Data Exchange (ETDEWEB)

    Gill, David Dennis; Kolb, William J.

    2013-07-01

    A three year plan for thermal energy storage (TES) research was created at Sandia National Laboratories in the spring of 2012. This plan included a strategic goal of providing test capability for Sandia and for the nation in which to evaluate high temperature storage (>650ÀC) technology. The plan was to scope, design, and build a flow loop that would be compatible with a multitude of high temperature heat transfer/storage fluids. The High Temperature Storage Loop (HTSL) would be reconfigurable so that it was useful for not only storage testing, but also for high temperature receiver testing and high efficiency power cycle testing as well. In that way, HTSL was part of a much larger strategy for Sandia to provide a research and testing platform that would be integral for the evaluation of individual technologies funded under the SunShot program. DOEs SunShot program seeks to reduce the price of solar technologies to 6/kWhr to be cost competitive with carbon-based fuels. The HTSL project sought to provide evaluation capability for these SunShot supported technologies. This report includes the scoping, design, and budgetary costing aspects of this effort

  3. Accelerating the loop expansion

    International Nuclear Information System (INIS)

    Ingermanson, R.

    1986-01-01

    This thesis introduces a new non-perturbative technique into quantum field theory. To illustrate the method, I analyze the much-studied phi 4 theory in two dimensions. As a prelude, I first show that the Hartree approximation is easy to obtain from the calculation of the one-loop effective potential by a simple modification of the propagator that does not affect the perturbative renormalization procedure. A further modification then susggests itself, which has the same nice property, and which automatically yields a convex effective potential. I then show that both of these modifications extend naturally to higher orders in the derivative expansion of the effective action and to higher orders in the loop-expansion. The net effect is to re-sum the perturbation series for the effective action as a systematic ''accelerated'' non-perturbative expansion. Each term in the accelerated expansion corresponds to an infinite number of terms in the original series. Each term can be computed explicitly, albeit numerically. Many numerical graphs of the various approximations to the first two terms in the derivative expansion are given. I discuss the reliability of the results and the problem of spontaneous symmetry-breaking, as well as some potential applications to more interesting field theories. 40 refs

  4. Probability safety assessment of LOOP accident to molten salt reactor

    International Nuclear Information System (INIS)

    Mei Mudan; Shao Shiwei; Yu Zhizhen; Chen Kun; Zuo Jiaxu

    2013-01-01

    Background: Loss of offsite power (LOOP) is a possible accident to any type of reactor, and this accident can reflect the main idea of reactor safety design. Therefore, it is very important to conduct a study on probabilistic safety assessment (PSA) of the molten salt reactor that is under LOOP circumstance. Purpose: The aim is to calculate the release frequency of molten salt radioactive material to the core caused by LOOP, and find out the biggest contributor to causing the radioactive release frequency. Methods: We carried out the PSA analysis of the LOOP using the PSA process risk spectrum, and assumed that the primary circuit had no valve and equipment reliability data based on the existing mature power plant equipment reliability data. Results: Through the PSA analysis, we got the accident sequences of the release of radioactive material to the core caused by LOOP and its frequency. The results show that the release frequency of molten salt radioactive material to the core caused by LOOP is about 2×10 -11 /(reactor ·year), which is far below that of the AP1000 LOOP. In addition, through the quantitative analysis, we obtained the point estimation and interval estimation of uncertainty analysis, and found that the biggest contributor to cause the release frequency of radioactive material to the core is the reactor cavity cooling function failure. Conclusion: This study provides effective help for the design and improvement of the following molten salt reactor system. (authors)

  5. STEM Education.

    Science.gov (United States)

    Xie, Yu; Fang, Michael; Shauman, Kimberlee

    2015-08-01

    Improving science, technology, engineering, and mathematics (STEM) education, especially for traditionally disadvantaged groups, is widely recognized as pivotal to the U.S.'s long-term economic growth and security. In this article, we review and discuss current research on STEM education in the U.S., drawing on recent research in sociology and related fields. The reviewed literature shows that different social factors affect the two major components of STEM education attainment: (1) attainment of education in general, and (2) attainment of STEM education relative to non-STEM education conditional on educational attainment. Cognitive and social psychological characteristics matter for both major components, as do structural influences at the neighborhood, school, and broader cultural levels. However, while commonly used measures of socioeconomic status (SES) predict the attainment of general education, social psychological factors are more important influences on participation and achievement in STEM versus non-STEM education. Domestically, disparities by family SES, race, and gender persist in STEM education. Internationally, American students lag behind those in some countries with less economic resources. Explanations for group disparities within the U.S. and the mediocre international ranking of US student performance require more research, a task that is best accomplished through interdisciplinary approaches.

  6. Mirror symmetry and loop operators

    Energy Technology Data Exchange (ETDEWEB)

    Assel, Benjamin [Department of Mathematics, King’s College London,The Strand, London WC2R 2LS (United Kingdom); Gomis, Jaume [Perimeter Institute for Theoretical Physics,Waterloo, Ontario, N2L 2Y5 (Canada)

    2015-11-09

    Wilson loops in gauge theories pose a fundamental challenge for dualities. Wilson loops are labeled by a representation of the gauge group and should map under duality to loop operators labeled by the same data, yet generically, dual theories have completely different gauge groups. In this paper we resolve this conundrum for three dimensional mirror symmetry. We show that Wilson loops are exchanged under mirror symmetry with Vortex loop operators, whose microscopic definition in terms of a supersymmetric quantum mechanics coupled to the theory encode in a non-trivial way a representation of the original gauge group, despite that the gauge groups of mirror theories can be radically different. Our predictions for the mirror map, which we derive guided by branes in string theory, are confirmed by the computation of the exact expectation value of Wilson and Vortex loop operators on the three-sphere.

  7. Reactor recirculation pump test loop

    International Nuclear Information System (INIS)

    Taka, Shusei; Kato, Hiroyuki

    1979-01-01

    A test loop for a reactor primary loop recirculation pumps (PLR pumps) has been constructed at Ebara's Haneda Plant in preparation for production of PLR pumps under license from Byron Jackson Pump Division of Borg-Warner Corporation. This loop can simulate operating conditions for test PLR pumps with 130 per cent of the capacity of pumps for a 1100 MWe BWR plant. A main loop, primary cooling system, water demineralizer, secondary cooling system, instrumentation and control equipment and an electric power supply system make up the test loop. This article describes the test loop itself and test results of two PLR pumps for Fukushima No. 2 N.P.S. Unit 1 and one main circulation pump for HAZ Demonstration Test Facility. (author)

  8. Commissioning of closed loop controls at CPP, HWP, Manuguru (Paper No. 3.5)

    International Nuclear Information System (INIS)

    Basu, Sukumar; Narasimham, P.L.

    1992-01-01

    The captive power plant (CPP) for Heavy Water Plant, Manuguru is equipped with 3x265 T/hr steam capacity boilers. The control system is built around ASEA master hardware for sequence interlocks, closed loop control, and data acquisition functions. This paper describes the configuration of the system hardware, the steps carried out during commissioning of closed loop controls in distributed digital control systems and also the problems faced during the commissioning of closed loops. (author). 3 figs

  9. Microbial Dark Matter: Unusual intervening sequences in 16S rRNA genes of candidate phyla from the deep subsurface

    Energy Technology Data Exchange (ETDEWEB)

    Jarett, Jessica; Stepanauskas, Ramunas; Kieft, Thomas; Onstott, Tullis; Woyke, Tanja

    2014-03-17

    The Microbial Dark Matter project has sequenced genomes from over 200 single cells from candidate phyla, greatly expanding our knowledge of the ecology, inferred metabolism, and evolution of these widely distributed, yet poorly understood lineages. The second phase of this project aims to sequence an additional 800 single cells from known as well as potentially novel candidate phyla derived from a variety of environments. In order to identify whole genome amplified single cells, screening based on phylogenetic placement of 16S rRNA gene sequences is being conducted. Briefly, derived 16S rRNA gene sequences are aligned to a custom version of the Greengenes reference database and added to a reference tree in ARB using parsimony. In multiple samples from deep subsurface habitats but not from other habitats, a large number of sequences proved difficult to align and therefore to place in the tree. Based on comparisons to reference sequences and structural alignments using SSU-ALIGN, many of these ?difficult? sequences appear to originate from candidate phyla, and contain intervening sequences (IVSs) within the 16S rRNA genes. These IVSs are short (39 - 79 nt) and do not appear to be self-splicing or to contain open reading frames. IVSs were found in the loop regions of stem-loop structures in several different taxonomic groups. Phylogenetic placement of sequences is strongly affected by IVSs; two out of three groups investigated were classified as different phyla after their removal. Based on data from samples screened in this project, IVSs appear to be more common in microbes occurring in deep subsurface habitats, although the reasons for this remain elusive.

  10. Efficiently computing exact geodesic loops within finite steps.

    Science.gov (United States)

    Xin, Shi-Qing; He, Ying; Fu, Chi-Wing

    2012-06-01

    Closed geodesics, or geodesic loops, are crucial to the study of differential topology and differential geometry. Although the existence and properties of closed geodesics on smooth surfaces have been widely studied in mathematics community, relatively little progress has been made on how to compute them on polygonal surfaces. Most existing algorithms simply consider the mesh as a graph and so the resultant loops are restricted only on mesh edges, which are far from the actual geodesics. This paper is the first to prove the existence and uniqueness of geodesic loop restricted on a closed face sequence; it contributes also with an efficient algorithm to iteratively evolve an initial closed path on a given mesh into an exact geodesic loop within finite steps. Our proposed algorithm takes only an O(k) space complexity and an O(mk) time complexity (experimentally), where m is the number of vertices in the region bounded by the initial loop and the resultant geodesic loop, and k is the average number of edges in the edge sequences that the evolving loop passes through. In contrast to the existing geodesic curvature flow methods which compute an approximate geodesic loop within a predefined threshold, our method is exact and can apply directly to triangular meshes without needing to solve any differential equation with a numerical solver; it can run at interactive speed, e.g., in the order of milliseconds, for a mesh with around 50K vertices, and hence, significantly outperforms existing algorithms. Actually, our algorithm could run at interactive speed even for larger meshes. Besides the complexity of the input mesh, the geometric shape could also affect the number of evolving steps, i.e., the performance. We motivate our algorithm with an interactive shape segmentation example shown later in the paper.

  11. DNA looping by FokI: the impact of twisting and bending rigidity on protein-induced looping dynamics

    Science.gov (United States)

    Laurens, Niels; Rusling, David A.; Pernstich, Christian; Brouwer, Ineke; Halford, Stephen E.; Wuite, Gijs J. L.

    2012-01-01

    Protein-induced DNA looping is crucial for many genetic processes such as transcription, gene regulation and DNA replication. Here, we use tethered-particle motion to examine the impact of DNA bending and twisting rigidity on loop capture and release, using the restriction endonuclease FokI as a test system. To cleave DNA efficiently, FokI bridges two copies of an asymmetric sequence, invariably aligning the sites in parallel. On account of the fixed alignment, the topology of the DNA loop is set by the orientation of the sites along the DNA. We show that both the separation of the FokI sites and their orientation, altering, respectively, the twisting and the bending of the DNA needed to juxtapose the sites, have profound effects on the dynamics of the looping interaction. Surprisingly, the presence of a nick within the loop does not affect the observed rigidity of the DNA. In contrast, the introduction of a 4-nt gap fully relaxes all of the torque present in the system but does not necessarily enhance loop stability. FokI therefore employs torque to stabilise its DNA-looping interaction by acting as a ‘torsional’ catch bond. PMID:22373924

  12. Learn About Stem Cells

    Science.gov (United States)

    ... Patient Handbook Stem Cell Glossary Search Toggle Nav Stem Cell Basics Stem cells are the foundation from which ... original cell’s DNA, cytoplasm and cell membrane. About stem cells Stem cells are the foundation of development in ...

  13. Loop Heat Pipe Startup Behaviors

    Science.gov (United States)

    Ku, Jentung

    2016-01-01

    A loop heat pipe must start successfully before it can commence its service. The startup transient represents one of the most complex phenomena in the loop heat pipe operation. This paper discusses various aspects of loop heat pipe startup behaviors. Topics include the four startup scenarios, the initial fluid distribution between the evaporator and reservoir that determines the startup scenario, factors that affect the fluid distribution between the evaporator and reservoir, difficulties encountered during the low power startup, and methods to enhance the startup success. Also addressed are the pressure spike and pressure surge during the startup transient, and repeated cycles of loop startup and shutdown under certain conditions.

  14. Modeling of compact loop antennas

    International Nuclear Information System (INIS)

    Baity, F.W.

    1987-01-01

    A general compact loop antenna model which treats all elements of the antenna as lossy transmission lines has been developed. In addition to capacitively-tuned resonant double loop (RDL) antennas the model treats stub-tuned resonant double loop antennas. Calculations using the model have been compared with measurements on full-scale mockups of resonant double loop antennas for ATF and TFTR in order to refine the transmission line parameters. Results from the model are presented for RDL antenna designs for ATF, TFTR, Tore Supra, and for the Compact Ignition Tokamak

  15. The complete mitochondrial genome of the pink stem borer, Sesamia inferens, in comparison with four other Noctuid moths.

    Science.gov (United States)

    Chai, Huan-Na; Du, Yu-Zhou

    2012-01-01

    The complete 15,413-bp mitochondrial genome (mitogenome) of Sesamia inferens (Walker) (Lepidoptera: Noctuidae) was sequenced and compared with those of four other noctuid moths. All of the mitogenomes analyzed displayed similar characteristics with respect to gene content, genome organization, nucleotide comparison, and codon usages. Twelve-one protein-coding genes (PCGs) utilized the standard ATN, but the cox1 gene used CGA as the initiation codon; cox1, cox2, and nad4 genes had the truncated termination codon T in the S. inferens mitogenome. All of the tRNA genes had typical cloverleaf secondary structures except for trnS1(AGN), in which the dihydrouridine (DHU) arm did not form a stable stem-loop structure. Both the secondary structures of rrnL and rrnS genes inferred from the S. inferens mitogenome closely resembled those of other noctuid moths. In the A+T-rich region, the conserved motif "ATAGA" followed by a long T-stretch was observed in all noctuid moths, but other specific tandem-repeat elements were more variable. Additionally, the S. inferens mitogenome contained a potential stem-loop structure, a duplicated 17-bp repeat element, a decuplicated segment, and a microsatellite "(AT)(7)", without a poly-A element upstream of the trnM in the A+T-rich region. Finally, the phylogenetic relationships were reconstructed based on amino acid sequences of mitochondrial 13 PCGs, which support the traditional morphologically based view of relationships within the Noctuidae.

  16. Vortex loops and Majoranas

    International Nuclear Information System (INIS)

    Chesi, Stefano; Jaffe, Arthur; Loss, Daniel; Pedrocchi, Fabio L.

    2013-01-01

    We investigate the role that vortex loops play in characterizing eigenstates of interacting Majoranas. We give some general results and then focus on ladder Hamiltonian examples as a test of further ideas. Two methods yield exact results: (i) A mapping of certain spin Hamiltonians to quartic interactions of Majoranas shows that the spectra of these two examples coincide. (ii) In cases with reflection-symmetric Hamiltonians, we use reflection positivity for Majoranas to characterize vortices in the ground states. Two additional methods suggest wider applicability of these results: (iii) Numerical evidence suggests similar behavior for certain systems without reflection symmetry. (iv) A perturbative analysis also suggests similar behavior without the assumption of reflection symmetry

  17. Inductance loop and partial

    CERN Document Server

    Paul, Clayton R

    2010-01-01

    "Inductance is an unprecedented text, thoroughly discussing "loop" inductance as well as the increasingly important "partial" inductance. These concepts and their proper calculation are crucial in designing modern high-speed digital systems. World-renowned leader in electromagnetics Clayton Paul provides the knowledge and tools necessary to understand and calculate inductance." "With the present and increasing emphasis on high-speed digital systems and high-frequency analog systems, it is imperative that system designers develop an intimate understanding of the concepts and methods in this book. Inductance is a much-needed textbook designed for senior and graduate-level engineering students, as well as a hands-on guide for working engineers and professionals engaged in the design of high-speed digital and high-frequency analog systems."--Jacket.

  18. Dynamic PID loop control

    International Nuclear Information System (INIS)

    Pei, L.; Klebaner, A.; Theilacker, J.; Soyars, W.; Martinez, A.; Bossert, R.; DeGraff, B.; Darve, C.

    2011-01-01

    The Horizontal Test Stand (HTS) SRF Cavity and Cryomodule 1 (CM1) of eight 9-cell, 1.3GHz SRF cavities are operating at Fermilab. For the cryogenic control system, how to hold liquid level constant in the cryostat by regulation of its Joule-Thompson JT-valve is very important after cryostat cool down to 2.0 K. The 72-cell cryostat liquid level response generally takes a long time delay after regulating its JT-valve; therefore, typical PID control loop should result in some cryostat parameter oscillations. This paper presents a type of PID parameter self-optimal and Time-Delay control method used to reduce cryogenic system parameters oscillation.

  19. Uranyl Nitrate Flow Loop

    International Nuclear Information System (INIS)

    Ladd-Lively, Jennifer L

    2008-01-01

    The objectives of the work discussed in this report were to: (1) develop a flow loop that would simulate the purified uranium-bearing aqueous stream exiting the solvent extraction process in a natural uranium conversion plant (NUCP); (2) develop a test plan that would simulate normal operation and disturbances that could be anticipated in an NUCP; (3) use the flow loop to test commercially available flowmeters for use as safeguards monitors; and (4) recommend a flowmeter for production-scale testing at an NUCP. There has been interest in safeguarding conversion plants because the intermediate products [uranium dioxide (UO 2 ), uranium tetrafluoride (UF 4 ), and uranium hexafluoride (UF 6 )] are all suitable uranium feedstocks for producing special nuclear materials. Furthermore, if safeguards are not applied virtually any nuclear weapons program can obtain these feedstocks without detection by the International Atomic Energy Agency (IAEA). Historically, IAEA had not implemented safeguards until the purified UF 6 product was declared as feedstock for enrichment plants. H. A. Elayat et al. provide a basic definition of a safeguards system: 'The function of a safeguards system on a chemical conversion plant is in general terms to verify that no useful nuclear material is being diverted to use in a nuclear weapons program'. The IAEA now considers all highly purified uranium compounds as candidates for safeguarding. DOE is currently interested in 'developing instruments, tools, strategies, and methods that could be of use to the IAEA in the application of safeguards' for materials found in the front end of the nuclear fuel cycle-prior to the production of the uranium hexafluoride or oxides that have been the traditional starting point for IAEA safeguards. Several national laboratories, including Oak Ridge, Los Alamos, Lawrence Livermore, and Brookhaven, have been involved in developing tools or techniques for safeguarding conversion plants. This study was sponsored by

  20. Loop Quantum Gravity.

    Science.gov (United States)

    Rovelli, Carlo

    2008-01-01

    The problem of describing the quantum behavior of gravity, and thus understanding quantum spacetime , is still open. Loop quantum gravity is a well-developed approach to this problem. It is a mathematically well-defined background-independent quantization of general relativity, with its conventional matter couplings. Today research in loop quantum gravity forms a vast area, ranging from mathematical foundations to physical applications. Among the most significant results obtained so far are: (i) The computation of the spectra of geometrical quantities such as area and volume, which yield tentative quantitative predictions for Planck-scale physics. (ii) A physical picture of the microstructure of quantum spacetime, characterized by Planck-scale discreteness. Discreteness emerges as a standard quantum effect from the discrete spectra, and provides a mathematical realization of Wheeler's "spacetime foam" intuition. (iii) Control of spacetime singularities, such as those in the interior of black holes and the cosmological one. This, in particular, has opened up the possibility of a theoretical investigation into the very early universe and the spacetime regions beyond the Big Bang. (iv) A derivation of the Bekenstein-Hawking black-hole entropy. (v) Low-energy calculations, yielding n -point functions well defined in a background-independent context. The theory is at the roots of, or strictly related to, a number of formalisms that have been developed for describing background-independent quantum field theory, such as spin foams, group field theory, causal spin networks, and others. I give here a general overview of ideas, techniques, results and open problems of this candidate theory of quantum gravity, and a guide to the relevant literature.

  1. Loop Quantum Gravity

    Directory of Open Access Journals (Sweden)

    Rovelli Carlo

    2008-07-01

    Full Text Available The problem of describing the quantum behavior of gravity, and thus understanding quantum spacetime, is still open. Loop quantum gravity is a well-developed approach to this problem. It is a mathematically well-defined background-independent quantization of general relativity, with its conventional matter couplings. Today research in loop quantum gravity forms a vast area, ranging from mathematical foundations to physical applications. Among the most significant results obtained so far are: (i The computation of the spectra of geometrical quantities such as area and volume, which yield tentative quantitative predictions for Planck-scale physics. (ii A physical picture of the microstructure of quantum spacetime, characterized by Planck-scale discreteness. Discreteness emerges as a standard quantum effect from the discrete spectra, and provides a mathematical realization of Wheeler’s “spacetime foam” intuition. (iii Control of spacetime singularities, such as those in the interior of black holes and the cosmological one. This, in particular, has opened up the possibility of a theoretical investigation into the very early universe and the spacetime regions beyond the Big Bang. (iv A derivation of the Bekenstein–Hawking black-hole entropy. (v Low-energy calculations, yielding n-point functions well defined in a background-independent context. The theory is at the roots of, or strictly related to, a number of formalisms that have been developed for describing background-independent quantum field theory, such as spin foams, group field theory, causal spin networks, and others. I give here a general overview of ideas, techniques, results and open problems of this candidate theory of quantum gravity, and a guide to the relevant literature.

  2. An evaluation of multiple annealing and looping based genome amplification using a synthetic bacterial community

    KAUST Repository

    Wang, Yong; Gao, Zhaoming; Xu, Ying; Li, Guangyu; He, Lisheng; Qian, Peiyuan

    2016-01-01

    -generation-sequencing technology. Using a synthetic bacterial community, the amplification efficiency of the Multiple Annealing and Looping Based Amplification Cycles (MALBAC) kit that is originally developed to amplify the single-cell genomic DNA of mammalian organisms

  3. The highly conserved codon following the slippery sequence supports -1 frameshift efficiency at the HIV-1 frameshift site.

    Directory of Open Access Journals (Sweden)

    Suneeth F Mathew

    Full Text Available HIV-1 utilises -1 programmed ribosomal frameshifting to translate structural and enzymatic domains in a defined proportion required for replication. A slippery sequence, U UUU UUA, and a stem-loop are well-defined RNA features modulating -1 frameshifting in HIV-1. The GGG glycine codon immediately following the slippery sequence (the 'intercodon' contributes structurally to the start of the stem-loop but has no defined role in current models of the frameshift mechanism, as slippage is inferred to occur before the intercodon has reached the ribosomal decoding site. This GGG codon is highly conserved in natural isolates of HIV. When the natural intercodon was replaced with a stop codon two different decoding molecules-eRF1 protein or a cognate suppressor tRNA-were able to access and decode the intercodon prior to -1 frameshifting. This implies significant slippage occurs when the intercodon is in the (perhaps distorted ribosomal A site. We accommodate the influence of the intercodon in a model of frame maintenance versus frameshifting in HIV-1.

  4. A totally diverting loop colostomy.

    Science.gov (United States)

    Merrett, N. D.; Gartell, P. C.

    1993-01-01

    A technique is described where the distal limb of a loop colostomy is tied with nylon or polydioxanone. This ensures total faecal diversion and dispenses with the supporting rod, enabling early application of stoma appliances. The technique does not interfere with the traditional transverse closure of a loop colostomy. PMID:8379632

  5. STEM Education

    Science.gov (United States)

    & Development (LDRD) National Security Education Center (NSEC) Office of Science Programs Richard P Databases National Security Education Center (NSEC) Center for Nonlinear Studies Engineering Institute Scholarships STEM Education Programs Teachers (K-12) Students (K-12) Higher Education Regional Education

  6. Higher dimensional loop quantum cosmology

    International Nuclear Information System (INIS)

    Zhang, Xiangdong

    2016-01-01

    Loop quantum cosmology (LQC) is the symmetric sector of loop quantum gravity. In this paper, we generalize the structure of loop quantum cosmology to the theories with arbitrary spacetime dimensions. The isotropic and homogeneous cosmological model in n + 1 dimensions is quantized by the loop quantization method. Interestingly, we find that the underlying quantum theories are divided into two qualitatively different sectors according to spacetime dimensions. The effective Hamiltonian and modified dynamical equations of n + 1 dimensional LQC are obtained. Moreover, our results indicate that the classical big bang singularity is resolved in arbitrary spacetime dimensions by a quantum bounce. We also briefly discuss the similarities and differences between the n + 1 dimensional model and the 3 + 1 dimensional one. Our model serves as a first example of higher dimensional loop quantum cosmology and offers the possibility to investigate quantum gravity effects in higher dimensional cosmology. (orig.)

  7. Role for cis-acting RNA sequences in the temperature-dependent expression of the multiadhesive lig proteins in Leptospira interrogans.

    Science.gov (United States)

    Matsunaga, James; Schlax, Paula J; Haake, David A

    2013-11-01

    The spirochete Leptospira interrogans causes a systemic infection that provokes a febrile illness. The putative lipoproteins LigA and LigB promote adhesion of Leptospira to host proteins, interfere with coagulation, and capture complement regulators. In this study, we demonstrate that the expression level of the LigA and LigB proteins was substantially higher when L. interrogans proliferated at 37°C instead of the standard culture temperature of 30°C. The RNA comprising the 175-nucleotide 5' untranslated region (UTR) and first six lig codons, whose sequence is identical in ligA and ligB, is predicted to fold into two distinct stem-loop structures separated by a single-stranded region. The ribosome-binding site is partially sequestered in double-stranded RNA within the second structure. Toeprint analysis revealed that in vitro formation of a 30S-tRNA(fMet)-mRNA ternary complex was inhibited unless a 5' deletion mutation disrupted the second stem-loop structure. To determine whether the lig sequence could mediate temperature-regulated gene expression in vivo, the 5' UTR and the first six codons were inserted between the Escherichia coli l-arabinose promoter and bgaB (β-galactosidase from Bacillus stearothermophilus) to create a translational fusion. The lig fragment successfully conferred thermoregulation upon the β-galactosidase reporter in E. coli. The second stem-loop structure was sufficient to confer thermoregulation on the reporter, while sequences further upstream in the 5' UTR slightly diminished expression at each temperature tested. Finally, the expression level of β-galactosidase was significantly higher when point mutations predicted to disrupt base pairs in the second structure were introduced into the stem. Compensatory mutations that maintained base pairing of the stem without restoring the wild-type sequence reinstated the inhibitory effect of the 5' UTR on expression. These results indicate that ligA and ligB expression is limited by double

  8. Contrasting HIV phylogenetic relationships and V3 loop protein similarities

    Energy Technology Data Exchange (ETDEWEB)

    Korber, B. (Los Alamos National Lab., NM (United States) Santa Fe Inst., NM (United States)); Myers, G. (Los Alamos National Lab., NM (United States))

    1992-01-01

    At least five distinct sequence subtypes of HIV-I can be identified from the major centers of the AMS pandemic. While it is too early to tell whether these subtypes are serologically or phenotypically similar or distinct in terms of properties such as pathogenicity and transmissibility, we can begin to investigate their potential for phenotypic divergence at the protein sequence level. Phylogenetic analysis of HIV DNA sequences is being widely used to examine lineages of different viral strains as they evolve and spread throughout the globe. We have identified five distinct HIV-1 subtypes (designated A-E), or clades, based on phylogenetic clustering patterns generated from genetic information from both the gag and envelope (env) genes from a spectrum of international isolates. Our initial observations concerning both HIV-1 and HIV-2 sequences indicate that conserved patterns in protein chemistry may indeed exist across distant lineages. Such patterns in V3 loop amino acid chemistry may be indicative of stable lineages or convergence within this highly variable, though functionally and immunologically critical, region. We think that there may be parallels between the apparently stable HIV-2 V3 lineage and the previously mentioned HIV-1 V3 loops which are very similar at the protein level despite being distant by cladistic analysis, and which do not possess the distinctive positively charged residues. Highly conserved V3 loop protein sequences are also encountered in SIVAGMs and CIVs (chimpanzee viral strains), which do not appear to be pathogenic in their wild-caught natural hosts.

  9. Contrasting HIV phylogenetic relationships and V3 loop protein similarities

    Energy Technology Data Exchange (ETDEWEB)

    Korber, B. [Los Alamos National Lab., NM (United States)]|[Santa Fe Inst., NM (United States); Myers, G. [Los Alamos National Lab., NM (United States)

    1992-12-31

    At least five distinct sequence subtypes of HIV-I can be identified from the major centers of the AMS pandemic. While it is too early to tell whether these subtypes are serologically or phenotypically similar or distinct in terms of properties such as pathogenicity and transmissibility, we can begin to investigate their potential for phenotypic divergence at the protein sequence level. Phylogenetic analysis of HIV DNA sequences is being widely used to examine lineages of different viral strains as they evolve and spread throughout the globe. We have identified five distinct HIV-1 subtypes (designated A-E), or clades, based on phylogenetic clustering patterns generated from genetic information from both the gag and envelope (env) genes from a spectrum of international isolates. Our initial observations concerning both HIV-1 and HIV-2 sequences indicate that conserved patterns in protein chemistry may indeed exist across distant lineages. Such patterns in V3 loop amino acid chemistry may be indicative of stable lineages or convergence within this highly variable, though functionally and immunologically critical, region. We think that there may be parallels between the apparently stable HIV-2 V3 lineage and the previously mentioned HIV-1 V3 loops which are very similar at the protein level despite being distant by cladistic analysis, and which do not possess the distinctive positively charged residues. Highly conserved V3 loop protein sequences are also encountered in SIVAGMs and CIVs (chimpanzee viral strains), which do not appear to be pathogenic in their wild-caught natural hosts.

  10. Rogowski Loop design for NSTX

    International Nuclear Information System (INIS)

    McCormack, B.; Kaita, R.; Kugel, H.; Hatcher, R.

    2000-01-01

    The Rogowski Loop is one of the most basic diagnostics for tokamak operations. On the National Spherical Torus Experiment (NSTX), the plasma current Rogowski Loop had the constraints of the very limited space available on the center stack, 5,000 volt isolation, flexibility requirements as it remained a part of the Center Stack assembly after the first phase of operation, and a +120 C temperature requirement. For the second phase of operation, four Halo Current Rogowski Loops under the Center Stack tiles will be installed having +600 C and limited space requirements. Also as part of the second operational phase, up to ten Rogowski Loops will installed to measure eddy currents in the Passive Plate support structures with +350 C, restricted space, and flexibility requirements. This presentation will provide the details of the material selection, fabrication techniques, testing, and installation results of the Rogowski Loops that were fabricated for the high temperature operational and bakeout requirements, high voltage isolation requirements, and the space and flexibility requirements imposed upon the Rogowski Loops. In the future operational phases of NSTX, additional Rogowski Loops could be anticipated that will measure toroidal plasma currents in the vacuum vessel and in the Passive Plate assemblies

  11. Two-loop hard-thermal-loop thermodynamics with quarks

    International Nuclear Information System (INIS)

    Andersen, Jens O.; Petitgirard, Emmanuel; Strickland, Michael

    2004-01-01

    We calculate the quark contribution to the free energy of a hot quark-gluon plasma to two-loop order using hard-thermal-loop (HTL) perturbation theory. All ultraviolet divergences can be absorbed into renormalizations of the vacuum energy and the HTL quark and gluon mass parameters. The quark and gluon HTL mass parameters are determined self-consistently by a variational prescription. Combining the quark contribution with the two-loop HTL perturbation theory free energy for pure glue we obtain the total two-loop QCD free energy. Comparisons are made with lattice estimates of the free energy for N f =2 and with exact numerical results obtained in the large-N f limit

  12. String breaking with Wilson loops?

    CERN Document Server

    Kratochvila, S; Kratochvila, Slavo; Forcrand, Philippe de

    2003-01-01

    A convincing, uncontroversial observation of string breaking, when the static potential is extracted from Wilson loops only, is still missing. This failure can be understood if the overlap of the Wilson loop with the broken string is exponentially small. In that case, the broken string ground state will only be seen if the Wilson loop is long enough. Our preliminary results show string breaking in the context of the 3d SU(2) adjoint static potential, using the L\\"uscher-Weisz exponential variance reduction approach. As a by-product, we measure the fundamental SU(2) static potential with improved accuracy and see clear deviations from Casimir scaling.

  13. BMN correlators by loop equations

    International Nuclear Information System (INIS)

    Eynard, Bertrand; Kristjansen, Charlotte

    2002-01-01

    In the BMN approach to N=4 SYM a large class of correlators of interest are expressible in terms of expectation values of traces of words in a zero-dimensional gaussian complex matrix model. We develop a loop-equation based, analytic strategy for evaluating such expectation values to any order in the genus expansion. We reproduce the expectation values which were needed for the calculation of the one-loop, genus one correction to the anomalous dimension of BMN-operators and which were earlier obtained by combinatorial means. Furthermore, we present the expectation values needed for the calculation of the one-loop, genus two correction. (author)

  14. Optical loop framing

    International Nuclear Information System (INIS)

    Kalibjian, R.; Chong, Y.P.; Prono, D.S.; Cavagnolo, H.R.

    1984-06-01

    The ATA provides an electron beam pulse of 70-ns duration at a 1-Hz rate. Our present optical diagnostics technique involve the imaging of the visible light generated by the beam incident onto the plant of a thin sheet of material. It has already been demonstrated that the light generated has a sufficiently fast temporal reponse in performing beam diagnostics. Notwithstanding possible beam emittance degradation due to scattering in the thin sheet, the observation of beam spatial profiles with relatively high efficiencies has provided data complementary to that obtained from beam wall current monitors and from various x-ray probes and other electrical probes. The optical image sensor consists of a gated, intensified television system. The gate pulse of the image intensifier can be appropriately delayed to give frames that are time-positioned from the head to the tail of the beam with a minimum gate time of 5-ns. The spatial correlation of the time frames from pulse to pulse is very good for a stable electron beam; however, when instabilities do occur, it is difficult to properly assess the spatial composition of the head and the tail of the beam on a pulse-to-pulse basis. Multiple gating within a pulse duration becomes desirable but cannot be performed because the recycle time (20-ms) of the TV system is much longer than the beam pulse. For this reason we have developed an optical-loop framing technique that will allow the recording of two frames within one pulse duration with our present gated/intensified TV system

  15. Acceleration of Feynman loop integrals in high-energy physics on many core GPUs

    International Nuclear Information System (INIS)

    Yuasa, F; Ishikawa, T; Hamaguchi, N; Koike, T; Nakasato, N

    2013-01-01

    The current and future colliders in high-energy physics require theorists to carry out a large scale computation for a precise comparison between experimental results and theoretical ones. In a perturbative approach several methods to evaluate Feynman loop integrals which appear in the theoretical calculation of cross-sections are well established in the one-loop level, however, more studies are necessary for higher-order levels. Direct Computation Method (DCM) is developed to evaluate multi-loop integrals. DCM is based on a combination of multidimensional numerical integration and extrapolation on a sequence of integrals. It is a fully numerical method and is applicable to a wide class of integrals with various physics parameters. The computation time depends on physics parameters and the topology of loop diagrams and it becomes longer for the two-loop integrals. In this paper we present our approach to the acceleration of the two-loop integrals by DCM on multiple GPU boards

  16. Stem Cell Basics

    Science.gov (United States)

    ... Tips Info Center Research Topics Federal Policy Glossary Stem Cell Information General Information Clinical Trials Funding Information Current ... Basics » Stem Cell Basics I. Back to top Stem Cell Basics I. Introduction: What are stem cells, and ...

  17. Stem Cells

    DEFF Research Database (Denmark)

    Sommerlund, Julie

    2004-01-01

    In his influential essay on markets, An essay on framing and overflowing (1998), Michel Callon writes that `the growing complexity of industrialized societies [is] due in large part to the movements of the technosciences, which are causing connections and interdependencies to proliferate'. This p...... and tantalizing than stem cells, in research, in medicine, or as products.......'. This paper is about tech-noscience, and about the proliferation of connections and interdependencies created by it.More specifically, the paper is about stem cells. Biotechnology in general has the power to capture the imagination. Within the field of biotechnology nothing seems more provocative...

  18. Therapeutic application of multipotent stem cells

    DEFF Research Database (Denmark)

    Mirzaei, Hamed; Sahebkar, Amirhossein; Sichani, Laleh Shiri

    2018-01-01

    Cell therapy is an emerging fields in the treatment of various diseases such as cardiovascular, pulmonary, hepatic, and neoplastic diseases. Stem cells are an integral tool for cell therapy. Multipotent stem cells are an important class of stem cells which have the ability to self-renew through...... been showed that multipotent stem cells exert their therapeutic effects via inhibition/activation of a sequence of cellular and molecular pathways. Although the advantages of multipotent stem cells are numerous, further investigation is still necessary to clarify the biology and safety of these cells...... before they could be considered as a potential treatment for different types of diseases. This review summarizes different features of multipotent stem cells including isolation, differentiation, and therapeutic applications....

  19. Distributed and multi-core computation of 2-loop integrals

    International Nuclear Information System (INIS)

    De Doncker, E; Yuasa, F

    2014-01-01

    For an automatic computation of Feynman loop integrals in the physical region we rely on an extrapolation technique where the integrals of the sequence are obtained with iterated/repeated adaptive methods from the QUADPACK 1D quadrature package. The integration rule evaluations in the outer level, corresponding to independent inner integral approximations, are assigned to threads dynamically via the OpenMP runtime in the parallel implementation. Furthermore, multi-level (nested) parallelism enables an efficient utilization of hyperthreading or larger numbers of cores. For a class of loop integrals in the unphysical region, which do not suffer from singularities in the interior of the integration domain, we find that the distributed adaptive integration methods in the multivariate PARINT package are highly efficient and accurate. We apply these techniques without resorting to integral transformations and report on the capabilities of the algorithms and the parallel performance for a test set including various types of two-loop integrals

  20. The complete mitogenome sequence of the Japanese oak silkmoth, Antheraea yamamai (Lepidoptera: Saturniidae).

    Science.gov (United States)

    Kim, Seong Ryeol; Kim, Man Il; Hong, Mee Yeon; Kim, Kee Young; Kang, Pil Don; Hwang, Jae Sam; Han, Yeon Soo; Jin, Byung Rae; Kim, Iksoo

    2009-09-01

    The 15,338-bp long complete mitochondrial genome (mitogenome) of the Japanese oak silkmoth, Antheraea yamamai (Lepidoptera: Saturniidae) was determined. This genome has a gene arrangement identical to those of all other sequenced lepidopteran insects, but differs from the most common type, as the result of the movement of tRNA(Met) to a position 5'-upstream of tRNA(Ile). No typical start codon of the A. yamamai COI gene is available. Instead, a tetranucleotide, TTAG, which is found at the beginning context of all sequenced lepidopteran insects was tentatively designated as the start codon for A. yamamai COI gene. Three of the 13 protein-coding genes (PCGs) harbor the incomplete termination codon, T or TA. All tRNAs formed stable stem-and-loop structures, with the exception of tRNA(Ser)(AGN), the DHU arm of which formed a simple loop as has been observed in many other metazoan mt tRNA(Ser)(AGN). The 334-bp long A + T-rich region is noteworthy in that it harbors tRNA-like structures, as has also been seen in the A + T-rich regions of other insect mitogenomes. Phylogenetic analyses of the available species of Bombycoidea, Pyraloidea, and Tortricidea bolstered the current morphology-based hypothesis that Bombycoidea and Pyraloidea are monophyletic (Obtectomera). As has been previously suggested, Bombycidae (Bombyx mori and B. mandarina) and Saturniidae (A. yamamai and Caligula boisduvalii) formed a reciprocal monophyletic group.

  1. Why STEM?

    Science.gov (United States)

    Mitts, Charles R.

    2016-01-01

    The International Technology and Engineering Educators Association (ITEEA) defines STEM as a new transdisciplinary subject in schools that integrates the disciplines of science, technology, engineering, and mathematics into a single course of study. There are three major problems with this definition: There is no consensus in support of the ITEEA…

  2. Topological and trivial magnetic oscillations in nodal loop semimetals

    Science.gov (United States)

    Oroszlány, László; Dóra, Balázs; Cserti, József; Cortijo, Alberto

    2018-05-01

    Nodal loop semimetals are close descendants of Weyl semimetals and possess a topologically dressed band structure. We argue by combining the conventional theory of magnetic oscillation with topological arguments that nodal loop semimetals host coexisting topological and trivial magnetic oscillations. These originate from mapping the topological properties of the extremal Fermi surface cross sections onto the physics of two dimensional semi-Dirac systems, stemming from merging two massless Dirac cones. By tuning the chemical potential and the direction of magnetic field, a sharp transition is identified from purely trivial oscillations, arising from the Landau levels of a normal two dimensional (2D) electron gas, to a phase where oscillations of topological and trivial origin coexist, originating from 2D massless Dirac and semi-Dirac points, respectively. These could in principle be directly identified in current experiments.

  3. Measure problem in slow roll inflation and loop quantum cosmology

    International Nuclear Information System (INIS)

    Corichi, Alejandro; Karami, Asieh

    2011-01-01

    We consider the measure problem in standard slow-roll inflationary models from the perspective of loop quantum cosmology (LQC). Following recent results by Ashtekar and Sloan, we study the probability of having enough e-foldings and focus on its dependence on the quantum gravity scale, including the transition of the theory to the limit where general relativity (GR) is recovered. Contrary to the standard expectation, the probability of having enough inflation, that is close to 1 in LQC, grows and tends to 1 as one approaches the GR limit. We study the origin of the tension between these results with those by Gibbons and Turok, and offer an explanation that brings these apparent contradictory results into a coherent picture. As we show, the conflicting results stem from different choices of initial conditions for the computation of probability. The singularity-free scenario of loop quantum cosmology offers a natural choice of initial conditions, and suggests that enough inflation is generic.

  4. Rapid and sensitive detection of Didymella bryoniae by visual loop-mediated isothermal amplification assay

    Directory of Open Access Journals (Sweden)

    Xiefeng Yao

    2016-08-01

    Full Text Available Didymella bryoniae is a pathogenic fungus that causes gummy stem blight (GSB in Cucurbitaceae crops (e.g. cantaloupe, muskmelon, cucumber, and watermelon. GSB produces lesions on the stems and leaves, and can also be spread by seeds. Here, we developed a rapid, visual, and sensitive loop-mediated amplification (LAMP assay for D. bryoniae detection based on sequence-characterized amplified regions (GenBank accession nos GQ872461 and GQ872462 common to the two random amplification of polymorphic DNA group genotypes (RGI and RGII of D. bryoniae; ideal conditions for detection were optimized for completion in 45 min at 63°C. The sensitivity and specificity of the LAMP assay were further analyzed in comparison with those of a conventional polymerase chain reaction (PCR. The sensitivity of the LAMP assay was 1000-fold higher than that of conventional PCR with a detection limit of 0.1 fg μL−1 of targeted DNA. The LAMP assay could be accomplished in about 45 min, with the results visible to the naked eye. The assay showed high specificity in discriminating all D. bryoniae isolates from seven other fungal pathogens that occur in Cucurbitaceae crops. The LAMP assay also detected D. bryoniae infection in young muskmelon leaves with suspected early symptoms of GSB disease. Hence, the technique has great potential for developing rapid and sensitive visual detection methods for the D. bryoniae pathogen in crops and seeds. This method has potential application in early prediction of disease and reducing the risk of epidemics.

  5. Loop equations in the theory of gravitation

    International Nuclear Information System (INIS)

    Makeenko, Yu.M.; Voronov, N.A.

    1981-01-01

    Loop-space variables (matrices of parallel transport) for the theory of gravitation are described. Loop equations, which are equivalent to the Einstein equations, are derived in the classical case. Loop equations are derived for gravity with cosmological constant as well. An analogy with the loop-space approach in Yang-Mills theory is discussed [ru

  6. Kalman Orbit Optimized Loop Tracking

    Science.gov (United States)

    Young, Lawrence E.; Meehan, Thomas K.

    2011-01-01

    Under certain conditions of low signal power and/or high noise, there is insufficient signal to noise ratio (SNR) to close tracking loops with individual signals on orbiting Global Navigation Satellite System (GNSS) receivers. In addition, the processing power available from flight computers is not great enough to implement a conventional ultra-tight coupling tracking loop. This work provides a method to track GNSS signals at very low SNR without the penalty of requiring very high processor throughput to calculate the loop parameters. The Kalman Orbit-Optimized Loop (KOOL) tracking approach constitutes a filter with a dynamic model and using the aggregate of information from all tracked GNSS signals to close the tracking loop for each signal. For applications where there is not a good dynamic model, such as very low orbits where atmospheric drag models may not be adequate to achieve the required accuracy, aiding from an IMU (inertial measurement unit) or other sensor will be added. The KOOL approach is based on research JPL has done to allow signal recovery from weak and scintillating signals observed during the use of GPS signals for limb sounding of the Earth s atmosphere. That approach uses the onboard PVT (position, velocity, time) solution to generate predictions for the range, range rate, and acceleration of the low-SNR signal. The low- SNR signal data are captured by a directed open loop. KOOL builds on the previous open loop tracking by including feedback and observable generation from the weak-signal channels so that the MSR receiver will continue to track and provide PVT, range, and Doppler data, even when all channels have low SNR.

  7. Hubungan Kekerabatan Sapi Aceh dengan Menggunakan Daerah Displacement-loop

    Directory of Open Access Journals (Sweden)

    Mohd. Agus Nashri Abdullah

    2008-10-01

    Full Text Available Relationship of aceh cattle using displacement-loop region ABSTRACT. The aims of this study were to describe relationship of D-loop of mtDNA Aceh cattle which is useful database for conducting conservation programme. The whole blood samples were collected (8 samples for D-loop analysis from four locations which were Aceh Besar, Pidie, North Aceh regencies and Banda Aceh city. Out group whole blood samples were collected from two samples from Bali cattles (Bali Island, Madura cattle (Madura Island, Pesisir cattle (West Sumatera respectively and one sample from PO cattle (West Java. Amplification of D-loop sequences of mtDNA with BIDLF and BIDLR primary have PCR product 980 bp. The Data were analyzed using Squint 1.02 and MEGA 4.0 programme. Result of analysis indicate that Aceh cattle have nearer relationship with zebu and there is items inset of genetik Bali cattle (Bos javanicus at the end sequences start ke-354 situs up to 483, so that the origin Aceh cattle was from Bos indicus which have hybridization with Bos javanicus.

  8. A type of loop algebra and the associated loop algebras

    International Nuclear Information System (INIS)

    Tam Honwah; Zhang Yufeng

    2008-01-01

    A higher-dimensional twisted loop algebra is constructed. As its application, a new Lax pair is presented, whose compatibility gives rise to a Liouville integrable hierarchy of evolution equations by making use of Tu scheme. One of the reduction cases of the hierarchy is an analogous of the well-known AKNS system. Next, the twisted loop algebra, furthermore, is extended to another higher dimensional loop algebra, from which a hierarchy of evolution equations with 11-potential component functions is obtained, whose reduction is just standard AKNS system. Especially, we prove that an arbitrary linear combination of the four Hamiltonian operators directly obtained from the recurrence relations is still a Hamiltonian operator. Therefore, the hierarchy with 11-potential functions possesses 4-Hamiltonian structures. Finally, an integrable coupling of the hierarchy is worked out

  9. Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures

    Science.gov (United States)

    Sloma, Michael F.; Mathews, David H.

    2016-01-01

    RNA secondary structure prediction is widely used to analyze RNA sequences. In an RNA partition function calculation, free energy nearest neighbor parameters are used in a dynamic programming algorithm to estimate statistical properties of the secondary structure ensemble. Previously, partition functions have largely been used to estimate the probability that a given pair of nucleotides form a base pair, the conditional stacking probability, the accessibility to binding of a continuous stretch of nucleotides, or a representative sample of RNA structures. Here it is demonstrated that an RNA partition function can also be used to calculate the exact probability of formation of hairpin loops, internal loops, bulge loops, or multibranch loops at a given position. This calculation can also be used to estimate the probability of formation of specific helices. Benchmarking on a set of RNA sequences with known secondary structures indicated that loops that were calculated to be more probable were more likely to be present in the known structure than less probable loops. Furthermore, highly probable loops are more likely to be in the known structure than the set of loops predicted in the lowest free energy structures. PMID:27852924

  10. Tritium Management Loop Design Status

    Energy Technology Data Exchange (ETDEWEB)

    Rader, Jordan D. [ORNL; Felde, David K. [ORNL; McFarlane, Joanna [ORNL; Greenwood, Michael Scott [ORNL; Qualls, A L. [ORNL; Calderoni, Pattrick [Idaho National Laboratory (INL)

    2017-12-01

    This report summarizes physical, chemical, and engineering analyses that have been done to support the development of a test loop to study tritium migration in 2LiF-BeF2 salts. The loop will operate under turbulent flow and a schematic of the apparatus has been used to develop a model in Mathcad to suggest flow parameters that should be targeted in loop operation. The introduction of tritium into the loop has been discussed as well as various means to capture or divert the tritium from egress through a test assembly. Permeation was calculated starting with a Modelica model for a transport through a nickel window into a vacuum, and modifying it for a FLiBe system with an argon sweep gas on the downstream side of the permeation interface. Results suggest that tritium removal with a simple tubular permeation device will occur readily. Although this system is idealized, it suggests that rapid measurement capability in the loop may be necessary to study and understand tritium removal from the system.

  11. Criteria for saturated magnetization loop

    International Nuclear Information System (INIS)

    Harres, A.; Mikhov, M.; Skumryev, V.; Andrade, A.M.H. de; Schmidt, J.E.; Geshev, J.

    2016-01-01

    Proper estimation of magnetization curve parameters is vital in studying magnetic systems. In the present article, criteria for discrimination non-saturated (minor) from saturated (major) hysteresis loops are proposed. These employ the analysis of (i) derivatives of both ascending and descending branches of the loop, (ii) remanent magnetization curves, and (iii) thermomagnetic curves. Computational simulations are used in order to demonstrate their validity. Examples illustrating the applicability of these criteria to well-known real systems, namely Fe_3O_4 and Ni fine particles, are provided. We demonstrate that the anisotropy-field value estimated from a visual examination of an only apparently major hysteresis loop could be more than two times lower than the real one. - Highlights: • Proper estimation of hysteresis-loop parameters is vital in magnetic studies. • We propose criteria for discrimination minor from major hysteresis loops. • The criteria analyze magnetization, remanence and ZFC/FC curves and/or their derivatives. • Examples of their application on real nanoparticles systems are given. • Using the criteria could avoid twofold or bigger saturation-field underestimation errors.

  12. Criteria for saturated magnetization loop

    Energy Technology Data Exchange (ETDEWEB)

    Harres, A. [Departamento de Física, UFSM, Santa Maria, 97105-900 Rio Grande do Sul (Brazil); Mikhov, M. [Faculty of Physics, University of Sofia, 1164 Sofia (Bulgaria); Skumryev, V. [Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona (Spain); Departament de Física, Universitat Autònoma de Barcelona, 08193 Barcelona (Spain); Andrade, A.M.H. de; Schmidt, J.E. [Instituto de Física, UFRGS, Porto Alegre, 91501-970 Rio Grande do Sul (Brazil); Geshev, J., E-mail: julian@if.ufrgs.br [Departament de Física, Universitat Autònoma de Barcelona, 08193 Barcelona (Spain); Instituto de Física, UFRGS, Porto Alegre, 91501-970 Rio Grande do Sul (Brazil)

    2016-03-15

    Proper estimation of magnetization curve parameters is vital in studying magnetic systems. In the present article, criteria for discrimination non-saturated (minor) from saturated (major) hysteresis loops are proposed. These employ the analysis of (i) derivatives of both ascending and descending branches of the loop, (ii) remanent magnetization curves, and (iii) thermomagnetic curves. Computational simulations are used in order to demonstrate their validity. Examples illustrating the applicability of these criteria to well-known real systems, namely Fe{sub 3}O{sub 4} and Ni fine particles, are provided. We demonstrate that the anisotropy-field value estimated from a visual examination of an only apparently major hysteresis loop could be more than two times lower than the real one. - Highlights: • Proper estimation of hysteresis-loop parameters is vital in magnetic studies. • We propose criteria for discrimination minor from major hysteresis loops. • The criteria analyze magnetization, remanence and ZFC/FC curves and/or their derivatives. • Examples of their application on real nanoparticles systems are given. • Using the criteria could avoid twofold or bigger saturation-field underestimation errors.

  13. DNA looping by FokI: the impact of synapse geometry on loop topology at varied site orientations

    Science.gov (United States)

    Rusling, David A.; Laurens, Niels; Pernstich, Christian; Wuite, Gijs J. L.; Halford, Stephen E.

    2012-01-01

    Most restriction endonucleases, including FokI, interact with two copies of their recognition sequence before cutting DNA. On DNA with two sites they act in cis looping out the intervening DNA. While many restriction enzymes operate symmetrically at palindromic sites, FokI acts asymmetrically at a non-palindromic site. The directionality of its sequence means that two FokI sites can be bridged in either parallel or anti-parallel alignments. Here we show by biochemical and single-molecule biophysical methods that FokI aligns two recognition sites on separate DNA molecules in parallel and that the parallel arrangement holds for sites in the same DNA regardless of whether they are in inverted or repeated orientations. The parallel arrangement dictates the topology of the loop trapped between sites in cis: the loop from inverted sites has a simple 180° bend, while that with repeated sites has a convoluted 360° turn. The ability of FokI to act at asymmetric sites thus enabled us to identify the synapse geometry for sites in trans and in cis, which in turn revealed the relationship between synapse geometry and loop topology. PMID:22362745

  14. Reconstruction of structural evolution in the trnL intron P6b loop of symbiotic Nostoc (Cyanobacteria).

    Science.gov (United States)

    Olsson, Sanna; Kaasalainen, Ulla; Rikkinen, Jouko

    2012-02-01

    In this study we reconstruct the structural evolution of the hyper-variable P6b region of the group I trnLeu intron in a monophyletic group of lichen-symbiotic Nostoc strains and establish it as a useful marker in the phylogenetic analysis of these organisms. The studied cyanobacteria occur as photosynthetic and/or nitrogen-fixing symbionts in lichen species of the diverse Nephroma guild. Phylogenetic analyses and secondary structure reconstructions are used to improve the understanding of the replication mechanisms in the P6b stem-loop and to explain the observed distribution patterns of indels. The variants of the P6b region in the Nostoc clade studied consist of different combinations of five sequence modules. The distribution of indels together with the ancestral character reconstruction performed enables the interpretation of the evolution of each sequence module. Our results indicate that the indel events are usually associated with single nucleotide changes in the P6b region and have occurred several times independently. In spite of their homoplasy, they provide phylogenetic information for closely related taxa. Thus we recognize that features of the P6b region can be used as molecular markers for species identification and phylogenetic studies involving symbiotic Nostoc cyanobacteria.

  15. Control Strategies for Islanded Microgrid using Enhanced Hierarchical Control Structure with Multiple Current-Loop Damping Schemes

    DEFF Research Database (Denmark)

    Han, Yang; Shen, Pan; Zhao, Xin

    2017-01-01

    In this paper, the modeling, controller design, and stability analysis of the islanded microgrid (MG) using enhanced hierarchical control structure with multiple current loop damping schemes is proposed. The islanded MG is consisted of the parallel-connected voltage source inverters using LCL...... output filters, and the proposed control structure includes: the primary control with additional phase-shift loop, the secondary control for voltage amplitude and frequency restoration, the virtual impedance loops which contains virtual positive- and negative-sequence impedance loops at fundamental...... frequency, and virtual variable harmonic impedance loop at harmonic frequencies, and the inner voltage and current loop controllers. A small-signal model for the primary and secondary controls with additional phase-shift loop is presented, which shows an over-damped feature from eigenvalue analysis...

  16. Thermodynamics in Loop Quantum Cosmology

    International Nuclear Information System (INIS)

    Li, L.F.; Zhu, J.Y.

    2009-01-01

    Loop quantum cosmology (LQC) is very powerful to deal with the behavior of early universe. Moreover, the effective loop quantum cosmology gives a successful description of the universe in the semiclassical region. We consider the apparent horizon of the Friedmann-Robertson-Walker universe as a thermodynamical system and investigate the thermodynamics of LQC in the semiclassical region. The effective density and effective pressure in the modified Friedmann equation from LQC not only determine the evolution of the universe in LQC scenario but also are actually found to be the thermodynamic quantities. This result comes from the energy definition in cosmology (the Misner-Sharp gravitational energy) and is consistent with thermodynamic laws. We prove that within the framework of loop quantum cosmology, the elementary equation of equilibrium thermodynamics is still valid.

  17. The nucleotide sequence of parsnip yellow fleck virus: a plant picorna-like virus.

    Science.gov (United States)

    Turnbull-Ross, A D; Reavy, B; Mayo, M A; Murant, A F

    1992-12-01

    The complete sequence of 9871 nucleotides (nts) of parsnip yellow fleck virus (PYFV; isolate P-121) was determined from cDNA clones and by direct sequencing of viral RNA. The RNA contains a large open reading frame between nts 279 and 9362 which encodes a polyprotein of 3027 amino acids with a calculated M(r) of 336212 (336K). A PYFV polyclonal antiserum reacted with the proteins expressed from phage carrying cDNA clones from the 5' half of the PYFV genome. Comparison of the polyprotein sequence of PYFV with other viral polyprotein sequences reveals similarities to the putative NTP-binding and RNA polymerase domains of cowpea mosaic comovirus, tomato black ring nepovirus and several animal picornaviruses. The 3' untranslated region of PYFV RNA is 509 nts long and does not have a poly(A) tail. The 3'-terminal 121 nts may form a stem-loop structure which resembles that formed in the genomic RNA of mosquito-borne flaviviruses.

  18. High pressure experimental water loop

    International Nuclear Information System (INIS)

    Grenon, M.

    1958-01-01

    A high pressure experimental water loop has been made for studying the detection and evolution of cladding failure in a pressurized reactor. The loop has been designed for a maximum temperature of 360 deg. C, a maximum of 160 kg/cm 2 and flow rates up to 5 m 3 /h. The entire loop consists of several parts: a main circuit with a canned rotor circulation pump, steam pressurizer, heating tubes, two hydro-cyclones (one de-gasser and one decanter) and one tubular heat exchanger; a continuous purification loop, connected in parallel, comprising pressure reducing valves and resin pots which also allow studies of the stability of resins under pressure, temperature and radiation; following the gas separator is a gas loop for studying the recombination of the radiolytic gases in the steam phase. The preceding circuits, as well as others, return to a low pressure storage circuit. The cold water of the low pressure storage flask is continuously reintroduced into the high pressure main circuit by means of a return pump at a maximum head of 160 kg /cm 2 , and adjusted to the pressurizer level. This loop is also a testing bench for the tight high pressure apparatus. The circulating pump and the connecting flanges (Oak Ridge type) are water-tight. The feed pump and the pressure reducing valves are not; the un-tight ones have a system of leak recovery. To permanently check the tightness the circuit has been fitted with a leak detection system (similar to the HRT one). (author) [fr

  19. Integrable systems and loop coproducts

    International Nuclear Information System (INIS)

    Musso, Fabio

    2010-01-01

    We present a generalization of a framework for the construction of classical integrable systems that we call loop coproduct formulation (Musso 2010 J. Phys. A: Math. Theor. 43 434026). In this paper, the loop coproduct formulation includes systems of Gelfand-Tsetlin type, the linear r-matrix formulation, the Sklyanin algebras, the reflection algebras, the coalgebra symmetry approach and some of its generalizations as particular cases, showing that all these apparently different approaches have a common algebraic origin. On the other hand, all these subcases do not exhaust the domain of applicability of this new technique, so that new possible directions of investigation do naturally emerge in this framework.

  20. Perturbations in loop quantum cosmology

    International Nuclear Information System (INIS)

    Nelson, W; Agullo, I; Ashtekar, A

    2014-01-01

    The era of precision cosmology has allowed us to accurately determine many important cosmological parameters, in particular via the CMB. Confronting Loop Quantum Cosmology with these observations provides us with a powerful test of the theory. For this to be possible, we need a detailed understanding of the generation and evolution of inhomogeneous perturbations during the early, quantum gravity phase of the universe. Here, we have described how Loop Quantum Cosmology provides a completion of the inflationary paradigm, that is consistent with the observed power spectra of the CMB

  1. LISA Pathfinder: OPD loop characterisation

    Science.gov (United States)

    Born, Michael; LPF Collaboration

    2017-05-01

    The optical metrology system (OMS) of the LISA Pathfinder mission is measuring the distance between two free-floating test masses with unprecedented precision. One of the four OMS heterodyne interferometers reads out the phase difference between the reference and the measurement laser beam. This phase from the reference interferometer is common to all other longitudinal interferometer read outs and therefore subtracted. In addition, the phase is fed back via the digital optical pathlength difference (OPD) control loop to keep it close to zero. Here, we analyse the loop parameters and compare them to on-ground measurement results.

  2. LOOP: engineering marvel, economic calamity

    Energy Technology Data Exchange (ETDEWEB)

    Brossard, E B

    1985-01-01

    The Louisiana Offshore Oil Port (LOOP) is the first superport built in the Lower 48. The United States was the only major oil-importing country that did not have a superport, and therefore, could not offload very large crude carriers (VLCCs). Unfortunately, a number of factors changed after it was decided to build LOOP, and these, plus the onerous provisions of the Deepwater Ports Act of 1974, which authorized superports, prevented LOOP from operating economically. LOOP's facilities consist of an offshore platform complex with three single-point-mooring (SPM) system buoys, 19 miles offshore in 110 feet of water, as well as a 32-million-barrel storage terminal 31 miles inland at Clovelly Salt Dome, and connecting pipelines offshore and onshore. By the time LOOP was started-up in May 1981, demand for oil had declined, because of rises in the price of oil, and the source of US oil imports had shifted back to the western hemisphere, away from the eastern hemisphere, closer to the US. The refinery mix in the US also changed, because of up-grading of a number of big refineries, which further reduced demand and made heavier crudes from countries like Mexico and Venezuela more economical. Because of reduced oil imports and shorter hauls, oil shippers started using or continued to use smaller tankers. Smaller tankers are not economical for LOOP, nor do they need LOOP. The start-up of the Trans-Alaska Pipeline System (TAPS) in mid-1977 backed out 1.5 million bd/sup -1/ of foreign imports. TAPS' capacity coincides with LOOP's offloading capacity of 1.4 million bd/sup -1/. US decontrol of domestic crude in 1981 and increased drilling, plus general energy conservation further reduced US oil imports. US consumption declined to 15.1 million bd/sup -1/ in 1983, from 18.8 million bd/sup -1/ in 1978. This award-winning superport needed federal decontrol and increased oil imports along with more VLCCs, in order to operate economically.

  3. Two-Loop Splitting Amplitudes

    International Nuclear Information System (INIS)

    Bern, Z.

    2004-01-01

    Splitting amplitudes govern the behavior of scattering amplitudes at the momenta of external legs become collinear. In this talk we outline the calculation of two-loop splitting amplitudes via the unitarity sewing method. This method retains the simple factorization properties of light-cone gauge, but avoids the need for prescriptions such as the principal value or Mandelstam-Leibbrandt ones. The encountered loop momentum integrals are then evaluated using integration-by-parts and Lorentz invariance identities. We outline a variety of applications for these splitting amplitudes

  4. Two-loop splitting amplitudes

    International Nuclear Information System (INIS)

    Bern, Z.; Dixon, L.J.; Kosower, D.A.

    2004-01-01

    Splitting amplitudes govern the behavior of scattering amplitudes at the momenta of external legs become collinear. In this talk we outline the calculation of two-loop splitting amplitudes via the unitarity sewing method. This method retains the simple factorization properties of light-cone gauge, but avoids the need for prescriptions such as the principal value or Mandelstam-Leibbrandt ones. The encountered loop momentum integrals are then evaluated using integration-by-parts and Lorentz invariance identities. We outline a variety of applications for these splitting amplitudes

  5. Fermions and loops on graphs: I. Loop calculus for determinants

    International Nuclear Information System (INIS)

    Chernyak, Vladimir Y; Chertkov, Michael

    2008-01-01

    This paper is the first in a series devoted to evaluation of the partition function in statistical models on graphs with loops in terms of the Berezin/fermion integrals. The paper focuses on a representation of the determinant of a square matrix in terms of a finite series, where each term corresponds to a loop on the graph. The representation is based on a fermion version of the loop calculus, previously introduced by the authors for graphical models with finite alphabets. Our construction contains two levels. First, we represent the determinant in terms of an integral over anti-commuting Grassmann variables, with some reparametrization/gauge freedom hidden in the formulation. Second, we show that a special choice of the gauge, called the BP (Bethe–Peierls or belief propagation) gauge, yields the desired loop representation. The set of gauge fixing BP conditions is equivalent to the Gaussian BP equations, discussed in the past as efficient (linear scaling) heuristics for estimating the covariance of a sparse positive matrix

  6. Robust fault detection in open loop vs. closed loop

    DEFF Research Database (Denmark)

    Niemann, Hans Henrik; Stoustrup, J.

    1997-01-01

    The robustness aspects of fault detection and isolation (FDI) for uncertain systems are considered. The FDI problem is considered in a standard problem formulation. The FDI design problem is analyzed both in the case where the control input signal is considered as a known external input signal (o...... (open loop) and when the input signal is generated by a feedback controller...

  7. A virtual closed loop method for closed loop identification

    NARCIS (Netherlands)

    Agüero, J.C.; Goodwin, G.C.; Hof, Van den P.M.J.

    2011-01-01

    Indirect methods for the identification of linear plant models on the basis of closed loop data are based on the use of (reconstructed) input signals that are uncorrelated with the noise. This generally requires exact (linear) controller knowledge. On the other hand, direct identification requires

  8. Sequence assembly

    DEFF Research Database (Denmark)

    Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria

    2009-01-01

    Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and...... in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html....

  9. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  10. Processing oscillatory signals by incoherent feedforward loops

    Science.gov (United States)

    Zhang, Carolyn; Wu, Feilun; Tsoi, Ryan; Shats, Igor; You, Lingchong

    From the timing of amoeba development to the maintenance of stem cell pluripotency,many biological signaling pathways exhibit the ability to differentiate between pulsatile and sustained signals in the regulation of downstream gene expression.While networks underlying this signal decoding are diverse,many are built around a common motif, the incoherent feedforward loop (IFFL),where an input simultaneously activates an output and an inhibitor of the output.With appropriate parameters,this motif can generate temporal adaptation,where the system is desensitized to a sustained input.This property serves as the foundation for distinguishing signals with varying temporal profiles.Here,we use quantitative modeling to examine another property of IFFLs,the ability to process oscillatory signals.Our results indicate that the system's ability to translate pulsatile dynamics is limited by two constraints.The kinetics of IFFL components dictate the input range for which the network can decode pulsatile dynamics.In addition,a match between the network parameters and signal characteristics is required for optimal ``counting''.We elucidate one potential mechanism by which information processing occurs in natural networks with implications in the design of synthetic gene circuits for this purpose. This work was partially supported by the National Science Foundation Graduate Research Fellowship (CZ).

  11. Deep sequencing of foot-and-mouth disease virus reveals RNA sequences involved in genome packaging.

    Science.gov (United States)

    Logan, Grace; Newman, Joseph; Wright, Caroline F; Lasecka-Dykes, Lidia; Haydon, Daniel T; Cottam, Eleanor M; Tuthill, Tobias J

    2017-10-18

    Non-enveloped viruses protect their genomes by packaging them into an outer shell or capsid of virus-encoded proteins. Packaging and capsid assembly in RNA viruses can involve interactions between capsid proteins and secondary structures in the viral genome as exemplified by the RNA bacteriophage MS2 and as proposed for other RNA viruses of plants, animals and human. In the picornavirus family of non-enveloped RNA viruses, the requirements for genome packaging remain poorly understood. Here we show a novel and simple approach to identify predicted RNA secondary structures involved in genome packaging in the picornavirus foot-and-mouth disease virus (FMDV). By interrogating deep sequencing data generated from both packaged and unpackaged populations of RNA we have determined multiple regions of the genome with constrained variation in the packaged population. Predicted secondary structures of these regions revealed stem loops with conservation of structure and a common motif at the loop. Disruption of these features resulted in attenuation of virus growth in cell culture due to a reduction in assembly of mature virions. This study provides evidence for the involvement of predicted RNA structures in picornavirus packaging and offers a readily transferable methodology for identifying packaging requirements in many other viruses. Importance In order to transmit their genetic material to a new host, non-enveloped viruses must protect their genomes by packaging them into an outer shell or capsid of virus-encoded proteins. For many non-enveloped RNA viruses the requirements for this critical part of the viral life cycle remain poorly understood. We have identified RNA sequences involved in genome packaging of the picornavirus foot-and-mouth disease virus. This virus causes an economically devastating disease of livestock affecting both the developed and developing world. The experimental methods developed to carry out this work are novel, simple and transferable to the

  12. Stem cell biobanks.

    Science.gov (United States)

    Bardelli, Silvana

    2010-04-01

    Stem cells contribute to innate healing and harbor a promising role for regenerative medicine. Stem cell banking through long-term storage of different stem cell platforms represents a fundamental source to preserve original features of stem cells for patient-specific clinical applications. Stem cell research and clinical translation constitute fundamental and indivisible modules catalyzed through biobanking activity, generating a return of investment.

  13. Free loop spaces and cyclohedra

    Czech Academy of Sciences Publication Activity Database

    Markl, Martin

    2003-01-01

    Roč. 71, - (2003), s. 151-157 R&D Projects: GA AV ČR IAA1019203 Institutional research plan: CEZ:AV0Z1019905; CEZ:AV0Z1019905 Keywords : cyclohedron * free loop space * recognition Subject RIV: BA - General Mathematics

  14. Feedback - closing the loop digitally

    International Nuclear Information System (INIS)

    Zagel, J.; Chase, B.

    1992-01-01

    Many feedback and feedforward systems are now using microprocessors within the loop. We describe the wide range of possibilities and problems that arise. We also propose some ideas for analysis and testing, including examples of motion control in the Flying Wire systems in Main Ring and Tevatron and Low Level RF control now being built for the Fermilab Linac upgrade. (author)

  15. Morbidity of temporary loop ileostomies

    NARCIS (Netherlands)

    Bakx, R.; Busch, O. R. C.; Bemelman, W. A.; Veldink, G. J.; Slors, J. F. M.; van Lanschot, J. J. B.

    2004-01-01

    Background/Aims: A temporary loop ileostomy is constructed to protect a distal colonic anastomosis. Closure is usually performed not earlier than 8 - 12 weeks after the primary operation. During this period, stoma-related complications can occur and enhance the adverse effect on quality of life. The

  16. Wilson loops in Kerr gravitation

    International Nuclear Information System (INIS)

    Bollini, C.G.; Giambiagi, J.J.; Tiomno, J.

    1981-01-01

    The ordered integrals for several paths in Kerr gravitation is computed in a compact form. When the path is closed its relation with the angular parallel displacement is discussed and the corresponding Wilson loop is calculated. The validity of Mandelstam relations for gauge fields is also explicitly verified. (Author) [pt

  17. Loop quantum cosmology: Recent progress

    Indian Academy of Sciences (India)

    Aspects of the full theory of loop quantum gravity can be studied in a simpler .... group) 1-forms and vector fields and Λ is an SO(3)-matrix indicating the internal ... are p and c which are related to the more familiar scale factor by the relations.

  18. PONDEROMOTIVE ACCELERATION IN CORONAL LOOPS

    Energy Technology Data Exchange (ETDEWEB)

    Dahlburg, R. B.; Obenschain, K. [LCP and FD, Naval Research Laboratory, Washington, DC 20375 (United States); Laming, J. M. [Space Science Division, Naval Research Laboratory, Washington, DC 20375 (United States); Taylor, B. D. [AFRL Eglin AFB, Pensacola, FL 32542 (United States)

    2016-11-10

    Ponderomotive acceleration has been asserted to be a cause of the first ionization potential (FIP) effect, the well-known enhancement in abundance by a factor of 3–4 over photospheric values of elements in the solar corona with FIP less than about 10 eV. It is shown here by means of numerical simulations that ponderomotive acceleration occurs in solar coronal loops, with the appropriate magnitude and direction, as a “by-product” of coronal heating. The numerical simulations are performed with the HYPERION code, which solves the fully compressible three-dimensional magnetohydrodynamic equations including nonlinear thermal conduction and optically thin radiation. Numerical simulations of coronal loops with an axial magnetic field from 0.005 to 0.02 T and lengths from 25,000 to 75,000 km are presented. In the simulations the footpoints of the axial loop magnetic field are convected by random, large-scale motions. There is a continuous formation and dissipation of field-aligned current sheets, which act to heat the loop. As a consequence of coronal magnetic reconnection, small-scale, high-speed jets form. The familiar vortex quadrupoles form at reconnection sites. Between the magnetic footpoints and the corona the reconnection flow merges with the boundary flow. It is in this region that the ponderomotive acceleration occurs. Mirroring the character of the coronal reconnection, the ponderomotive acceleration is also found to be intermittent.

  19. Loop quantum cosmology and singularities.

    Science.gov (United States)

    Struyve, Ward

    2017-08-15

    Loop quantum gravity is believed to eliminate singularities such as the big bang and big crunch singularity. This belief is based on studies of so-called loop quantum cosmology which concerns symmetry-reduced models of quantum gravity. In this paper, the problem of singularities is analysed in the context of the Bohmian formulation of loop quantum cosmology. In this formulation there is an actual metric in addition to the wave function, which evolves stochastically (rather than deterministically as the case of the particle evolution in non-relativistic Bohmian mechanics). Thus a singularity occurs whenever this actual metric is singular. It is shown that in the loop quantum cosmology for a homogeneous and isotropic Friedmann-Lemaître-Robertson-Walker space-time with arbitrary constant spatial curvature and cosmological constant, coupled to a massless homogeneous scalar field, a big bang or big crunch singularity is never obtained. This should be contrasted with the fact that in the Bohmian formulation of the Wheeler-DeWitt theory singularities may exist.

  20. PONDEROMOTIVE ACCELERATION IN CORONAL LOOPS

    International Nuclear Information System (INIS)

    Dahlburg, R. B.; Obenschain, K.; Laming, J. M.; Taylor, B. D.

    2016-01-01

    Ponderomotive acceleration has been asserted to be a cause of the first ionization potential (FIP) effect, the well-known enhancement in abundance by a factor of 3–4 over photospheric values of elements in the solar corona with FIP less than about 10 eV. It is shown here by means of numerical simulations that ponderomotive acceleration occurs in solar coronal loops, with the appropriate magnitude and direction, as a “by-product” of coronal heating. The numerical simulations are performed with the HYPERION code, which solves the fully compressible three-dimensional magnetohydrodynamic equations including nonlinear thermal conduction and optically thin radiation. Numerical simulations of coronal loops with an axial magnetic field from 0.005 to 0.02 T and lengths from 25,000 to 75,000 km are presented. In the simulations the footpoints of the axial loop magnetic field are convected by random, large-scale motions. There is a continuous formation and dissipation of field-aligned current sheets, which act to heat the loop. As a consequence of coronal magnetic reconnection, small-scale, high-speed jets form. The familiar vortex quadrupoles form at reconnection sites. Between the magnetic footpoints and the corona the reconnection flow merges with the boundary flow. It is in this region that the ponderomotive acceleration occurs. Mirroring the character of the coronal reconnection, the ponderomotive acceleration is also found to be intermittent.

  1. Independent SU(2)-loop variables

    International Nuclear Information System (INIS)

    Loll, R.

    1991-04-01

    We give a reduction procedure for SU(2)-trace variables and introduce a complete set of indepentent, gauge-invariant and almost local loop variables for the configuration space of SU(2)-lattice gauge theory in 2+1 dimensions. (orig.)

  2. An experimental study of dislocation loop nucleation

    International Nuclear Information System (INIS)

    Bounaud, J.Y.; Leteurtre, J.

    1975-01-01

    The nucleation of dislocation loops is experimentally studied by observing the demixion of the Burgers vectors of dislocation loops nucleated in copper whiskers irradiated in flexion by fission fragments at room temperature. The demixion of Burgers vectors is observed by the dimensional effects of dislocation loops: after irradiation, the applied stress is removed; the whisker shows a residual strain that is due to loops because, after an annealing treatment to evaporate dislocation loops, each whisker recovers its initial straight shape. Everywhere along the whisker, the radius of curvature is measured and plotted vs the max. applied stress. Estimations of the interstitial and vacancy dislocation loop nuclei are derived [fr

  3. The nucleotide sequence of the RNA-2 of an isolate of the English serotype of tomato black ring virus: RNA recombination in the history of nepoviruses.

    Science.gov (United States)

    Le Gall, O L; Lanneau, M; Candresse, T; Dunez, J

    1995-05-01

    The RNA-2 of a carrot isolate from the English serotype of tomato black ring nepovirus (TBRV-ED) has been sequenced. It is 4618 nucleotides long and contains one open reading frame encoding a polypeptide of 1344 amino acids. The 5' non-coding region contains three repetitions of a stem-loop structure also conserved in TBRV-Scottish and grapevine chrome mosaic nepovirus (GCMV). The coat protein domain was mapped to the carboxy-terminal one-third of the polyprotein. Sequence comparisons indicate that TBRV-ED RNA-2 probably arose by an RNA recombination event that resulted in the exchange of the putative movement protein gene between TBRV and GCMV.

  4. A complex approach to the blue-loop problem

    Science.gov (United States)

    Ostrowski, Jakub; Daszynska-Daszkiewicz, Jadwiga

    2015-08-01

    The problem of the blue loops during the core helium burning, outstanding for almost fifty years, is one of the most difficult and poorly understood problems in stellar astrophysics. Most of the work focused on the blue loops done so far has been performed with old stellar evolution codes and with limited computational resources. In the end the obtained conclusions were based on a small sample of models and could not have taken into account more advanced effects and interactions between them.The emergence of the blue loops depends on many details of the evolution calculations, in particular on chemical composition, opacity, mixing processes etc. The non-linear interactions between these factors contribute to the statement that in most cases it is hard to predict without a precise stellar modeling whether a loop will emerge or not. The high sensitivity of the blue loops to even small changes of the internal structure of a star yields one more issue: a sensitivity to numerical problems, which are common in calculations of stellar models on advanced stages of the evolution.To tackle this problem we used a modern stellar evolution code MESA. We calculated a large grid of evolutionary tracks (about 8000 models) with masses in the range of 3.0 - 25.0 solar masses from the zero age main sequence to the depletion of helium in the core. In order to make a comparative analysis, we varied metallicity, helium abundance and different mixing parameters resulting from convective overshooting, rotation etc.The better understanding of the properties of the blue loops is crucial for our knowledge of the population of blue supergiants or pulsating variables such as Cepheids, α-Cygni or Slowly Pulsating B-type supergiants. In case of more massive models it is also of great importance for studies of the progenitors of supernovae.

  5. Catalog of gene expression in adult neural stem cells and their in vivo microenvironment

    International Nuclear Information System (INIS)

    Williams, Cecilia; Wirta, Valtteri; Meletis, Konstantinos; Wikstroem, Lilian; Carlsson, Leif; Frisen, Jonas; Lundeberg, Joakim

    2006-01-01

    Stem cells generally reside in a stem cell microenvironment, where cues for self-renewal and differentiation are present. However, the genetic program underlying stem cell proliferation and multipotency is poorly understood. Transcriptome analysis of stem cells and their in vivo microenvironment is one way of uncovering the unique stemness properties and provides a framework for the elucidation of stem cell function. Here, we characterize the gene expression profile of the in vivo neural stem cell microenvironment in the lateral ventricle wall of adult mouse brain and of in vitro proliferating neural stem cells. We have also analyzed an Lhx2-expressing hematopoietic-stem-cell-like cell line in order to define the transcriptome of a well-characterized and pure cell population with stem cell characteristics. We report the generation, assembly and annotation of 50,792 high-quality 5'-end expressed sequence tag sequences. We further describe a shared expression of 1065 transcripts by all three stem cell libraries and a large overlap with previously published gene expression signatures for neural stem/progenitor cells and other multipotent stem cells. The sequences and cDNA clones obtained within this framework provide a comprehensive resource for the analysis of genes in adult stem cells that can accelerate future stem cell research

  6. Light-by-light-type corrections to the muon anomalous magnetic moment at four-loop order

    International Nuclear Information System (INIS)

    Kurz, Alexander; Smirnov, Alexander V.; Smirnov, Vladimir A.

    2015-08-01

    The numerically dominant QED contributions to the anomalous magnetic moment of the muon stem from Feynman diagrams with internal electron loops. We consider such corrections and present a calculation of the four-loop light-by-light-type corrections where the external photon couples to a closed electron or muon loop. We perform an asymptotic expansion in the ratio of electron and muon mass and reduce the resulting integrals to master integrals which we evaluate using analytical and numerical methods. We confirm the results present in the literature which are based on different computational methods.

  7. The phonological loop unmasked? A comment on the evidence for a "perceptual-gestural" alternative.

    Science.gov (United States)

    Baddeley, Alan D; Larsen, Janet D

    2007-04-01

    Jones et al. (Jones, Hughes, & Macken, 2006; Jones, Macken, & Nicholls, 2004) identify the interaction between phonological similarity, articulatory suppression, and stimulus presentation mode in verbal short-term memory as potentially providing important support for the phonological loop hypothesis. They find such an interaction but attribute it to "perceptual organization masquerading as phonological storage". We present data using shorter letter sequences and find clear evidence of the interaction predicted by the phonological loop hypothesis, which, unlike the evidence of Jones et al., is not limited to recency, and which provides continued support for the phonological loop hypothesis.

  8. Chained learning architectures in a simple closed-loop behavioural context

    DEFF Research Database (Denmark)

    Kulvicius, Tomas; Porr, Bernd; Wörgötter, Florentin

    2007-01-01

    are very simple and consist of single learning unit. The current study is trying to solve this problem focusing on chained learning architectures in a simple closed-loop behavioural context. METHODS: We applied temporal sequence learning (Porr B and Wörgötter F 2006) in a closed-loop behavioural system...... where a driving robot learns to follow a line. Here for the first time we introduced two types of chained learning architectures named linear chain and honeycomb chain. We analyzed such architectures in an open and closed-loop context and compared them to the simple learning unit. CONCLUSIONS...

  9. Two- and three-loop amplitudes in covariant loop calculus

    International Nuclear Information System (INIS)

    Roland, K.

    1988-04-01

    We study 2- and 3-loop vacuum-amplitudes for the closed bosonic string. We compare two sets of expressions for the corresponding density on moduli space: One, based on the covariant Reggeon loop calculus (where modular invariance is not manifest). The other, based on analytic geometry. We want to prove identity between the two sets of expressions. Quite apart from demonstrating modular invariance of the Reggeon results, this would in itself be a remarkable mathematical feature. Identity is established to 'high' order in some moduli and exactly in others. The expansions reveal an essentially number-theoretical structure. Agreement is found only by exploiting the connection between the 4 Jacobi θ-functions and number theory. (orig.)

  10. Two- and three-loop amplitudes in covariant loop calculus

    International Nuclear Information System (INIS)

    Roland, K.

    1989-01-01

    We study two- and three-loop vacuum amplitudes for the closed bosonic string. We compare two sets of expressions for the corresponding density on moduli space. One is based on the covariant reggeon loop calculus (where modular invariance is not manifest). The other is based on analytic geometry. We want to prove identity between the two sets of expressions. Quite apart from demonstrating modular invariance of the reggeon results, this would in itself be a remarkable mathematical feature. Identity is established to ''high'' order in some moduli and exactly in others. The expansions reveal an essentially number-theoretic structure. Agreement is found only by exploiting the connection between the four Jacobi θ-functions and number theory. (orig.)

  11. Estimation of complex permittivity using loop antenna

    DEFF Research Database (Denmark)

    Lenler-Eriksen, Hans-Rudolph; Meincke, Peter

    2004-01-01

    A method for estimating the complex permittivity of materials in the vicinity of a loop antenna is proposed. The method is based on comparing measured and numerically calculated input admittances for the loop antenna.......A method for estimating the complex permittivity of materials in the vicinity of a loop antenna is proposed. The method is based on comparing measured and numerically calculated input admittances for the loop antenna....

  12. A True Open-Loop Synchronization Technique

    DEFF Research Database (Denmark)

    Golestan, Saeed; Vidal, Ana; Yepes, Alejandro G.

    2016-01-01

    Synchronization techniques can be broadly classified into two major categories: Closed-loop and open-loop methods. The open-loop synchronization (OLS) techniques, contrary to the closed-loop ones, are unconditionally stable and benefit from a fast dynamic response. Their performance, however, tends...... is to develop a true OLS (and therefore, unconditionally stable) technique without any need for the calculation of sine and cosine functions. The effectiveness of the proposed synchronization technique is confirmed through the simulation and experimental results....

  13. Study of mitochondria D-loop gene to detect the heterogeneity of gemak in Turnicidae family

    Science.gov (United States)

    Setiati, N.; Partaya

    2018-03-01

    As a part of life biodiversity, birds in Turnicidae family should be preserved from the extinction and its type heterogeneity decline. One effort for giving the strategic base of plasma nutfah conservation is through genetic heterogeneity study. The aim of the research is to analyze D-loop gen from DNA mitochondria of gemak bird in Turnicidae family molecularly. From the result of the analysis, it may be known the genetic heterogeneity of gemak bird based on the sequence of D-loop gen. The collection of both types of gemak of Turnicidae family is still easy since we can find them in ricefield area after harvest particularly for Gemakloreng (Turnix sylvatica), it means while gemak tegalan (Turnixsusciator) is getting difficult to find. Based on the above DNA quantification standard, the blood sample of Gemak in this research is mostly grouped into pure blood (ranges from 1,63 – 1,90), and it deserves to be used for PCR analysis. The sequencing analysis has not detected the sequence of nucleotide completely. However, it indicates sequence polymorphism of base as the arranger of D-loop gen. D-loop gen may identify genetic heterogeneity of gemak bird of Turnicidae family, but it is necessary to perform further sequencing analysis with PCR-RFLP technique. This complete nucleotide sequence is obtained and easy to detect after being cut restriction enzyme.

  14. Automation of loop amplitudes in numerical approach

    International Nuclear Information System (INIS)

    Fujimoto, J.; Ishikawa, T.; Shimizu, Y.; Kato, K.; Nakazawa, N.; Kaneko, T.

    1997-01-01

    An automatic calculating system GRACE-L1 of one-loop Feynman amplitude is reviewed. This system can be applied to 2 to 2-body one-loop processes. A sample calculation of 2 to 3-body one-loop amplitudes is also presented. (orig.)

  15. Complete Sequence of the mitochondrial genome of the tapeworm Hymenolepis diminuta: Gene arrangements indicate that platyhelminths are eutrochozoans

    Energy Technology Data Exchange (ETDEWEB)

    von Nickisch-Rosenegk, Markus; Brown, Wesley M.; Boore, Jeffrey L.

    2001-01-01

    Using ''long-PCR'' we have amplified in overlapping fragments the complete mitochondrial genome of the tapeworm Hymenolepis diminuta (Platyhelminthes: Cestoda) and determined its 13,900 nucleotide sequence. The gene content is the same as that typically found for animal mitochondrial DNA (mtDNA) except that atp8 appears to be lacking, a condition found previously for several other animals. Despite the small size of this mtDNA, there are two large non-coding regions, one of which contains 13 repeats of a 31 nucleotide sequence and a potential stem-loop structure of 25 base pairs with an 11-member loop. Large potential secondary structures are identified also for the non-coding regions of two other cestode mtDNAs. Comparison of the mitochondrial gene arrangement of H. diminuta with those previously published supports a phylogenetic position of flatworms as members of the Eutrochozoa, rather than being basal to either a clade of protostomes or a clade of coelomates.

  16. Fluctuation current in superconducting loops

    International Nuclear Information System (INIS)

    Berger, Jorge

    2012-01-01

    A superconducting loop that encloses noninteger flux holds a permanent current. On the average, this current is also present above T c , and has been measured in recent years. We are able to evaluate the permanent current within the TDGL or the Kramer-Watts-Tobin models for loops of general configuration, i.e., we don't require uniform cross section, material or temperature. We can also consider situations in which the width is not negligible in comparison to the radius. Our results agree with experiments. The situations with which we deal at present include fluctuation superconductivity in two-band superconductors, equilibrium thermal fluctuations of supercurrent along a weak link, and ratchet effects.

  17. Loop connectors in dentogenic diastema

    Directory of Open Access Journals (Sweden)

    Sanjna Nayar

    2015-01-01

    Full Text Available Patients with a missing tooth along with diastema have limited treatment options to restore the edentulous space. The use of a conventional fixed partial denture (FPD to replace the missing tooth may result in too wide anterior teeth leading to poor esthetics. Loss of anterior teeth with existing diastema may result in excess space available for pontic. This condition presents great esthetic challenge for prosthodontist. If implant supported prosthesis is not possible because of inadequate bone support, FPD along with loop connector may be a treatment option to maintain the diastema and provide optimal esthetic restoration. Here, we report a clinical case where FPD along with loop connector was used to achieve esthetic rehabilitation in maxillary anterior region in which midline diastema has been maintained.

  18. In pile helium loop ''COMEDIE''

    International Nuclear Information System (INIS)

    Abassin, J.J.; Blanchard, R.J.; Gentil, J.

    1981-01-01

    The SR1 test in the COMEDIE loop has permitted to demonstrate particularly the device operation reliability with a fuel loading. The post-irradiation examinations have pointed out the good filter efficiency and have enabled to determine the deposition profiles either for the activation products (e.g.: 51 Cr, 60 Co) or for the fission products (e.g.: sup(110m)Ag, 131 I, 134 Cs, 137 Cs). (author)

  19. Dispersion relations in loop calculations

    International Nuclear Information System (INIS)

    Kniehl, B.A.

    1996-01-01

    These lecture notes give a pedagogical introduction to the use of dispersion relations in loop calculations. We first derive dispersion relations which allow us to recover the real part of a physical amplitude from the knowledge of its absorptive part along the branch cut. In perturbative calculations, the latter may be constructed by means of Cutkosky's rule, which is briefly discussed. For illustration, we apply this procedure at one loop to the photon vacuum-polarization function induced by leptons as well as to the γf anti-f vertex form factor generated by the exchange of a massive vector boson between the two fermion legs. We also show how the hadronic contribution to the photon vacuum polarization may be extracted from the total cross section of hadron production in e + e - annihilation measured as a function of energy. Finally, we outline the application of dispersive techniques at the two-loop level, considering as an example the bosonic decay width of a high-mass Higgs boson. (author)

  20. Detection and differentiation of Fusarium oxysporum f. sp. lycopersici race 1 using loop-mediated isothermal amplification with three primer sets.

    Science.gov (United States)

    Ayukawa, Y; Komatsu, K; Kashiwa, T; Akai, K; Yamada, M; Teraoka, T; Arie, T

    2016-09-01

    Fusarium oxysporum f. sp. lycopersici (Fol) causes tomato wilt. Based on the difference in pathogenicity towards tomato cultivars, Fol is classified into three races. In this study, a rapid method is developed for the detection and discrimination of Fol race 1 using a loop-mediated isothermal amplification (LAMP) assay with two primer sets targeting a region of the nucleotide sequence of the SIX4 gene specific for race 1 and a primer set targeting the SIX5 gene, conserved in all known Fol isolates. Upon LAMP reaction, amplification using all three primer sets was observed only when DNA of Fol race 1 was used as a template, and not when DNA of other Fol races or other fungal species was used. This method could detect 300 fg of Fol race 1 DNA, a 100-fold higher sensitivity than that obtained by conventional PCR. The method can also detect DNA extracted from soil artificially infested with Fol race 1. It is now possible to detect Fol race 1 in colonies and infected tomato stems without DNA isolation. This method is a rapid and simple tool for discrimination of Fol race 1. This study developed a loop-mediated isothermal amplification (LAMP) assay for detection and differentiation of Fusarium oxysporum f. sp. lycopersici (Fol) race 1 by using three primer sets targeting for the SIX4 and SIX5 genes. These genes are present together only in Fol race 1. This method can detect Fol race 1 in infected tomato stems without DNA extraction, affording an efficient diagnosis of Fusarium wilt on tomatoes in the field. © 2016 The Society for Applied Microbiology.

  1. Complete nucleotide sequence and organization of the mitogenome ...

    African Journals Online (AJOL)

    STORAGESEVER

    2010-02-01

    Feb 1, 2010 ... In this study, the complete mitochondrial genome (mitogenome) of E. autonoe was .... skew” was calculated for the PCGs between two strands and the ..... codon stem and 7 bp in the anticodon loop, but also con- tained a ...

  2. Oscillation damping of chiral string loops

    International Nuclear Information System (INIS)

    Babichev, Eugeny; Dokuchaev, Vyacheslav

    2002-01-01

    Chiral cosmic string loops tend to the stationary (vorton) configuration due to energy loss into gravitational and electromagnetic radiation. We describe the asymptotic behavior of near stationary chiral loops and their fading to vortons. General limits on the gravitational and electromagnetic energy losses by near stationary chiral loops are found. For these loops we estimate the oscillation damping time. We present solvable examples of gravitational radiation energy loss by some chiral loop configurations. The analytical dependence of string energy with time is found in the case of the chiral ring with small amplitude radial oscillations

  3. Modular invariance and covariant loop calculus

    International Nuclear Information System (INIS)

    Petersen, J.L.; Roland, K.O.; Sidenius, J.R.

    1988-01-01

    The covariant loop calculus provides and efficient technique for computing explicit expressions for the density on moduli space corresponding to arbitrary (bosonic string) loop diagrams. Since modular invariance is not manifest, however, we carry out a detailed comparison with known explicit 2- and 3- loop results derived using analytic geometry (1 loop is known to be ok). We establish identity to 'high' order in some moduli and exactly in others. Agreement is found as a result of various non-trivial cancellations, in part related to number theory. We feel our results provide very strong support for the correctness of the covariant loop calculus approach. (orig.)

  4. Functional Fourier transforms and the loop equation

    International Nuclear Information System (INIS)

    Bershadskii, M.A.; Vaisburd, I.D.; Migdal, A.A.

    1986-01-01

    The Migdal-Makeenko momentum-space loop equation is investigated. This equation is derived from the ordinary loop equation by taking the Fourier transform of the Wilson functional. A perturbation theory is constructed for the new equation and it is proved that the action of the loop operator is determined by vertex functions which coincide with those of the previous equation. It is shown how the ghost loop arises in direct iterations of the momentum-space equation with respect to the coupling constant. A simple example is used to illustrate the mechanism of appearance of an integration in the interior loops in transition to observables

  5. Modular invariance and covariant loop calculus

    International Nuclear Information System (INIS)

    Petersen, J.L.; Roland, K.O.; Sidenius, J.R.

    1988-01-01

    The covariant loop calculus provides an efficient technique for computing explicit expressions for the density on moduli space corresponding to arbitrary (bosonic string) loop diagrams. Since modular invariance is not manifest, however, we carry out a detailed comparison with known explicit two- and three-loop results derived using analytic geometry (one loop is known to be okay). We establish identity to 'high' order in some moduli and exactly in others. Agreement is found as a result of various nontrivial cancellations, in part related to number theory. We feel our results provide very strong support for the correctness of the covariant loop calculus approach. (orig.)

  6. A systematic classification of Plasmodium falciparum P-loop NTPases: structural and functional correlation

    Directory of Open Access Journals (Sweden)

    Chauhan Virander S

    2009-04-01

    Full Text Available Abstract Background The P-loop NTPases constitute one of the largest groups of globular protein domains that play highly diverse functional roles in most of the organisms. Even with the availability of nearly 300 different Hidden Markov Models representing the P-loop NTPase superfamily, not many P-loop NTPases are known in Plasmodium falciparum. A number of characteristic attributes of the genome have resulted into the lack of knowledge about this functionally diverse, but important class of proteins. Method In the study, protein sequences with characteristic motifs of NTPase domain (Walker A and Walker B are computationally extracted from the P. falciparum database. A detailed secondary structure analysis, functional classification, phylogenetic and orthology studies of the NTPase domain of repertoire of 97 P. falciparum P-loop NTPases is carried out. Results Based upon distinct sequence features and secondary structure profile of the P-loop domain of obtained sequences, a cladistic classification is also conceded: nucleotide kinases and GTPases, ABC and SMC family, SF1/2 helicases, AAA+ and AAA protein families. Attempts are made to identify any ortholog(s for each of these proteins in other Plasmodium sp. as well as its vertebrate host, Homo sapiens. A number of P. falciparum P-loop NTPases that have no homologue in the host, as well as those annotated as hypothetical proteins and lack any characteristic functional domain are identified. Conclusion The study suggests a strong correlation between sequence and secondary structure profile of P-loop domains and functional roles of these proteins and thus provides an opportunity to speculate the role of many hypothetical proteins. The study provides a methodical framework for the characterization of biologically diverse NTPases in the P. falciparum genome. The efforts made in the analysis are first of its kind; and the results augment to explore the functional role of many of these proteins from

  7. Hyperstaticity and loops in frictional granular packings

    Science.gov (United States)

    Tordesillas, Antoinette; Lam, Edward; Metzger, Philip T.

    2009-06-01

    The hyperstatic nature of granular packings of perfectly rigid disks is analyzed algebraically and through numerical simulation. The elementary loops of grains emerge as a fundamental element in addressing hyperstaticity. Loops consisting of an odd number of grains behave differently than those with an even number. For odd loops, the latent stresses are exterior and are characterized by the sum of frictional forces around each loop. For even loops, the latent stresses are interior and are characterized by the alternating sum of frictional forces around each loop. The statistics of these two types of loop sums are found to be Gibbsian with a "temperature" that is linear with the friction coefficient μ when μ<1.

  8. Potency of Stem Cells

    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. Potency of Stem Cells. Totipotent Stem Cells (Zygote + first 2 divisions). -Can form placenta, embryo, and any cell of the body. Pluripotent (Embryonic Stem Cells). -Can form any cell of the body but can not form placenta, hence no embryo. Multipotent (Adult stem cells).

  9. Optimal packaging of FIV genomic RNA depends upon a conserved long-range interaction and a palindromic sequence within gag.

    Science.gov (United States)

    Rizvi, Tahir A; Kenyon, Julia C; Ali, Jahabar; Aktar, Suriya J; Phillip, Pretty S; Ghazawi, Akela; Mustafa, Farah; Lever, Andrew M L

    2010-10-15

    The feline immunodeficiency virus (FIV) is a lentivirus that is related to human immunodeficiency virus (HIV), causing a similar pathology in cats. It is a potential small animal model for AIDS and the FIV-based vectors are also being pursued for human gene therapy. Previous studies have mapped the FIV packaging signal (ψ) to two or more discontinuous regions within the 5' 511 nt of the genomic RNA and structural analyses have determined its secondary structure. The 5' and 3' sequences within ψ region interact through extensive long-range interactions (LRIs), including a conserved heptanucleotide interaction between R/U5 and gag. Other secondary structural elements identified include a conserved 150 nt stem-loop (SL2) and a small palindromic stem-loop within gag open reading frame that might act as a viral dimerization initiation site. We have performed extensive mutational analysis of these sequences and structures and ascertained their importance in FIV packaging using a trans-complementation assay. Disrupting the conserved heptanucleotide LRI to prevent base pairing between R/U5 and gag reduced packaging by 2.8-5.5 fold. Restoration of pairing using an alternative, non-wild type (wt) LRI sequence restored RNA packaging and propagation to wt levels, suggesting that it is the structure of the LRI, rather than its sequence, that is important for FIV packaging. Disrupting the palindrome within gag reduced packaging by 1.5-3-fold, but substitution with a different palindromic sequence did not restore packaging completely, suggesting that the sequence of this region as well as its palindromic nature is important. Mutation of individual regions of SL2 did not have a pronounced effect on FIV packaging, suggesting that either it is the structure of SL2 as a whole that is necessary for optimal packaging, or that there is redundancy within this structure. The mutational analysis presented here has further validated the previously predicted RNA secondary structure of FIV

  10. Complete sequences of the mitochondrial DNA of the wild Gracilariopsis lemaneiformis and two mutagenic cultivated breeds (Gracilariaceae, Rhodophyta.

    Directory of Open Access Journals (Sweden)

    Lei Zhang

    Full Text Available The complete mitochondrial DNA (mtDNA of Gracilariopsis lemaneiformis was sequenced (25883 bp and mapped to a circular model. The A+T composition was 72.5%. Forty six genes and two potentially functional open reading frames were identified. They include 24 protein-coding genes, 2 rRNA genes, 20 tRNA genes and 2 ORFs (orf60, orf142. There is considerable sequence synteny across the five red algal mtDNAs falling into Florideophyceae including Gr. lemaneiformis in this study and previously sequenced species. A long stem-loop and a hairpin structure were identified in intergenic regions of mt genome of Gr. lemaneiformis, which are believed to be involved with transcription and replication. In addition, the mtDNAs of two mutagenic cultivated breeds ("981" and "07-2" were also sequenced. Compared with the mtDNA of wild Gr. lemaneiformis, the genome size and gene length and order of three strains were completely identical except nine base mutations including eight in the protein-coding genes and one in the tRNA gene. None of the base mutations caused frameshift or a premature stop codon in the mtDNA genes. Phylogenetic analyses based on mitochondrial protein-coding genes and rRNA genes demonstrated Gracilariopsis andersonii had closer phylogenetic relationship with its parasite Gracilariophila oryzoides than Gracilariopsis lemaneiformis which was from the same genus of Gracilariopsis.

  11. Complete sequences of the mitochondrial DNA of the wild Gracilariopsis lemaneiformis and two mutagenic cultivated breeds (Gracilariaceae, Rhodophyta).

    Science.gov (United States)

    Zhang, Lei; Wang, Xumin; Qian, Hao; Chi, Shan; Liu, Cui; Liu, Tao

    2012-01-01

    The complete mitochondrial DNA (mtDNA) of Gracilariopsis lemaneiformis was sequenced (25883 bp) and mapped to a circular model. The A+T composition was 72.5%. Forty six genes and two potentially functional open reading frames were identified. They include 24 protein-coding genes, 2 rRNA genes, 20 tRNA genes and 2 ORFs (orf60, orf142). There is considerable sequence synteny across the five red algal mtDNAs falling into Florideophyceae including Gr. lemaneiformis in this study and previously sequenced species. A long stem-loop and a hairpin structure were identified in intergenic regions of mt genome of Gr. lemaneiformis, which are believed to be involved with transcription and replication. In addition, the mtDNAs of two mutagenic cultivated breeds ("981" and "07-2") were also sequenced. Compared with the mtDNA of wild Gr. lemaneiformis, the genome size and gene length and order of three strains were completely identical except nine base mutations including eight in the protein-coding genes and one in the tRNA gene. None of the base mutations caused frameshift or a premature stop codon in the mtDNA genes. Phylogenetic analyses based on mitochondrial protein-coding genes and rRNA genes demonstrated Gracilariopsis andersonii had closer phylogenetic relationship with its parasite Gracilariophila oryzoides than Gracilariopsis lemaneiformis which was from the same genus of Gracilariopsis.

  12. Near-native protein loop sampling using nonparametric density estimation accommodating sparcity.

    Science.gov (United States)

    Joo, Hyun; Chavan, Archana G; Day, Ryan; Lennox, Kristin P; Sukhanov, Paul; Dahl, David B; Vannucci, Marina; Tsai, Jerry

    2011-10-01

    Unlike the core structural elements of a protein like regular secondary structure, template based modeling (TBM) has difficulty with loop regions due to their variability in sequence and structure as well as the sparse sampling from a limited number of homologous templates. We present a novel, knowledge-based method for loop sampling that leverages homologous torsion angle information to estimate a continuous joint backbone dihedral angle density at each loop position. The φ,ψ distributions are estimated via a Dirichlet process mixture of hidden Markov models (DPM-HMM). Models are quickly generated based on samples from these distributions and were enriched using an end-to-end distance filter. The performance of the DPM-HMM method was evaluated against a diverse test set in a leave-one-out approach. Candidates as low as 0.45 Å RMSD and with a worst case of 3.66 Å were produced. For the canonical loops like the immunoglobulin complementarity-determining regions (mean RMSD 7.0 Å), this sampling method produces a population of loop structures to around 3.66 Å for loops up to 17 residues. In a direct test of sampling to the Loopy algorithm, our method demonstrates the ability to sample nearer native structures for both the canonical CDRH1 and non-canonical CDRH3 loops. Lastly, in the realistic test conditions of the CASP9 experiment, successful application of DPM-HMM for 90 loops from 45 TBM targets shows the general applicability of our sampling method in loop modeling problem. These results demonstrate that our DPM-HMM produces an advantage by consistently sampling near native loop structure. The software used in this analysis is available for download at http://www.stat.tamu.edu/~dahl/software/cortorgles/.

  13. Cool transition region loops observed by the Interface Region Imaging Spectrograph

    Science.gov (United States)

    Huang, Z.; Xia, L.; Li, B.; Madjarska, M. S.

    2015-12-01

    An important class of loops in the solar atmosphere, cool transition region loops, have received little attention mainly due to instrumental limitations. We analyze a cluster of these loops in the on-disk active region NOAA 11934 recorded in a Si IV 1402.8 Å spectral raster and 1400Å slit-jaw (SJ) images taken by the Interface Region Imaging Spectrograph. We divide these loops into three groups and study their dynamics, evolution and interaction.The first group comprises geometrically relatively stable loops, which are finely scaled with 382~626 km cross-sections. Siphon flows in these loops are suggested by the Doppler velocities gradually changing from -10 km/s (blue-shifts) in one end to 20 km/s (red-shifts) in the other. Nonthermal velocities from 15 to 25 km/s were determined. The obtained physical properties suggest that these loops are impulsively heated by magnetic reconnection occurring at the blue-shifted footpoints where magnetic cancellation with a rate of 1015 Mx/s is found. The released magnetic energy is redistributed by the siphon flows. The second group corresponds to two active footpoints rooted in mixed-magnetic-polarity regions. Magnetic reconnection in both footpoints is suggested by explosive-event line profiles with enhanced wings up to 200 km/s and magnetic cancellation with a rate of ~1015 Mx/s. In the third group, an interaction between two cool loop systems is observed. Mixed-magnetic polarities are seen in their conjunction area where explosive-event line profiles and magnetic cancellation with a rate of 3×1015 Mx/s are found. This is a clear indication that magnetic reconnection occurs between these two loop systems. Our observations suggest that the cool transition region loops are heated impulsively most likely by sequences of magnetic reconnection events.

  14. Near-native protein loop sampling using nonparametric density estimation accommodating sparcity.

    Directory of Open Access Journals (Sweden)

    Hyun Joo

    2011-10-01

    Full Text Available Unlike the core structural elements of a protein like regular secondary structure, template based modeling (TBM has difficulty with loop regions due to their variability in sequence and structure as well as the sparse sampling from a limited number of homologous templates. We present a novel, knowledge-based method for loop sampling that leverages homologous torsion angle information to estimate a continuous joint backbone dihedral angle density at each loop position. The φ,ψ distributions are estimated via a Dirichlet process mixture of hidden Markov models (DPM-HMM. Models are quickly generated based on samples from these distributions and were enriched using an end-to-end distance filter. The performance of the DPM-HMM method was evaluated against a diverse test set in a leave-one-out approach. Candidates as low as 0.45 Å RMSD and with a worst case of 3.66 Å were produced. For the canonical loops like the immunoglobulin complementarity-determining regions (mean RMSD 7.0 Å, this sampling method produces a population of loop structures to around 3.66 Å for loops up to 17 residues. In a direct test of sampling to the Loopy algorithm, our method demonstrates the ability to sample nearer native structures for both the canonical CDRH1 and non-canonical CDRH3 loops. Lastly, in the realistic test conditions of the CASP9 experiment, successful application of DPM-HMM for 90 loops from 45 TBM targets shows the general applicability of our sampling method in loop modeling problem. These results demonstrate that our DPM-HMM produces an advantage by consistently sampling near native loop structure. The software used in this analysis is available for download at http://www.stat.tamu.edu/~dahl/software/cortorgles/.

  15. Near-Native Protein Loop Sampling Using Nonparametric Density Estimation Accommodating Sparcity

    Science.gov (United States)

    Day, Ryan; Lennox, Kristin P.; Sukhanov, Paul; Dahl, David B.; Vannucci, Marina; Tsai, Jerry

    2011-01-01

    Unlike the core structural elements of a protein like regular secondary structure, template based modeling (TBM) has difficulty with loop regions due to their variability in sequence and structure as well as the sparse sampling from a limited number of homologous templates. We present a novel, knowledge-based method for loop sampling that leverages homologous torsion angle information to estimate a continuous joint backbone dihedral angle density at each loop position. The φ,ψ distributions are estimated via a Dirichlet process mixture of hidden Markov models (DPM-HMM). Models are quickly generated based on samples from these distributions and were enriched using an end-to-end distance filter. The performance of the DPM-HMM method was evaluated against a diverse test set in a leave-one-out approach. Candidates as low as 0.45 Å RMSD and with a worst case of 3.66 Å were produced. For the canonical loops like the immunoglobulin complementarity-determining regions (mean RMSD 7.0 Å), this sampling method produces a population of loop structures to around 3.66 Å for loops up to 17 residues. In a direct test of sampling to the Loopy algorithm, our method demonstrates the ability to sample nearer native structures for both the canonical CDRH1 and non-canonical CDRH3 loops. Lastly, in the realistic test conditions of the CASP9 experiment, successful application of DPM-HMM for 90 loops from 45 TBM targets shows the general applicability of our sampling method in loop modeling problem. These results demonstrate that our DPM-HMM produces an advantage by consistently sampling near native loop structure. The software used in this analysis is available for download at http://www.stat.tamu.edu/~dahl/software/cortorgles/. PMID:22028638

  16. Loop diagrams without γ matrices

    International Nuclear Information System (INIS)

    McKeon, D.G.C.; Rebhan, A.

    1993-01-01

    By using a quantum-mechanical path integral to compute matrix elements of the form left-angle x|exp(-iHt)|y right-angle, radiative corrections in quantum-field theory can be evaluated without encountering loop-momentum integrals. In this paper we demonstrate how Dirac γ matrices that occur in the proper-time ''Hamiltonian'' H lead to the introduction of a quantum-mechanical path integral corresponding to a superparticle analogous to one proposed recently by Fradkin and Gitman. Direct evaluation of this path integral circumvents many of the usual algebraic manipulations of γ matrices in the computation of quantum-field-theoretical Green's functions involving fermions

  17. Perturbation calculations with Wilson loop

    International Nuclear Information System (INIS)

    Peixoto Junior, L.B.

    1984-01-01

    We present perturbative calculations with the Wilson loop (WL). The dimensional regularization method is used with a special attention concerning to the problem of divergences in the WL expansion in second and fourth orders, in three and four dimensions. We show that the residue in the pole, in 4d, of the fourth order graphs contribution sum is important for the charge renormalization. We compute up to second order the exact expression of the WL, in three-dimensional gauge theories with topological mass as well as its assimptotic behaviour for small and large distances. the author [pt

  18. Resistance of Subtype C HIV-1 Strains to Anti-V3 Loop Antibodies

    Directory of Open Access Journals (Sweden)

    David Almond

    2012-01-01

    Full Text Available HIV-1’s subtype C V3 loop consensus sequence exhibits increased resistance to anti-V3 antibody-mediated neutralization as compared to the subtype B consensus sequence. The dynamic 3D structure of the consensus C V3 loop crown, visualized by ab initio folding, suggested that the resistance derives from structural rigidity and non-β-strand secondary protein structure in the N-terminal strand of the β-hairpin of the V3 loop crown, which is where most known anti-V3 loop antibodies bind. The observation of either rigidity or non-β-strand structure in this region correlated with observed resistance to antibody-mediated neutralization in a series of chimeric pseudovirus (psV mutants. The results suggest the presence of an epitope-independent, neutralization-relevant structural difference in the antibody-targeted region of the V3 loop crown between subtype C and subtype B, a difference that we hypothesize may contribute to the divergent pattern of global spread between these subtypes. As antibodies to a variable loop were recently identified as an inverse correlate of risk for HIV infection, the structure-function relationships discussed in this study may have relevance to HIV vaccine research.

  19. Consistent probabilities in loop quantum cosmology

    International Nuclear Information System (INIS)

    Craig, David A; Singh, Parampreet

    2013-01-01

    A fundamental issue for any quantum cosmological theory is to specify how probabilities can be assigned to various quantum events or sequences of events such as the occurrence of singularities or bounces. In previous work, we have demonstrated how this issue can be successfully addressed within the consistent histories approach to quantum theory for Wheeler–DeWitt-quantized cosmological models. In this work, we generalize that analysis to the exactly solvable loop quantization of a spatially flat, homogeneous and isotropic cosmology sourced with a massless, minimally coupled scalar field known as sLQC. We provide an explicit, rigorous and complete decoherent-histories formulation for this model and compute the probabilities for the occurrence of a quantum bounce versus a singularity. Using the scalar field as an emergent internal time, we show for generic states that the probability for a singularity to occur in this model is zero, and that of a bounce is unity, complementing earlier studies of the expectation values of the volume and matter density in this theory. We also show from the consistent histories point of view that all states in this model, whether quantum or classical, achieve arbitrarily large volume in the limit of infinite ‘past’ or ‘future’ scalar ‘time’, in the sense that the wave function evaluated at any arbitrary fixed value of the volume vanishes in that limit. Finally, we briefly discuss certain misconceptions concerning the utility of the consistent histories approach in these models. (paper)

  20. Gauge theory loop operators and Liouville theory

    International Nuclear Information System (INIS)

    Drukker, Nadav; Teschner, Joerg

    2009-10-01

    We propose a correspondence between loop operators in a family of four dimensional N=2 gauge theories on S 4 - including Wilson, 't Hooft and dyonic operators - and Liouville theory loop operators on a Riemann surface. This extends the beautiful relation between the partition function of these N=2 gauge theories and Liouville correlators found by Alday, Gaiotto and Tachikawa. We show that the computation of these Liouville correlators with the insertion of a Liouville loop operator reproduces Pestun's formula capturing the expectation value of a Wilson loop operator in the corresponding gauge theory. We prove that our definition of Liouville loop operators is invariant under modular transformations, which given our correspondence, implies the conjectured action of S-duality on the gauge theory loop operators. Our computations in Liouville theory make an explicit prediction for the exact expectation value of 't Hooft and dyonic loop operators in these N=2 gauge theories. The Liouville loop operators are also found to admit a simple geometric interpretation within quantum Teichmueller theory as the quantum operators representing the length of geodesics. We study the algebra of Liouville loop operators and show that it gives evidence for our proposal as well as providing definite predictions for the operator product expansion of loop operators in gauge theory. (orig.)

  1. Gauge theory loop operators and Liouville theory

    Energy Technology Data Exchange (ETDEWEB)

    Drukker, Nadav [Humboldt Univ. Berlin (Germany). Inst. fuer Physik; Gomis, Jaume; Okuda, Takuda [Perimeter Inst. for Theoretical Physics, Waterloo, ON (Canada); Teschner, Joerg [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)

    2009-10-15

    We propose a correspondence between loop operators in a family of four dimensional N=2 gauge theories on S{sup 4} - including Wilson, 't Hooft and dyonic operators - and Liouville theory loop operators on a Riemann surface. This extends the beautiful relation between the partition function of these N=2 gauge theories and Liouville correlators found by Alday, Gaiotto and Tachikawa. We show that the computation of these Liouville correlators with the insertion of a Liouville loop operator reproduces Pestun's formula capturing the expectation value of a Wilson loop operator in the corresponding gauge theory. We prove that our definition of Liouville loop operators is invariant under modular transformations, which given our correspondence, implies the conjectured action of S-duality on the gauge theory loop operators. Our computations in Liouville theory make an explicit prediction for the exact expectation value of 't Hooft and dyonic loop operators in these N=2 gauge theories. The Liouville loop operators are also found to admit a simple geometric interpretation within quantum Teichmueller theory as the quantum operators representing the length of geodesics. We study the algebra of Liouville loop operators and show that it gives evidence for our proposal as well as providing definite predictions for the operator product expansion of loop operators in gauge theory. (orig.)

  2. Phylogenetic footprinting of non-coding RNA: hammerhead ribozyme sequences in a satellite DNA family of Dolichopoda cave crickets (Orthoptera, Rhaphidophoridae

    Directory of Open Access Journals (Sweden)

    Venanzetti Federica

    2010-01-01

    Full Text Available Abstract Background The great variety in sequence, length, complexity, and abundance of satellite DNA has made it difficult to ascribe any function to this genome component. Recent studies have shown that satellite DNA can be transcribed and be involved in regulation of chromatin structure and gene expression. Some satellite DNAs, such as the pDo500 sequence family in Dolichopoda cave crickets, have a catalytic hammerhead (HH ribozyme structure and activity embedded within each repeat. Results We assessed the phylogenetic footprints of the HH ribozyme within the pDo500 sequences from 38 different populations representing 12 species of Dolichopoda. The HH region was significantly more conserved than the non-hammerhead (NHH region of the pDo500 repeat. In addition, stems were more conserved than loops. In stems, several compensatory mutations were detected that maintain base pairing. The core region of the HH ribozyme was affected by very few nucleotide substitutions and the cleavage position was altered only once among 198 sequences. RNA folding of the HH sequences revealed that a potentially active HH ribozyme can be found in most of the Dolichopoda populations and species. Conclusions The phylogenetic footprints suggest that the HH region of the pDo500 sequence family is selected for function in Dolichopoda cave crickets. However, the functional role of HH ribozymes in eukaryotic organisms is unclear. The possible functions have been related to trans cleavage of an RNA target by a ribonucleoprotein and regulation of gene expression. Whether the HH ribozyme in Dolichopoda is involved in similar functions remains to be investigated. Future studies need to demonstrate how the observed nucleotide changes and evolutionary constraint have affected the catalytic efficiency of the hammerhead.

  3. Sequence-specific inhibition of microRNA-130a gene by CRISPR/Cas9 system in breast cancer cell line

    Science.gov (United States)

    Ainina Abdollah, Nur; Das Kumitaa, Theva; Yusof Narazah, Mohd; Razak, Siti Razila Abdul

    2017-05-01

    MicroRNAs (miRNAs) are short stranded noncoding RNA that play important roles in apoptosis, cell survival, development and cell proliferation. However, gene expression control via small regulatory RNA, particularly miRNA in breast cancer is still less explored. Therefore, this project aims to develop an approach to target microRNA-130a using the Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/Cas9 system in MCF7, breast cancer cell line. The 20 bp sequences target at stem loop, 3ʹ and 5ʹ end of miR130a were cloned into pSpCas9(BB)-2A-GFP (PX458) plasmid, and the positive clones were confirmed by sequencing. A total of 5 μg of PX458-miR130a was transfected to MCF7 using Lipofectamine® 3000 according to manufacturer’s protocol. The transfected cells were maintained in the incubator at 37 °C under humidified 5% CO2. After 48 hours, cells were harvested and total RNA was extracted using miRNeasy Mini Kit (Qiagen). cDNAs were synthesised specific to miR-130a using TaqMan MicroRNA Reverse Transcription Kit (Applied Biosystems). Then, qRT-PCR was carried out using TaqMan Universal Master Mix (Applied Biosystems) to quantify the knockdown level of mature miRNAs in the cells. Result showed that miR-130a-5p was significantly downregulated in MCF7 cell line. However, no significant changes were observed for sequences targeting miR-130a-3p and stem loop. Thus, this study showed that the expression of miR-130a-5p was successfully down-regulated using CRISPR silencing system. This technique may be useful to manipulate the level of miRNA in various cell types to answer clinical questions at the molecular level.

  4. Senataxin Mutation Reveals How R-Loops Promote Transcription by Blocking DNA Methylation at Gene Promoters.

    Science.gov (United States)

    Grunseich, Christopher; Wang, Isabel X; Watts, Jason A; Burdick, Joshua T; Guber, Robert D; Zhu, Zhengwei; Bruzel, Alan; Lanman, Tyler; Chen, Kelian; Schindler, Alice B; Edwards, Nancy; Ray-Chaudhury, Abhik; Yao, Jianhua; Lehky, Tanya; Piszczek, Grzegorz; Crain, Barbara; Fischbeck, Kenneth H; Cheung, Vivian G

    2018-02-01

    R-loops are three-stranded nucleic acid structures found abundantly and yet often viewed as by-products of transcription. Studying cells from patients with a motor neuron disease (amyotrophic lateral sclerosis 4 [ALS4]) caused by a mutation in senataxin, we uncovered how R-loops promote transcription. In ALS4 patients, the senataxin mutation depletes R-loops with a consequent effect on gene expression. With fewer R-loops in ALS4 cells, the expression of BAMBI, a negative regulator of transforming growth factor β (TGF-β), is reduced; that then leads to the activation of the TGF-β pathway. We uncovered that genome-wide R-loops influence promoter methylation of over 1,200 human genes. DNA methyl-transferase 1 favors binding to double-stranded DNA over R-loops. Thus, in forming R-loops, nascent RNA blocks DNA methylation and promotes further transcription. Hence, our results show that nucleic acid structures, in addition to sequences, influence the binding and activity of regulatory proteins. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. The Complete Mitochondrial Genome Sequence of Bactericera cockerelli and Comparison with Three Other Psylloidea Species.

    Directory of Open Access Journals (Sweden)

    Fengnian Wu

    Full Text Available Potato psyllid (Bactericera cockerelli is an important pest of potato, tomato and pepper. Not only could a toxin secreted by nymphs results in serious phytotoxemia in some host plants, but also over the past few years B. cockerelli was shown to transmit "Candidatus Liberibacter solanacearum", the putative bacterial pathogen of potato zebra chip (ZC disease, to potato and tomato. ZC has caused devastating losses to potato production in the western U.S., Mexico, and elsewhere. New knowledge of the genetic diversity of the B. cockerelli is needed to develop improved strategies to manage pest populations. Mitochondrial genome (mitogenome sequencing provides important knowledge about insect evolution and diversity in and among populations. This report provides the first complete B. cockerelli mitogenome sequence as determined by next generation sequencing technology (Illumina MiSeq. The circular B. cockerelli mitogenome had a size of 15,220 bp with 13 protein-coding gene (PCGs, 2 ribosomal RNA genes (rRNAs, 22 transfer RNA genes (tRNAs, and a non-coding region of 975 bp. The overall gene order of the B. cockerelli mitogenome is identical to three other published Psylloidea mitogenomes: one species from the Triozidae, Paratrioza sinica; and two species from the Psyllidae, Cacopsylla coccinea and Pachypsylla venusta. This suggests all of these species share a common ancestral mitogenome. However, sequence analyses revealed differences between and among the insect families, in particular a unique region that can be folded into three stem-loop secondary structures present only within the B. cockerelli mitogenome. A phylogenetic tree based on the 13 PCGs matched an existing taxonomy scheme that was based on morphological characteristics. The available complete mitogenome sequence makes it accessible to all genes for future population diversity evaluation of B. cockerelli.

  6. Complete nucleotide sequence and organization of the mitogenome of the silk moth Caligula boisduvalii (Lepidoptera: Saturniidae) and comparison with other lepidopteran insects.

    Science.gov (United States)

    Hong, Mee Yeon; Lee, Eun Mee; Jo, Yong Hun; Park, Hae Chul; Kim, Seong Ryul; Hwang, Jae Sam; Jin, Byung Rae; Kang, Pil Don; Kim, Ki-Gyoung; Han, Yeon Soo; Kim, Iksoo

    2008-04-30

    The 15,360-bp long complete mitogenome of Caligula boisduvalii possesses a gene arrangement and content identical to other completely sequenced lepidopteran mitogenomes, but different from the common arrangement found in most insect order, as the result of the movement of tRNA(Met) to a position 5'-upstream of tRNA Ile. The 330-bp A+T-rich region is apparently capable of forming a stem-and-loop structure, which harbors the conserved flanking sequences at both ends. Dissimilar to what has been seen in other sequenced lepidopteran insects, the initiation codon for C. boisduvalii COI appears to be TTG, which is a rare, but apparently possible initiation codon. The ATP8, ATP6, ND4L, and ND6 genes, which neighbor another PCG at their 3' end, all harbored potential sequences for the formation of a hairpin structure. This is suggestive of the importance of such structures for the precise cleavage of the mRNA of mature PCGs. Phylogenetic analyses of available sequenced species of Bombycoidea, Pyraloidea, and Tortricidea supported the morphology-based current hypothesis that Bombycoidea and Pyraloidea are monophyletic (Obtectomera). As previously suggested, Bombycidae (Bombyx mori and B. mandarina) and Saturniidae (Antheraea pernyi and C. boisduvalii) formed a reciprocal monophyletic group.

  7. Loop quantization as a continuum limit

    International Nuclear Information System (INIS)

    Manrique, Elisa; Oeckl, Robert; Weber, Axel; Zapata, Jose A

    2006-01-01

    We present an implementation of Wilson's renormalization group and a continuum limit tailored for loop quantization. The dynamics of loop-quantized theories is constructed as a continuum limit of the dynamics of effective theories. After presenting the general formalism we show as a first explicit example the 2D Ising field theory, an interacting relativistic quantum field theory with local degrees of freedom quantized by loop quantization techniques

  8. Quantum chromodynamics as dynamics of loops

    International Nuclear Information System (INIS)

    Makeenko, Yu.M.; Migdal, A.A.

    1981-01-01

    QCD is entirely reformulated in terms of white composite fields - the traces of the loop products. The 1/N expansion turns out to be the WKB (Hartree-Fock) approximation for these fields. The 'classical' equation describing the N = infinite case is reduced tp a bootstrap form. New, manifestly gauge-invariant perturbation theory in the loop space, reproducing asymptotic freedom, is developed by iterations of this equation. The area law appears to be a self-consistent solution at large loops. (orig.)

  9. Lattice QED in the loop space

    International Nuclear Information System (INIS)

    Fort, H.

    1994-01-01

    We present a survey on the state of the art in the formulation of lattice compact QED in the space of loops. In a first part we review our most recent Hamiltonian results which signal a second order transition for (3+1) compact QED. We devote the second part to the Lagrangian loop formalism, showing the equivalence of the recently proposed loop action with the Villain form. (orig.)

  10. LMFBR with booster pump in pumping loop

    International Nuclear Information System (INIS)

    Rubinstein, H.J.

    1975-01-01

    A loop coolant circulation system is described for a liquid metal fast breeder reactor (LMFBR) utilizing a low head, high specific speed booster pump in the hot leg of the coolant loop with the main pump located in the cold leg of the loop, thereby providing the advantages of operating the main pump in the hot leg with the reliability of cold leg pump operation

  11. Soft Neutrosophic Loops and Their Generalization

    Directory of Open Access Journals (Sweden)

    Mumtaz Ali

    2014-06-01

    Full Text Available Soft set theory is a general mathematical tool for dealing with uncertain, fuzzy, not clearly defined objects. In this paper we introduced soft neutrosophic loop,soft neutosophic biloop, soft neutrosophic N -loop with the discuission of some of their characteristics. We also introduced a new type of soft neutrophic loop, the so called soft strong neutrosophic loop which is of pure neutrosophic character. This notion also found in all the other corresponding notions of soft neutrosophic thoery. We also given some of their properties of this newly born soft structure related to the strong part of neutrosophic theory.

  12. Vertically Polarized Omnidirectional Printed Slot Loop Antenna

    DEFF Research Database (Denmark)

    Kammersgaard, Nikolaj Peter Iversen; Kvist, Søren H.; Thaysen, Jesper

    2015-01-01

    A novel vertically polarized omnidirectional printed slot loop antenna has been designed, simulated, fabricated and measured. The slot loop works as a magnetic loop. The loop is loaded with inductors to insure uniform and in-phase fields in the slot in order to obtain an omnidirectional radiation...... pattern. The antenna is designed for the 2.45 GHz Industrial, Scientific and Medical band. Applications of the antenna are many. One is for on-body applications since it is ideal for launching a creeping waves due to the polarization....

  13. Quantum chromodynamics as dynamics of loops

    International Nuclear Information System (INIS)

    Makeenko, Yu.; Migdal, A.A.

    1980-01-01

    The problem of a possibility of reformulating quantum chromodynamics (QCD) in terms of colourless composite fields instead of coloured quarks and gluons is considered. The role of such fields is played by the gauge invariant loop functionals. The Shwinger equations of motion is derived in the loop space which completely describe dynamics of the loop fields. New manifestly gauge invariant diagram technique in the loop space is developed. These diagrams reproduce asymptotic freedom in the ultraviolet range and are consistent with the confinement law in the infrared range

  14. In pile helium loop ''Comedie''

    International Nuclear Information System (INIS)

    Blanchard, R.J.

    1985-01-01

    The loop is located in the SILOE reactor at Centre d'Etudes Nucleaires de Grenoble. The purpose and objectives are divided into two groups, principal and secondary. The primary objective was to provide basic data on the deposition behavior of important condensable fission products on a variety of steel surfaces, i.e. temperature (sorption isotherms) and mass transfer (physical adsorption) dependencies; to provide information concerning the degree of penetration of important fission products into the metals comprising the heat exchanger-recuperator tubes as a function of alloy type and/or metal temperature; to provide complementary information on the reentrainment (liftoff) of important fission and activation products by performing out-of-pile blowdown experiments on tube samples representative of the alloy types used in the heat exchanger-recuperator and of the surface temperatures experienced during plateout. The secondary objective was to provide information concerning the migration of important fission products through graphite. To this end, concentration profiles in the web between the fuel rods containing the fission product source and the coolant channels and in the graphite diffusion sample will be measured to study the corrosion of metallic specimens placed in the conditions of high temperature gas cooled reactor. The first experiment SRO enables to determine the loop characteristics and possibilities related to thermal, thermodynamic, chemical and neutronic properties. The second experiment has been carried out in high temperature gas cooled reactor operating conditions. It enables to determine in particular the deposition axial profile of activation and fission products in the plateout section constituting the heat exchanger, the fission products balance trapped in the different filter components, and the cumulated released fraction of solid fission products. The SR1 test permits to demonstrate in particular the Comedie loop operation reliability, either

  15. New application of dynamic reliability assessment of the mid-loop operation

    International Nuclear Information System (INIS)

    Moosung, Jae; Goon Cherl Park; Chang Hyun Chung

    1995-01-01

    This paper presents a new approach for assessing the dynamic reliability in a complex system such as a nuclear power plant. The method is applied to a dynamic analysis of the potential accident sequences that may occur during mid-loop operation

  16. Rapid Simulation of Flat Knitting Loops Based On the Yarn Texture and Loop Geometrical Model

    Directory of Open Access Journals (Sweden)

    Lu Zhiwen

    2017-06-01

    Full Text Available In order to create realistic loop primitives suitable for the fast computer-aided design (CAD of the flat knitted fabric, we have a research on the geometric model of the loop as well as the variation of the loop surface. Establish the texture variation model based on the changing process from the normal yarn to loop that provides the realistic texture of the simulative loop. Then optimize the simulative loop based on illumination variation. This paper develops the computer program with the optimization algorithm and achieves the loop simulation of different yarns to verify the feasibility of the proposed algorithm. Our work provides a fast CAD of the flat knitted fabric with loop simulation, and it is not only more realistic but also material adjustable. Meanwhile it also provides theoretical value for the flat knitted fabric computer simulation.

  17. Lose Your Loops with Numpy

    CERN Multimedia

    CERN. Geneva

    2016-01-01

    Developing in python is fast. Computation, however, can often be another story. Or at least that is how it may seem. When working with arrays and numerical datasets one can subvert many of python’s computational limitations by utilizing numpy. Numpy is python’s standard matrix computation library. Many python users only use numpy to store and generate arrays, failing to utilize one of python’s most powerful computational tools. By leveraging numpy’s ufuncs, aggregation, broadcasting and slicing/masking/indexing functionality one can cut back on slow python loops and increase the speed of their programs by as much as 100x. This talk aims at teaching attendees how to use these tools through toy examples.

  18. Closed loop steam cooled airfoil

    Science.gov (United States)

    Widrig, Scott M.; Rudolph, Ronald J.; Wagner, Gregg P.

    2006-04-18

    An airfoil, a method of manufacturing an airfoil, and a system for cooling an airfoil is provided. The cooling system can be used with an airfoil located in the first stages of a combustion turbine within a combined cycle power generation plant and involves flowing closed loop steam through a pin array set within an airfoil. The airfoil can comprise a cavity having a cooling chamber bounded by an interior wall and an exterior wall so that steam can enter the cavity, pass through the pin array, and then return to the cavity to thereby cool the airfoil. The method of manufacturing an airfoil can include a type of lost wax investment casting process in which a pin array is cast into an airfoil to form a cooling chamber.

  19. Generic Safety Issue (GSI) 171 -- Engineered Safety Feature (ESF) failure from a loop subsequent to LOCA: Assessment of plant vulnerability and CDF contributions

    International Nuclear Information System (INIS)

    Martinez-Guridi, G.; Samanta, P.; Chu, L.; Yang, J.

    1998-01-01

    Generic Safety Issue 171 (GSI-171), Engineered Safety Feature (ESF) from a Loss Of Offsite Power (LOOP) subsequent to a Loss Of Coolant Accident (LOCA), deals with an accident sequence in which a LOCA is followed by a LOOP. This issue was later broadened to include a LOOP followed by a LOCA. Plants are designed to handle a simultaneous LOCA and LOOP. In this paper, the authors address the unique issues that are involved i LOCA with delayed LOOP (LOCA/LOOP) and LOOP with delayed LOCA (LOOP/LOCA) accident sequences. LOCA/LOOP accidents are analyzed further by developing event-tree/fault-tree models to quantify their contributions to core-damage frequency (CDF) in a pressurized water reactor and a boiling water reactor (PWR and a BWR). Engineering evaluation and judgments are used during quantification to estimate the unique conditions that arise in a LOCA/LOOP accident. The results show that the CDF contribution of such an accident can be a dominant contributor to plant risk, although BWRs are less vulnerable than PWRs

  20. Stem Cell Transplant

    Science.gov (United States)

    ... Graft-versus-host disease: A potential risk when stem cells come from donors If you receive a transplant ... medications and blood products into your body. Collecting stem cells for transplant If a transplant using your own ...

  1. Stem Cell Information: Glossary

    Science.gov (United States)

    ... Tips Info Center Research Topics Federal Policy Glossary Stem Cell Information General Information Clinical Trials Funding Information Current ... here Home » Glossary Back to top Glossary Adult stem cell Astrocyte Blastocoel Blastocyst Bone marrow stromal cells Bone ...

  2. Plant stem cell niches.

    Science.gov (United States)

    Stahl, Yvonne; Simon, Rüdiger

    2005-01-01

    Stem cells are required to support the indeterminate growth style of plants. Meristems are a plants stem cell niches that foster stem cell survival and the production of descendants destined for differentiation. In shoot meristems, stem cell fate is decided at the populational level. The size of the stem cell domain at the meristem tip depends on signals that are exchanged with cells of the organizing centre underneath. In root meristems, individual stem cells are controlled by direct interaction with cells of the quiescent centre that lie in the immediate neighbourhood. Analysis of the interactions and signaling processes in the stem cell niches has delivered some insights into the molecules that are involved and revealed that the two major niches for plant stem cells are more similar than anticipated.

  3. Neocortical electrical stimulation for epilepsy : Closed-loop versus open-loop

    NARCIS (Netherlands)

    Vassileva, Albena; van Blooijs, Dorien; Leijten, Frans; Huiskamp, Geertjan

    2018-01-01

    The aim of this review is to evaluate whether open-loop or closed-loop neocortical electrical stimulation should be the preferred approach to manage seizures in intractable epilepsy. Twenty cases of open-loop neocortical stimulation with an implanted device have been reported, in 5 case studies.

  4. Hardware-in-the-loop grid simulator system and method

    Science.gov (United States)

    Fox, John Curtiss; Collins, Edward Randolph; Rigas, Nikolaos

    2017-05-16

    A hardware-in-the-loop (HIL) electrical grid simulation system and method that combines a reactive divider with a variable frequency converter to better mimic and control expected and unexpected parameters in an electrical grid. The invention provides grid simulation in a manner to allow improved testing of variable power generators, such as wind turbines, and their operation once interconnected with an electrical grid in multiple countries. The system further comprises an improved variable fault reactance (reactive divider) capable of providing a variable fault reactance power output to control a voltage profile, therein creating an arbitrary recovery voltage. The system further comprises an improved isolation transformer designed to isolate zero-sequence current from either a primary or secondary winding in a transformer or pass the zero-sequence current from a primary to a secondary winding.

  5. A Unified Theoretical Framework for Cognitive Sequencing.

    Science.gov (United States)

    Savalia, Tejas; Shukla, Anuj; Bapi, Raju S

    2016-01-01

    The capacity to sequence information is central to human performance. Sequencing ability forms the foundation stone for higher order cognition related to language and goal-directed planning. Information related to the order of items, their timing, chunking and hierarchical organization are important aspects in sequencing. Past research on sequencing has emphasized two distinct and independent dichotomies: implicit vs. explicit and goal-directed vs. habits. We propose a theoretical framework unifying these two streams. Our proposal relies on brain's ability to implicitly extract statistical regularities from the stream of stimuli and with attentional engagement organizing sequences explicitly and hierarchically. Similarly, sequences that need to be assembled purposively to accomplish a goal require engagement of attentional processes. With repetition, these goal-directed plans become habits with concomitant disengagement of attention. Thus, attention and awareness play a crucial role in the implicit-to-explicit transition as well as in how goal-directed plans become automatic habits. Cortico-subcortical loops basal ganglia-frontal cortex and hippocampus-frontal cortex loops mediate the transition process. We show how the computational principles of model-free and model-based learning paradigms, along with a pivotal role for attention and awareness, offer a unifying framework for these two dichotomies. Based on this framework, we make testable predictions related to the potential influence of response-to-stimulus interval (RSI) on developing awareness in implicit learning tasks.

  6. A Unified Theoretical Framework for Cognitive Sequencing

    Directory of Open Access Journals (Sweden)

    Tejas Savalia

    2016-11-01

    Full Text Available The capacity to sequence information is central to human performance. Sequencing ability forms the foundation stone for higher order cognition related to language and goal-directed planning. Information related to the order of items, their timing, chunking and hierarchical organization are important aspects in sequencing. Past research on sequencing has emphasized two distinct and independent dichotomies: implicit versus explicit and goal-directed versus habits. We propose a theoretical framework unifying these two streams. Our proposal relies on brain's ability to implicitly extract statistical regularities from the stream of stimuli and with attentional engagement organizing sequences explicitly and hierarchically. Similarly, sequences that need to be assembled purposively to accomplish a goal require engagement of attentional processes. With repetition, these goal-directed plans become habits with concomitant disengagement of attention. Thus attention and awareness play a crucial role in the implicit-to-explicit transition as well as in how goal-directed plans become automatic habits. Cortico-subcortical loops ─ basal ganglia-frontal cortex and hippocampus-frontal cortex loops ─ mediate the transition process. We show how the computational principles of model-free and model-based learning paradigms, along with a pivotal role for attention and awareness, offer a unifying framework for these two dichotomies. Based on this framework, we make testable predictions related to the potential influence of response-to-stimulus interval (RSI on developing awareness in implicit learning tasks.

  7. Studying the influence of stem composition in pH-sensitive molecular beacons onto their sensing properties.

    Science.gov (United States)

    Dembska, Anna; Kierzek, Elzbieta; Juskowiak, Bernard

    2017-10-16

    Intracellular sensing using fluorescent molecular beacons is a potentially useful strategy for real-time, in vivo monitoring of important cellular events. This work is focused on evaluation of pyrene excimer signaling molecular beacons (MBs) for the monitoring of pH changes in vitro as well as inside living cells. The recognition element in our MB called pHSO (pH-sensitive oligonucleotide) is the loop enclosing cytosine-rich fragment that is able to form i-motif structure in a specific pH range. However, alteration of a sequence of the 6 base pairs containing stem of MB allowed the design of pHSO probes that exhibited different dynamic pH range and possessed slightly different transition midpoint between i-motif and open loop configuration. Moreover, this conformational transition was accompanied by spectral changes showing developed probes different pyrene excimer-monomer emission ratio triggered by pH changes. The potential of these MBs for intracellular pH sensing is demonstrated on the example of HeLa cells line. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Creative Teaching in STEM

    Science.gov (United States)

    Pollard, Vikki; Hains-Wesson, Rachael; Young, Karen

    2018-01-01

    If Science, Technology, Engineering and Mathematics (STEM) disciplines in higher education are to retain students, there needs to be a shift towards teaching in more enriching and interesting ways. Creative teaching needs to become more prominent in STEM. This article presents a study that defines creative teaching in the STEM context and…

  9. Brain network dynamics in the human articulatory loop.

    Science.gov (United States)

    Nishida, Masaaki; Korzeniewska, Anna; Crone, Nathan E; Toyoda, Goichiro; Nakai, Yasuo; Ofen, Noa; Brown, Erik C; Asano, Eishi

    2017-08-01

    The articulatory loop is a fundamental component of language function, involved in the short-term buffer of auditory information followed by its vocal reproduction. We characterized the network dynamics of the human articulatory loop, using invasive recording and stimulation. We measured high-gamma activity 70-110 Hz recorded intracranially when patients with epilepsy either only listened to, or listened to and then reproduced two successive tones by humming. We also conducted network analyses, and analyzed behavioral responses to cortical stimulation. Presentation of the initial tone elicited high-gamma augmentation bilaterally in the superior-temporal gyrus (STG) within 40ms, and in the precentral and inferior-frontal gyri (PCG and IFG) within 160ms after sound onset. During presentation of the second tone, high-gamma augmentation was reduced in STG but enhanced in IFG. The task requiring tone reproduction further enhanced high-gamma augmentation in PCG during and after sound presentation. Event-related causality (ERC) analysis revealed dominant flows within STG immediately after sound onset, followed by reciprocal interactions involving PCG and IFG. Measurement of cortico-cortical evoked-potentials (CCEPs) confirmed connectivity between distant high-gamma sites in the articulatory loop. High-frequency stimulation of precentral high-gamma sites in either hemisphere induced speech arrest, inability to control vocalization, or forced vocalization. Vocalization of tones was accompanied by high-gamma augmentation over larger extents of PCG. Bilateral PCG rapidly and directly receives feed-forward signals from STG, and may promptly initiate motor planning including sub-vocal rehearsal for short-term buffering of auditory stimuli. Enhanced high-gamma augmentation in IFG during presentation of the second tone may reflect high-order processing of the tone sequence. The articulatory loop employs sustained reciprocal propagation of neural activity across a network of

  10. Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction.

    Science.gov (United States)

    Xiang, Zhexin; Soto, Cinque S; Honig, Barry

    2002-05-28

    In this paper, we introduce a method to account for the shape of the potential energy curve in the evaluation of conformational free energies. The method is based on a procedure that generates a set of conformations, each with its own force-field energy, but adds a term to this energy that favors conformations that are close in structure (have a low rmsd) to other conformations. The sum of the force-field energy and rmsd-dependent term is defined here as the "colony energy" of a given conformation, because each conformation that is generated is viewed as representing a colony of points. The use of the colony energy tends to select conformations that are located in broad energy basins. The approach is applied to the ab initio prediction of the conformations of all of the loops in a dataset of 135 nonredundant proteins. By using an rmsd from a native criterion based on the superposition of loop stems, the average rmsd of 5-, 6-, 7-, and 8-residue long loops is 0.85, 0.92, 1.23, and 1.45 A, respectively. For 8-residue loops, 60 of 61 predictions have an rmsd of less than 3.0 A. The use of the colony energy is found to improve significantly the results obtained from the potential function alone. (The loop prediction program, "Loopy," can be downloaded at http://trantor.bioc.columbia.edu.)

  11. Newtonian gravity in loop quantum gravity

    OpenAIRE

    Smolin, Lee

    2010-01-01

    We apply a recent argument of Verlinde to loop quantum gravity, to conclude that Newton's law of gravity emerges in an appropriate limit and setting. This is possible because the relationship between area and entropy is realized in loop quantum gravity when boundaries are imposed on a quantum spacetime.

  12. Holonomy loops, spectral triples and quantum gravity

    DEFF Research Database (Denmark)

    Johannes, Aastrup; Grimstrup, Jesper Møller; Nest, Ryszard

    2009-01-01

    We review the motivation, construction and physical interpretation of a semi-finite spectral triple obtained through a rearrangement of central elements of loop quantum gravity. The triple is based on a countable set of oriented graphs and the algebra consists of generalized holonomy loops...

  13. Feedback loop compensates for rectifier nonlinearity

    Science.gov (United States)

    1966-01-01

    Signal processing circuit with two negative feedback loops rectifies two sinusoidal signals which are 180 degrees out of phase and produces a single full-wave rectified output signal. Each feedback loop incorporates a feedback rectifier to compensate for the nonlinearity of the circuit.

  14. Loop calculus for lattice gauge theories

    International Nuclear Information System (INIS)

    Gambini, R.; Leal, L.; Trias, A.; Departamento de Fisica Aplicada, Facultad de Ingenieria, Universidad Central de Venezuela, Apartado 47724, Caracas 1051, Venezuela; Departament de Matematiques, Universitat Politecnica de Catalunya, Escuela Tecnica Superior de Enginyers de Telecomunicaciones, Barcelona 08034, Spain)

    1989-01-01

    Hamiltonian calculations are performed using a loop-labeled basis where the full set of identities for the SU(N) gauge models has been incorporated. The loops are classified as clusterlike structures and the eigenvalue problem leads to a linear set of finite-difference equations easily amenable to numerical treatment. Encouraging results are reported for SU(2) at spatial dimension 2

  15. Design Principles for Closed Loop Supply Chains

    NARCIS (Netherlands)

    H.R. Krikke (Harold); C.P. Pappis (Costas); G.T. Tsoulfas; J.M. Bloemhof-Ruwaard (Jacqueline)

    2001-01-01

    textabstractIn this paper we study design principles for closed loop supply chains. Closed loop supply chains aim at closing material flows thereby limiting emission and residual waste, but also providing customer service at low cost. We study 'traditional' and 'new' design principles known in the

  16. Complete nucleotide sequence of the RNA-2 of grapevine deformation and Grapevine Anatolian ringspot viruses.

    Science.gov (United States)

    Ghanem-Sabanadzovic, Nina Abou; Sabanadzovic, Sead; Digiaro, Michele; Martelli, Giovanni P

    2005-05-01

    The nucleotide sequence of RNA-2 of Grapevine Anatolian ringspot virus (GARSV) and Grapevine deformation virus (GDefV), two recently described nepoviruses, has been determined. These RNAs are 3753 nt (GDefV) and 4607 nt (GARSV) in size and contain a single open reading frame encoding a polyprotein of 122 kDa (GDefV) and 150 kDa (GARSV). Full-length nucleotide sequence comparison disclosed 71-73% homology between GDefV RNA-2 and that of Grapevine fanleaf virus (GFLV) and Arabis mosaic virus (ArMV), and 62-64% homology between GARSV RNA-2 and that of Grapevine chrome mosaic virus (GCMV) and Tomato black ring virus (TBRV). As previously observed in other nepoviruses, the 5' non-coding regions of both RNAs are capable of forming stem-loop structures. Phylogenetic analysis of the three proteins encoded by RNA-2 (i.e. protein 2A, movement protein and coat protein) confirmed that GDefV and GARSV are distinct viruses which can be assigned as definitive species in subgroup A and subgroup B of the genus Nepovirus, respectively.

  17. Knotted vs. unknotted proteins: evidence of knot-promoting loops.

    Directory of Open Access Journals (Sweden)

    Raffaello Potestio

    Full Text Available Knotted proteins, because of their ability to fold reversibly in the same topologically entangled conformation, are the object of an increasing number of experimental and theoretical studies. The aim of the present investigation is to assess, on the basis of presently available structural data, the extent to which knotted proteins are isolated instances in sequence or structure space, and to use comparative schemes to understand whether specific protein segments can be associated to the occurrence of a knot in the native state. A significant sequence homology is found among a sizeable group of knotted and unknotted proteins. In this family, knotted members occupy a primary sub-branch of the phylogenetic tree and differ from unknotted ones only by additional loop segments. These "knot-promoting" loops, whose virtual bridging eliminates the knot, are found in various types of knotted proteins. Valuable insight into how knots form, or are encoded, in proteins could be obtained by targeting these regions in future computational studies or excision experiments.

  18. The Wilson loop and some applications

    International Nuclear Information System (INIS)

    Bezerra, V.B.

    1983-04-01

    A simple relation between the classical Wilson loop and the angular deviation in the parallel displacement is found. An example of potentials which give field copies and which suplly the same classical Wilson loop for a particular trajectory is exhibited. The asymptotic behaviour of the Wilson loop for the BPST instanton and the meron, is discussed. By using the dimensional regularization technique to calculate the second order term of the quantum Wilson loop, the influence of geometrical factors for the residue in the pole due to contact points, cuspides and intersections, in function of the space-time ν, is investigated. Charge renormalization in Quantum electrodynamics is finally calculated by using the quantum Wilson loop. (L.C.) [pt

  19. The Wilson loop and some applications

    International Nuclear Information System (INIS)

    Bezerra, V.B.

    1983-01-01

    A simple relation between the classical Wilson loop and the angular deviation in the parallel shift is found. An example of potential which given field copies and which give the same classical Wilson loop for a given trajectory is exchibited. Afterwards, the asymptotic behaviour of the Wilson loop for the BPST instanton and meron is discussed. Using the dimensional regularization technique to calculate the second order term of Quantum Wilson loop, the influence of geometrical factors for the residue in the polo due to contact points, cusp and intersections, in function of the upsilon dimension of the space-time is investigated. Finally, the charge renormalization in Quantum Electrodynamics using Quantum Wilson loop is calculated. (L.C.) [pt

  20. Hydraulic loop: practices using open control systems

    International Nuclear Information System (INIS)

    Carrasco, J.A.; Alonso, L.; Sanchez, F.

    1998-01-01

    The Tecnatom Hydraulic Loop is a dynamic training platform. It has been designed with the purpose of improving the work in teams. With this system, the student can obtain a full scope vision of a system. The hydraulic Loop is a part of the Tecnatom Maintenance Centre. The first objective of the hydraulic Loop is the instruction in components, process and process control using open control system. All the personal of an electric power plant can be trained in the Hydraulic Loop with specific courses. The development of a dynamic tool for tests previous to plant installations has been an additional objective of the Hydraulic Loop. The use of this platform is complementary to the use of full-scope simulators in order to debug and to analyse advanced control strategies. (Author)

  1. Osmotic mechanism of the loop extrusion process

    Science.gov (United States)

    Yamamoto, Tetsuya; Schiessel, Helmut

    2017-09-01

    The loop extrusion theory assumes that protein factors, such as cohesin rings, act as molecular motors that extrude chromatin loops. However, recent single molecule experiments have shown that cohesin does not show motor activity. To predict the physical mechanism involved in loop extrusion, we here theoretically analyze the dynamics of cohesin rings on a loop, where a cohesin loader is in the middle and unloaders at the ends. Cohesin monomers bind to the loader rather frequently and cohesin dimers bind to this site only occasionally. Our theory predicts that a cohesin dimer extrudes loops by the osmotic pressure of cohesin monomers on the chromatin fiber between the two connected rings. With this mechanism, the frequency of the interactions between chromatin segments depends on the loading and unloading rates of dimers at the corresponding sites.

  2. Feedback Loop Gains and Feedback Behavior (1996)

    DEFF Research Database (Denmark)

    Kampmann, Christian Erik

    2012-01-01

    Linking feedback loops and system behavior is part of the foundation of system dynamics, yet the lack of formal tools has so far prevented a systematic application of the concept, except for very simple systems. Having such tools at their disposal would be a great help to analysts in understanding...... large, complicated simulation models. The paper applies tools from graph theory formally linking individual feedback loop strengths to the system eigenvalues. The significance of a link or a loop gain and an eigenvalue can be expressed in the eigenvalue elasticity, i.e., the relative change...... of an eigenvalue resulting from a relative change in the gain. The elasticities of individual links and loops may be found through simple matrix operations on the linearized system. Even though the number of feedback loops can grow rapidly with system size, reaching astronomical proportions even for modest systems...

  3. Stem cell therapy: MRI guidance and monitoring.

    Science.gov (United States)

    Kraitchman, Dara L; Gilson, Wesley D; Lorenz, Christine H

    2008-02-01

    With the recent advances in magnetic resonance (MR) labeling of cellular therapeutics, it is natural that interventional MRI techniques for targeting would be developed. This review provides an overview of the current methods of stem cell labeling and the challenges that are created with respect to interventional MRI administration. In particular, stem cell therapies will require specialized, MR-compatible devices as well as integration of graphical user interfaces with pulse sequences designed for interactive, real-time delivery in many organs. Specific applications that are being developed will be reviewed as well as strategies for future translation to the clinical realm. (Copyright) 2008 Wiley-Liss, Inc.

  4. Genome Editing in Human Pluripotent Stem Cells.

    Science.gov (United States)

    Carlson-Stevermer, Jared; Saha, Krishanu

    2017-01-01

    Genome editing in human pluripotent stem cells (hPSCs) enables the generation of reporter lines and knockout cell lines. Zinc finger nucleases, transcription activator-like effector nucleases (TALENs), and CRISPR/Cas9 technology have recently increased the efficiency of proper gene editing by creating double strand breaks (DSB) at defined sequences in the human genome. These systems typically use plasmids to transiently transcribe nucleases within the cell. Here, we describe the process for preparing hPSCs for transient expression of nucleases via electroporation and subsequent analysis to create genetically modified stem cell lines.

  5. Deep-sequencing protocols influence the results obtained in small-RNA sequencing.

    Directory of Open Access Journals (Sweden)

    Joern Toedling

    Full Text Available Second-generation sequencing is a powerful method for identifying and quantifying small-RNA components of cells. However, little attention has been paid to the effects of the choice of sequencing platform and library preparation protocol on the results obtained. We present a thorough comparison of small-RNA sequencing libraries generated from the same embryonic stem cell lines, using different sequencing platforms, which represent the three major second-generation sequencing technologies, and protocols. We have analysed and compared the expression of microRNAs, as well as populations of small RNAs derived from repetitive elements. Despite the fact that different libraries display a good correlation between sequencing platforms, qualitative and quantitative variations in the results were found, depending on the protocol used. Thus, when comparing libraries from different biological samples, it is strongly recommended to use the same sequencing platform and protocol in order to ensure the biological relevance of the comparisons.

  6. Transcription-factor-mediated DNA looping probed by high-resolution, single-molecule imaging in live E. coli cells.

    Directory of Open Access Journals (Sweden)

    Zach Hensel

    Full Text Available DNA looping mediated by transcription factors plays critical roles in prokaryotic gene regulation. The "genetic switch" of bacteriophage λ determines whether a prophage stays incorporated in the E. coli chromosome or enters the lytic cycle of phage propagation and cell lysis. Past studies have shown that long-range DNA interactions between the operator sequences O(R and O(L (separated by 2.3 kb, mediated by the λ repressor CI (accession number P03034, play key roles in regulating the λ switch. In vitro, it was demonstrated that DNA segments harboring the operator sequences formed loops in the presence of CI, but CI-mediated DNA looping has not been directly visualized in vivo, hindering a deep understanding of the corresponding dynamics in realistic cellular environments. We report a high-resolution, single-molecule imaging method to probe CI-mediated DNA looping in live E. coli cells. We labeled two DNA loci with differently colored fluorescent fusion proteins and tracked their separations in real time with ∼40 nm accuracy, enabling the first direct analysis of transcription-factor-mediated DNA looping in live cells. Combining looping measurements with measurements of CI expression levels in different operator mutants, we show quantitatively that DNA looping activates transcription and enhances repression. Further, we estimated the upper bound of the rate of conformational change from the unlooped to the looped state, and discuss how chromosome compaction may impact looping kinetics. Our results provide insights into transcription-factor-mediated DNA looping in a variety of operator and CI mutant backgrounds in vivo, and our methodology can be applied to a broad range of questions regarding chromosome conformations in prokaryotes and higher organisms.

  7. A kinematic view of loop closure.

    Science.gov (United States)

    Coutsias, Evangelos A; Seok, Chaok; Jacobson, Matthew P; Dill, Ken A

    2004-03-01

    We consider the problem of loop closure, i.e., of finding the ensemble of possible backbone structures of a chain segment of a protein molecule that is geometrically consistent with preceding and following parts of the chain whose structures are given. We reduce this problem of determining the loop conformations of six torsions to finding the real roots of a 16th degree polynomial in one variable, based on the robotics literature on the kinematics of the equivalent rotator linkage in the most general case of oblique rotators. We provide a simple intuitive view and derivation of the polynomial for the case in which each of the three pair of torsional axes has a common point. Our method generalizes previous work on analytical loop closure in that the torsion angles need not be consecutive, and any rigid intervening segments are allowed between the free torsions. Our approach also allows for a small degree of flexibility in the bond angles and the peptide torsion angles; this substantially enlarges the space of solvable configurations as is demonstrated by an application of the method to the modeling of cyclic pentapeptides. We give further applications to two important problems. First, we show that this analytical loop closure algorithm can be efficiently combined with an existing loop-construction algorithm to sample loops longer than three residues. Second, we show that Monte Carlo minimization is made severalfold more efficient by employing the local moves generated by the loop closure algorithm, when applied to the global minimization of an eight-residue loop. Our loop closure algorithm is freely available at http://dillgroup. ucsf.edu/loop_closure/. Copyright 2004 Wiley Periodicals, Inc. J Comput Chem 25: 510-528, 2004

  8. The Complete Mitochondrial Genome of the Pink Stem Borer, Sesamia inferens, in Comparison with Four Other Noctuid Moths

    Directory of Open Access Journals (Sweden)

    Yu-Zhou Du

    2012-08-01

    Full Text Available The complete 15,413-bp mitochondrial genome (mitogenome of Sesamia inferens (Walker (Lepidoptera: Noctuidae was sequenced and compared with those of four other noctuid moths. All of the mitogenomes analyzed displayed similar characteristics with respect to gene content, genome organization, nucleotide comparison, and codon usages. Twelve-one protein-coding genes (PCGs utilized the standard ATN, but the cox1 gene used CGA as the initiation codon; cox1, cox2, and nad4 genes had the truncated termination codon T in the S. inferens mitogenome. All of the tRNA genes had typical cloverleaf secondary structures except for trnS1(AGN, in which the dihydrouridine (DHU arm did not form a stable stem-loop structure. Both the secondary structures of rrnL and rrnS genes inferred from the S. inferens mitogenome closely resembled those of other noctuid moths. In the A+T-rich region, the conserved motif “ATAGA” followed by a long T-stretch was observed in all noctuid moths, but other specific tandem-repeat elements were more variable. Additionally, the S. inferens mitogenome contained a potential stem-loop structure, a duplicated 17-bp repeat element, a decuplicated segment, and a microsatellite “(AT7”, without a poly-A element upstream of the trnM in the A+T-rich region. Finally, the phylogenetic relationships were reconstructed based on amino acid sequences of mitochondrial 13 PCGs, which support the traditional morphologically based view of relationships within the Noctuidae.

  9. Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing

    Directory of Open Access Journals (Sweden)

    Chen Shou-Yi

    2011-01-01

    Full Text Available Abstract Background MicroRNAs (miRNAs regulate gene expression by mediating gene silencing at transcriptional and post-transcriptional levels in higher plants. miRNAs and related target genes have been widely studied in model plants such as Arabidopsis and rice; however, the number of identified miRNAs in soybean (Glycine max is limited, and global identification of the related miRNA targets has not been reported in previous research. Results In our study, a small RNA library and a degradome library were constructed from developing soybean seeds for deep sequencing. We identified 26 new miRNAs in soybean by bioinformatic analysis and further confirmed their expression by stem-loop RT-PCR. The miRNA star sequences of 38 known miRNAs and 8 new miRNAs were also discovered, providing additional evidence for the existence of miRNAs. Through degradome sequencing, 145 and 25 genes were identified as targets of annotated miRNAs and new miRNAs, respectively. GO analysis indicated that many of the identified miRNA targets may function in soybean seed development. Additionally, a soybean homolog of Arabidopsis SUPPRESSOR OF GENE SLIENCING 3 (AtSGS3 was detected as a target of the newly identified miRNA Soy_25, suggesting the presence of feedback control of miRNA biogenesis. Conclusions We have identified large numbers of miRNAs and their related target genes through deep sequencing of a small RNA library and a degradome library. Our study provides more information about the regulatory network of miRNAs in soybean and advances our understanding of miRNA functions during seed development.

  10. Plant stem cell niches.

    Science.gov (United States)

    Aichinger, Ernst; Kornet, Noortje; Friedrich, Thomas; Laux, Thomas

    2012-01-01

    Multicellular organisms possess pluripotent stem cells to form new organs, replenish the daily loss of cells, or regenerate organs after injury. Stem cells are maintained in specific environments, the stem cell niches, that provide signals to block differentiation. In plants, stem cell niches are situated in the shoot, root, and vascular meristems-self-perpetuating units of organ formation. Plants' lifelong activity-which, as in the case of trees, can extend over more than a thousand years-requires that a robust regulatory network keep the balance between pluripotent stem cells and differentiating descendants. In this review, we focus on current models in plant stem cell research elaborated during the past two decades, mainly in the model plant Arabidopsis thaliana. We address the roles of mobile signals on transcriptional modules involved in balancing cell fates. In addition, we discuss shared features of and differences between the distinct stem cell niches of Arabidopsis.

  11. Stem Cell Pathology.

    Science.gov (United States)

    Fu, Dah-Jiun; Miller, Andrew D; Southard, Teresa L; Flesken-Nikitin, Andrea; Ellenson, Lora H; Nikitin, Alexander Yu

    2018-01-24

    Rapid advances in stem cell biology and regenerative medicine have opened new opportunities for better understanding disease pathogenesis and the development of new diagnostic, prognostic, and treatment approaches. Many stem cell niches are well defined anatomically, thereby allowing their routine pathological evaluation during disease initiation and progression. Evaluation of the consequences of genetic manipulations in stem cells and investigation of the roles of stem cells in regenerative medicine and pathogenesis of various diseases such as cancer require significant expertise in pathology for accurate interpretation of novel findings. Therefore, there is an urgent need for developing stem cell pathology as a discipline to facilitate stem cell research and regenerative medicine. This review provides examples of anatomically defined niches suitable for evaluation by diagnostic pathologists, describes neoplastic lesions associated with them, and discusses further directions of stem cell pathology.

  12. TS LOOP ALCOVE VENTILATION ANALYSIS

    International Nuclear Information System (INIS)

    T.M. Lahnalampi

    2000-01-01

    The scope of this analysis is to examine the existing, constructor installed, physical ventilation installations located in each of the Exploratory Studies Facility (ESF) Topopah Springs (TS) Loop Alcoves No.1, No.2, No.3, No.4, No.6, and No.7. Alcove No.5 is excluded from the scope of this analysis since it is an A/E design system. Each ventilation installation will be analyzed for the purpose of determining if requirements for acceptance into the A/E design technical baseline have been met. The ventilation installations will be evaluated using Occupational Safety and Health Administration (OSHA) standards and Exploratory Studies Facility Design Requirements (ESFDR) (YMP 1997) requirements. The end product will be a technical analysis that will define ventilation installation compliance issues, any outstanding field changes, and use-as-is design deviations that are required to bring the ventilation installations into compliance with requirements for acceptance into the A/E design technical baseline. The analysis will provide guidance for alcove ventilation component design modifications to be developed to correct any deficient components that do not meet minimum requirements and standards

  13. Loops in hierarchical channel networks

    Science.gov (United States)

    Katifori, Eleni; Magnasco, Marcelo

    2012-02-01

    Nature provides us with many examples of planar distribution and structural networks having dense sets of closed loops. An archetype of this form of network organization is the vasculature of dicotyledonous leaves, which showcases a hierarchically-nested architecture. Although a number of methods have been proposed to measure aspects of the structure of such networks, a robust metric to quantify their hierarchical organization is still lacking. We present an algorithmic framework that allows mapping loopy networks to binary trees, preserving in the connectivity of the trees the architecture of the original graph. We apply this framework to investigate computer generated and natural graphs extracted from digitized images of dicotyledonous leaves and animal vasculature. We calculate various metrics on the corresponding trees and discuss the relationship of these quantities to the architectural organization of the original graphs. This algorithmic framework decouples the geometric information from the metric topology (connectivity and edge weight) and it ultimately allows us to perform a quantitative statistical comparison between predictions of theoretical models and naturally occurring loopy graphs.

  14. Towards conformal loop quantum gravity

    International Nuclear Information System (INIS)

    Wang, Charles H-T

    2006-01-01

    A discussion is given of recent developments in canonical gravity that assimilates the conformal analysis of gravitational degrees of freedom. The work is motivated by the problem of time in quantum gravity and is carried out at the metric and the triad levels. At the metric level, it is shown that by extending the Arnowitt-Deser-Misner (ADM) phase space of general relativity (GR), a conformal form of geometrodynamics can be constructed. In addition to the Hamiltonian and Diffeomorphism constraints, an extra first class constraint is introduced to generate conformal transformations. This phase space consists of York's mean extrinsic curvature time, conformal three-metric and their momenta. At the triad level, the phase space of GR is further enlarged by incorporating spin-gauge as well as conformal symmetries. This leads to a canonical formulation of GR using a new set of real spin connection variables. The resulting gravitational constraints are first class, consisting of the Hamiltonian constraint and the canonical generators for spin-gauge and conformorphism transformations. The formulation has a remarkable feature of being parameter-free. Indeed, it is shown that a conformal parameter of the Barbero-Immirzi type can be absorbed by the conformal symmetry of the extended phase space. This gives rise to an alternative approach to loop quantum gravity that addresses both the conceptual problem of time and the technical problem of functional calculus in quantum gravity

  15. Identification of lignin genes and regulatory sequences involved in secondary cell wall formation in Acacia auriculiformis and Acacia mangium via de novo transcriptome sequencing

    Directory of Open Access Journals (Sweden)

    Cannon Charles H

    2011-07-01

    Full Text Available Abstract Background Acacia auriculiformis × Acacia mangium hybrids are commercially important trees for the timber and pulp industry in Southeast Asia. Increasing pulp yield while reducing pulping costs are major objectives of tree breeding programs. The general monolignol biosynthesis and secondary cell wall formation pathways are well-characterized but genes in these pathways are poorly characterized in Acacia hybrids. RNA-seq on short-read platforms is a rapid approach for obtaining comprehensive transcriptomic data and to discover informative sequence variants. Results We sequenced transcriptomes of A. auriculiformis and A. mangium from non-normalized cDNA libraries synthesized from pooled young stem and inner bark tissues using paired-end libraries and a single lane of an Illumina GAII machine. De novo assembly produced a total of 42,217 and 35,759 contigs with an average length of 496 bp and 498 bp for A. auriculiformis and A. mangium respectively. The assemblies of A. auriculiformis and A. mangium had a total length of 21,022,649 bp and 17,838,260 bp, respectively, with the largest contig 15,262 bp long. We detected all ten monolignol biosynthetic genes using Blastx and further analysis revealed 18 lignin isoforms for each species. We also identified five contigs homologous to R2R3-MYB proteins in other plant species that are involved in transcriptional regulation of secondary cell wall formation and lignin deposition. We searched the contigs against public microRNA database and predicted the stem-loop structures of six highly conserved microRNA families (miR319, miR396, miR160, miR172, miR162 and miR168 and one legume-specific family (miR2086. Three microRNA target genes were predicted to be involved in wood formation and flavonoid biosynthesis. By using the assemblies as a reference, we discovered 16,648 and 9,335 high quality putative Single Nucleotide Polymorphisms (SNPs in the transcriptomes of A. auriculiformis and A. mangium

  16. Performance Improvement of a Prefiltered Synchronous-Reference-Frame PLL By Using a PID-Type Loop Filter

    DEFF Research Database (Denmark)

    Golestan, Saeed; Monfared, Mohammad; Frejeido, Francisco

    2014-01-01

    Control Parameters design of a three-phase synchronous reference frame phase locked loop (SRF-PLL) with a pre-filtering stage (acting as the sequence separator) is not a trivial task. The conventional way to deal with this problem is to neglect the interaction between the SRF-PLL and pre-filterin......Control Parameters design of a three-phase synchronous reference frame phase locked loop (SRF-PLL) with a pre-filtering stage (acting as the sequence separator) is not a trivial task. The conventional way to deal with this problem is to neglect the interaction between the SRF-PLL and pre......-integral-derivative controller as the loop filter (instead of the commonly adopted proportionalintegral controller) and arranging a pole-zero cancellation. The suggested method is simple and efficient, and is applicable to the joint operation of different sequence separation techniques and the SRF-PLL. The effectiveness...

  17. Stability, structure, and evolution of cool loops

    International Nuclear Information System (INIS)

    Cally, P.S.; Robb, T.D.

    1991-01-01

    The criteria for the existence and stability of cool loops are reexamined. It is found that the stability of the loops strongly depends on the form of the heating and radiative loss functions and that if the Ly-alpha peak which appears in most calculations of the radiative loss function is real, cool loops are almost certainly unstable. Removing the hydrogen contribution from the recent loss function Q(T) by Cook et al. (1989) does not produce the much-used result, Q proportional to T-cubed, which is so favorable to cool loop stability. Even using the probably unrealistically favorable loss function Q1 of Cook et al. with the hydrogen contribution removed, the maximum temperature attainable in stable cool loops is a factor of 2-3 too small to account for the excess emission observed in lower transition region lines. Dynamical simulations of cool loop instabilities reveal that the final state of such a model is the hot loop equilibrium. 26 refs

  18. Negative Sequence Droop Method based Hierarchical Control for Low Voltage Ride-Through in Grid-Interactive Microgrids

    DEFF Research Database (Denmark)

    Zhao, Xin; Firoozabadi, Mehdi Savaghebi; Quintero, Juan Carlos Vasquez

    2015-01-01

    . In this paper, a voltage support strategy based on negative sequence droop control, which regulate the positive/negative sequence active and reactive power flow by means of sending proper voltage reference to the inner control loop, is proposed for the grid connected MGs to ride through voltage sags under...... complex line impedance conditions. In this case, the MGs should inject a certain amount of positive and negative sequence power to the grid so that the voltage quality at load side can be maintained at a satisfied level. A two layer hierarchical control strategy is proposed in this paper. The primary...... control loop consists of voltage and current inner loops, conventional droop control and virtual impedance loop while the secondary control loop is based on positive/negative sequence droop control which can achieve power injection under voltage sags. Experimental results with asymmetrical voltage sags...

  19. The hormone response element mimic sequence of GAS5 lncRNA is sufficient to induce apoptosis in breast cancer cells

    Science.gov (United States)

    Pickard, Mark R.; Williams, Gwyn T.

    2016-01-01

    Growth arrest-specific 5 (GAS5) lncRNA promotes apoptosis, and its expression is down-regulated in breast cancer. GAS5 lncRNA is a decoy of glucocorticoid/related receptors; a stem-loop sequence constitutes the GAS5 hormone response element mimic (HREM), which is essential for the regulation of breast cancer cell apoptosis. This preclinical study aimed to determine if the GAS5 HREM sequence alone promotes the apoptosis of breast cancer cells. Nucleofection of hormone-sensitive and –insensitive breast cancer cell lines with a GAS5 HREM DNA oligonucleotide increased both basal and ultraviolet-C-induced apoptosis, and decreased culture viability and clonogenic growth, similar to GAS5 lncRNA. The HREM oligonucleotide demonstrated similar sequence specificity to the native HREM for its functional activity and had no effect on endogenous GAS5 lncRNA levels. Certain chemically modified HREM oligonucleotides, notably DNA and RNA phosphorothioates, retained pro-apoptotic. activity. Crucially the HREM oligonucleotide could overcome apoptosis resistance secondary to deficient endogenous GAS5 lncRNA levels. Thus, the GAS5 lncRNA HREM sequence alone is sufficient to induce apoptosis in breast cancer cells, including triple-negative breast cancer cells. These findings further suggest that emerging knowledge of structure/function relationships in the field of lncRNA biology can be exploited for the development of entirely novel, oligonucleotide mimic-based, cancer therapies. PMID:26862727

  20. Loop-quantum-gravity vertex amplitude.

    Science.gov (United States)

    Engle, Jonathan; Pereira, Roberto; Rovelli, Carlo

    2007-10-19

    Spin foam models are hoped to provide the dynamics of loop-quantum gravity. However, the most popular of these, the Barrett-Crane model, does not have the good boundary state space and there are indications that it fails to yield good low-energy n-point functions. We present an alternative dynamics that can be derived as a quantization of a Regge discretization of Euclidean general relativity, where second class constraints are imposed weakly. Its state space matches the SO(3) loop gravity one and it yields an SO(4)-covariant vertex amplitude for Euclidean loop gravity.

  1. Technical specification of HANARO fuel test loop

    Energy Technology Data Exchange (ETDEWEB)

    Kim, J. Y

    1998-03-01

    The design and installation of the irradiation test facility for verification test of the fuel performance are very important in connection with maximization of the utilization of HANARO. HANARO fuel test loop was designed in accordance with the same code and standards of nuclear power plant because HANARO FTL will be operated the high pressure and temperature same as nuclear power plant operation conditions. The objective of this study is to confirm the operation limit, safety limit, operation condition and checking points of HANARO fuel test loop. This results will become guidances for the planning of irradiation testing and operation of HANARO fuel test loop. (author). 13 refs., 13 tabs., 8 figs.

  2. Numerical approach to one-loop integrals

    International Nuclear Information System (INIS)

    Fujimoto, Junpei; Shimizu, Yoshimitsu; Kato, Kiyoshi; Oyanagi, Yoshio.

    1992-01-01

    Two numerical methods are proposed for the calculation of one-loop scalar integrals. In the first method, the singularity is cancelled by the symmetrization of the integrand and the integration is done by a Monte-Carlo method. In the second one, after the transform of the integrand into a standard form, the integral is reduced into a regular numerical integral. These methods provide us practical tools to evaluate one-loop Feynman diagrams with desired numerical accuracy. They are extended to the integral with numerator and the treatment of the one-loop virtual correction to the cross section is also presented. (author)

  3. Zero point energy of renormalized Wilson loops

    International Nuclear Information System (INIS)

    Hidaka, Yoshimasa; Pisarski, Robert D.

    2009-01-01

    The quark-antiquark potential, and its associated zero point energy, can be extracted from lattice measurements of the Wilson loop. We discuss a unique prescription to renormalize the Wilson loop, for which the perturbative contribution to the zero point energy vanishes identically. A zero point energy can arise nonperturbatively, which we illustrate by considering effective string models. The nonperturbative contribution to the zero point energy vanishes in the Nambu model, but is nonzero when terms for extrinsic curvature are included. At one loop order, the nonperturbative contribution to the zero point energy is negative, regardless of the sign of the extrinsic curvature term.

  4. Loop corrections to primordial non-Gaussianity

    Science.gov (United States)

    Boran, Sibel; Kahya, E. O.

    2018-02-01

    We discuss quantum gravitational loop effects to observable quantities such as curvature power spectrum and primordial non-Gaussianity of cosmic microwave background (CMB) radiation. We first review the previously shown case where one gets a time dependence for zeta-zeta correlator due to loop corrections. Then we investigate the effect of loop corrections to primordial non-Gaussianity of CMB. We conclude that, even with a single scalar inflaton, one might get a huge value for non-Gaussianity which would exceed the observed value by at least 30 orders of magnitude. Finally we discuss the consequences of this result for scalar driven inflationary models.

  5. Sigma models and renormalization of string loops

    International Nuclear Information System (INIS)

    Tseytlin, A.A.

    1989-05-01

    An extension of the ''σ-model β-functions - string equations of motion'' correspondence to the string loop level is discussed. Special emphasis is made on how the renormalization group acts in string loops and, in particular, on the renormalizability property of the generating functional Z-circumflex for string amplitudes (related to the σ model partition function integrated over moduli). Renormalization of Z-circumflex at one and two loop order is analyzed in some detail. We also discuss an approach to renormalization based on operators of insertion of topological fixtures. (author). 70 refs

  6. Construction of the blowdown and condensation loop

    Energy Technology Data Exchange (ETDEWEB)

    Park, Choon Kyung; Song, Chul Kyung; Cho, Seok; Chun, S. Y.; Chung, Moon Ki

    1997-12-01

    The blowdown and condensation loop (B and C loop) has been constructed to get experimental data for designing the safety depressurization system (SDS) and steam sparger which are considered to implement in the Korea Next Generation Reactor (KNGR). In this report, system description on the B and C loop is given in detail, which includes the drawings and technical specification of each component, instrumentation and control system, and the operational procedures and the results of the performance testing. (author). 7 refs., 11 tabs., 48 figs.

  7. Eigenvalue distributions of Wilson loops

    International Nuclear Information System (INIS)

    Lohmayer, Robert

    2010-01-01

    In the first part of this thesis, we focus on the distribution of the eigenvalues of the unitary Wilson loop matrix in the two-dimensional case at arbitrary finite N. To characterize the distribution of the eigenvalues, we introduce three density functions (the ''symmetric'', the ''antisymmetric'', and the ''true'' eigenvalue density) which differ at finite N but possess the same infinite-N limit, exhibiting the Durhuus-Olesen phase transition. Using expansions of determinants and inverse determinants in characters of totally symmetric or totally antisymmetric representations of SU(N), the densities at finite N can be expressed in terms of simple sums involving only dimensions and quadratic Casimir invariants of certain irreducible representations of SU(N), allowing for a numerical computation of the densities at arbitrary N to any desired accuracy. We find that the true eigenvalue density, adding N oscillations to the monotonic symmetric density, is in some sense intermediate between the symmetric and the antisymmetric density, which in turn is given by a sum of N delta peaks located at the zeros of the average of the characteristic polynomial. Furthermore, we show that the dependence on N can be made explicit by deriving integral representations for the resolvents associated to the three eigenvalue densities. Using saddle-point approximations, we confirm that all three densities reduce to the Durhuus-Olesen result in the infinite-N limit. In the second part, we study an exponential form of the multiplicative random complex matrix model introduced by Gudowska-Nowak et al. Varying a parameter which can be identified with the area of the Wilson loop in the unitary case, the region of non-vanishing eigenvalue density of the N-dimensional complex product matrix undergoes a topological change at a transition point in the infinite-N limit. We study the transition by a detailed analysis of the average of the modulus square of the characteristic polynomial. Furthermore

  8. Eigenvalue distributions of Wilson loops

    Energy Technology Data Exchange (ETDEWEB)

    Lohmayer, Robert

    2010-07-01

    In the first part of this thesis, we focus on the distribution of the eigenvalues of the unitary Wilson loop matrix in the two-dimensional case at arbitrary finite N. To characterize the distribution of the eigenvalues, we introduce three density functions (the ''symmetric'', the ''antisymmetric'', and the ''true'' eigenvalue density) which differ at finite N but possess the same infinite-N limit, exhibiting the Durhuus-Olesen phase transition. Using expansions of determinants and inverse determinants in characters of totally symmetric or totally antisymmetric representations of SU(N), the densities at finite N can be expressed in terms of simple sums involving only dimensions and quadratic Casimir invariants of certain irreducible representations of SU(N), allowing for a numerical computation of the densities at arbitrary N to any desired accuracy. We find that the true eigenvalue density, adding N oscillations to the monotonic symmetric density, is in some sense intermediate between the symmetric and the antisymmetric density, which in turn is given by a sum of N delta peaks located at the zeros of the average of the characteristic polynomial. Furthermore, we show that the dependence on N can be made explicit by deriving integral representations for the resolvents associated to the three eigenvalue densities. Using saddle-point approximations, we confirm that all three densities reduce to the Durhuus-Olesen result in the infinite-N limit. In the second part, we study an exponential form of the multiplicative random complex matrix model introduced by Gudowska-Nowak et al. Varying a parameter which can be identified with the area of the Wilson loop in the unitary case, the region of non-vanishing eigenvalue density of the N-dimensional complex product matrix undergoes a topological change at a transition point in the infinite-N limit. We study the transition by a detailed analysis of the average of the

  9. Temperature dependence of looping rates in a short peptide.

    Science.gov (United States)

    Roccatano, Danilo; Sahoo, Harekrushna; Zacharias, Martin; Nau, Werner M

    2007-03-15

    Knowledge of the influence of chain length and amino acid sequence on the structural and dynamic properties of small peptides in solution provides essential information on protein folding pathways. The combination of time-resolved optical spectroscopy and molecular dynamics (MD) simulation methods has become a powerful tool to investigate the kinetics of end-to-end collisions (looping rates) in short peptides, which are relevant in early protein folding events. We applied the combination of both techniques to study temperature-dependent (280-340 K) looping rates of the Dbo-AlaGlyGln-Trp-NH2 peptide, where Dbo represents a 2,3-diazabicyclo[2.2.2]oct-2-ene-labeled asparagine, which served as a fluorescent probe in the time-resolved spectroscopic experiments. The experimental looping rates increased from 4.8 x 10(7) s(-1) at 283 K to 2.0 x 10(8) s(-1) at 338 K in H2O. The corresponding Arrhenius plot provided as activation parameters Ea = 21.5 +/- 1.0 kJ mol(-1) and ln(A/s-1) = 26.8 +/- 0.2 in H2O. The results in D2O were consistent with a slight solvent viscosity effect, i.e., the looping rates were 10-20% slower. MD simulations were performed with the GROMOS96 force field in a water solvent model, which required first a parametrization of the synthetic amino acid Dbo. After corrections for solvent viscosity effects, the calculated looping rates varied from 1.5 x 10(8) s(-1) at 280 K to 8.2 x 10(8) s(-1) at 340 K in H2O, which was about four times larger than the experimental data. The calculated activation parameters were Ea = 24.7 +/- 1.5 kJ mol(-1) and ln(A/s(-1)) = 29.4 +/- 0.1 in H2O.

  10. Identification of Candidate Genes Responsible for Stem Pith Production Using Expression Analysis in Solid-Stemmed Wheat.

    Science.gov (United States)

    Oiestad, A J; Martin, J M; Cook, J; Varella, A C; Giroux, M J

    2017-07-01

    The wheat stem sawfly (WSS) is an economically important pest of wheat in the Northern Great Plains. The primary means of WSS control is resistance associated with the single quantitative trait locus (QTL) , which controls most stem solidness variation. The goal of this study was to identify stem solidness candidate genes via RNA-seq. This study made use of 28 single nucleotide polymorphism (SNP) makers derived from expressed sequence tags (ESTs) linked to contained within a 5.13 cM region. Allele specific expression of EST markers was examined in stem tissue for solid and hollow-stemmed pairs of two spring wheat near isogenic lines (NILs) differing for the QTL. Of the 28 ESTs, 13 were located within annotated genes and 10 had detectable stem expression. Annotated genes corresponding to four of the ESTs were differentially expressed between solid and hollow-stemmed NILs and represent possible stem solidness gene candidates. Further examination of the 5.13 cM region containing the 28 EST markers identified 260 annotated genes. Twenty of the 260 linked genes were up-regulated in hollow NIL stems, while only seven genes were up-regulated in solid NIL stems. An -methyltransferase within the region of interest was identified as a candidate based on differential expression between solid and hollow-stemmed NILs and putative function. Further study of these candidate genes may lead to the identification of the gene(s) controlling stem solidness and an increased ability to select for wheat stem solidness and manage WSS. Copyright © 2017 Crop Science Society of America.

  11. Complete Sequence and Analysis of the Mitochondrial Genome of Hemiselmis andersenii CCMP644 (Cryptophyceae

    Directory of Open Access Journals (Sweden)

    Bowman Sharen

    2008-05-01

    Full Text Available Abstract Background Cryptophytes are an enigmatic group of unicellular eukaryotes with plastids derived by secondary (i.e., eukaryote-eukaryote endosymbiosis. Cryptophytes are unusual in that they possess four genomes–a host cell-derived nuclear and mitochondrial genome and an endosymbiont-derived plastid and 'nucleomorph' genome. The evolutionary origins of the host and endosymbiont components of cryptophyte algae are at present poorly understood. Thus far, a single complete mitochondrial genome sequence has been determined for the cryptophyte Rhodomonas salina. Here, the second complete mitochondrial genome of the cryptophyte alga Hemiselmis andersenii CCMP644 is presented. Results The H. andersenii mtDNA is 60,553 bp in size and encodes 30 structural RNAs and 36 protein-coding genes, all located on the same strand. A prominent feature of the genome is the presence of a ~20 Kbp long intergenic region comprised of numerous tandem and dispersed repeat units of between 22–336 bp. Adjacent to these repeats are 27 copies of palindromic sequences predicted to form stable DNA stem-loop structures. One such stem-loop is located near a GC-rich and GC-poor region and may have a regulatory function in replication or transcription. The H. andersenii mtDNA shares a number of features in common with the genome of the cryptophyte Rhodomonas salina, including general architecture, gene content, and the presence of a large repeat region. However, the H. andersenii mtDNA is devoid of inverted repeats and introns, which are present in R. salina. Comparative analyses of the suite of tRNAs encoded in the two genomes reveal that the H. andersenii mtDNA has lost or converted its original trnK(uuu gene and possesses a trnS-derived 'trnK(uuu', which appears unable to produce a functional tRNA. Mitochondrial protein coding gene phylogenies strongly support a variety of previously established eukaryotic groups, but fail to resolve the relationships among higher

  12. TREE STEM RECONSTRUCTION USING VERTICAL FISHEYE IMAGES: A PRELIMINARY STUDY

    Directory of Open Access Journals (Sweden)

    A. Berveglieri

    2016-06-01

    Full Text Available A preliminary study was conducted to assess a tree stem reconstruction technique with panoramic images taken with fisheye lenses. The concept is similar to the Structure from Motion (SfM technique, but the acquisition and data preparation rely on fisheye cameras to generate a vertical image sequence with height variations of the camera station. Each vertical image is rectified to four vertical planes, producing horizontal lateral views. The stems in the lateral view are rectified to the same scale in the image sequence to facilitate image matching. Using bundle adjustment, the stems are reconstructed, enabling later measurement and extraction of several attributes. The 3D reconstruction was performed with the proposed technique and compared with SfM. The preliminary results showed that the stems were correctly reconstructed by using the lateral virtual images generated from the vertical fisheye images and with the advantage of using fewer images and taken from one single station.

  13. The Universal One-Loop Effective Action

    CERN Document Server

    Drozd, Aleksandra; Quevillon, Jérémie; You, Tevong

    2016-01-01

    We present the universal one-loop effective action for all operators of dimension up to six obtained by integrating out massive, non-degenerate multiplets. Our general expression may be applied to loops of heavy fermions or bosons, and has been checked against partial results available in the literature. The broad applicability of this approach simplifies one-loop matching from an ultraviolet model to a lower-energy effective field theory (EFT), a procedure which is now reduced to the evaluation of a combination of matrices in our universal expression, without any loop integrals to evaluate. We illustrate the relationship of our results to the Standard Model (SM) EFT, using as an example the supersymmetric stop and sbottom squark Lagrangian and extracting from our universal expression the Wilson coefficients of dimension-six operators composed of SM fields.

  14. The universal one-loop effective action

    International Nuclear Information System (INIS)

    Drozd, Aleksandra; Ellis, John; Quevillon, Jérémie; You, Tevong

    2016-01-01

    We present the universal one-loop effective action for all operators of dimension up to six obtained by integrating out massive, non-degenerate multiplets. Our general expression may be applied to loops of heavy fermions or bosons, and has been checked against partial results available in the literature. The broad applicability of this approach simplifies one-loop matching from an ultraviolet model to a lower-energy effective field theory (EFT), a procedure which is now reduced to the evaluation of a combination of matrices in our universal expression, without any loop integrals to evaluate. We illustrate the relationship of our results to the Standard Model (SM) EFT, using as an example the supersymmetric stop and sbottom squark Lagrangian and extracting from our universal expression the Wilson coefficients of dimension-six operators composed of SM fields.

  15. Mathematical Modeling of Loop Heat Pipes

    Science.gov (United States)

    Kaya, Tarik; Ku, Jentung; Hoang, Triem T.; Cheung, Mark L.

    1998-01-01

    The primary focus of this study is to model steady-state performance of a Loop Heat Pipe (LHP). The mathematical model is based on the steady-state energy balance equations at each component of the LHP. The heat exchange between each LHP component and the surrounding is taken into account. Both convection and radiation environments are modeled. The loop operating temperature is calculated as a function of the applied power at a given loop condition. Experimental validation of the model is attempted by using two different LHP designs. The mathematical model is tested at different sink temperatures and at different elevations of the loop. Tbc comparison of the calculations and experimental results showed very good agreement (within 3%). This method proved to be a useful tool in studying steady-state LHP performance characteristics.

  16. CHY loop integrands from holomorphic forms

    Energy Technology Data Exchange (ETDEWEB)

    Gomez, Humberto [Facultad de Ciencias Basicas, Universidad Santiago de Cali,Calle 5 62-00 Barrio Pampalinda, Cali, Valle (Colombia); Perimeter Institute for Theoretical Physics,31 Caroline Street N, Waterloo, ON N2L 2Y5 (Canada); Mizera, Sebastian; Zhang, Guojun [Perimeter Institute for Theoretical Physics,31 Caroline Street N, Waterloo, ON N2L 2Y5 (Canada); Department of Physics & Astronomy, University of Waterloo,Waterloo, ON N2L 3G1 (Canada)

    2017-03-16

    Recently, the Cachazo-He-Yuan (CHY) approach for calculating scattering amplitudes has been extended beyond tree level. In this paper, we introduce a way of constructing CHY integrands for Φ{sup 3} theory up to two loops from holomorphic forms on Riemann surfaces. We give simple rules for translating Feynman diagrams into the corresponding CHY integrands. As a complementary result, we extend the L-algorithm, originally introduced in https://arxiv.org/abs/1604.05373, to two loops. Using this approach, we are able to analytically verify our prescription for the CHY integrands up to seven external particles at two loops. In addition, it gives a natural way of extending to higher-loop orders.

  17. Observing string breaking with Wilson loops

    CERN Document Server

    Kratochvila, S; Kratochvila, Slavo; Forcrand, Philippe de

    2003-01-01

    An uncontroversial observation of adjoint string breaking is proposed, while measuring the static potential from Wilson loops only. The overlap of the Wilson loop with the broken-string state is small, but non-vanishing, so that the broken-string groundstate can be seen if the Wilson loop is long enough. We demonstrate this in the context of the (2+1)d SU(2) adjoint static potential, using an improved version of the Luscher-Weisz exponential variance reduction. To complete the picture we perform the more usual multichannel analysis with two basis states, the unbroken-string state and the broken-string state (two so-called gluelumps). As by-products, we obtain the temperature-dependent static potential measured from Polyakov loop correlations, and the fundamental SU(2) static potential with improved accuracy. Comparing the latter with the adjoint potential, we see clear deviations from Casimir scaling.

  18. Hardware-in-the-Loop Testing

    Data.gov (United States)

    Federal Laboratory Consortium — RTC has a suite of Hardware-in-the Loop facilities that include three operational facilities that provide performance assessment and production acceptance testing of...

  19. Loop Diuretics in the Treatment of Hypertension.

    Science.gov (United States)

    Malha, Line; Mann, Samuel J

    2016-04-01

    Loop diuretics are not recommended in current hypertension guidelines largely due to the lack of outcome data. Nevertheless, they have been shown to lower blood pressure and to offer potential advantages over thiazide-type diuretics. Torsemide offers advantages of longer duration of action and once daily dosing (vs. furosemide and bumetanide) and more reliable bioavailability (vs. furosemide). Studies show that the previously employed high doses of thiazide-type diuretics lower BP more than furosemide. Loop diuretics appear to have a preferable side effect profile (less hyponatremia, hypokalemia, and possibly less glucose intolerance). Studies comparing efficacy and side effect profiles of loop diuretics with the lower, currently widely prescribed, thiazide doses are needed. Research is needed to fill gaps in knowledge and common misconceptions about loop diuretic use in hypertension and to determine their rightful place in the antihypertensive arsenal.

  20. Possible hysteresis loops of resonatorless optical bistability

    International Nuclear Information System (INIS)

    Nguyen Ba An; Le Thi Cat Tuong.

    1990-05-01

    We qualitatively show that hysteresis loops of intrinsic optical bistability phenomena without any additional feedback may be of various shapes including those of a butterfly and a three-winged bow. (author). 15 refs, 4 figs

  1. Closed loop solar chemical heat pipe

    International Nuclear Information System (INIS)

    Levy, M.; Levitan, R.; Rosin, H.; Rubin, R.

    1991-01-01

    The system used for the closed loop operation of the solar chemical heat pipe comprises a reformer, heated by the solar furnace, a methanator and a storage assembly containing a compressor and storage cylinders. (authors). 7 figs

  2. Nonequilibrium Chromosome Looping via Molecular Slip Links

    Science.gov (United States)

    Brackley, C. A.; Johnson, J.; Michieletto, D.; Morozov, A. N.; Nicodemi, M.; Cook, P. R.; Marenduzzo, D.

    2017-09-01

    We propose a model for the formation of chromatin loops based on the diffusive sliding of molecular slip links. These mimic the behavior of molecules like cohesin, which, along with the CTCF protein, stabilize loops which contribute to organizing the genome. By combining 3D Brownian dynamics simulations and 1D exactly solvable nonequilibrium models, we show that diffusive sliding is sufficient to account for the strong bias in favor of convergent CTCF-mediated chromosome loops observed experimentally. We also find that the diffusive motion of multiple slip links along chromatin is rectified by an intriguing ratchet effect that arises if slip links bind to the chromatin at a preferred "loading site." This emergent collective behavior favors the extrusion of loops which are much larger than the ones formed by single slip links.

  3. A theory of desynchronisable closed loop system

    Directory of Open Access Journals (Sweden)

    Harsh Beohar

    2010-10-01

    Full Text Available The task of implementing a supervisory controller is non-trivial, even though different theories exist that allow automatic synthesis of these controllers in the form of automata. One of the reasons for this discord is due to the asynchronous interaction between a plant and its controller in implementations, whereas the existing supervisory control theories assume synchronous interaction. As a consequence the implementation suffer from the so-called inexact synchronisation problem. In this paper we address the issue of inexact synchronisation in a process algebraic setting, by solving a more general problem of refinement. We construct an asynchronous closed loop system by introducing a communication medium in a given synchronous closed loop system. Our goal is to find sufficient conditions under which a synchronous closed loop system is branching bisimilar to its corresponding asynchronous closed loop system.

  4. Global Collaborative STEM Education

    Science.gov (United States)

    Meabh Kelly, Susan; Smith, Walter

    2016-04-01

    Global Collaborative STEM Education, as the name suggests, simultaneously supports two sets of knowledge and skills. The first set is STEM -- science, technology, engineering and math. The other set of content knowledge and skills is that of global collaboration. Successful global partnerships require awareness of one's own culture, the biases embedded within that culture, as well as developing awareness of the collaborators' culture. Workforce skills fostered include open-mindedness, perseverance when faced with obstacles, and resourceful use of technological "bridges" to facilitate and sustain communication. In respect for the 2016 GIFT Workshop focus, Global Collaborative STEM Education projects dedicated to astronomy research will be presented. The projects represent different benchmarks within the Global Collaborative STEM Education continuum, culminating in an astronomy research experience that fully reflects how the global STEM workforce collaborates. To facilitate wider engagement in Global Collaborative STEM Education, project summaries, classroom resources and contact information for established international collaborative astronomy research projects will be disseminated.

  5. A multiple-pass ring oscillator based dual-loop phase-locked loop

    International Nuclear Information System (INIS)

    Chen Danfeng; Ren Junyan; Deng Jingjing; Li Wei; Li Ning

    2009-01-01

    A dual-loop phase-locked loop (PLL) for wideband operation is proposed. The dual-loop architecture combines a coarse-tuning loop with a fine-tuning one, enabling a wide tuning range and low voltage-controlled oscillator (VCO) gain without poisoning phase noise and reference spur suppression performance. An analysis of the phase noise and reference spur of the dual-loop PLL is emphasized. A novel multiple-pass ring VCO is designed for the dual-loop application. It utilizes both voltage-control and current-control simultaneously in the delay cell. The PLL is fabricated in Jazz 0.18-μm RF CMOS technology. The measured tuning range is from 4.2 to 5.9 GHz. It achieves a low phase noise of -99 dBc/Hz - 1 MHz offset from a 5.5 GHz carrier.

  6. A multiple-pass ring oscillator based dual-loop phase-locked loop

    Energy Technology Data Exchange (ETDEWEB)

    Chen Danfeng; Ren Junyan; Deng Jingjing; Li Wei; Li Ning, E-mail: dfchen@fudan.edu.c [State Key Laboratory of ASIC and System, Fudan University, Shanghai 201203 (China)

    2009-10-15

    A dual-loop phase-locked loop (PLL) for wideband operation is proposed. The dual-loop architecture combines a coarse-tuning loop with a fine-tuning one, enabling a wide tuning range and low voltage-controlled oscillator (VCO) gain without poisoning phase noise and reference spur suppression performance. An analysis of the phase noise and reference spur of the dual-loop PLL is emphasized. A novel multiple-pass ring VCO is designed for the dual-loop application. It utilizes both voltage-control and current-control simultaneously in the delay cell. The PLL is fabricated in Jazz 0.18-{mu}m RF CMOS technology. The measured tuning range is from 4.2 to 5.9 GHz. It achieves a low phase noise of -99 dBc/Hz - 1 MHz offset from a 5.5 GHz carrier.

  7. Selfdual strings and loop space Nahm equations

    International Nuclear Information System (INIS)

    Gustavsson, Andreas

    2008-01-01

    We give two independent arguments why the classical membrane fields should be take values in a loop algebra. The first argument comes from how we may construct selfdual strings in the M5 brane from a loop space version of the Nahm equations. The second argument is that there appears to be no infinite set of finite-dimensional Lie algebras (such as su(N) for any N) that satisfies the algebraic structure of the membrane theory

  8. Laser welding closed-loop power control

    DEFF Research Database (Denmark)

    Bagger, Claus; Olsen, Flemming Ove

    2003-01-01

    A closed-loop control system is developed to maintain an even seam width on the root side of a laser weld by continually controlling the output laser power of a 1500 W CO2 laser.......A closed-loop control system is developed to maintain an even seam width on the root side of a laser weld by continually controlling the output laser power of a 1500 W CO2 laser....

  9. FMFT. Fully massive four-loop tadpoles

    Energy Technology Data Exchange (ETDEWEB)

    Pikelner, Andrey [Hamburg Univ. (Germany). 2. Inst. fuer Theoretische Physik

    2017-07-15

    We present FMFT - a package written in FORM that evaluates four-loop fully massive tadpole Feynman diagrams. It is a successor of the MATAD package that has been successfully used to calculate many renormalization group functions at three-loop order in a wide range of quantum field theories especially in the Standard Model. We describe an internal structure of the package and provide some examples of its usage.

  10. Higgs Decay to Photons at Two Loops

    International Nuclear Information System (INIS)

    Fugel, F.

    2007-01-01

    The calculation of the two-loop corrections to the partial width of an intermediate-mass Higgs boson decaying into a pair of photons is reviewed. The main focus lies on the electroweak (EW) contributions. The sum of the EW corrections ranges from -4% to 0% for a Higgs mass between 100 GeV and 150 GeV, while the complete correction at two-loop order amounts to less than ± 1.5% in this regime. (author)

  11. Piles of dislocation loops in real crystals

    International Nuclear Information System (INIS)

    Dubinko, V.I.; Turkin, A.A.; Yanovskij, V.V.

    1985-01-01

    Behaviour of piles of dislocation loops in crystals was studied in order to define metal swelling under irradiation. Energy of pile interaction with point defects and intrinsic pile energy are studied in the framework of the linear elasticity theory. Preference of dislocation pile calculated in the paper decreases with radiation dose hence, material swelling rate also decreases. Creation of conditions, which assume an existence of piles of dislocation loops being stable under irradiation, is of particular interest

  12. Zero Point Energy of Renormalized Wilson Loops

    OpenAIRE

    Hidaka, Yoshimasa; Pisarski, Robert D.

    2009-01-01

    The quark antiquark potential, and its associated zero point energy, can be extracted from lattice measurements of the Wilson loop. We discuss a unique prescription to renormalize the Wilson loop, for which the perturbative contribution to the zero point energy vanishes identically. A zero point energy can arise nonperturbatively, which we illustrate by considering effective string models. The nonperturbative contribution to the zero point energy vanishes in the Nambu model, but is nonzero wh...

  13. FMFT: fully massive four-loop tadpoles

    Science.gov (United States)

    Pikelner, Andrey

    2018-03-01

    We present FMFT - a package written in FORM that evaluates four-loop fully massive tadpole Feynman diagrams. It is a successor of the MATAD package that has been successfully used to calculate many renormalization group functions at three-loop order in a wide range of quantum field theories especially in the Standard Model. We describe an internal structure of the package and provide some examples of its usage.

  14. Quantum Kinematics of Bosonic Vortex Loops

    International Nuclear Information System (INIS)

    Goldin, G.A.; Owczarek, R.; Sharp, D.H.

    1999-01-01

    Poisson structure for vortex filaments (loops and arcs) in 2D ideal incompressible fluid is analyzed in detail. Canonical coordinates and momenta on coadjoint orbits of the area-preserving diffeomorphism group, associated with such vortices, are found. The quantum space of states in the simplest case of ''bosonic'' vortex loops is built within a geometric quantization approach to the description of a quantum fluid. Fock-like structure and non-local creation and annihilation operators of quantum vortex filaments are introduced

  15. Next-generation small RNA sequencing for microRNAs profiling in the honey bee Apis mellifera.

    Science.gov (United States)

    Chen, X; Yu, X; Cai, Y; Zheng, H; Yu, D; Liu, G; Zhou, Q; Hu, S; Hu, F

    2010-12-01

    MicroRNAs (miRNAs) are key regulators in various physiological and pathological processes via post-transcriptional regulation of gene expression. The honey bee (Apis mellifera) is a key model for highly social species, and its complex social behaviour can be interpreted theoretically as changes in gene regulation, in which miRNAs are thought to be involved. We used the SOLiD sequencing system to identify the repertoire of miRNAs in the honey bee by sequencing a mixed small RNA library from different developmental stages. We obtained a total of 36,796,459 raw sequences; of which 5,491,100 short sequences were fragments of mRNA and other noncoding RNAs (ncRNA), and 1,759,346 reads mapped to the known miRNAs. We predicted 267 novel honey bee miRNAs representing 380,182 short reads, including eight miRNAs of other insects in 14,107,583 genome-mapped sequences. We verified 50 of them using stem-loop reverse-transcription PCR (RT-PCR), in which 35 yielded PCR products. Cross-species analyses showed 81 novel miRNAs with homologues in other insects, suggesting that they were authentic miRNAs and have similar functions. The results of this study provide a basis for studies of the miRNA-modulating networks in development and some intriguing phenomena such as caste differentiation in A. mellifera. © 2010 The Authors. Insect Molecular Biology © 2010 The Royal Entomological Society.

  16. Dental pulp stem cells

    DEFF Research Database (Denmark)

    Ashri, N. Y.; Ajlan, S. A.; Aldahmash, Abdullah M.

    2015-01-01

    scaffold, and guided through signaling molecules. Dental pulp stem cells have been used in an increasing number of studies in dental tissue engineering. Those cells show mesenchymal (stromal) stem cell-like properties including self-renewal and multilineage differentiation potentials, aside from...... an updated review on dental pulp stem cells and their applications in periodontal regeneration, in combination with different scaffolds and growth factors....

  17. Loop space representation of quantum general relativity and the group of loops

    International Nuclear Information System (INIS)

    Gambini, R.

    1991-01-01

    The action of the constraints of quantum general relativity on a general state in the loop representation is coded in terms of loop derivatives. These differential operators are related to the infinitesimal generators of the group of loops and generalize the area derivative first considered by Mandelstam. A new sector of solutions of the physical states space of nonperturbative quantum general relativity is found. (orig.)

  18. Multiple Flow Loop SCADA System Implemented on the Production Prototype Loop

    Energy Technology Data Exchange (ETDEWEB)

    Baily, Scott A. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Dalmas, Dale Allen [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Wheat, Robert Mitchell [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Woloshun, Keith Albert [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Dale, Gregory E. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-11-16

    The following report covers FY 15 activities to develop supervisory control and data acquisition (SCADA) system for the Northstar Moly99 production prototype gas flow loop. The goal of this effort is to expand the existing system to include a second flow loop with a larger production-sized blower. Besides testing the larger blower, this system will demonstrate the scalability of our solution to multiple flow loops.

  19. Liquid Lead-Bismuth Materials Test Loop

    International Nuclear Information System (INIS)

    Tcharnotskaia, Valentina; Ammerman, Curtt; Darling, Timothy; King, Joe; Li, Ning; Shaw, Don; Snodgrass, Leon; Woloshun, Keith

    2002-01-01

    We designed and built the Liquid Lead-Bismuth Materials Test Loop (MTL) to study the materials behavior in a flow of molten lead-bismuth eutectic (LBE). In this paper we present a description of the loop with main components and their functions. Stress distribution in the piping due to sustained, occasional and expansion loads is shown. The loop is designed so that a difference of 100 deg. C can be attained between the coldest and the hottest parts at a nominal flow rate of 8.84 GPM. Liquid LBE flow can be activated by a mechanical sump pump or by natural convection. In order to maintain a self-healing protective film on the surface of the stainless steel pipe, a certain concentration of oxygen has to be maintained in the liquid metal. We developed oxygen sensors and an oxygen control system to be implemented in the loop. The loop is outfitted with a variety of instruments that are controlled from a computer based data acquisition system. Initial experiments include preconditioning the loop, filling it up with LBE, running at uniform temperature and tuning the oxygen control system. We will present some preliminary results and discuss plans for the future tests. (authors)

  20. Integrative STEM Education Defined

    OpenAIRE

    Sanders, Mark E.

    2015-01-01

    “My work with integrative STEM education began in 1990 with the NSF-funded Technology, Science, Mathematics Integration Project… By 2008, I was convinced “STEM Education” was (and always would be) a hopelessly ambiguous phrase, and therefore felt we absolutely needed to rename our “STEM Education” graduate program and develop a tight operational definition of the central idea underlying our program, in hopes of preventing the sort of hopeless ambiguity that ruined the term “STEM education” fr...

  1. Stem Cells and Aging.

    Science.gov (United States)

    Koliakos, George

    2017-02-01

    The article is a presentation at the 4th Conference of ESAAM, which took place on October 30-31, 2015, in Athens, Greece. Its purpose was not to cover all aspects of cellular aging but to share with the audience of the Conference, in a 15-minute presentation, current knowledge about the rejuvenating and repairing somatic stem cells that are distinct from other stem cell types (such as embryonic or induced pluripotent stem cells), emphasize that our body in old age cannot take advantage of these rejuvenating cells, and provide some examples of novel experimental stem cell applications in the field of rejuvenation and antiaging biomedical research.

  2. Distribution of sizes of erased loops for loop-erased random walks

    OpenAIRE

    Dhar, Deepak; Dhar, Abhishek

    1997-01-01

    We study the distribution of sizes of erased loops for loop-erased random walks on regular and fractal lattices. We show that for arbitrary graphs the probability $P(l)$ of generating a loop of perimeter $l$ is expressible in terms of the probability $P_{st}(l)$ of forming a loop of perimeter $l$ when a bond is added to a random spanning tree on the same graph by the simple relation $P(l)=P_{st}(l)/l$. On $d$-dimensional hypercubical lattices, $P(l)$ varies as $l^{-\\sigma}$ for large $l$, whe...

  3. Hybrid Combustion-Gasification Chemical Looping

    Energy Technology Data Exchange (ETDEWEB)

    Herbert Andrus; Gregory Burns; John Chiu; Gregory Lijedahl; Peter Stromberg; Paul Thibeault

    2009-01-07

    For the past several years Alstom Power Inc. (Alstom), a leading world-wide power system manufacturer and supplier, has been in the initial stages of developing an entirely new, ultra-clean, low cost, high efficiency power plant for the global power market. This new power plant concept is based on a hybrid combustion-gasification process utilizing high temperature chemical and thermal looping technology The process consists of the oxidation, reduction, carbonation, and calcination of calcium-based compounds, which chemically react with coal, biomass, or opportunity fuels in two chemical loops and one thermal loop. The chemical and thermal looping technology can be alternatively configured as (i) a combustion-based steam power plant with CO{sub 2} capture, (ii) a hybrid combustion-gasification process producing a syngas for gas turbines or fuel cells, or (iii) an integrated hybrid combustion-gasification process producing hydrogen for gas turbines, fuel cells or other hydrogen based applications while also producing a separate stream of CO{sub 2} for use or sequestration. In its most advanced configuration, this new concept offers the promise to become the technology link from today's Rankine cycle steam power plants to tomorrow's advanced energy plants. The objective of this work is to develop and verify the high temperature chemical and thermal looping process concept at a small-scale pilot facility in order to enable AL to design, construct and demonstrate a pre-commercial, prototype version of this advanced system. In support of this objective, Alstom and DOE started a multi-year program, under this contract. Before the contract started, in a preliminary phase (Phase 0) Alstom funded and built the required small-scale pilot facility (Process Development Unit, PDU) at its Power Plant Laboratories in Windsor, Connecticut. Construction was completed in calendar year 2003. The objective for Phase I was to develop the indirect combustion loop with CO{sub 2

  4. The stem factor challenge

    International Nuclear Information System (INIS)

    Russell, M.J.; Steele, R. Jr.; DeWall, K.G.; Watkins, J.C.; Bramwell, D.

    1994-01-01

    One of the most important challenges that still needs to be met in the effort to understand the operation of motor-operated, rising-stem valves is the ability to determine stem factor throughout the valve's load range. The stem factor represents the conversion of operator torque to stem thrust. Determining the stem factor is important because some motor-operated valves (MOVs) cannot be tested in the plant at design basis conditions. The ability of these valves to perform their design basis function (typically, to operate against specified flow and pressure loads) must be ensured by analytical methods or by extrapolating from the results of tests conducted at lower loads. Because the stem factor tends to vary in response to friction and lubrication phenomena that occur during loading and wedging, analytical methods and extrapolation methods have been difficult to develop and implement. Early investigations into variability in the stem factor tended to look only at the tip of the iceberg; they focused on what was happening at torque switch trip, which usually occurs at full wedging. In most stems, the stem factor is better (lower) in the wedging transient than before wedging, so working with torque switch trip data alone led many early researchers to false conclusions about the relationship between stem factor and load. However, research at the Idaho National Engineering Laboratory (INEL) has taken a closer look at what happens during the running portion of the closing stroke along with the wedging portion. This shift in focus is important, because functional failure of a valve typically consists of a failure to isolate flow, not a failure to achieve full wedging. Thus, the stem factor that must be determined for a valve's design basis closing requirements is the one that corresponds with the running load before wedging

  5. Donating Peripheral Blood Stem Cells

    Science.gov (United States)

    ... Print this page My Cart Donating peripheral blood stem cells Peripheral blood stem cell (PBSC) donation is a nonsurgical procedure to collect ... Donating bone marrow Donor experiences videos Peripheral blood stem cell (PBSC) donation is one of two methods of ...

  6. Stem Cell Transplants (For Teens)

    Science.gov (United States)

    ... Safe Videos for Educators Search English Español Stem Cell Transplants KidsHealth / For Teens / Stem Cell Transplants What's ... Take to Recover? Coping Print What Are Stem Cells? As you probably remember from biology class, every ...

  7. Decreased HIV diversity after allogeneic stem cell transplantation of an HIV-1 infected patient: a case report

    Directory of Open Access Journals (Sweden)

    Thielen Alexander

    2010-03-01

    Full Text Available Abstract The human immunodeficiency virus type 1 (HIV-1 coreceptor use and viral evolution were analyzed in blood samples from an HIV-1 infected patient undergoing allogeneic stem cell transplantation (SCT. Coreceptor use was predicted in silico from sequence data obtained from the third variable loop region of the viral envelope gene with two software tools. Viral diversity and evolution was evaluated on the same samples by Bayesian inference and maximum likelihood methods. In addition, phenotypic analysis was done by comparison of viral growth in peripheral blood mononuclear cells and in a CCR5 (R5-deficient T-cell line which was controlled by a reporter assay confirming viral tropism. In silico coreceptor predictions did not match experimental determinations that showed a consistent R5 tropism. Anti-HIV directed antibodies could be detected before and after the SCT. These preexisting antibodies did not prevent viral rebound after the interruption of antiretroviral therapy during the SCT. Eventually, transplantation and readministration of anti-retroviral drugs lead to sustained increase in CD4 counts and decreased viral load to undetectable levels. Unexpectedly, viral diversity decreased after successful SCT. Our data evidence that only R5-tropic virus was found in the patient before and after transplantation. Therefore, blocking CCR5 receptor during stem cell transplantation might have had beneficial effects and this might apply to more patients undergoing allogeneic stem cell transplantation. Furthermore, we revealed a scenario of HIV-1 dynamic different from the commonly described ones. Analysis of viral evolution shows the decrease of viral diversity even during episodes with bursts in viral load.

  8. Incremental Closed-loop Identification of Linear Parameter Varying Systems

    DEFF Research Database (Denmark)

    Bendtsen, Jan Dimon; Trangbæk, Klaus

    2011-01-01

    , closed-loop system identification is more difficult than open-loop identification. In this paper we prove that the so-called Hansen Scheme, a technique known from linear time-invariant systems theory for transforming closed-loop system identification problems into open-loop-like problems, can be extended...

  9. High-temperature helium-loop facility

    International Nuclear Information System (INIS)

    Tokarz, R.D.

    1981-09-01

    The high-temperature helium loop is a facility for materials testing in ultrapure helium gas at high temperatures. The closed loop system is capable of recirculating high-purity helium or helium with controlled impurities. The gas loop maximum operating conditions are as follows: 300 psi pressure, 500 lb/h flow rate, and 2100 0 F temperature. The two test sections can accept samples up to 3.5 in. diameter and 5 ft long. The gas loop is fully instrumented to continuously monitor all parameters of loop operation as well as helium impurities. The loop is fully automated to operate continuously and requires only a daily servicing by a qualified operator to replenish recorder charts and helium makeup gas. Because of its versatility and high degree of parameter control, the helium loop is applicable to many types of materials research. This report describes the test apparatus, operating parameters, peripheral systems, and instrumentation system. The experimental capabilities and test conand presents the results that have been obtained. The study has been conducted using a four-phase approach. The first phase develops the solution to the steady-state radon-diffusion equation in one-dimensieered barriers; disposal charge analysis; analysis of spent fuel policy implementation; spent f water. Field measurements and observations are reported for each site. Analytical data and field measurements are presented in tables and maps. Uranium concentrations in the sediments which were above detection limits ranged from 0.10 t 51.2 ppM. The mean of the logarithms of the uranium concentrations was 0.53. A group of high uranium concentrations occurs near the junctions of quadrangles AB, AC, BB, a 200 mK. In case 2), x-ray studies of isotopic phase separation in 3 He-- 4 He bcc solids were carried out by B. A. Fraass

  10. Two-phase Heating in Flaring Loops

    Science.gov (United States)

    Zhu, Chunming; Qiu, Jiong; Longcope, Dana W.

    2018-03-01

    We analyze and model a C5.7 two-ribbon solar flare observed by the Solar Dynamics Observatory, Hinode, and GOES on 2011 December 26. The flare is made of many loops formed and heated successively over one and half hours, and their footpoints are brightened in the UV 1600 Å before enhanced soft X-ray and EUV missions are observed in flare loops. Assuming that anchored at each brightened UV pixel is a half flaring loop, we identify more than 6700 half flaring loops, and infer the heating rate of each loop from the UV light curve at the footpoint. In each half loop, the heating rate consists of two phases: intense impulsive heating followed by a low-rate heating that is persistent for more than 20 minutes. Using these heating rates, we simulate the evolution of their coronal temperatures and densities with the model of the “enthalpy-based thermal evolution of loops.” In the model, suppression of thermal conduction is also considered. This model successfully reproduces total soft X-ray and EUV light curves observed in 15 passbands by four instruments GOES, AIA, XRT, and EVE. In this flare, a total energy of 4.9 × 1030 erg is required to heat the corona, around 40% of this energy is in the slow-heating phase. About two-fifths of the total energy used to heat the corona is radiated by the coronal plasmas, and the other three fifth transported to the lower atmosphere by thermal conduction.

  11. Clustering of HIV-1 Subtypes Based on gp120 V3 Loop electrostatic properties

    Directory of Open Access Journals (Sweden)

    López de Victoria Aliana

    2012-02-01

    Full Text Available Abstract Background The V3 loop of the glycoprotein gp120 of HIV-1 plays an important role in viral entry into cells by utilizing as coreceptor CCR5 or CXCR4, and is implicated in the phenotypic tropisms of HIV viruses. It has been hypothesized that the interaction between the V3 loop and CCR5 or CXCR4 is mediated by electrostatics. We have performed hierarchical clustering analysis of the spatial distributions of electrostatic potentials and charges of V3 loop structures containing consensus sequences of HIV-1 subtypes. Results Although the majority of consensus sequences have a net charge of +3, the spatial distribution of their electrostatic potentials and charges may be a discriminating factor for binding and infectivity. This is demonstrated by the formation of several small subclusters, within major clusters, which indicates common origin but distinct spatial details of electrostatic properties. Some of this information may be present, in a coarse manner, in clustering of sequences, but the spatial details are largely lost. We show the effect of ionic strength on clustering of electrostatic potentials, information that is not present in clustering of charges or sequences. We also make correlations between clustering of electrostatic potentials and net charge, coreceptor selectivity, global prevalence, and geographic distribution. Finally, we interpret coreceptor selectivity based on the N6X7T8|S8X9 sequence glycosylation motif, the specific positive charge location according to the 11/24/25 rule, and the overall charge and electrostatic potential distribution. Conclusions We propose that in addition to the sequence and the net charge of the V3 loop of each subtype, the spatial distributions of electrostatic potentials and charges may also be important factors for receptor recognition and binding and subsequent viral entry into cells. This implies that the overall electrostatic potential is responsible for long-range recognition of the V3

  12. Clustering of HIV-1 Subtypes Based on gp120 V3 Loop electrostatic properties

    International Nuclear Information System (INIS)

    López de Victoria, Aliana; Kieslich, Chris A; Rizos, Apostolos K; Krambovitis, Elias; Morikis, Dimitrios

    2012-01-01

    The V3 loop of the glycoprotein gp120 of HIV-1 plays an important role in viral entry into cells by utilizing as coreceptor CCR5 or CXCR4, and is implicated in the phenotypic tropisms of HIV viruses. It has been hypothesized that the interaction between the V3 loop and CCR5 or CXCR4 is mediated by electrostatics. We have performed hierarchical clustering analysis of the spatial distributions of electrostatic potentials and charges of V3 loop structures containing consensus sequences of HIV-1 subtypes. Although the majority of consensus sequences have a net charge of +3, the spatial distribution of their electrostatic potentials and charges may be a discriminating factor for binding and infectivity. This is demonstrated by the formation of several small subclusters, within major clusters, which indicates common origin but distinct spatial details of electrostatic properties. Some of this information may be present, in a coarse manner, in clustering of sequences, but the spatial details are largely lost. We show the effect of ionic strength on clustering of electrostatic potentials, information that is not present in clustering of charges or sequences. We also make correlations between clustering of electrostatic potentials and net charge, coreceptor selectivity, global prevalence, and geographic distribution. Finally, we interpret coreceptor selectivity based on the N 6 X 7 T 8 |S 8 X 9 sequence glycosylation motif, the specific positive charge location according to the 11/24/25 rule, and the overall charge and electrostatic potential distribution. We propose that in addition to the sequence and the net charge of the V3 loop of each subtype, the spatial distributions of electrostatic potentials and charges may also be important factors for receptor recognition and binding and subsequent viral entry into cells. This implies that the overall electrostatic potential is responsible for long-range recognition of the V3 loop with coreceptors CCR5/CXCR4, whereas the charge

  13. Structural and sequence diversity of the transposon Galileo in the Drosophila willistoni genome.

    Science.gov (United States)

    Gonçalves, Juliana W; Valiati, Victor Hugo; Delprat, Alejandra; Valente, Vera L S; Ruiz, Alfredo

    2014-09-13

    Galileo is one of three members of the P superfamily of DNA transposons. It was originally discovered in Drosophila buzzatii, in which three segregating chromosomal inversions were shown to have been generated by ectopic recombination between Galileo copies. Subsequently, Galileo was identified in six of 12 sequenced Drosophila genomes, indicating its widespread distribution within this genus. Galileo is strikingly abundant in Drosophila willistoni, a neotropical species that is highly polymorphic for chromosomal inversions, suggesting a role for this transposon in the evolution of its genome. We carried out a detailed characterization of all Galileo copies present in the D. willistoni genome. A total of 191 copies, including 133 with two terminal inverted repeats (TIRs), were classified according to structure in six groups. The TIRs exhibited remarkable variation in their length and structure compared to the most complete copy. Three copies showed extended TIRs due to internal tandem repeats, the insertion of other transposable elements (TEs), or the incorporation of non-TIR sequences into the TIRs. Phylogenetic analyses of the transposase (TPase)-encoding and TIR segments yielded two divergent clades, which we termed Galileo subfamilies V and W. Target-site duplications (TSDs) in D. willistoni Galileo copies were 7- or 8-bp in length, with the consensus sequence GTATTAC. Analysis of the region around the TSDs revealed a target site motif (TSM) with a 15-bp palindrome that may give rise to a stem-loop secondary structure. There is a remarkable abundance and diversity of Galileo copies in the D. willistoni genome, although no functional copies were found. The TIRs in particular have a dynamic structure and extend in different ways, but their ends (required for transposition) are more conserved than the rest of the element. The D. willistoni genome harbors two Galileo subfamilies (V and W) that diverged ~9 million years ago and may have descended from an ancestral

  14. Colorectal cancer stem cells.

    Science.gov (United States)

    Salama, Paul; Platell, Cameron

    2009-10-01

    Somatic stem cells reside at the base of the crypts throughout the colonic mucosa. These cells are essential for the normal regeneration of the colonic epithelium. The stem cells reside within a special 'niche' comprised of intestinal sub-epithelial myofibroblasts that tightly control their function. It has been postulated that mutations within these adult colonic stem cells may induce neoplastic changes. Such cells can then dissociate from the epithelium and travel into the mesenchyme and thus form invasive cancers. This theory is based on the observation that within a colon cancer, less than 1% of the neoplastic cells have the ability to regenerate the tumour. It is this group of cells that exhibits characteristics of colonic stem cells. Although anti-neoplastic agents can induce remissions by inhibiting cell division, the stem cells appear to be remarkably resistant to both standard chemotherapy and radiotherapy. These stem cells may therefore persist after treatment and form the nucleus for cancer recurrence. Hence, future treatment modalities should focus specifically on controlling the cancer stem cells. In this review, we discuss the biology of normal and malignant colonic stem cells.

  15. Aneuploidy in stem cells

    NARCIS (Netherlands)

    Garcia-Martinez, Jorge; Bakker, Bjorn; Schukken, Klaske M; Simon, Judith E; Foijer, Floris

    2016-01-01

    Stem cells hold enormous promise for regenerative medicine as well as for engineering of model systems to study diseases and develop new drugs. The discovery of protocols that allow for generating induced pluripotent stem cells (IPSCs) from somatic cells has brought this promise steps closer to

  16. Dazlin' pluripotent stem cells

    NARCIS (Netherlands)

    Welling, M.A.

    2014-01-01

    Pluripotent embryonic stem cells (ESCs) can be isolated from the inner cell mass (ICM) of blastocyst embryos and differentiate into all three germ layers in vitro. However, despite their similar origin, mouse embryonic stem cells represent a more naïve ICM-like pluripotent state whereas human

  17. Cancer stem cells revisited

    NARCIS (Netherlands)

    Batlle, Eduard; Clevers, Hans

    2017-01-01

    The cancer stem cell (CSC) concept was proposed four decades ago, and states that tumor growth, analogous to the renewal of healthy tissues, is fueled by small numbers of dedicated stem cells. It has gradually become clear that many tumors harbor CSCs in dedicated niches, and yet their

  18. The Hidden STEM Economy

    Science.gov (United States)

    Rothwell, Jonathan

    2013-01-01

    Workers in STEM (science, technology, engineering, and math) fields play a direct role in driving economic growth. Yet, because of how the STEM economy has been defined, policymakers have mainly focused on supporting workers with at least a bachelor's (BA) degree, overlooking a strong potential workforce of those with less than a BA. This report…

  19. A mutation in the envelope protein fusion loop attenuates mouse neuroinvasiveness of the NY99 strain of West Nile virus

    International Nuclear Information System (INIS)

    Zhang Shuliu; Li Li; Woodson, Sara E.; Huang, Claire Y.-H.; Kinney, Richard M.; Barrett, Alan D.T.; Beasley, David W.C.

    2006-01-01

    Substitutions were engineered individually and in combinations at the fusion loop, receptor-binding domain and a stem-helix structure of the envelope protein of a West Nile virus strain, NY99, and their effects on mouse virulence and presentation of epitopes recognized by monoclonal antibodies (MAbs) were assessed. A single substitution within the fusion loop (L107F) attenuated mouse neuroinvasiveness of NY99. No substitutions attenuated NY99 neurovirulence. The L107F mutation also abolished binding of a non-neutralizing MAb, 3D9, whose epitope had not been previously identified. MAb 3D9 was subsequently shown to be broadly cross-reactive with other flaviviruses, consistent with binding near the highly conserved fusion loop

  20. Detection of HbsAg and hATIII genetically modified goats (Caprahircus) by loop-mediated isothermal amplification.

    Science.gov (United States)

    Tao, Chenyu; Zhang, Qingde; Zhai, Shanli; Liu, Bang

    2013-11-01

    In this study, sensitive and rapid detection systems were designed using a loop-mediated isothermal amplification (LAMP) method to detect the genetically modified goats. A set of 4 primers were designed for each exogenous nucleic acids HBsAg and hATIII. The DNA samples were first amplified with the outer and inner primers and released a single-stranded DNA,of which both ends were stem-loop structure. Then one inner primer hybridized with the loop, and initiated displacement synthesis in less than 1 h. The result could be visualized by both agarose gel electrophoresis and unaided eyes directly after adding SYBR GREEN 1. The detection limit of LAMP was ten copies of target molecules, indicating that LAMP was tenfold more sensitive than the classical PCR. Furthermore, all the samples of genetically modified goats were tested positively by LAMP, and the results demonstrated that the LAMP was a rapid and sensitive method for detecting the genetically modified organism.

  1. Conformation and dynamics of nucleotides in bulges and symmetric internal loops in duplex DNA studied by EPR and fluorescence spectroscopies

    International Nuclear Information System (INIS)

    Cekan, Pavol; Sigurdsson, Snorri Th.

    2012-01-01

    Highlights: ► Bulges and loops were studied by both EPR and fluorescence spectroscopies using the probe Ç/Ç f . ► One-base bulge was in a temperature-dependent equilibrium between looped-out and stacked states. ► Bases in two- and three-base bulges were stacked at all temperatures, resulting in DNA bending. ► Bases were stacked in symmetrical two- to five-base internal loops, according to EPR data. ► Unexpectedly high fluorescence for the smaller loops indicated local structural perturbations. -- Abstract: The dynamics and conformation of base bulges and internal loops in duplex DNA were studied using the bifunctional spectroscopic probe Ç, which becomes fluorescent (Ç f ) upon reduction of the nitroxide functional group, along with EPR and fluorescence spectroscopies. A one-base bulge was in a conformational equilibrium between looped-out and stacked states, the former favored at higher temperature and the latter at lower temperature. Stacking of bulge bases was favored in two- and three-base bulges, independent of temperature, resulting in DNA bending as evidenced by increased fluorescence of Ç f . EPR spectra of Ç-labeled three-, four- and five-base symmetrical interior DNA bulges at 20 °C showed low mobility, indicating that the spin-label was stacked within the loop. The spin-label mobility at 37 °C increased as the loops became larger. A considerable variation in fluorescence between different loops was observed, as well as a temperature-dependence within constructs. Fluorescence unexpectedly increased as the size of the loop decreased at 2 °C. Fluorescence of the smallest loops, where a single T·T mismatch was located between the stem region and the probe, was even larger than for the single strand, indicating a considerable local structural deformation of these loops from regular B-DNA. These results show the value of combining EPR and fluorescence spectroscopy to study non-helical regions of nucleic acids.

  2. An algorithm to find all palindromic sequences in proteins

    Indian Academy of Sciences (India)

    2013-01-20

    Jan 20, 2013 ... 1976; Karrer and Gall 1976; Vogt and Braun 1976) and (iii) in the formation of hairpin loops in the newly transcribed RNA. Palindromic sequences are observed in various classes of proteins like histones (Cheng et al. 1989), prion proteins (Sulkowski 1992; Kazim 1993),. DNA-binding proteins (Suzuki 1992; ...

  3. Role of the NC-loop in catalytic activity and stability in lipase from Fervidobacterium changbaicum.

    Directory of Open Access Journals (Sweden)

    Binchun Li

    Full Text Available Flexible NC-loops between the catalytic domain and the cap domain of the α/β hydrolase fold enzymes show remarkable diversity in length, sequence, and configuration. Recent investigations have suggested that the NC-loop might be involved in catalysis and substrate recognition in many enzymes from the α/β hydrolase fold superfamily. To foster a deep understanding of its role in catalysis, stability, and divergent evolution, we here systemically investigated the function of the NC-loop (residues 131-151 in a lipase (FClip1 from thermophilic bacterium Fervidobacterium changbaicum by loop deletion, alanine-scanning mutagenesis and site-directed mutagenesis. We found that the upper part of the NC-loop (residues 131-138 was of great importance to enzyme catalysis. Single substitutions in this region could fine-tune the activity of FClip1 as much as 41-fold, and any deletions from this region rendered the enzyme completely inactive. The lower part of the NC-loop (residues 139-151 was capable of enduring extensive deletions without loss of activity. The shortened mutants in this region were found to show both improved activity and increased stability simultaneously. We therefore speculated that the NC-loop, especially the lower part, would be a perfect target for enzyme engineering to optimize the enzymatic properties, and might present a hot zone for the divergent evolution of α/β hydrolases. Our findings may provide an opportunity for better understanding of the mechanism of divergent evolution in the α/β hydrolase fold superfamily, and may also guide the design of novel biocatalysts for industrial applications.

  4. Activation loop targeting strategy for design of receptor-interacting protein kinase 2 (RIPK2) inhibitors.

    Science.gov (United States)

    Suebsuwong, Chalada; Pinkas, Daniel M; Ray, Soumya S; Bufton, Joshua C; Dai, Bing; Bullock, Alex N; Degterev, Alexei; Cuny, Gregory D

    2018-02-15

    Development of selective kinase inhibitors remains a challenge due to considerable amino acid sequence similarity among family members particularly in the ATP binding site. Targeting the activation loop might offer improved inhibitor selectivity since this region of kinases is less conserved. However, the strategy presents difficulties due to activation loop flexibility. Herein, we report the design of receptor-interacting protein kinase 2 (RIPK2) inhibitors based on pan-kinase inhibitor regorafenib that aim to engage basic activation loop residues Lys169 or Arg171. We report development of CSR35 that displayed >10-fold selective inhibition of RIPK2 versus VEGFR2, the target of regorafenib. A co-crystal structure of CSR35 with RIPK2 revealed a resolved activation loop with an ionic interaction between the carboxylic acid installed in the inhibitor and the side-chain of Lys169. Our data provides principle feasibility of developing activation loop targeting type II inhibitors as a complementary strategy for achieving improved selectivity. Copyright © 2018 The Author(s). Published by Elsevier Ltd.. All rights reserved.

  5. The Basic/Helix-Loop-Helix Protein Family in Gossypium: Reference Genes and Their Evolution during Tetraploidization.

    Directory of Open Access Journals (Sweden)

    Qian Yan

    Full Text Available Basic/helix-loop-helix (bHLH proteins comprise one of the largest transcription factor families and play important roles in diverse cellular and molecular processes. Comprehensive analyses of the composition and evolution of the bHLH family in cotton are essential to elucidate their functions and the molecular basis of cotton development. By searching bHLH homologous genes in sequenced diploid cotton genomes (Gossypium raimondii and G. arboreum, a set of cotton bHLH reference genes containing 289 paralogs were identified and named as GobHLH001-289. Based on their phylogenetic relationships, these cotton bHLH proteins were clustered into 27 subfamilies. Compared to those in Arabidopsis and cacao, cotton bHLH proteins generally increased in number, but unevenly in different subfamilies. To further uncover evolutionary changes of bHLH genes during tetraploidization of cotton, all genes of S5a and S5b subfamilies in upland cotton and its diploid progenitors were cloned and compared, and their transcript profiles were determined in upland cotton. A total of 10 genes of S5a and S5b subfamilies (doubled from A- and D-genome progenitors maintained in tetraploid cottons. The major sequence changes in upland cotton included a 15-bp in-frame deletion in GhbHLH130D and a long terminal repeat retrotransposon inserted in GhbHLH062A, which eliminated GhbHLH062A expression in various tissues. The S5a and S5b bHLH genes of A and D genomes (except GobHLH062 showed similar transcription patterns in various tissues including roots, stems, leaves, petals, ovules, and fibers, while the A- and D-genome genes of GobHLH110 and GobHLH130 displayed clearly different transcript profiles during fiber development. In total, this study represented a genome-wide analysis of cotton bHLH family, and revealed significant changes in sequence and expression of these genes in tetraploid cottons, which paved the way for further functional analyses of bHLH genes in the cotton genus.

  6. Short hairpin-loop-structured oligodeoxynucleotides reduce HSV-1 replication

    Directory of Open Access Journals (Sweden)

    Heinrich Jochen

    2009-04-01

    Full Text Available Abstract The Herpes simplex virus (HSV is known as an infectious agent and widespread in the human population. The symptoms of HSV infections can range from mild to life threatening, especially in immune-compromised individuals. HSV infections are commonly treated with the guanosine analogue Aciclovir, but reports of resistance are increasing. Efforts are made to establish single-stranded antisense oligodeoxynucleotides (as and small interfering ribonucleic acids (siRNAs for antiviral treatment. Recently, another class of short interfering nucleic acids, partially double-stranded hairpin loop-structured 54 mer oligodeoxynucleotides (ODNs, was shown to allow hydrolysis of HIV RNA by binding to the viral RNA. This leads to a substrate for the viral RNase H. To assess the potential of such ODNs for inhibition of HSV-1 replication, five partially double-stranded ODNs were designed based on the sequences of known siRNAs against HSV-1 with antiviral activity. Three of them are directed against early and two against leaky late genes. Primary human lung fibroblasts, MRC-5, and African green monkey kidney cells, Vero, were transfected with ODNs and subsequently infected. The effect on HSV-1 replication was determined by analyzing the virus titer in cell culture supernatants by quantitative PCR and plaque assays. An inhibitory effect was observed with all five selected ODNs, with two cases showing statistical significance in both cell types. The observed effect was sequence-specific and dose dependent. In one case the ODN was more efficient than a previously described siRNA directed against the same target site in the mRNA of UL5, a component of the helicase/primase complex. HSV-1 virions and ODNs can be applied simultaneously without transfection reagent, but at a 50-fold higher concentration to Vero cells with similar efficiencies. The results underline the potential of partially double-stranded hairpin loop-structured ODNs as antiviral agents.

  7. Operation of the hot test loop facilities

    International Nuclear Information System (INIS)

    Cheong, Moon Ki; Park, Choon Kyeong; Won, Soon Yeon; Yang, Sun Kyu; Cheong, Jang Whan; Cheon, Se Young; Song, Chul Hwa; Jeon, Hyeong Kil; Chang, Suk Kyu; Jeong, Heung Jun; Cho, Young Ro; Kim, Bok Duk; Min, Kyeong Ho

    1994-12-01

    The objective of this project is to obtain the available experimental data and to develop the measuring techniques through taking full advantage of the facilities. The facilities operated by the thermal hydraulics department have been maintained and repaired in order to carry out the thermal hydraulics tests necessary for providing the available data. The performance tests for double grid type bottom end piece which was improved on the debris filtering effectivity were performed using the PWR-Hot Test Loop. The CANDU-Hot Test Loop was operated to carry out the pressure drop tests and strength tests of fuel. The Cold Test Loop was used to obtain the local velocity data in subchannel within fuel bundle and to understand the characteristic of pressure drop required for improving the nuclear fuel and to develop the advanced measuring techniques. RCS Loop, which is used to measure the CHF, is presently under design and construction. B and C Loop is designed and constructed to assess the automatic depressurization safety system behavior. 4 tabs., 79 figs., 7 refs. (Author) .new

  8. Mass inflation in the loop black hole

    International Nuclear Information System (INIS)

    Brown, Eric G.; Mann, Robert; Modesto, Leonardo

    2011-01-01

    In classical general relativity the Cauchy horizon within a two-horizon black hole is unstable via a phenomenon known as mass inflation, in which the mass parameter (and the spacetime curvature) of the black hole diverges at the Cauchy horizon. Here we study this effect for loop black holes - quantum gravitationally corrected black holes from loop quantum gravity - whose construction alleviates the r=0 singularity present in their classical counterparts. We use a simplified model of mass inflation, which makes use of the generalized Dray-'t Hooft relation, to conclude that the Cauchy horizon of loop black holes indeed results in a curvature singularity similar to that found in classical black holes. The Dray-'t Hooft relation is of particular utility in the loop black hole because it does not directly rely upon Einstein's field equations. We elucidate some of the interesting and counterintuitive properties of the loop black hole, and corroborate our results using an alternate model of mass inflation due to Ori.

  9. One-loop calculations with massive particles

    International Nuclear Information System (INIS)

    Oldenborgh, G.J. van.

    1990-01-01

    In this thesis some techniques for performing one-loop calculations with massive particles are presented. Numerical techniques are presented necessary for evaluating one-loop integrals which occur in one-loop calculations of photon-photon scattering. The algorithms have been coded in FORTRAN (to evaluate the scalar integrals) and the algebraic language FORM (to reduce the tensor integrals to scalar integrals). Applications are made in the theory of the strong interaction, QCD, i.e. in handling one-loop integrals with massive particles, in order to regulate the infinities by mass parameters encountered in this theory. However this simplifies the computation considerably, the description of the proton structure functions have to be renormalized in order to obtain physical results. This renormalization is different from the published results for the gluon and thus has to be redone. The first physics results that have been obtained with these new methods are presented. These concern heavy quark production in semi-leptonic interactions, for instance neutrino charm production and top production at the electron-proton (ep) collider HERA and the proposed LEP/LHC combination. Total and differential cross-sections for one-loop corrections to top production at the HERA and proposed LEP/HLC ep colliders are given and structure functions for charmed quark production are compared with previously published results. (author). 58 refs.; 18 figs.; 5 tabs

  10. Bootstrapping the Three-Loop Hexagon

    Energy Technology Data Exchange (ETDEWEB)

    Dixon, Lance J.; /CERN /SLAC; Drummond, James M.; /CERN /Annecy, LAPTH; Henn, Johannes M.; /Humboldt U., Berlin /Santa Barbara, KITP

    2011-11-08

    We consider the hexagonal Wilson loop dual to the six-point MHV amplitude in planar N = 4 super Yang-Mills theory. We apply constraints from the operator product expansion in the near-collinear limit to the symbol of the remainder function at three loops. Using these constraints, and assuming a natural ansatz for the symbol's entries, we determine the symbol up to just two undetermined constants. In the multi-Regge limit, both constants drop out from the symbol, enabling us to make a non-trivial confirmation of the BFKL prediction for the leading-log approximation. This result provides a strong consistency check of both our ansatz for the symbol and the duality between Wilson loops and MHV amplitudes. Furthermore, we predict the form of the full three-loop remainder function in the multi-Regge limit, beyond the leading-log approximation, up to a few constants representing terms not detected by the symbol. Our results confirm an all-loop prediction for the real part of the remainder function in multi-Regge 3 {yields} 3 scattering. In the multi-Regge limit, our result for the remainder function can be expressed entirely in terms of classical polylogarithms. For generic six-point kinematics other functions are required.

  11. Double switching hysteresis loop in a single layer Fe3Pt alloy thin films

    International Nuclear Information System (INIS)

    Nahid, M.A.I.; Suzuki, Takao

    2008-01-01

    The Fe 3 Pt alloy thin films were epitaxially grown on MgO(100) substrate by e-beam evaporation. The films were partially ordered at the substrate deposition temperature above 350 deg. C. These partially ordered films exhibit very large biaxial magnetic anisotropy constant in the order of 10 5 J/m 3 and produce double switching in the hysteresis loops. The difference of the switching field of these films can be up to about 3 x 10 5 A/m by tuning the angle of the applied field with respect to the easy axes. This double switching behavior stems from the large biaxial magnetic anisotropy of the films

  12. New heavy flavor contributions to DIS at the 3-loop order: different masses and nested topologies

    Energy Technology Data Exchange (ETDEWEB)

    Ablinger, Jakob; Schneider, Carsten [RISC - JKU Linz (Austria); Bluemlein, Johannes; Wissbrock, Fabian [DESY (Germany)

    2013-07-01

    We present recent results on the heavy flavor Wilson coefficients of the deep-inelastic structure function F{sub 2} stemming from diagrams which contain both charm- and bottom-quarks. Starting at 3-loop order these contributions cannot be incorporated into the variable flavor number scheme (VFSN). We also present new results on the computation of diagrams of more advanced topologies (knotted ladder, Benz, and others) which have been obtained via the method of hyperlogarithms. They require the use of extensions to the basic formalism leading to the more general class of generalized hyperlogarithms, resp. the associated nested sums. Both the x- and Mellin N-space representations are discussed.

  13. Variational solution of the loop equation in QCD

    International Nuclear Information System (INIS)

    Agishtein, M.E.; Migdal, A.A.

    1988-01-01

    A new technique for the large N loop equation of QCD is worked out. The Wilson loop W(C) is approximated by a Gaussian functional. The parameters are fitted to the loop equation, after which the equation is statisfied up to 0.2%. The resulting Wilson loop corresponds to linearly rising Regge trajectories. The problem of tachyon is still present, but it could be cured by iteration of the loop equation starting from this variational solution. (orig.)

  14. Variational solution of the loop equation in QCD

    International Nuclear Information System (INIS)

    Agishtein, M.E.; Migdal, A.A.

    1988-01-01

    A new technique for the large N loop equation of QCD is worked out. The Wilson loop W(C) is approximated by a Gaussian functional. The parameters are fitted to the loop equation, after which the equation is satisfied up to 0.2%. The resulting Wilson loop corresponds to linearly rising Regge trajectories. The problem of tachyon is still present, but it could be cured by iteration of the loop equation starting from this variational solution

  15. BPS Wilson loops and Bremsstrahlung function in ABJ(M): a two loop analysis

    Energy Technology Data Exchange (ETDEWEB)

    Bianchi, Marco S. [Institut für Physik, Humboldt-Universität zu Berlin,Newtonstraße 15, 12489 Berlin (Germany); Griguolo, Luca [Dipartimento di Fisica e Scienze della Terra, Università di Parmaand INFN Gruppo Collegato di Parma,Viale G.P. Usberti 7/A, 43100 Parma (Italy); Leoni, Matias [Physics Department, FCEyN-UBA & IFIBA-CONICETCiudad Universitaria, Pabellón I, 1428, Buenos Aires (Argentina); Penati, Silvia [Dipartimento di Fisica, Università di Milano-Bicoccaand INFN, Sezione di Milano-Bicocca,Piazza della Scienza 3, I-20126 Milano (Italy); Seminara, Domenico [Dipartimento di Fisica, Università di Firenzeand INFN Sezione di Firenze,via G. Sansone 1, 50019 Sesto Fiorentino (Italy)

    2014-06-19

    We study a family of circular BPS Wilson loops in N=6 super Chern-Simons-matter theories, generalizing the usual 1/2-BPS circle. The scalar and fermionic couplings depend on two deformation parameters and these operators can be considered as the ABJ(M) counterpart of the DGRT latitudes defined in N=4 SYM. We perform a complete two-loop analysis of their vacuum expectation value, discuss the appearance of framing-like phases and propose a general relation with cohomologically equivalent bosonic operators. We make an all-loop proposal for computing the Bremsstrahlung function associated to the 1/2-BPS cusp in terms of these generalized Wilson loops. When applied to our two-loop result it reproduces the known expression. Finally, we comment on the generalization of this proposal to the bosonic 1/6-BPS case.

  16. Shotgun protein sequencing.

    Energy Technology Data Exchange (ETDEWEB)

    Faulon, Jean-Loup Michel; Heffelfinger, Grant S.

    2009-06-01

    A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

  17. Flat Knitting Loop Deformation Simulation Based on Interlacing Point Model

    Directory of Open Access Journals (Sweden)

    Jiang Gaoming

    2017-12-01

    Full Text Available In order to create realistic loop primitives suitable for the faster CAD of the flat-knitted fabric, we have performed research on the model of the loop as well as the variation of the loop surface. This paper proposes an interlacing point-based model for the loop center curve, and uses the cubic Bezier curve to fit the central curve of the regular loop, elongated loop, transfer loop, and irregular deformed loop. In this way, a general model for the central curve of the deformed loop is obtained. The obtained model is then utilized to perform texture mapping, texture interpolation, and brightness processing, simulating a clearly structured and lifelike deformed loop. The computer program LOOP is developed by using the algorithm. The deformed loop is simulated with different yarns, and the deformed loop is applied to design of a cable stitch, demonstrating feasibility of the proposed algorithm. This paper provides a loop primitive simulation method characterized by lifelikeness, yarn material variability, and deformation flexibility, and facilitates the loop-based fast computer-aided design (CAD of the knitted fabric.

  18. An improved design of virtual output impedance loop for droop-controlled parallel three-phase Voltage Source Inverters

    DEFF Research Database (Denmark)

    Wang, Xiongfei; Blaabjerg, Frede; Chen, Zhe

    2012-01-01

    -sequence virtual resistance even in the case of feeding a balanced three-phase load. Furthermore, to adapt to the variety of unbalanced loads, a dynamically-tuned negative-sequence resistance loop is designed, such that a good compromise between the quality of inverter output voltage and the performance of load......The virtual output impedance loop is known as an effective way to enhance the load sharing stability and quality of droop-controlled parallel inverters. This paper proposes an improved design of virtual output impedance loop for parallel three-phase voltage source inverters. In the approach...... sharing can be obtained. Finally, laboratory test results of two parallel three-phase voltage source inverters are shown to confirm the validity of the proposed method....

  19. What is a stem cell?

    Science.gov (United States)

    Slack, Jonathan M W

    2018-05-15

    The historical roots of the stem cell concept are traced with respect to its usage in embryology and in hematology. The modern consensus definition of stem cells, comprising both pluripotent stem cells in culture and tissue-specific stem cells in vivo, is explained and explored. Methods for identifying stem cells are discussed with respect to cell surface markers, telomerase, label retention and transplantability, and properties of the stem cell niche are explored. The CreER method for identifying stem cells in vivo is explained, as is evidence in favor of a stochastic rather than an obligate asymmetric form of cell division. In conclusion, it is found that stem cells do not possess any unique and specific molecular markers; and stem cell behavior depends on the environment of the cell as well as the stem cell's intrinsic qualities. Furthermore, the stochastic mode of division implies that stem cell behavior is a property of a cell population not of an individual cell. In this sense, stem cells do not exist in isolation but only as a part of multicellular system. This article is categorized under: Adult Stem Cells, Tissue Renewal, and Regeneration > Tissue Stem Cells and Niches Adult Stem Cells, Tissue Renewal, and Regeneration > Methods and Principles Adult Stem Cells, Tissue Renewal, and Regeneration > Environmental Control of Stem Cells. © 2018 Wiley Periodicals, Inc.

  20. Transition probability spaces in loop quantum gravity

    Science.gov (United States)

    Guo, Xiao-Kan

    2018-03-01

    We study the (generalized) transition probability spaces, in the sense of Mielnik and Cantoni, for spacetime quantum states in loop quantum gravity. First, we show that loop quantum gravity admits the structures of transition probability spaces. This is exemplified by first checking such structures in covariant quantum mechanics and then identifying the transition probability spaces in spin foam models via a simplified version of general boundary formulation. The transition probability space thus defined gives a simple way to reconstruct the discrete analog of the Hilbert space of the canonical theory and the relevant quantum logical structures. Second, we show that the transition probability space and in particular the spin foam model are 2-categories. Then we discuss how to realize in spin foam models two proposals by Crane about the mathematical structures of quantum gravity, namely, the quantum topos and causal sites. We conclude that transition probability spaces provide us with an alternative framework to understand various foundational questions of loop quantum gravity.

  1. Solar flare loops observations and interpretations

    CERN Document Server

    Huang, Guangli; Ji, Haisheng; Ning, Zongjun

    2018-01-01

    This book provides results of analysis of typical solar events, statistical analysis, the diagnostics of energetic electrons and magnetic field, as well as the global behavior of solar flaring loops such as their contraction and expansion. It pays particular attention to analyzing solar flare loops with microwave, hard X-ray, optical and EUV emissions, as well as the theories of their radiation, and electron acceleration/transport. The results concerning influence of the pitch-angle anisotropy of non-thermal electrons on their microwave and hard X-ray emissions, new spectral behaviors in X-ray and microwave bands, and results related to the contraction of flaring loops, are widely discussed in the literature of solar physics. The book is useful for graduate students and researchers in solar and space physics.

  2. Automatic Loop Parallelization via Compiler Guided Refactoring

    DEFF Research Database (Denmark)

    Larsen, Per; Ladelsky, Razya; Lidman, Jacob

    For many parallel applications, performance relies not on instruction-level parallelism, but on loop-level parallelism. Unfortunately, many modern applications are written in ways that obstruct automatic loop parallelization. Since we cannot identify sufficient parallelization opportunities...... for these codes in a static, off-line compiler, we developed an interactive compilation feedback system that guides the programmer in iteratively modifying application source, thereby improving the compiler’s ability to generate loop-parallel code. We use this compilation system to modify two sequential...... benchmarks, finding that the code parallelized in this way runs up to 8.3 times faster on an octo-core Intel Xeon 5570 system and up to 12.5 times faster on a quad-core IBM POWER6 system. Benchmark performance varies significantly between the systems. This suggests that semi-automatic parallelization should...

  3. Microwave emission from flaring magnetic loops

    International Nuclear Information System (INIS)

    Vlahos, L.

    1980-01-01

    The microwave emission from a flaring loop is considered. In particular the author examines the question: What will be the characteristics of the radio emission at centimeter wavelengths from a small compact flaring loop when the mechanism which pumps magnetic energy into the plasma in the form of heating and/or electron acceleration satisfies the conditions: (a) the magnetic energy is released in a small volume compared to the volume of the loop, and the rate at which magnetic energy is transformed into plasma energy is faster than the energy losses from the same volume. This causes a local enhancement of the temperature by as much as one or two orders of magnitude above the coronal temperature; (b) The bulk of the energy released goes into heating the plasma and heats primarily the electrons. (Auth.)

  4. Experimental loop for SH2 (LECS)

    International Nuclear Information System (INIS)

    Strehar, N.R.; Bruzzoni, Pablo; Moras, J.J.; Cogozzo, E.O.

    1981-01-01

    An experimental loop is described for circulation of SH 2 that operates at 2 x 10 6 Pascal and 33 deg C. It was designed and constructed with the purpose of experimentally studying the hydraulic instability phenomenon that can be detected in cold isotopic exchange columns in the Girdler-Sulfide (GS) process of heavy water production. The main features of the different components of the loop are described, as well as the materials, the measurement and control instruments and the auxiliary equipment used, and finally the measuring methods to qualify and quantify the formation of froth. Furthermore, the loop's transportable metallic container is described, which allows to transport and connect it to CNEA's experimental heavy water plant or to any other heavy water plants using the GS method. Some tests made with inert gases that intended to verify the equipment's performance and to select the most adequate sieve trays for its operation are discussed. (M.E.L.) [es

  5. Automated one-loop calculations with GOSAM

    International Nuclear Information System (INIS)

    Cullen, Gavin; Greiner, Nicolas; Heinrich, Gudrun; Reiter, Thomas; Luisoni, Gionata

    2011-11-01

    We present the program package GoSam which is designed for the automated calculation of one-loop amplitudes for multi-particle processes in renormalisable quantum field theories. The amplitudes, which are generated in terms of Feynman diagrams, can be reduced using either D-dimensional integrand-level decomposition or tensor reduction. GoSam can be used to calculate one-loop QCD and/or electroweak corrections to Standard Model processes and offers the flexibility to link model files for theories Beyond the Standard Model. A standard interface to programs calculating real radiation is also implemented. We demonstrate the flexibility of the program by presenting examples of processes with up to six external legs attached to the loop. (orig.)

  6. Automated one-loop calculations with GOSAM

    Energy Technology Data Exchange (ETDEWEB)

    Cullen, Gavin [Edinburgh Univ. (United Kingdom). School of Physics and Astronomy; Deutsches Elektronen-Synchrotron, Zeuthen [DESY; Germany; Greiner, Nicolas [Illinois Univ., Urbana-Champaign, IL (United States). Dept. of Physics; Max-Planck-Institut fuer Physik, Muenchen (Germany); Heinrich, Gudrun; Reiter, Thomas [Max-Planck-Institut fuer Physik, Muenchen (Germany); Luisoni, Gionata [Durham Univ. (United Kingdom). Inst. for Particle Physics Phenomenology; Mastrolia, Pierpaolo [Max-Planck-Institut fuer Physik, Muenchen (Germany); Padua Univ. (Italy). Dipt. di Fisica; Ossola, Giovanni [New York City Univ., NY (United States). New York City College of Technology; New York City Univ., NY (United States). The Graduate School and University Center; Tramontano, Francesco [European Organization for Nuclear Research (CERN), Geneva (Switzerland)

    2011-11-15

    We present the program package GoSam which is designed for the automated calculation of one-loop amplitudes for multi-particle processes in renormalisable quantum field theories. The amplitudes, which are generated in terms of Feynman diagrams, can be reduced using either D-dimensional integrand-level decomposition or tensor reduction. GoSam can be used to calculate one-loop QCD and/or electroweak corrections to Standard Model processes and offers the flexibility to link model files for theories Beyond the Standard Model. A standard interface to programs calculating real radiation is also implemented. We demonstrate the flexibility of the program by presenting examples of processes with up to six external legs attached to the loop. (orig.)

  7. Covariant diagrams for one-loop matching

    International Nuclear Information System (INIS)

    Zhang, Zhengkang

    2016-10-01

    We present a diagrammatic formulation of recently-revived covariant functional approaches to one-loop matching from an ultraviolet (UV) theory to a low-energy effective field theory. Various terms following from a covariant derivative expansion (CDE) are represented by diagrams which, unlike conventional Feynman diagrams, involve gaugecovariant quantities and are thus dubbed ''covariant diagrams.'' The use of covariant diagrams helps organize and simplify one-loop matching calculations, which we illustrate with examples. Of particular interest is the derivation of UV model-independent universal results, which reduce matching calculations of specific UV models to applications of master formulas. We show how such derivation can be done in a more concise manner than the previous literature, and discuss how additional structures that are not directly captured by existing universal results, including mixed heavy-light loops, open covariant derivatives, and mixed statistics, can be easily accounted for.

  8. Covariant diagrams for one-loop matching

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Zhengkang [Michigan Center for Theoretical Physics (MCTP), University of Michigan,450 Church Street, Ann Arbor, MI 48109 (United States); Deutsches Elektronen-Synchrotron (DESY),Notkestraße 85, 22607 Hamburg (Germany)

    2017-05-30

    We present a diagrammatic formulation of recently-revived covariant functional approaches to one-loop matching from an ultraviolet (UV) theory to a low-energy effective field theory. Various terms following from a covariant derivative expansion (CDE) are represented by diagrams which, unlike conventional Feynman diagrams, involve gauge-covariant quantities and are thus dubbed “covariant diagrams.” The use of covariant diagrams helps organize and simplify one-loop matching calculations, which we illustrate with examples. Of particular interest is the derivation of UV model-independent universal results, which reduce matching calculations of specific UV models to applications of master formulas. We show how such derivation can be done in a more concise manner than the previous literature, and discuss how additional structures that are not directly captured by existing universal results, including mixed heavy-light loops, open covariant derivatives, and mixed statistics, can be easily accounted for.

  9. Defect networks and supersymmetric loop operators

    Energy Technology Data Exchange (ETDEWEB)

    Bullimore, Mathew [Perimeter Institute for Theoretical Physics, 31 Caroline Street North, Waterloo, ON N2L 2Y5 (Canada)

    2015-02-10

    We consider topological defect networks with junctions in A{sub N−1} Toda CFT and the connection to supersymmetric loop operators in N=2 theories of class S on a four-sphere. Correlation functions in the presence of topological defect networks are computed by exploiting the monodromy of conformal blocks, generalising the notion of a Verlinde operator. Concentrating on a class of topological defects in A{sub 2} Toda theory, we find that the Verlinde operators generate an algebra whose structure is determined by a set of generalised skein relations that encode the representation theory of a quantum group. In the second half of the paper, we explore the dictionary between topological defect networks and supersymmetric loop operators in the N=2{sup ∗} theory by comparing to exact localisation computations. In this context, the the generalised skein relations are related to the operator product expansion of loop operators.

  10. Covariant diagrams for one-loop matching

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Zhengkang [Michigan Univ., Ann Arbor, MI (United States). Michigan Center for Theoretical Physics; Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)

    2016-10-15

    We present a diagrammatic formulation of recently-revived covariant functional approaches to one-loop matching from an ultraviolet (UV) theory to a low-energy effective field theory. Various terms following from a covariant derivative expansion (CDE) are represented by diagrams which, unlike conventional Feynman diagrams, involve gaugecovariant quantities and are thus dubbed ''covariant diagrams.'' The use of covariant diagrams helps organize and simplify one-loop matching calculations, which we illustrate with examples. Of particular interest is the derivation of UV model-independent universal results, which reduce matching calculations of specific UV models to applications of master formulas. We show how such derivation can be done in a more concise manner than the previous literature, and discuss how additional structures that are not directly captured by existing universal results, including mixed heavy-light loops, open covariant derivatives, and mixed statistics, can be easily accounted for.

  11. Covariant diagrams for one-loop matching

    International Nuclear Information System (INIS)

    Zhang, Zhengkang

    2017-01-01

    We present a diagrammatic formulation of recently-revived covariant functional approaches to one-loop matching from an ultraviolet (UV) theory to a low-energy effective field theory. Various terms following from a covariant derivative expansion (CDE) are represented by diagrams which, unlike conventional Feynman diagrams, involve gauge-covariant quantities and are thus dubbed “covariant diagrams.” The use of covariant diagrams helps organize and simplify one-loop matching calculations, which we illustrate with examples. Of particular interest is the derivation of UV model-independent universal results, which reduce matching calculations of specific UV models to applications of master formulas. We show how such derivation can be done in a more concise manner than the previous literature, and discuss how additional structures that are not directly captured by existing universal results, including mixed heavy-light loops, open covariant derivatives, and mixed statistics, can be easily accounted for.

  12. Proteins mediating DNA loops effectively block transcription.

    Science.gov (United States)

    Vörös, Zsuzsanna; Yan, Yan; Kovari, Daniel T; Finzi, Laura; Dunlap, David

    2017-07-01

    Loops are ubiquitous topological elements formed when proteins simultaneously bind to two noncontiguous DNA sites. While a loop-mediating protein may regulate initiation at a promoter, the presence of the protein at the other site may be an obstacle for RNA polymerases (RNAP) transcribing a different gene. To test whether a DNA loop alters the extent to which a protein blocks transcription, the lac repressor (LacI) was used. The outcome of in vitro transcription along templates containing two LacI operators separated by 400 bp in the presence of LacI concentrations that produced both looped and unlooped molecules was visualized with scanning force microscopy (SFM). An analysis of transcription elongation complexes, moving for 60 s at an average of 10 nt/s on unlooped DNA templates, revealed that they more often surpassed LacI bound to the lower affinity O2 operator than to the highest affinity Os operator. However, this difference was abrogated in looped DNA molecules where LacI became a strong roadblock independently of the affinity of the operator. Recordings of transcription elongation complexes, using magnetic tweezers, confirmed that they halted for several minutes upon encountering a LacI bound to a single operator. The average pause lifetime is compatible with RNAP waiting for LacI dissociation, however, the LacI open conformation visualized in the SFM images also suggests that LacI could straddle RNAP to let it pass. Independently of the mechanism by which RNAP bypasses the LacI roadblock, the data indicate that an obstacle with looped topology more effectively interferes with transcription. © 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

  13. Coronal Loops: Evolving Beyond the Isothermal Approximation

    Science.gov (United States)

    Schmelz, J. T.; Cirtain, J. W.; Allen, J. D.

    2002-05-01

    Are coronal loops isothermal? A controversy over this question has arisen recently because different investigators using different techniques have obtained very different answers. Analysis of SOHO-EIT and TRACE data using narrowband filter ratios to obtain temperature maps has produced several key publications that suggest that coronal loops may be isothermal. We have constructed a multi-thermal distribution for several pixels along a relatively isolated coronal loop on the southwest limb of the solar disk using spectral line data from SOHO-CDS taken on 1998 Apr 20. These distributions are clearly inconsistent with isothermal plasma along either the line of sight or the length of the loop, and suggested rather that the temperature increases from the footpoints to the loop top. We speculated originally that these differences could be attributed to pixel size -- CDS pixels are larger, and more `contaminating' material would be expected along the line of sight. To test this idea, we used CDS iron line ratios from our data set to mimic the isothermal results from the narrowband filter instruments. These ratios indicated that the temperature gradient along the loop was flat, despite the fact that a more complete analysis of the same data showed this result to be false! The CDS pixel size was not the cause of the discrepancy; rather, the problem lies with the isothermal approximation used in EIT and TRACE analysis. These results should serve as a strong warning to anyone using this simplistic method to obtain temperature. This warning is echoed on the EIT web page: ``Danger! Enter at your own risk!'' In other words, values for temperature may be found, but they may have nothing to do with physical reality. Solar physics research at the University of Memphis is supported by NASA grant NAG5-9783. This research was funded in part by the NASA/TRACE MODA grant for Montana State University.

  14. Amino Acids in the TM4-TM5 loop of Na,K-ATPase Are Important for Biosynthesis

    DEFF Research Database (Denmark)

    Jørgensen, Jesper Roland; Houghton-Larsen, Jens; Jacobsen, Mette Dorph

    2003-01-01

    -sensitive folding mutants, as they induce the unfolded protein response at 30°C but not at 15°C. We used an algorithm to predict that residues 868ENGFLIPIHLL878 in the L78 loop exposed to the endoplasmic reticulum lumen constitute the most likely BiP binding site. Correct folding of this sequence may be important...

  15. High-Order Frequency-Locked Loops

    DEFF Research Database (Denmark)

    Golestan, Saeed; Guerrero, Josep M.; Quintero, Juan Carlos Vasquez

    2017-01-01

    In very recent years, some attempts for designing high-order frequency-locked loops (FLLs) have been made. Nevertheless, the advantages and disadvantages of these structures, particularly in comparison with a standard FLL and high-order phase-locked loops (PLLs), are rather unclear. This lack...... study, and its small-signal modeling, stability analysis, and parameter tuning are presented. Finally, to gain insight about advantages and disadvantages of high-order FLLs, a theoretical and experimental performance comparison between the designed second-order FLL and a standard FLL (first-order FLL...

  16. Accident analysis of HANARO fuel test loop

    Energy Technology Data Exchange (ETDEWEB)

    Kim, J. Y.; Chi, D. Y

    1998-03-01

    Steady state fuel test loop will be equipped in HANARO to obtain the development and betterment of advanced fuel and materials through the irradiation tests. The HANARO fuel test loop was designed to match the CANDU and PWR fuel operating conditions. The accident analysis was performed by RELAP5/MOD3 code based on FTL system designs and determined the detail engineering specification of in-pile test section and out-pile systems. The accident analysis results of FTL system could be used for the fuel and materials designer to plan the irradiation testing programs. (author). 23 refs., 20 tabs., 178 figs.

  17. A keyboard control method for loop measurement

    International Nuclear Information System (INIS)

    Gao, Z.W.

    1994-01-01

    This paper describes a keyboard control mode based on the DEC VAX computer. The VAX Keyboard code can be found under running of a program was developed. During the loop measurement or multitask operation, it ables to be distinguished from a keyboard code to stop current operation or transfer to another operation while previous information can be held. The combining of this mode, the author successfully used one key control loop measurement for test Dual Input Memory module which is used in a rearrange Energy Trigger system for LEP 8 Bunch operation

  18. Anomaly freedom in perturbative loop quantum gravity

    International Nuclear Information System (INIS)

    Bojowald, Martin; Hossain, Golam Mortuza; Kagan, Mikhail; Shankaranarayanan, S.

    2008-01-01

    A fully consistent linear perturbation theory for cosmology is derived in the presence of quantum corrections as they are suggested by properties of inverse volume operators in loop quantum gravity. The underlying constraints present a consistent deformation of the classical system, which shows that the discreteness in loop quantum gravity can be implemented in effective equations without spoiling space-time covariance. Nevertheless, nontrivial quantum corrections do arise in the constraint algebra. Since correction terms must appear in tightly controlled forms to avoid anomalies, detailed insights for the correct implementation of constraint operators can be gained. The procedures of this article thus provide a clear link between fundamental quantum gravity and phenomenology.

  19. Logical inference techniques for loop parallelization

    DEFF Research Database (Denmark)

    Oancea, Cosmin Eugen; Rauchwerger, Lawrence

    2012-01-01

    the parallelization transformation by verifying the independence of the loop's memory references. To this end it represents array references using the USR (uniform set representation) language and expresses the independence condition as an equation, S={}, where S is a set expression representing array indexes. Using...... of their estimated complexities. We evaluate our automated solution on 26 benchmarks from PERFECT-CLUB and SPEC suites and show that our approach is effective in parallelizing large, complex loops and obtains much better full program speedups than the Intel and IBM Fortran compilers....

  20. Description of the sodium loop ML-3

    International Nuclear Information System (INIS)

    Torre, de la M.; Melches, I; Lapena, J.; Martinez, T.A.; Miguel, de D.; Duran, F.

    1979-01-01

    The sodium loop ML-3 is described. The main objective of this facility is to obtain mechanical property data for LMFBR materials in creep and low cycle fatigue testing in flowing sodium. ML-3 includes 10 test stations for creep and two for fatigue. It is possible to operate simultaneously at three different temperature levels. The maximum operating temperature is 650 deg C at flow velocities up to 5 m/s. The ML-3 loop has been located in a manner that permits the fill/dump tank cover gas and security systems to be shared with an earlier circuit, the ML-1. (author)

  1. Tuning OpenACC loop execution

    KAUST Repository

    Feki, Saber

    2017-01-07

    The purpose of this chapter is to help OpenACC developer who is already familiar with the basic and essential directives to further improve his code performance by adding more descriptive clauses to OpenACC loop constructs. At the end of this chapter the reader will: • Have a better understanding of the purpose of the OpenACC loop construct and its associated clauses illustrated with use cases • Use the acquired knowledge in practice to further improve the performance of OpenACC accelerated codes

  2. Topspin networks in loop quantum gravity

    International Nuclear Information System (INIS)

    Duston, Christopher L

    2012-01-01

    We discuss the extension of loop quantum gravity to topspin networks, a proposal which allows topological information to be encoded in spin networks. We will show that this requires minimal changes to the phase space, C*-algebra and Hilbert space of cylindrical functions. We will also discuss the area and Hamiltonian operators, and show how they depend on the topology. This extends the idea of ‘background independence’ in loop quantum gravity to include topology as well as geometry. It is hoped this work will confirm the usefulness of the topspin network formalism and open up several new avenues for research into quantum gravity. (paper)

  3. Loop quantum gravity in asymptotically flat spaces

    International Nuclear Information System (INIS)

    Arnsdorf, M.

    2000-01-01

    This thesis describes applications and extensions of the loop variable approach to non-perturbative quantum gravity. The common theme of the work presented, is the need to generalise loop quantum gravity to be applicable in cases where space is asymptotically flat, and no longer compact as is usually assumed. This is important for the study of isolated gravitational systems. It also presents a natural context in which to search for the semi-classical limit, one of the main outstanding problems in loop quantum gravity. In the first part of the thesis we study how isolated gravitational systems can be attributed particle-like properties. In particular, we show how spinorial states can arise in pure loop quantum gravity if spatial topology is non-trivial, thus confirming an old conjecture of Friedman and Sorkin. Heuristically, this corresponds to the idea that we can rotate isolated regions of spatial topology relative to the environment at infinity, and that only a 4π-rotation will take us back to the original configuration. To do this we extend the standard loop quantum gravity formalism by introducing a compactification of our non-compact spatial manifold, and study the knotting of embedded graphs. The second part of the thesis takes a more systematic approach to the study of loop quantum gravity on non-compact spaces. We look for new representations of the loop algebra, which give rise to quantum theories that are inequivalent to the standard one. These theories naturally describe excitations of a fiducial background state, which is specified via the choice of its vacuum expectation values. In particular, we can choose background states that describe the geometries of non-compact manifolds. We also discuss how suitable background states can be constructed that can approximate classical phase space data, in our case holonomies along embedded paths and geometrical quantities related to areas and volumes. These states extend the notion of the weave and provide a

  4. Automation of one-loop QCD corrections

    CERN Document Server

    Hirschi, Valentin; Frixione, Stefano; Garzelli, Maria Vittoria; Maltoni, Fabio; Pittau, Roberto

    2011-01-01

    We present the complete automation of the computation of one-loop QCD corrections, including UV renormalization, to an arbitrary scattering process in the Standard Model. This is achieved by embedding the OPP integrand reduction technique, as implemented in CutTools, into the MadGraph framework. By interfacing the tool so constructed, which we dub MadLoop, with MadFKS, the fully automatic computation of any infrared-safe observable at the next-to-leading order in QCD is attained. We demonstrate the flexibility and the reach of our method by calculating the production rates for a variety of processes at the 7 TeV LHC.

  5. Multimodal sequence learning.

    Science.gov (United States)

    Kemény, Ferenc; Meier, Beat

    2016-02-01

    While sequence learning research models complex phenomena, previous studies have mostly focused on unimodal sequences. The goal of the current experiment is to put implicit sequence learning into a multimodal context: to test whether it can operate across different modalities. We used the Task Sequence Learning paradigm to test whether sequence learning varies across modalities, and whether participants are able to learn multimodal sequences. Our results show that implicit sequence learning is very similar regardless of the source modality. However, the presence of correlated task and response sequences was required for learning to take place. The experiment provides new evidence for implicit sequence learning of abstract conceptual representations. In general, the results suggest that correlated sequences are necessary for implicit sequence learning to occur. Moreover, they show that elements from different modalities can be automatically integrated into one unitary multimodal sequence. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. Sequence Read Archive (SRA)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome...

  7. Prunus necrotic ringspot ilarvirus: nucleotide sequence of RNA3 and the relationship to other ilarviruses based on coat protein comparison.

    Science.gov (United States)

    Guo, D; Maiss, E; Adam, G; Casper, R

    1995-05-01

    The RNA3 of prunus necrotic ringspot ilarvirus (PNRSV) has been cloned and its entire sequence determined. The RNA3 consists of 1943 nucleotides (nt) and possesses two large open reading frames (ORFs) separated by an intergenic region of 74 nt. The 5' proximal ORF is 855 nt in length and codes for a protein of molecular mass 31.4 kDa which has homologies with the putative movement protein of other members of the Bromoviridae. The 3' proximal ORF of 675 nt is the cistron for the coat protein (CP) and has a predicted molecular mass of 24.9 kDa. The sequence of the 3' non-coding region (NCR) of PNRSV RNA3 showed a high degree of similarity with those of tobacco streak virus (TSV), prune dwarf virus (PDV), apple mosaic virus (ApMV) and also alfalfa mosaic virus (AIMV). In addition it contained potential stem-loop structures with interspersed AUGC motifs characteristic for ilar- and alfamoviruses. This conserved primary and secondary structure in all 3' NCRs may be responsible for the interaction with homologous and heterologous CPs and subsequent activation of genome replication. The CP gene of an ApMV isolate (ApMV-G) of 657 nt has also been cloned and sequenced. Although ApMV and PNRSV have a distant serological relationship, the deduced amino acid sequences of their CPs have an identity of only 51.8%. The N termini of PNRSV and ApMV CPs have in common a zinc-finger motif and the potential to form an amphipathic helix.

  8. C-terminal low-complexity sequence repeats of Mycobacterium smegmatis Ku modulate DNA binding.

    Science.gov (United States)

    Kushwaha, Ambuj K; Grove, Anne

    2013-01-24

    Ku protein is an integral component of the NHEJ (non-homologous end-joining) pathway of DSB (double-strand break) repair. Both eukaryotic and prokaryotic Ku homologues have been characterized and shown to bind DNA ends. A unique feature of Mycobacterium smegmatis Ku is its basic C-terminal tail that contains several lysine-rich low-complexity PAKKA repeats that are absent from homologues encoded by obligate parasitic mycobacteria. Such PAKKA repeats are also characteristic of mycobacterial Hlp (histone-like protein) for which they have been shown to confer the ability to appose DNA ends. Unexpectedly, removal of the lysine-rich extension enhances DNA-binding affinity, but an interaction between DNA and the PAKKA repeats is indicated by the observation that only full-length Ku forms multiple complexes with a short stem-loop-containing DNA previously designed to accommodate only one Ku dimer. The C-terminal extension promotes DNA end-joining by T4 DNA ligase, suggesting that the PAKKA repeats also contribute to efficient end-joining. We suggest that low-complexity lysine-rich sequences have evolved repeatedly to modulate the function of unrelated DNA-binding proteins.

  9. A Single Electrochemical Probe Used for Analysis of Multiple Nucleic Acid Sequences

    Science.gov (United States)

    Mills, Dawn M.; Calvo-Marzal, Percy; Pinzon, Jeffer M.; Armas, Stephanie; Kolpashchikov, Dmitry M.; Chumbimuni-Torres, Karin Y.

    2017-01-01

    Electrochemical hybridization sensors have been explored extensively for analysis of specific nucleic acids. However, commercialization of the platform is hindered by the need for attachment of separate oligonucleotide probes complementary to a RNA or DNA target to an electrode’s surface. Here we demonstrate that a single probe can be used to analyze several nucleic acid targets with high selectivity and low cost. The universal electrochemical four-way junction (4J)-forming (UE4J) sensor consists of a universal DNA stem-loop (USL) probe attached to the electrode’s surface and two adaptor strands (m and f) which hybridize to the USL probe and the analyte to form a 4J associate. The m adaptor strand was conjugated with a methylene blue redox marker for signal ON sensing and monitored using square wave voltammetry. We demonstrated that a single sensor can be used for detection of several different DNA/RNA sequences and can be regenerated in 30 seconds by a simple water rinse. The UE4J sensor enables a high selectivity by recognition of a single base substitution, even at room temperature. The UE4J sensor opens a venue for a re-useable universal platform that can be adopted at low cost for the analysis of DNA or RNA targets. PMID:29371782

  10. Identification of microRNAs and their targets in Finger millet by high throughput sequencing.

    Science.gov (United States)

    Usha, S; Jyothi, M N; Sharadamma, N; Dixit, Rekha; Devaraj, V R; Nagesh Babu, R

    2015-12-15

    MicroRNAs are short non-coding RNAs which play an important role in regulating gene expression by mRNA cleavage or by translational repression. The majority of identified miRNAs were evolutionarily conserved; however, others expressed in a species-specific manner. Finger millet is an important cereal crop; nonetheless, no practical information is available on microRNAs to date. In this study, we have identified 95 conserved microRNAs belonging to 39 families and 3 novel microRNAs by high throughput sequencing. For the identified conserved and novel miRNAs a total of 507 targets were predicted. 11 miRNAs were validated and tissue specificity was determined by stem loop RT-qPCR, Northern blot. GO analyses revealed targets of miRNA were involved in wide range of regulatory functions. This study implies large number of known and novel miRNAs found in Finger millet which may play important role in growth and development. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. Rapid and Sensitive Isothermal Detection of Nucleic-acid Sequence by Multiple Cross Displacement Amplification.

    Science.gov (United States)

    Wang, Yi; Wang, Yan; Ma, Ai-Jing; Li, Dong-Xun; Luo, Li-Juan; Liu, Dong-Xin; Jin, Dong; Liu, Kai; Ye, Chang-Yun

    2015-07-08

    We have devised a novel amplification strategy based on isothermal strand-displacement polymerization reaction, which was termed multiple cross displacement amplification (MCDA). The approach employed a set of ten specially designed primers spanning ten distinct regions of target sequence and was preceded at a constant temperature (61-65 °C). At the assay temperature, the double-stranded DNAs were at dynamic reaction environment of primer-template hybrid, thus the high concentration of primers annealed to the template strands without a denaturing step to initiate the synthesis. For the subsequent isothermal amplification step, a series of primer binding and extension events yielded several single-stranded DNAs and single-stranded single stem-loop DNA structures. Then, these DNA products enabled the strand-displacement reaction to enter into the exponential amplification. Three mainstream methods, including colorimetric indicators, agarose gel electrophoresis and real-time turbidity, were selected for monitoring the MCDA reaction. Moreover, the practical application of the MCDA assay was successfully evaluated by detecting the target pathogen nucleic acid in pork samples, which offered advantages on quick results, modest equipment requirements, easiness in operation, and high specificity and sensitivity. Here we expounded the basic MCDA mechanism and also provided details on an alternative (Single-MCDA assay, S-MCDA) to MCDA technique.

  12. Multi-loop PWR modeling and hardware-in-the-loop testing using ACSL

    International Nuclear Information System (INIS)

    Thomas, V.M.; Heibel, M.D.; Catullo, W.J.

    1989-01-01

    Westinghouse has developed an Advanced Digital Feedwater Control System (ADFCS) which is aimed at reducing feedwater related reactor trips through improved control performance for pressurized water reactor (PWR) power plants. To support control system setpoint studies and functional design efforts for the ADFCS, an ACSL based model of the nuclear steam supply system (NSSS) of a Westinghouse (PWR) was generated. Use of this plant model has been extended from system design to system testing through integration of the model into a Hardware-in-Loop test environment for the ADFCS. This integration includes appropriate interfacing between a Gould SEL 32/87 computer, upon which the plant model executes in real time, and the Westinghouse Distributed Processing family (WDPF) test hardware. A development program has been undertaken to expand the existing ACSL model to include capability to explicitly model multiple plant loops, steam generators, and corresponding feedwater systems. Furthermore, the program expands the ADFCS Hardware-in-Loop testing to include the multi-loop plant model. This paper provides an overview of the testing approach utilized for the ADFCS with focus on the role of Hardware-in-Loop testing. Background on the plant model, methodology and test environment is also provided. Finally, an overview is presented of the program to expand the model and associated Hardware-in-Loop test environment to handle multiple loops

  13. Fundamental and Harmonic Oscillations in Neighboring Coronal Loops

    Science.gov (United States)

    Li, Hongbo; Liu, Yu; Vai Tam, Kuan

    2017-06-01

    We present observations of multimode (fundamental and harmonic) oscillations in a loop system, which appear to be simultaneously excited by a GOES C-class flare. Analysis of the periodic oscillations reveals that (1) the primary loop with a period of P a ≈ 4 minutes and a secondary loop with two periods of P a ≈ 4 minutes and P b ≈ 2 minutes are detected simultaneously in closely spaced loop strands; (2) both oscillation components have their peak amplitudes near the loop apex, while in the second loop the low-frequency component P a dominates in a loop segment that is two times larger than the high-frequency component P b ; (3) the harmonic mode P b shows the largest deviation from a sinusoidal loop shape at the loop apex. We conclude that multiple harmonic modes with different displacement profiles can be excited simultaneously even in closely spaced strands, similar to the overtones of a violin string.

  14. The Adenovirus Type 3 Dodecahedron's RGD Loop Comprises an HSPG Binding Site That Influences Integrin Binding

    Directory of Open Access Journals (Sweden)

    E. Gout

    2010-01-01

    Full Text Available Human type 3 adenovirus dodecahedron (a virus like particle made of twelve penton bases features the ability to enter cells through Heparan Sulphate Proteoglycans (HSPGs and integrins interaction and is used as a versatile vector to deliver DNA or proteins. Cryo-EM reconstruction of the pseudoviral particle with Heparan Sulphate (HS oligosaccharide shows an extradensity on the RGD loop. A set of mutants was designed to study the respective roles of the RGD sequence (RGE mutant and of a basic sequence located just downstream. Results showed that the RGE mutant binding to the HS deficient CHO-2241 cells was abolished and unexpectedly, mutation of the basic sequence (KQKR to AQAS dramatically decreased integrin recognition by the viral pseudoparticle. This basic sequence is thus involved in integrin docking, showing a close interplay between HSPGs and integrin receptors.

  15. PHOTOSPHERIC PROPERTIES OF WARM EUV LOOPS AND HOT X-RAY LOOPS

    Energy Technology Data Exchange (ETDEWEB)

    Kano, R. [National Astronomical Observatory of Japan, 2-21-1 Osawa, Mitaka, Tokyo 181-8588 (Japan); Ueda, K. [Department of Astronomy, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Tsuneta, S., E-mail: ryouhei.kano@nao.ac.jp [Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency, 3-1-1 Yoshinodai, Chuo, Sagamihara, Kanagawa 252-5210 (Japan)

    2014-02-20

    We investigate the photospheric properties (vector magnetic fields and horizontal velocity) of a well-developed active region, NOAA AR 10978, using the Hinode Solar Optical Telescope specifically to determine what gives rise to the temperature difference between ''warm loops'' (1-2 MK), which are coronal loops observed in EUV wavelengths, and ''hot loops'' (>3 MK), coronal loops observed in X-rays. We found that outside sunspots, the magnetic filling factor in the solar network varies with location and is anti-correlated with the horizontal random velocity. If we accept that the observed magnetic features consist of unresolved magnetic flux tubes, this anti-correlation can be explained by the ensemble average of flux-tube motion driven by small-scale random flows. The observed data are consistent with a flux tube width of ∼77 km and horizontal flow at ∼2.6 km s{sup –1} with a spatial scale of ∼120 km. We also found that outside sunspots, there is no significant difference between warm and hot loops either in the magnetic properties (except for the inclination) or in the horizontal random velocity at their footpoints, which are identified with the Hinode X-Ray Telescope and the Transition Region and Coronal Explorer. The energy flux injected into the coronal loops by the observed photospheric motion of the magnetic fields is estimated to be 2 × 10{sup 6} erg s{sup –1} cm{sup –2}, which is the same for both warm and hot loops. This suggests that coronal properties (e.g., loop length) play a more important role in giving rise to temperature differences of active-region coronal loops than photospheric parameters.

  16. A Comparative Transcriptomic Analysis Reveals Conserved Features of Stem Cell Pluripotency in Planarians and Mammals

    Science.gov (United States)

    Labbé, Roselyne M.; Irimia, Manuel; Currie, Ko W.; Lin, Alexander; Zhu, Shu Jun; Brown, David D.R.; Ross, Eric J.; Voisin, Veronique; Bader, Gary D.; Blencowe, Benjamin J.; Pearson, Bret J.

    2014-01-01

    Many long-lived species of animals require the function of adult stem cells throughout their lives. However, the transcriptomes of stem cells in invertebrates and vertebrates have not been compared, and consequently, ancestral regulatory circuits that control stem cell populations remain poorly defined. In this study, we have used data from high-throughput RNA sequencing to compare the transcriptomes of pluripotent adult stem cells from planarians with the transcriptomes of human and mouse pluripotent embryonic stem cells. From a stringently defined set of 4,432 orthologs shared between planarians, mice and humans, we identified 123 conserved genes that are ≥5-fold differentially expressed in stem cells from all three species. Guided by this gene set, we used RNAi screening in adult planarians to discover novel stem cell regulators, which we found to affect the stem cell-associated functions of tissue homeostasis, regeneration, and stem cell maintenance. Examples of genes that disrupted these processes included the orthologs of TBL3, PSD12, TTC27, and RACK1. From these analyses, we concluded that by comparing stem cell transcriptomes from diverse species, it is possible to uncover conserved factors that function in stem cell biology. These results provide insights into which genes comprised the ancestral circuitry underlying the control of stem cell self-renewal and pluripotency. PMID:22696458

  17. Innovation and STEM Schools

    Science.gov (United States)

    Roberts, Julia Link

    2015-01-01

    How do schools with a focus on science, technology, engineering, and mathematics (STEM) fit in with state goals to increase innovation and to boost the economy? This article briefly discusses how educators can encourage creativity and innovation.

  18. [STEM on Station Education

    Science.gov (United States)

    Lundebjerg, Kristen

    2016-01-01

    The STEM on Station team is part of Education which is part of the External Relations organization (ERO). ERO has traditional goals based around BHAG (Big Hairy Audacious Goal). The BHAG model is simplified to a saying: Everything we do stimulates actions by others to advance human space exploration. The STEM on Station education initiate is a project focused on bringing off the earth research and learning into classrooms. Educational resources such as lesson plans, activities to connect with the space station and STEM related contests are available and hosted by the STEM on Station team along with their partners such as Texas Instruments. These educational activities engage teachers and students in the current happenings aboard the international space station, inspiring the next generation of space explorers.

  19. STEM Education Programs

    Science.gov (United States)

    & Development (LDRD) National Security Education Center (NSEC) Office of Science Programs Richard P Databases National Security Education Center (NSEC) Center for Nonlinear Studies Engineering Institute Scholarships STEM Education Programs Teachers (K-12) Students (K-12) Higher Education Regional Education

  20. Parallelizing More Loops with Compiler Guided Refactoring

    DEFF Research Database (Denmark)

    Larsen, Per; Ladelsky, Razya; Lidman, Jacob

    2012-01-01

    an interactive compilation feedback system that guides programmers in iteratively modifying their application source code. This helps leverage the compiler’s ability to generate loop-parallel code. We employ our system to modify two sequential benchmarks dealing with image processing and edge detection...