Sample records for binary hammerhead ribozymes

  1. LNA nucleotides improve cleavage efficiency of singular and binary hammerhead ribozymes

    Christiansen, Janne K; Lobedanz, Sune; Arar, Khalil;


    concentrations, it was found that insertion of LNA monomers into the substrate binding arms allowed these to be shortened and results in a very active enzyme under both single and multiple turnover conditions. Incorporation of a mix of LNA and DNA residues further increased the multiple turnover cleavage...... activity. At high Mg(2+) concentrations or high substrate and ribozyme concentrations, the enhancing effect of LNA incorporation was even more prominent. Using LNA in the stem of Helix II diminished cleavage activity, but allowed deletion of the tetra-loop and thus separating the ribozyme into two...

  2. Kinetic characterization of two I/II format hammerhead ribozymes.

    Clouet-d'Orval, B.; Uhlenbeck, O C


    Five new hammerhead ribozymes were designed that assemble through the formation of helices I and II (I/II format) instead of the more standard assembly through helices I and III (I/III format). The substrate binding and cleavage properties of such hammerheads could potentially be different due to the absence of loop II and the requirement for the entire catalytic core to assemble. Two I/II format hammerheads, HHalpha1 and HHalpha5, which show structural homogeneity on native gels, were charac...

  3. Ionic interactions and the global conformations of the hammerhead ribozyme

    Bassi, G S; Møllegaard, N E; Murchie, A I;


    Here we investigate the global conformation of the hammerhead ribozyme. Electrophoretic studies demonstrate that the structure is folded in response to the concentration and type of ions present. Folding based on colinear alignment of arms II and III is suggested, with a variable angle subtended ...

  4. Automated design of hammerhead ribozymes and validation by targeting the PABPN1 gene transcript.

    Kharma, Nawwaf; Varin, Luc; Abu-Baker, Aida; Ouellet, Jonathan; Najeh, Sabrine; Ehdaeivand, Mohammad-Reza; Belmonte, Gabriel; Ambri, Anas; Rouleau, Guy; Perreault, Jonathan


    We present a new publicly accessible web-service, RiboSoft, which implements a comprehensive hammerhead ribozyme design procedure. It accepts as input a target sequence (and some design parameters) then generates a set of ranked hammerhead ribozymes, which target the input sequence. This paper describes the implemented procedure, which takes into consideration multiple objectives leading to a multi-objective ranking of the computer-generated ribozymes. Many ribozymes were assayed and validated, including four ribozymes targeting the transcript of a disease-causing gene (a mutant version of PABPN1). These four ribozymes were successfully tested in vitro and in vivo, for their ability to cleave the targeted transcript. The wet-lab positive results of the test are presented here demonstrating the real-world potential of both hammerhead ribozymes and RiboSoft. RiboSoft is freely available at the website PMID:26527730

  5. Experimental cancer gene therapy by multiple anti-survivin hammerhead ribozymes

    Qi Fei; Yuwen Ke; Xuebiao Yao; Jingde Zhu; Hongyu Zhang; Lili Fu; Xinlan Dai; Baomei Gao; Min Ni; Chao Ge; Jinjun Li; Xia Ding


    To improve the efficacy of gene therapy for cancer, we designed four hammerhead ribozyme adenoviruses (R1 to R4) targeting the exposed regions of survivin mRNA. In addition to the in vitro characterization, which included a determination of the sequence specificity of cleavage by primer extension, assays for cell proliferation and for in vivo tumor growth were used to score for ribozyme efficiency.The resulting suppression of survivin expression induced mitotic catastrophe and cell death via the caspase-3-dependent pathway. Importantly, administration of the ribozyme adenoviruses inhibited tumor growth in a hepato-cellular carcinoma xenograft mouse model. Co-expression of R1, R3 and R4 ribozymes synergistically suppressed survivin and, as this combination targets all major forms of the survivin transcripts, produced the most potent anti-cancer effects. The adenoviruses carrying the multiple hammerhead ribozymes described in this report offered a robust gene therapy strategy against cancer.

  6. Capturing hammerhead ribozyme structures in action by modulating general base catalysis.

    Young-In Chi


    Full Text Available We have obtained precatalytic (enzyme-substrate complex and postcatalytic (enzyme-product complex crystal structures of an active full-length hammerhead RNA that cleaves in the crystal. Using the natural satellite tobacco ringspot virus hammerhead RNA sequence, the self-cleavage reaction was modulated by substituting the general base of the ribozyme, G12, with A12, a purine variant with a much lower pKa that does not significantly perturb the ribozyme's atomic structure. The active, but slowly cleaving, ribozyme thus permitted isolation of enzyme-substrate and enzyme-product complexes without modifying the nucleophile or leaving group of the cleavage reaction, nor any other aspect of the substrate. The predissociation enzyme-product complex structure reveals RNA and metal ion interactions potentially relevant to transition-state stabilization that are absent in precatalytic structures.

  7. Expression and in vitro cleavage activity of anti-caspase-7 hammerhead ribozymes

    Wei Zhang; Qing Xie; Xia-Qiu Zhou; Shan Jiang; You-Xin Jin


    AIM: To prepare hammerhead ribozymes against mouse caspase-7 and identify their cleavage activityin vitro, in order to select a ribozyme with specific cleavage activity against mouse caspase-7 as a potential gene therapy for apoptosis-related diseases.METHODS: Anti-caspase-7 ribozymes targeting sites 333and 394 (named Rz333 and Rz394) were designed by computer software, and their DNA sequences encoding ribozymes were synthesized. Caspase-7 DNA sequence was acquired by RT-PCR. Ribozymes and caspase-7 DNA obtained byin vitro transcription were cloned into pBSKneo U6' and pGEM-T vectors, respectively. The cleavage activity of ribozymes against mouse caspase-7 was identified by cleavage experimentsin vitro.RESULTS: Rz333 and Rz394 were designed and their DNA sequences were synthesized respectively. The expression vector of caspase-7 and plasmids containing Rz333 and Rz394 were reconstructed successfully. Ribozymes and caspase-7 mRNA were expressed byin vitro transcription.In vitro cleavage experiment showed that 243-nt and 744-nt segments were produced after caspase-7 mRNA was mixed with Rz333 in equivalent, and the cleavage efficiency was 67.98%. No cleaved segment was observed when caspase-7 mRNA was mixed with Rz394.CONCLUSION: Rz333 can site-specific cleave mouse caspase-7 mRNA, and it shows a potential for gene therapy of apoptosis-related diseases by down-regulating gene expression of caspase-7.

  8. Connective tissue growth factor hammerhead ribozyme attenuates human hepatic stellate cell function

    Run-Ping Gao; David R Brigstock


    AIM: To determine the effect of hammerhead ribozyme targeting connective tissue growth factor (CCN2) on human hepatic stellate cell (HSC) function. METHODS: CCN2 hammerhead ribozyme cDNA plus two self-cleaving sequences were inserted into pTriEx2 to produce pTriCCN2-Rz. Each vector was individually transfected into cultured LX-2 human HSCs, which were then stimulated by addition of transforming growth factor (TGF)-b1 to the culture medium. Semiquantitative RT-PCR was used to determine mRNA levels for CCN2 or collagen Ⅰ, while protein levels of each molecule in cell lysates and conditioned medium were measured by ELISA. Cell-cycle progression of the transfected cells was assessed by flow cytometry. RESULTS: In pTriEx2-transfected LX-2 cells, TGF-β1 treatment caused an increase in the mRNA level for CCN2 or collagen Ⅰ, and an increase in produced and secreted CCN2 or extracellular collagen Ⅰ protein levels. pTriCCN2-Rz-transfected LX-2 cells showed decreased basal CCN2 or collagen mRNA levels, as well as produced and secreted CCN2 or collagen Ⅰ protein. Furthermore, the TGF-b1-induced increase in mRNA or protein for CCN2 or collagen Ⅰ was inhibited partially in pTriCCN2-Rz-transfected LX-2 cells. Inhibition of CCN2 using hammerhead ribozyme cDNA resulted in fewer of the cells transitioning into S phase. CONCLUSION: Endogenous CCN2 is a mediator of basal or TGF-b1-induced collagen Ⅰ production in human HSCs and regulates entry of the cells into Sphase.

  9. Fast and simple purification of chemically modified hammerhead ribozymes using a lipophilic capture tag.

    Sproat, B S; Rupp, T; Menhardt, N; Keane, D.; Beijer, B


    A new type of 5'-lipophilic capture tag is described, enabling the facile reverse phase HPLC purification of chemically modified hammerhead ribozymes (oligozymes) whilst still carrying the 2'-O-tert.-butyldimethylsilyl protection of the essential riboses. In its most convenient form, the capture tag consists of a simple diol, such as hexan-1,6-diol, which at one end is attached via a silyl residue to a highly lipophilic entity such as tocopherol (vitamin E) or cholesterol, and the other end i...

  10. Targeted cleavage of hepatitis E virus 3' end RNA mediated by hammerhead ribozymes inhibits viral RNA replication

    The 3' end of hepatitis E virus (HEV) contains cis-acting regulatory element, which plays an important role in viral replication. To develop specific replication inhibitor at the molecular level, mono- and di-hammerhead ribozymes (Rz) were designed and synthesized against the conserved 3' end sequences of HEV, which cleave at nucleotide positions 7125 and 7112/7125, respectively. Di-hammerhead ribozyme with two catalytic motifs in tandem was designed to cleave simultaneously at two sites spaced 13 nucleotides apart, which increases the overall cleavage efficiency and prevents the development of escape mutants. Specific cleavage products were obtained with both the ribozymes in vitro at physiological conditions. The inactive control ribozymes showed no cleavage. The ribozymes showed specific inhibition of HEV 3' end fused-luciferase reporter gene expression by ∼37 and ∼60%, respectively in HepG2 cells. These results demonstrate a feasible approach to inhibit the HEV replication to a limited extent by targeting the cis-acting 3' end of HEV with hammerhead ribozymes

  11. Activity identification of chimeric anti-caspase-3 mRNA hammerhead ribozyme in vitro and in vivo

    XU; Renhuan; (


    [1]Andrew, F., Gerard, E., A license to kill, Cell, 1996, 85: 781-784.[2]Thornberry, N. A., Lazebnik, Y., Caspases: Enemies within, Science, 1998, 281: 1312-1316.[3]Kijima, H., Ishida, H., Ohkawa, T. et al., Therapeutic application of ribozymes, Pharmacol. Ther., 1995, 68: 247-264.[4]Phylactou, L. A., Kilpatrick, M. W., Wood, M. J., Ribozymes as therapeutic tools for genetic disease, Hum. Mol. Genet., 1998, 7(10): 1649-1653.[5]Bettrand, E., Pictet, R ., Grange, T., Can heamerhead ribozymes be efficient tools inactivate gene function? Nucleic Acids Res., 1994, 22: 293-300.[6]Lieber, A., Strauss, M., Selection of efficient cleavage sites in target RNAs by using a ribozyme expression library, Mol. Cell Biol., 1995, 15: 540-551.[7]Xu, R. H., Zhou, X. Q., Xie, Q. et al., Preparation and identification of hammerhead ribozyme in vitro against rat caspase-3 mRNA fragment, Chin. J. Hepatol., 2000,8: 361-363.[8]Liu, J., Jin, Y. X., Wang, D. B., A novel vector for abundant expression of antisense RNA, triplex-forming RNA and ribozyme in vivo, High Technology Letters, 2000, 6: 84-88.[9]Sambrook, J., Fritsch, E. F., Maniatis, T., Molecular Cloning: A Laboratory Manual, 2nd ed., New York: Cold Spring Harbor Laboratory Press, 1989.[10]Porter, A. G., J?nicke, R. U., Emerging roles of caspase-3 in apoptosis, Cell Death Differ, 1999, 6: 99-104.[11]Cryns, V., Yuan, J., Proteases to die for, Genes Dev., 1998, 12: 1551-1570.[12]Narendra, K. V., Anikumar, R. K., Fritz, E., Recent developments in the hammerhead ribozyme field, Nucleic Acids Research, 1998, 26: 5237-5242.

  12. Preparation of anti-mouse caspase-12 mRNA hammerhead ribozyme and identification of its activity in vitro

    Shan Jiang; Qing Xie; Wei Zhang; Xia-Qiu Zhou; You-Xin Jin


    AIM: To prepare and identify specific anti-mouse caspase12 hammerhead ribozymes in vitro, in order to select a more effective ribozyme against mouse caspase-12 as a potential tool to rescue cells from endoplasmic reticulum stress induced apoptosis.METHODS: Two hammerhead ribozymes directed separately against 138 and 218 site of nucleotide of mouse caspase-12 mRNA were designed by computer software,and their DNA sequences were synthesized. The synthesized ribozymes were cloned into an eukaryotic expression vector-neorpBSKU6 and embedded in U6 SnRNA context for further study. Mouse caspase-12 gene segment was cloned into PGEM-T vector under the control of T7 RNA polymerase promoter (containing gene sequence from positions nt 41 to nt 894) as target. In vitro transcription both the ribozymes and target utilize T7 promoter. The target was labeled with [α-32P]UTP, while ribozymes were not labeled. After gel purification the RNAs were dissolved in RNase free water. Ribozyme and target were incubated for 90 min at 37 ℃ in reaction buffer (40 mmol/L Tris-HCL,pH 7.5, 10 mmol/L Mg2+). Molar ratio of ribozyme vs target was 30:1. Samples were analyzed on 6% PAGE (containing 8 mol/L urea).RESULTS: Both caspase-12 and ribozyme gene sequences were successfully cloned into expression vector confirmed by sequencing. Ribozymes and caspase-12 mRNA were obtained by in vitro transcription. Cleavage experiment showed that in a physiological similar condition (37 ℃,pH 7.5), Rz138 and Rz218 both cleaved targets at predicted sites, for Rz138 the cleavage efficiency was about 100%,for Rz218 the value was 36.66%.CONCLUSION: Rz138 prepared in vitro can site specific cleave mouse caspase-12 mRNA with an excellent efficiency. It shows a potential to suppress the expression of caspase-12 in vivo, thus provided a new way to protect cells from ER stress induced apoptosis.


    Anderson, Michael


    As a relatively simple and well-studied molecule, the hammerhead ribozyme is an ideal system to study RNA catalysis and structure. A deeper understanding of the hammerhead catalytic mechanism and the role of divalent ions in catalysis lends support to the exploration of more complex RNA machinery such as the ribosome, and ultimately may assist in the design of new medical therapies. Kinetic study of the hammerhead ribozyme to date has largely derived from bulk assays monitoring millions of ...

  14. Inhibition of Hepatitis B Virus Replication and Expression in Vitro and in Vivo by the Hammerhead Ribozymes Targeted Different Sites

    Wei; Dai; Rong; Zhou; Hong; Yu; Xiao-juan; Li


    Objective To develop an effective and specific medicine targeting hepatitis B virus(HBV) pregenome. Based on the identified accessible target sites for hammerhead ribozyme in our previous researches, a recombinant hepatitis delta virus(HDV) ribozyme was chosen and used to demonstrate the effective cleavage in vitro and in vivo. Methods Three hammerhead ribozymes for potential target sites(S, X and C genes) and co-expression plasmid(pTr-dB, pTdδ-dB, pTrX-dB and pTrC-dB) as well as four HDV-ribozyme chimera constructs with HBV(pTdXX, pTdXC, pTdSX and pTdSC) were severally chosen to validate the inhibition of the replication and expression of HBV. The co-expression plasmids(pTdδ and pTr-Db) in physiological saline were hydrodynamically injected to mice by tail vein. Results Compared with the group injected with pTr-dB in Huh-7 cell, hepatitis B surface antigen(HBsAg) was reduced by 31% in the group injected with pTdδ-dB, by 54%, 26%, 72% and 97% in the group injected with recombinant-ribozymes pTdSX, pTdSC, pTdXC and pTdXX, respectively. The inhibiting effects of endogenous ribozymes RzX and RzC on the HBsAg expression were 66% and 57%, respectively. Compared with the positive control, the amount of HBsAg was decreased in mice injected with pTdXX through tail vein by 88% and 96% on the second day and the third day, respectively. HBsAg was undetectable on the 6th day and could not primitively be detected on the 9th day in the sera from all mice. HBV DNA was not detected in the sera of BALB/c mice injected with pTdXX-dB, pTrX-dB or replicating-defective plasmid pHBV, while HBV DNA replication in control group could be detected on the 6th day. While HBcAg could not be detected in liver tissues of mice injected with plasmid pTdXX-dB on the 3rd day. Conclusions Encoding regions of HBV S, C and X gene were the effective cleavage sites for hammerhead ribozyme in vitro and in vivo, which provides basis for further construction of therapeutic recombinant HDV and the

  15. Antiviral Hammerhead Ribozymes Are Effective for Developing Transgenic Suppression of Chikungunya Virus in Aedes aegypti Mosquitoes.

    Mishra, Priya; Furey, Colleen; Balaraman, Velmurugan; Fraser, Malcolm J


    The chikungunya virus (CHIKV) is an emerging pathogen with widespread distribution in regions of Africa, India, and Asia that threatens to spread into temperate climates with the introduction of its major vector, Aedes albopictus. CHIKV causes a disease frequently misdiagnosed as dengue fever, with potentially life-threatening symptoms that can result in a longer-term debilitating arthritis. The increasing risk of spread from endemic regions via human travel and commerce and the current absence of a vaccine put a significant proportion of the world population at risk for this disease. In this study we designed and tested hammerhead ribozymes (hRzs) targeting CHIKV structural protein genes of the RNA genome as potential antivirals both at the cellular and in vivo level. We employed the CHIKV strain 181/25, which exhibits similar infectivity rates in both Vero cell cultures and mosquitoes. Virus suppression assay performed on transformed Vero cell clones of all seven hRzs demonstrated that all are effective at inhibiting CHIKV in Vero cells, with hRz #9 and #14 being the most effective. piggyBac transformation vectors were constructed using the Ae. aegypti t-RNA(val) Pol III promoted hRz #9 and #14 effector genes to establish a total of nine unique transgenic Higgs White Eye (HWE) Ae. aegypti lines. Following confirmation of transgene expression by real-time polymerase chain reaction (RT-PCR), comparative TCID50-IFA analysis, in situ Immuno-fluorescent Assays (IFA) and analysis of salivary CHIKV titers demonstrated effective suppression of virus replication at 7 dpi in heterozygous females of each of these transgenic lines compared with control HWE mosquitoes. This report provides a proof that appropriately engineered hRzs are powerful antiviral effector genes suitable for population replacement strategies. PMID:27294950

  16. Mechanistic studies of copper(II)-aminoglycoside mediated DNA damage and magnesium catalyzed nuclease activity of hammerhead ribozyme

    Patwardhan, Anjali A.

    The antibacterial activity of aminoglycosides stems from their high affinity binding to the 16S rRNA in bacteria resulting in inhibition of protein synthesis. Used to treat acute bacterial infections these antibiotics have limited applications due to their high dosage requirements and the emergence of resistant strains. We have synthesized and characterized Cu(II) derivatives of the aminoglycosides, kanamycin A, tobramycin, neamine, kanamycin B, neomycin B, and paromomycin. The first three exhibit preferential and tight binding to Cu(II) as against neomycin B and kanamycin B and paromomycin. EPR of frozen solutions and UV-visible spectroscopy suggest a change in geometry around the Cu(II) but the stabilities of the complexes in water differ. These copper derivatives efficiently cleave plasmid DNA at micromolar concentrations (hydrolytic) and at nanomolar concentrations in the presence co-reactants like hydrogen peroxide or ascorbic acid. Hydrolysis is multi turnover and exhibits Michelis-Menten kinetics with enzyme-like behavior whereas oxidative cleavage is highly specific with C-4' H abstraction resulting in characteristic base propenal and nucleotide base products. Hydroxyl radicals generated are copper based and are generated in close proximity of the substrate. Hammerhead ribozymes are selectively hydrolyzed in the presence of divalent ions with Mg2+ being the metal ion of choice in vivo . Our studies with complex ions like cobalt hexaammine and fac-triamminetriaquochromium(III) establish outer sphere interactions of Mg2+ with the hammerhead in the catalytic site. There are two sets of sites, one structural and one catalytic. Complex ions in the catalytic site and divalent ions in the structural site result in a slow but active hammerhead ribozyme suggesting that the complex ions are not inhibitory, contrary to what was suggested previously.

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

    Venanzetti Federica


    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.

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

    Venanzetti Federica; Johnsen Arild; Martinsen Lene; Bachmann Lutz


    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. Resul...

  19. Zinc-dependent cleavage in the catalytic core of the hammerhead ribozyme: evidence for a pH-dependent conformational change

    Borda, Emily J.; Markley, John C.; Sigurdsson, Snorri Th.


    We have characterized a novel Zn2+-catalyzed cleavage site between nucleotides C3 and U4 in the catalytic core of the hammerhead ribozyme. In contrast to previously described divalent metal-ion-dependent cleavage of RNA, U4 cleavage is only observed in the presence of Zn2+. This new cleavage site has an unusual pH dependence, in that U4 cleavage products are only observed above pH 7.9 and reach a maximum yield at about pH 8.5. These data, together with the fact that no metal ion-binding site ...

  20. Secondary structure in solution of two anti-HIV-1 hammerhead ribozymes as investigated by two-dimensional 1H 500 MHz NMR spectroscopy in water

    Sarma, R. H.; Sarma, M. H.; Rein, R.; Shibata, M.; Setlik, R. S.; Ornstein, R. L.; Kazim, A. L.; Cairo, A.; Tomasi, T. B.


    Two hammerhead chimeric RNA/DNA ribozymes (HRz) were synthesized in pure form. Both were 30 nucleotides long, and the sequences were such that they could be targeted to cleave the HIV-1 gag RNA. Named HRz-W and HRz-M, the former had its invariable core region conserved, the latter had a uridine in the invariable region replaced by a guanine. Their secodary structures were determined by 2D NOESY 1H 500 MHz NMR spectroscopy in 90% water and 10% D2(0), following the imino protons. The data show that both HRz-M and HRz-W form identical secondary structures with stem regions consisting of continuous stacks of AT and GT pairs. An energy minimized computer model of this stem region is provided. The results suggest that the loss of catalytic activity that is known to result when an invariant core residue is replaced is not related to the secondary structure of the ribozymes in the absence of substrate.

  1. Spiegelzymes® mirror-image hammerhead ribozymes and mirror-image DNAzymes, an alternative to siRNAs and microRNAs to cleave mRNAs in vivo?

    Eliza Wyszko

    Full Text Available With the discovery of small non-coding RNA (ncRNA molecules as regulators for cellular processes, it became intriguing to develop technologies by which these regulators can be applied in molecular biology and molecular medicine. The application of ncRNAs has significantly increased our knowledge about the regulation and functions of a number of proteins in the cell. It is surprising that similar successes in applying these small ncRNAs in biotechnology and molecular medicine have so far been very limited. The reasons for these observations may lie in the high complexity in which these RNA regulators function in the cells and problems with their delivery, stability and specificity. Recently, we have described mirror-image hammerhead ribozymes and DNAzymes (Spiegelzymes® which can sequence-specifically hydrolyse mirror-image nucleic acids, such as our mirror-image aptamers (Spiegelmers discovered earlier. In this paper, we show for the first time that Spiegelzymes are capable of recognising complementary enantiomeric substrates (D-nucleic acids, and that they efficiently hydrolyse them at submillimolar magnesium concentrations and at physiologically relevant conditions. The Spiegelzymes are very stable in human sera, and do not require any protein factors for their function. They have the additional advantages of being non-toxic and non-immunogenic. The Spiegelzymes can be used for RNA silencing and also as therapeutic and diagnostic tools in medicine. We performed extensive three-dimensional molecular modelling experiments with mirror-image hammerhead ribozymes and DNAzymes interacting with D-RNA targets. We propose a model in which L/D-double helix structures can be formed by natural Watson-Crick base pairs, but where the nucleosides of one of the two strands will occur in an anticlinal conformation. Interestingly enough, the duplexes (L-RNA/D-RNA and L-DNA/D-RNA in these models can show either right- or left-handedness. This is a very new

  2. The effect of structure in a long target RNA on ribozyme cleavage efficiency.

    Campbell, T B; McDonald, C K; Hagen, M.


    Inhibition of gene expression by catalytic RNA (ribozymes) requires that ribozymes efficiently cleave specific sites within large target RNAs. However, the cleavage of long target RNAs by ribozymes is much less efficient than cleavage of short oligonucleotide substrates because of higher order structure in the long target RNA. To further study the effects of long target RNA structure on ribozyme cleavage efficiency, we determined the accessibility of seven hammerhead ribozyme cleavage sites i...

  3. Engineering a ribozyme cleavage-induced split fluorescent aptamer complementation assay

    Ausländer, Simon; Fuchs, David; Hürlemann, Samuel; Ausländer, David; Fussenegger, Martin


    Hammerhead ribozymes are self-cleaving RNA molecules capable of regulating gene expression in living cells. Their cleavage performance is strongly influenced by intra-molecular loop–loop interactions, a feature not readily accessible through modern prediction algorithms. Ribozyme engineering and efficient implementation of ribozyme-based genetic switches requires detailed knowledge of individual self-cleavage performances. By rational design, we devised fluorescent aptamer-ribozyme RNA archit...

  4. Structure of an anti-HIV-1 hammerhead ribozyme complex with a 17-mer DNA substrate analog of HIV-1 gag RNA and a mechanism for the cleavage reaction: 750 MHz NMR and computer experiments

    Ojha, R. P.; Dhingra, M. M.; Sarma, M. H.; Myer, Y. P.; Setlik, R. F.; Shibata, M.; Kazim, A. L.; Ornstein, R. L.; Rein, R.; Turner, C. J.; Sarma, R. H.


    The structure of an anti-HIV-1 ribozyme-DNA abortive substrate complex was investigated by 750 MHz NMR and computer modeling experiments. The ribozyme was a chimeric molecule with 30 residues-18 DNA nucleotides, and 12 RNA residues in the conserved core. The DNA substrate analog had 17 residues. The chimeric ribozyme and the DNA substrate formed a shortened ribozyme-abortive substrate complex of 47 nucleotides with two DNA stems (stems I and III) and a loop consisting of the conserved core residues. Circular dichroism spectra showed that the DNA stems assume A-family conformation at the NMR concentration and a temperature of 15 degrees C, contrary to the conventional wisdom that DNA duplexes in aqueous solution populate entirely in the B-form. It is proposed that the A-family RNA residues at the core expand the A-family initiated at the core into the DNA stems because of the large free energy requirement for the formation of A/B junctions. Assignments of the base H8/H6 protons and H1' of the 47 residues were made by a NOESY walk. In addition to the methyl groups of all T's, the imino resonances of stems I and III and AH2's were assigned from appropriate NOESY walks. The extracted NMR data along with available crystallographic data, were used to derive a structural model of the complex. Stems I and III of the final model displayed a remarkable similarity to the A form of DNA; in stem III, a GC base pair was found to be moving into the floor of the minor groove defined by flanking AT pairs; data suggest the formation of a buckled rhombic structure with the adjacent pair; in addition, the base pair at the interface of stem III and the loop region displayed deformed geometry. The loop with the catalytic core, and the immediate region of the stems displayed conformational multiplicity within the NMR time scale. A catalytic mechanism for ribozyme action based on the derived structure, and consistent with biochemical data in the literature, is proposed. The complex

  5. Ultrasensitive monitoring of ribozyme cleavage product using molecular-beacon-ligation system

    MENG XiangXian; TANG ZhiWen; WANG KeMin; TAN WeiHong; YANG XiaoHai; LI Jun; GUO QiuPing


    This paper reports a new approach to detect ribozyme cleavage product based on the molecular- beacon-ligation system. The molecular beacon, designed in such a way that one-half of its loop is complementary to ribozyme cleavage product, is used to monitor ligation process of RNA/DNA complex in a homogeneous solution and to convert directly cleavage product information into fluorescence signal. The method need not label ribozyme and ribozyme substrate, which is fast, simple and ultrasensitive for detection of cleavage product. Detection limit of the assay is 0.05 nmol/L. The cleavage product of hammerhead ribozyme against hepatitis C virus RNA (HCV-RNA) was detected perfectly based on this assay. Owing to its ultrasensitivity, excellent specificity, convenience and fidelity, this method might hold out great promise in ribozyme reaction and ribozyme gene therapy.

  6. Construction of Multi-ribozyme Expression System and Its Characterization of Cleavage on the MDR1/MRP1 Double Target Substrate in vitro

    TIAN Sheng-li; ZHENG Suo; LIU Shi-de; ZHANG Jian-hua; XU Dong-ping; OHNUMA Takao


    To improve catalytic activity of ribozyme on its substrate,the multi-ribozyme expression system was designed and constructed from 20 cis-acting hammerhead ribozymes undergoing self-cleavage with 10 trans-acting hammerhead ribozymes inserted altematively regularly and the plasmid of pGEM-MDRI/MRPI used to transcribe the M DRI/MRPI(196/210) substrate containing double target sites was also constructed by DNA recombination.Endonuclease digestion analysis and DNA sequencing indicate all the recombinant plasmids were correct.The cleavage activities were evaluated for the multi-ribozyme expression system on the MDR1/MRP1 substrate in the cell free system.The results demonstrate that the cis-acting hammerhead ribozymes in the multi-ribozyme expression system were able to cleave themselves and the 72 nt of 196Rz and the 71 nt of 210Rz trans-acting hammerhead ribozymes were liberated effectively,and the trans-acting hammerhead ribozymes released were able to act on the MDR1/MRP1 double target RNA substrate and cleave the target RNA at specific sites effectively.The multiribozyme expression system of the [Coat'A196Rz/Coat'B210Rz]5 is more significantly superior to that of the [Coat'A 196Rz/Coat'B210Rz]1 in cleavage of RNA substrate.The fractions cleaved by [Coat'A196Rz/Coat'B210Rz]5 on the MDR1/MRP1 substrate for 8 h at observed temperatures showed no marked difference.The studies of Mg2+ on cleavage efficiency indicate that cleavage reaction is dependent on Mg2+ ions concentration.The plot of Ig(kobs) vs.Igc(Mg2+) displays a linear relationship between 2.5 mmol/L and 20 mmol/L Mg2..It suggests that Mg2+ ions play a crucial role in multi-ribozyme cleavage on the substrate.

  7. Ribozyme-mediated reversal of the multidrug-resistant phenotype.

    Scanlon, K J; Ishida, H.; Kashani-Sabet, M


    This study examined the effects of suppressing c-fos oncogene expression on multidrug resistance (MDR). A2780S human ovarian carcinoma cells with resistance to actinomycin D were isolated and the resultant A2780AD cells exhibited the MDR phenotype. A hammerhead ribozyme designed to cleave fos RNA cloned into the pMAMneo plasmid was transfected into A2780AD cells. Induction of the ribozyme resulted in decreased expression of c-fos, as well as that of the MDR gene (mdr-1), c-jun, and mutant p53...

  8. 碱基切除修复基因HOGG1特异性锤头状核酶表达载体的构建及其功能的初步研究%Constructing the Eukaryotic Expression Vector to Study Preliminarily the Functions of Hammerhead Ribozyme Targeting Base Excision Repair Gene HOGG1

    张遵真; 张勤; 吴媚


    Objective Adriamycin is widely used as an effective anti-tumor drug clinically treating a number of human cancers, but the effect of adriamycin is limited by drug resistance. The various kinds of investigations indicated that the anti-tumor activity of adriamycin resulted from drug-induced free radical formation. The free radicals could lead to oxidative DNA damage, and the lesion would be repaired by base excision repair (BER) pathway. Human 8-oxoguanine DNA glycosylase 1 (HOGG1) is a key enzyme on BER pathway. To study the influence and biological mechanism of the HOGG1 to adriamycin drug-sensitivity, the eukaryotic expression vector with gene of hammerhead ribozyme targeting HOGG1 mRNA would be constructed and identified, and then the change of drug-sensitivity in lung cancer A549 cells would be investigated. Methods According to computer design, two specific restriction site BamHⅠ and EcoRⅠ were added to both ends of the ribozyme gene, then the modified ribozyme gene was synthesized and cloned into the eukaryotic expression vector pcDNA3.1(+). The positive recombinants were screened by ampicillin resistance, and plasmids were extracted from the positive recombinants and digested by BamH Ⅰ and EcoR Ⅰ, and then were analyzed by agarose gel electrophoresis and DNA sequencing. The recombinants were transiently transfected into A549 cells. The positive recombinants were identified by reverse transcription-polymerase chain reaction (RT-PCR) targeting to NEO gene, which was a neomycin resistance gene for selection of stable cell lines and only existed in vectors. The changes of HOGG1 mRNA in A549 cells were detected by RT-PCR. Then the cellular sensitivity to adriamycin was tested by comparison between untransfected cells and transfected cells by MTT assay. The adriamycin-induced DNA damage was investigated by comet assay or single cell gel electrophoresis (SCGE) between untransfected and transfected cells. Results The recombinants containing the ribozyme gene

  9. Group I intron ribozymes

    Nielsen, Henrik


    Group I intron ribozymes constitute one of the main classes of ribozymes and have been a particularly important model in the discovery of key concepts in RNA biology as well as in the development of new methods. Compared to other ribozyme classes, group I intron ribozymes display considerable...... intronic products of these pathways have the potential to integrate into targets and to form various types of circular RNA molecules. Thus, group I intron ribozymes and associated elements found within group I introns is a rich source of biological phenomena. This chapter provides a strategy and protocols...... for initial characterization of new group I intron ribozymes....

  10. Kinetics of hairpin ribozyme cleavage in yeast.

    Donahue, C P; Fedor, M J


    Hairpin ribozymes catalyze a self-cleavage reaction that provides a simple model for quantitative analyses of intracellular mechanisms of RNA catalysis. Decay rates of chimeric mRNAs containing self-cleaving ribozymes give a direct measure of intracellular cleavage kinetics in yeast. Intracellular ribozyme-mediated cleavage occurs at similar rates and shows similar inhibition by ribozyme mutations as ribozyme-mediated reactions in vitro, but only when ribozymes are located in a favorable mRNA...

  11. Ribozyme-based aminoglycoside switches of gene expression engineered by genetic selection in S. cerevisiae.

    Klauser, Benedikt; Atanasov, Janina; Siewert, Lena K; Hartig, Jörg S


    Systems for conditional gene expression are powerful tools in basic research as well as in biotechnology. For future applications, it is of great importance to engineer orthogonal genetic switches that function reliably in diverse contexts. RNA-based switches have the advantage that effector molecules interact immediately with regulatory modules inserted into the target RNAs, getting rid of the need of transcription factors usually mediating genetic control. Artificial riboswitches are characterized by their simplicity and small size accompanied by a high degree of modularity. We have recently reported a series of hammerhead ribozyme-based artificial riboswitches that allow for post-transcriptional regulation of gene expression via switching mRNA, tRNA, or rRNA functions. A more widespread application was so far hampered by moderate switching performances and a limited set of effector molecules available. Here, we report the re-engineering of hammerhead ribozymes in order to respond efficiently to aminoglycoside antibiotics. We first established an in vivo selection protocol in Saccharomyces cerevisiae that enabled us to search large sequence spaces for optimized switches. We then envisioned and characterized a novel strategy of attaching the aptamer to the ribozyme catalytic core, increasing the design options for rendering the ribozyme ligand-dependent. These innovations enabled the development of neomycin-dependent RNA modules that switch gene expression up to 25-fold. The presented aminoglycoside-responsive riboswitches belong to the best-performing RNA-based genetic regulators reported so far. The developed in vivo selection protocol should allow for sampling of large sequence spaces for engineering of further optimized riboswitches. PMID:24871672

  12. RiboSubstrates: a web application addressing the cleavage specificities of ribozymes in designated genomes

    Bergeron Lucien


    Full Text Available Abstract Background RNA-dependent gene silencing is becoming a routine tool used in laboratories worldwide. One of the important remaining hurdles in the selection of the target sequence, if not the most important one, is the designing of tools that have minimal off-target effects (i.e. cleaves only the desired sequence. Increasingly, in the current dawn of the post-genomic era, there is a heavy reliance on tools that are suitable for high-throughput functional genomics, consequently more and more bioinformatic software is becoming available. However, to date none have been designed to satisfy the ever-increasing need for the accurate selection of targets for a specific silencing reagent. Results In order to overcome this hurdle we have developed RiboSubstrates This integrated bioinformatic software permits the searching of a cDNA database for all potential substrates for a given ribozyme. This includes the mRNAs that perfectly match the specific requirements of a given ribozyme, as well those including Wobble base pairs and mismatches. The results generated allow rapid selection of sequences suitable as targets for RNA degradation. The current web-based RiboSubstrates version permits the identification of potential gene targets for both SOFA-HDV ribozymes and for hammerhead ribozymes. Moreover, a minimal template for the search of siRNAs is also available. This flexible and reliable tool is easily adaptable for use with any RNA tool (i.e. other ribozymes, deoxyribozymes and antisense, and may use the information present in any cDNA bank. Conclusion RiboSubstrates should become an essential step for all, even including "non-RNA biologists", who endeavor to develop a gene-inactivation system.

  13. Inhibition of telomerase in tumor cells by ribozyme targeting telomerase RNA component

    LIU; Bailin(刘柏林); QU; Yi(屈艺); LIU; Shuqiu(刘菽秋); OUYANG; Xuesong(欧阳雪松)


    Telomerase plays an important role in cell proliferation and carcinogenesis and is believed to be a good target for anti-cancer drugs. Elimination of template function of telomerase RNA may repress the telomerase activity. A hammer-headed ribozyme(telomerase ribozyme, teloRZ) directed against the RNA component of human telomerase(hTR) was designed and synthesized. TeloRZ showed a specific cleavage activity against the hTR. The cleavage efficacy reached 60%. A eukaryotic expression plasmid containing teloRZ gene was inducted into HeLa cells by lipofectamine, the telomerase activity in HeLa cells expressing teloRZ decreased to one eighth of that in the control cells. The doubling time increased significantly and the apoptosis ratio was elevated with increasing population doublings(PDS). After 19-20 PDS 95% cells were apoptotic. To further investigate the effect of teloRZ on tumor growth, the eukaryotic expression plasmid containing teloRZ was injected into transplanted tumor of nude mouse. The teloRZ effectively inhibited the telomerase activity in transplanted tumor, promoted apoptosis of the transplanted tumor cells, and decreased the tumor size significantly. These results indicate that teloRZ can effectively inhibit telomerase activity and growth of tumor cells, and suggest the potential use of this ribozyme in anti-cancer therapy.

  14. Viroid Replication: Rolling-Circles, Enzymes and Ribozymes

    Marcos De la Peña


    Full Text Available Viroids, due to their small size and lack of protein-coding capacity, must rely essentially on their hosts for replication. Intriguingly, viroids have evolved the ability to replicate in two cellular organella, the nucleus (family Pospiviroidae and the chloroplast (family Avsunviroidae. Viroid replication proceeds through an RNA-based rolling-circle mechanism with three steps that, with some variations, operate in both polarity strands: i synthesis of longer-than-unit strands catalyzed by either the nuclear RNA polymerase II or a nuclear-encoded chloroplastic RNA polymerase, in both instances redirected to transcribe RNA templates, ii cleavage to unit-length, which in the family Avsunviroidae is mediated by hammerhead ribozymes embedded in both polarity strands, while in the family Pospiviroidae the oligomeric RNAs provide the proper conformation but not the catalytic activity, and iii circularization. The host RNA polymerases, most likely assisted by additional host proteins, start transcription from specific sites, thus implying the existence of viroid promoters. Cleavage and ligation in the family Pospiviroidae is probably catalyzed by an RNase III-like enzyme and an RNA ligase able to circularize the resulting 5’ and 3’ termini. Whether a chloroplastic RNA ligase mediates circularization in the family Avsunviroidae, or this reaction is autocatalytic, remains an open issue.

  15. Hidden ribozymes in eukaryotic genome sequence

    Sean P Ryder


    The small self-cleaving ribozymes fold into complex tertiary structures to promote autocatalytic cleavage or ligation at a precise position within their sequence. Until recently, relatively few examples had been identified. Two papers now reveal that self-cleaving ribozymes are prevalent in eukaryotic genomes and, in some cases, might play a role in regulating gene expression.

  16. Molecular modelling of the GIR1 branching ribozyme gives new insight into evolution of structurally related ribozymes

    Beckert, Bertrand Dominique; Nielsen, Henrik; Einvik, Christer;


    Twin-ribozyme introns contain a branching ribozyme (GIR1) followed by a homing endonuclease (HE) encoding sequence embedded in a peripheral domain of a group I splicing ribozyme (GIR2). GIR1 catalyses the formation of a lariat with 3 nt in the loop, which caps the HE mRNA. GIR1 is structurally...

  17. Helium ion beam induced growth of hammerhead AFM probes

    Nanda, G.; Van Veldhoven, E.; Maas, D.; Sadeghian, H.; Alkemade, P.F.A.


    The authors report the direct-write growth of hammerhead atomic force microscope(AFM) probes by He+beam induced deposition of platinum-carbon. In order to grow a thin nanoneedle on top of a conventional AFM probe, the authors move a focused He+beam during exposure to a PtC precursor gas. In the fina

  18. Helium ion beam induced growth of hammerhead AFM probes

    Nanda, G.; Veldhoven, E. van; Maas, D.J.; Sadeghian Marnani, H.; Alkemade, P.F.A.


    The authors report the direct-write growth of hammerhead atomic force microscope (AFM) probes by He+ beam induced deposition of platinum-carbon. In order to grow a thin nanoneedle on top of a conventional AFM probe, the authors move a focused He+ beam during exposure to a PtC precursor gas. In the f

  19. Chemical fidelity of an RNA polymerase ribozyme

    Attwater, J.; Tagami, S.; Kimoto, M.;


    strands. Our results indicate specificity mechanisms that are found in functionally analogous forms in natural polymerases. They also reveal a level of chemical fidelity over multiple catalytic steps that is remarkable for a comparatively unoptimized enzyme developed de novo from a random sequence pool....... The convergent evolution of specificity mechanisms in phylogenetically unrelated proteinaceous polymerases and polymerase ribozymes suggests that chemical as well as informational fidelity are emergent properties of polymerase enzymes. © 2013 The Royal Society of Chemistry....

  20. MM 99.58 Physical modelling of Hammerhead forging, Vertical and Lateral load history

    Arentoft, Mogens; Eriksen, Morten; Wanheim, Tarras;


    The present report presents a laboratory setup with hammerhead forging, where the vertical and lateral force history is obtained under different process conditions......The present report presents a laboratory setup with hammerhead forging, where the vertical and lateral force history is obtained under different process conditions...

  1. Molecular characterization of a new member of the lariat capping twin-ribozyme introns

    Tang, Yunjia; Nielsen, Henrik; Masquida, Benoît;


    BACKGROUND: Twin-ribozyme introns represent a complex class of mobile group I introns that harbour a lariat capping (LC) ribozyme and a homing endonuclease gene embedded in a conventional self-splicing group I ribozyme (GIR2). Twin-ribozyme introns have so far been confined to nucleolar DNA in...... Naegleria amoeboflagellates and the myxomycete Didymium iridis. RESULTS: We characterize structural organization, catalytic properties and molecular evolution of a new twin-ribozyme intron in Allovahlkampfia (Heterolobosea). The intron contains two ribozyme domains with different functions in ribosomal RNA...... efficient self-cleaving ribozyme that generates a small 2',5' lariat cap at the 5' end of the homing endonuclease mRNA, and thus contributes to intron mobility. CONCLUSIONS: The discovery of a twin-ribozyme intron in a member of Heterolobosea expands the distribution pattern of LC ribozymes. We identify a...

  2. Chemistry and Biology of Self-Cleaving Ribozymes.

    Jimenez, Randi M; Polanco, Julio A; Lupták, Andrej


    Self-cleaving ribozymes were discovered 30 years ago, but their biological distribution and catalytic mechanisms are only beginning to be defined. Each ribozyme family is defined by a distinct structure, with unique active sites accelerating the same transesterification reaction across the families. Biochemical studies show that general acid-base catalysis is the most common mechanism of self-cleavage, but metal ions and metabolites can be used as cofactors. Ribozymes have been discovered in highly diverse genomic contexts throughout nature, from viroids to vertebrates. Their biological roles include self-scission during rolling-circle replication of RNA genomes, co-transcriptional processing of retrotransposons, and metabolite-dependent gene expression regulation in bacteria. Other examples, including highly conserved mammalian ribozymes, suggest that many new biological roles are yet to be discovered. PMID:26481500

  3. Kinetic framework for ligation by an efficient RNA ligase ribozyme.

    Bergman, N H; Johnston, W K; Bartel, D P


    The class I RNA ligase ribozyme, isolated previously from random sequences, performs an efficient RNA ligation reaction. It ligates two substrate RNAs, promoting the attack of the 3'-hydroxyl of one substrate upon the 5'-triphosphate of the other substrate with release of pyrophosphate. This ligation reaction has similarities to the reaction catalyzed by RNA polymerases. Using data from steady-state kinetic measurements and pulse-chase/pH-jump experiments, we have constructed minimal kinetic frameworks for two versions of the class I ligase, named 207t and 210t. For both ligases, as well as for the self-ligating parent ribozyme, the rate constant for the chemical step (k(c)) is log-linear with pH in the range 5.7-8.0. At physiological pH, the k(c) is 100 min(-1), a value similar to those reported for the fastest naturally occurring ribozymes. At higher pH, product release is limiting for both 207t and 210t. The 210t ribozyme, with its faster product release, attains multiple-turnover rates (k(cat) = 360 min(-1), pH 9.0) exceeding those of 207t and other reported ribozyme reactions. The kinetic framework for the 210t ribozyme describes the limits of this catalysis and suggests how key steps can be targeted for improvement using design or combinatorial approaches. PMID:10715133

  4. Electroreception in juvenile scalloped hammerhead and sandbar sharks.

    Kajiura, Stephen M; Holland, Kim N


    The unique head morphology of sphyrnid sharks might have evolved to enhance electrosensory capabilities. The 'enhanced electroreception' hypothesis was tested by comparing the behavioral responses of similarly sized carcharhinid and sphyrnid sharks to prey-simulating electric stimuli. Juvenile scalloped hammerhead sharks Sphyrna lewini and sandbar sharks Carcharhinus plumbeus oriented to dipole electric fields from the same maximum distance (approximately 30 cm) and thus demonstrated comparable behavioral-response thresholds (shark bent its trunk to orient to the center of the dipole. By contrast, sandbars swam in a broader arc towards the center of the dipole. The different orientation patterns are attributed to the hydrodynamic properties of the cephalofoil, which enables the hammerheads to execute sharp turns at high speed. The greater trunk width of the sandbar sharks prevented them from demonstrating the same degree of flexibility. Therefore, although the sphyrnid head morphology does not appear to confer a greater sensitivity to prey-simulating dipole electric fields, it does provide (1). a greater lateral search area, which may increase the probability of prey encounter, and (2). enhanced maneuverability, which may aid in prey capture. PMID:12409487

  5. Modulation of Group I Ribozyme Activity by Cationic Porphyrins

    Shigeyoshi Matsumura


    Full Text Available The effects of cationic porphyrins on the catalytic activities of four group I ribozymes were investigated. A cationic porphyrin possessing four pyridinium moieties (pPyP inhibited two group IC3 ribozymes (Syn Rz and Azo Rz and a group IC1 ribozyme (Tet Rz. In the case of a group IA2 ribozyme (Td Rz, however, pPyP served not only as an inhibitor but also as an activator, and the effects of pPyP were dependent on its concentration. To analyze the structural and electronic factors determining the effects of pPyP on group I ribozymes, three cationic porphyrins (pPyNCP, pPyF4P, and TMPyP were also examined. As interactions between small organic molecules and nucleic acids are attractive and important issues in biochemistry and biotechnology, this study contributes to the development of porphyrin-based molecules that can modulate functions of structured RNA molecules.

  6. Constructional morphology within the head of hammerhead sharks (sphyrnidae).

    Mara, Kyle R; Motta, Philip J; Martin, Andrew P; Hueter, Robert E


    The study of functional trade-offs is important if a structure, such as the cranium, serves multiple biological roles, and is, therefore, shaped by multiple selective pressures. The sphyrnid cephalofoil presents an excellent model for investigating potential trade-offs among sensory, neural, and feeding structures. In this study, hammerhead shark species were chosen to represent differences in head form through phylogeny. A combination of surface-based geometric morphometrics, computed tomography (CT) volumetric analysis, and phylogenetic analyses were utilized to investigate potential trade-offs within the head. Hammerhead sharks display a diversity of cranial morphologies where the position of the eyes and nares vary among species, with only minor changes in shape, position, and volume of the feeding apparatus through phylogeny. The basal winghead shark, Eusphyra blochii, has small anteriorly positioned eyes. Through phylogeny, the relative size and position of the eyes change, such that derived species have larger, more medially positioned eyes. The lateral position of the external nares is highly variable, showing no phylogenetic trend. Mouth size and position are conserved, remaining relatively unchanged. Volumetric CT analyses reveal no trade-offs between the feeding apparatus and the remaining cranial structures. The few trade-offs were isolated to the nasal capsule volume's inverse correlation with braincase, chondrocranial, and total cephalofoil volume. Eye volume also decreased as cephalofoil width increased. These data indicate that despite considerable changes in head shape, much of the head is morphologically conserved through sphyrnid phylogeny, particularly the jaw cartilages and their associated feeding muscles, with shape change and morphological trade-offs being primarily confined to the lateral wings of the cephalofoil and their associated sensory structures. PMID:25684106

  7. Speciation of a group I intron into a lariat capping ribozyme

    Meyer, Mélanie; Nielsen, Henrik; Oliéric, Vincent;


    The lariat-capping (LC) ribozyme is a natural ribozyme isolated from eukaryotic microorganisms. Despite apparent structural similarity to group I introns, the LC ribozyme catalyzes cleavage by a 2',5' branching reaction, leaving the 3' product with a 3-nt lariat cap that functionally substitutes...... for a conventional mRNA cap in the downstream pre-mRNA encoding a homing endonuclease. We describe the crystal structures of the precleavage and postcleavage LC ribozymes, which suggest that structural features inherited from group I ribozymes have undergone speciation due to profound changes in...

  8. Cleavage of highly structured viral RNA molecules by combinatorial libraries of hairpin ribozymes. The most effective ribozymes are not predicted by substrate selection rules.

    Yu, Q; Pecchia, D B; Kingsley, S L; Heckman, J E; Burke, J M


    Combinatorial libraries of hairpin ribozymes representing all possible cleavage specificities (>10(5)) were used to evaluate all ribozyme cleavage sites within a large (4.2-kilobase) and highly structured viral mRNA, the 26 S subgenomic RNA of Sindbis virus. The combinatorial approach simultaneously accounts for target site structure and dynamics, together with ribozyme folding, and the sequences that result in a ribozyme-substrate complex with maximal activity. Primer extension was used to map and rank the relative activities of the ribozyme pool against individual sites and revealed two striking findings. First, only a small fraction of potential recognition sites are effectively cleaved (activity-selected sites). Second, nearly all of the most effectively cleaved sites deviated substantially from the established consensus selection rules for the hairpin ribozyme and were not predicted by examining the sequence, or through the use of computer-assisted predictions of RNA secondary structure. In vitro selection methods were used to isolate ribozymes with increased activity against substrates that deviate from the GUC consensus sequence. trans-Acting ribozymes targeting nine of the activity-selected sites were synthesized, together with ribozymes targeting four sites with a perfect match to the cleavage site consensus (sequence-selected sites). Activity-selected ribozymes have much higher cleavage activity against the long, structured RNA molecules than do sequence-selected ribozymes, although the latter are effective in cleaving oligoribonucleotides, as predicted. These results imply that, for Sindbis virus 26 S RNA, designing ribozymes based on matches to the consensus sequence may be an ineffective strategy. PMID:9722591

  9. Fluorescent RNA labeling using self-alkylating ribozymes.

    Sharma, Ashwani K; Plant, Joshua J; Rangel, Alexandra E; Meek, Kirsten N; Anamisis, April J; Hollien, Julie; Heemstra, Jennifer M


    The ability to fluorescently label specific RNA sequences is of significant utility for both in vitro and live cell applications. Currently, most RNA labeling methods utilize RNA-nucleic acid or RNA-protein molecular recognition. However, in the search for improved RNA labeling methods, harnessing the small-molecule recognition capabilities of RNA is rapidly emerging as a promising alternative. Along these lines, we propose a novel strategy in which a ribozyme acts to promote self-alkylation with a fluorophore, providing a robust, covalent linkage between the RNA and the fluorophore. Here we describe the selection and characterization of ribozymes that promote self-labeling with fluorescein iodoacetamide (FIA). Kinetic studies reveal a second-order rate constant that is on par with those of other reactions used for biomolecular labeling. Additionally, we demonstrate that labeling is specific to the ribozyme sequences, as FIA does not react nonspecifically with RNA. PMID:24896502

  10. The Structural Basis of Ribozyme-Catalyzed RNA Assembly

    Robertson, M.P.; Scott, W.G.; /UC, Santa Cruz


    Life originated, according to the RNA World hypothesis, from self-replicating ribozymes that catalyzed ligation of RNA fragments. We have solved the 2.6 angstrom crystal structure of a ligase ribozyme that catalyzes regiospecific formation of a 5' to 3' phosphodiester bond between the 5'-triphosphate and the 3'-hydroxyl termini of two RNA fragments. Invariant residues form tertiary contacts that stabilize a flexible stem of the ribozyme at the ligation site, where an essential magnesium ion coordinates three phosphates. The structure of the active site permits us to suggest how transition-state stabilization and a general base may catalyze the ligation reaction required for prebiotic RNA assembly.

  11. Structural studies on an internal loop from a hairpin ribozyme

    Cai, Z.; SantaLucia, J. Jr.; Tinoco, I. Jr. [Univ. of California, Berkeley, CA (United States)


    Ribozymes, RNA enzymes, catalyze site-specific RNA cleavage and ligation reactions. We are studying the three-dimensional structure of a hairpin ribozyme derived from the minus strand of tobacco ring spot virus satellite RNA ((-)sTRSV), which has been engineering to specifically cleave the HIV-1 RNA. The minimum structure for the catalytic reaction involves a 50-nucleotide ribozyme and a 14-nucleotide substrate. The proposed secondary structure of the ribozyme-substrate complex consists of four short helices separated by two internal loops. The relatively large size (64-nucleotide) of the ribozyme-substrate complex presents formidable problems in solving the structure using NMR. Therefore we are studying smaller structural subunits of the complex. We are determining the high resolution structure of the symmetric internal loop involving the cleavage site and the flanking helices. One strand of the internal loop was selectively {sup 13}C-labeled at C8 of each purine and C6 of each pyrimidine. By using {sup 13}C-edited two-dimensional NMR, the proton NOESY spectrum was greatly simplified. This allowed unambiguous sequential proton resonance assignments along each strand. Three-dimensional {sup 1}-{sup 13}C HMQC-NOESY was used to further facilitate resonance assignments. We are also enzymatically synthesizing the entire 50-nucleotide ribozyme and will combine it with the {sup 13}C-labeled substrate. Through comparison of the NOE connectivities of the labeled nucleotides from the internal loop alone with those from the entire complex, the differences between the two structures can be elucidated.

  12. Kinetic partitioning mechanism of HDV ribozyme folding

    Chen, Jiawen; Gong, Sha; Wang, Yujie; Zhang, Wenbing, E-mail: [Department of Physics, Wuhan University, Wuhan, Hubei 430072 (China)


    RNA folding kinetics is directly tied to RNA biological functions. We introduce here a new approach for predicting the folding kinetics of RNA secondary structure with pseudoknots. This approach is based on our previous established helix-based method for predicting the folding kinetics of RNA secondary structure. In this approach, the transition rates for an elementary step: (1) formation, (2) disruption of a helix stem, and (3) helix formation with concomitant partial melting of an incompatible helix, are calculated with the free energy landscape. The folding kinetics of the Hepatitis delta virus (HDV) ribozyme and the mutated sequences are studied with this method. The folding pathways are identified by recursive searching the states with high net flux-in(out) population starting from the native state. The theory results are in good agreement with that of the experiments. The results indicate that the bi-phasic folding kinetics for the wt HDV sequence is ascribed to the kinetic partitioning mechanism: Part of the population will quickly fold to the native state along the fast pathway, while another part of the population will fold along the slow pathway, in which the population is trapped in a non-native state. Single mutation not only changes the folding rate but also the folding pathway.

  13. Reconciling Ligase Ribozyme Activity with Fatty Acid Vesicle Stability

    Fabrizio Anella; Christophe Danelon


    The “RNA world” and the “Lipid world” theories for the origin of cellular life are often considered incompatible due to the differences in the environmental conditions at which they can emerge. One obstacle resides in the conflicting requirements for divalent metal ions, in particular Mg2+, with respect to optimal ribozyme activity, fatty acid vesicle stability and protection against RNA strand cleavage. Here, we report on the activity of a short L1 ligase ribozyme in the presence of myristol...

  14. 78 FR 24701 - Endangered and Threatened Wildlife; 90-Day Finding on Petitions To List the Great Hammerhead...


    ... hammerhead shark is considered to be a candidate species (69 FR 19975; April 15, 2004). Within 12 months of..., to list the great hammerhead shark range-wide as threatened, and to designate critical habitat. The...'' for the purposes of listing, delisting, and reclassifying a species under the ESA (61 FR...

  15. Kinematics and critical swimming speed of juvenile scalloped hammerhead sharks



    Kinematics and critical swimming speed (Ucrit) of juvenile scalloped hammerhead sharks Sphyrna lewini were measured in a Brett-type flume (635 l). Kinematic parameters were also measured in sharks swimming in a large pond for comparison with those of sharks swimming in the flume. Sharks in the flume exhibited a mean Ucrit of 65±11 cm s-1 (± s.d.) or 1.17±0.21 body lengths per second (L s-1), which are similar to values for other species of sharks. In both the flume and pond, tailbeat frequency (TBF) and stride length (LS) increased linearly with increases in relative swimming speed (Urel=body lengths traveled per second). In the flume, tailbeat amplitude (TBA) decreased with increasing speed whereas TBA did not change with speed in the pond. Differences in TBF and LS between sharks swimming in the flume and the pond decreased with increases in Urel. Sharks swimming at slow speeds (e.g. 0.55 L s-1) in the pond had LS 19 % longer and TBF 21 % lower than sharks in the flume at the same Urel. This implies that sharks in the flume expended more energy while swimming at comparable velocities. Comparative measurements of swimming kinematics from sharks in the pond can be used to correct for effects of the flume on shark swimming kinematics and energetics. PMID:9320537

  16. A Hairpin Ribozyme Inhibits Expression of Diverse Strains of Human Immunodeficiency Virus Type 1

    Yu, Mang; Ojwang, Joshua; Yamada, Osamu; Hampel, Arnold; Rapapport, Jay; Looney, David; Wong-Staal, Flossie


    Ribozymes have enormous potential as antiviral agents. We have previously reported that a hairpin ribozyme expressed under the control of the β-actin promoter that cleaves human immunodeficiency virus type 1 (HIV-1) RNA in the leader sequence can inhibit HIV-1 (pHXB2gpt) expression. For such a ribozyme in a retroviral vector delivery system to be useful in gene therapy for the treatment of HIV-1 infection, it must be able to inhibit the expression of multiple HIV-1 strains. We have now cloned this ribozyme into various regular expression vectors (including retroviral vectors) by using various gene expression control strategies. Here we show by transient transfection that inhibition of expression of diverse strains of HIV-1 can be achieved by this ribozyme expressed in the proper vectors. These data further support the potential of this hairpin ribozyme as a therapeutic agent for HIV-1.

  17. An mRNA is capped by a 2', 5' lariat catalyzed by a group I-like ribozyme

    Nielsen, Henrik; Westhof, Eric; Johansen, Steinar


    Twin-ribozyme introns are formed by two ribozymes belonging to the group I family and occur in some ribosomal RNA transcripts. The group I-like ribozyme, GIR1, liberates the 5' end of a homing endonuclease messenger RNA in the slime mold Didymium iridis. We demonstrate that this cleavage occurs...

  18. Reconciling Ligase Ribozyme Activity with Fatty Acid Vesicle Stability

    Fabrizio Anella


    Full Text Available The “RNA world” and the “Lipid world” theories for the origin of cellular life are often considered incompatible due to the differences in the environmental conditions at which they can emerge. One obstacle resides in the conflicting requirements for divalent metal ions, in particular Mg2+, with respect to optimal ribozyme activity, fatty acid vesicle stability and protection against RNA strand cleavage. Here, we report on the activity of a short L1 ligase ribozyme in the presence of myristoleic acid (MA vesicles at varying concentrations of Mg2+. The ligation rate is significantly lower at low-Mg2+ conditions. However, the loss of activity is overcompensated by the increased stability of RNA leading to a larger amount of intact ligated substrate after long reaction periods. Combining RNA ligation assays with fatty acid vesicles we found that MA vesicles made of 5 mM amphiphile are stable and do not impair ligase ribozyme activity in the presence of approximately 2 mM Mg2+. These results provide a scenario in which catalytic RNA and primordial membrane assembly can coexist in the same environment.

  19. Social organization of schools of the Scalloped Hammerhead shark, Sphyrna lewini (Griffith and Smith), in the Gulf of California

    Klimley, A. Peter


    The social behavior of the scalloped hammerhead shark is described with an emphasis on determining the function of its polarized schooling. . This shark possesses a refuging social system in which individuals remain in groups in a small core of their home range during the inactive phase of their diel cycle and disperse into the surrounding environment during the active phase. Scalloped hammerhead sharks, followed by ultrasonic telemetry, swam slowly back and forth during the day along the rid...

  20. Generation and Development of RNA Ligase Ribozymes with Modular Architecture Through “Design and Selection”

    Yuki Fujita


    Full Text Available In vitro selection with long random RNA libraries has been used as a powerful method to generate novel functional RNAs, although it often requires laborious structural analysis of isolated RNA molecules. Rational RNA design is an attractive alternative to avoid this laborious step, but rational design of catalytic modules is still a challenging task. A hybrid strategy of in vitro selection and rational design has been proposed. With this strategy termed “design and selection,” new ribozymes can be generated through installation of catalytic modules onto RNA scaffolds with defined 3D structures. This approach, the concept of which was inspired by the modular architecture of naturally occurring ribozymes, allows prediction of the overall architectures of the resulting ribozymes, and the structural modularity of the resulting ribozymes allows modification of their structures and functions. In this review, we summarize the design, generation, properties, and engineering of four classes of ligase ribozyme generated by design and selection.

  1. Intracellular ribozyme-catalyzed trans-cleavage of RNA monitored by fluorescence resonance energy transfer.

    Vitiello, D; Pecchia, D B; Burke, J M


    Small catalytic RNAs like the hairpin ribozyme are proving to be useful intracellular tools; however, most attempts to demonstrate trans-cleavage of RNA by ribozymes in cells have been frustrated by rapid cellular degradation of the cleavage products. Here, we describe a fluorescence resonance energy transfer (FRET) assay that directly monitors cleavage of target RNA in tissue-culture cells. An oligoribonucleotide substrate was modified to inhibit cellular ribonuclease degradation without interfering with ribozyme cleavage, and donor (fluorescein) and acceptor (tetramethylrhodamine) fluorophores were introduced at positions flanking the cleavage site. In simple buffers, the intact substrate produces a strong FRET signal that is lost upon cleavage, resulting in a red-to-green shift in dominant fluorescence emission. Hairpin ribozyme and fluorescent substrate were microinjected into murine fibroblasts under conditions in which substrate cleavage can occur only inside the cell. A strong FRET signal was observed by fluorescence microscopy when substrate was injected, but rapid decay of the FRET signal occurred when an active, cognate ribozyme was introduced with the substrate. No acceleration in cleavage rates was observed in control experiments utilizing a noncleavable substrate, inactive ribozyme, or an active ribozyme with altered substrate specificity. Subsequently, the fluorescent substrates were injected into clonal cell lines that expressed cognate or noncognate ribozymes. A decrease in FRET signal was observed only when substrate was microinjected into cells expressing its cognate ribozyme. These results demonstrate trans-cleavage of RNA within mammalian cells, and provide an experimental basis for quantitative analysis of ribozyme activity and specificity within the cell. PMID:10786853

  2. In vitro evolution of coenzyme-independent variants from the glmS ribozyme structural scaffold.

    Lau, Matthew W L; Ferré-D'Amaré, Adrian R


    Uniquely among known natural ribozymes that cleave RNA sequence-specifically, the glmS ribozyme-riboswitch employs a small molecule, glucosamine-6-phosphate (GlcN6P) as a catalytic cofactor. In vitro selection was employed to search for coenzyme-independent variants of this ribozyme. In addition to shedding light on the catalytic mechanism of the ribozyme, such variants could resemble the evolutionary ancestors of the modern, GlcN6P-regulated ribozyme-riboswitch. A mutant pool was constructed such that the secondary structure elements, which define the triply-pseudoknotted global fold of the ribozyme, was preserved. A stringent selection scheme that relies on thiol-mercury affinity chromatography for separating active and inactive sequences ultimately yielded a triple mutant with a cleavage rate exceeding 3min(-1) that only requires divalent cations for activity. Mutational analysis demonstrated that a point reversion of the variant toward the wild-type sequence was sufficient to partially restore GlcN6P-dependence, suggesting that coenzyme dependence can be readily be acquired by RNAs that adopt the glmS ribozyme fold. The methods employed to perform this selection experiment are described in detail in this review. PMID:27130889

  3. Age validation of great hammerhead shark (Sphyrna mokarran), determined by bomb radiocarbon analysis

    Passerotti, Michelle S.; John K. Carlson; Piercy, Andrew N.; Campana, Steven E.


    Preliminary validation of annual growth band deposition in vertebrae of great hammerhead shark (Sphyrna mokarran) was conducted by using bomb radiocarbon analysis. Adult specimens (n=2) were collected and thin sections of vertebral centra were removed for visual aging and use in radiocarbon assays. Vertebral band counts were used to estimate age, and year of formation was assigned to each growth band by subtracting estimated age from the year of capture. A total of 10 samples were extra...

  4. Effects of fasting and refeeding on intestinal cell proliferation and apoptosis in hammerhead shark (Sphyrna lewini)

    Hideya Takahashi; Susumu Hyodo; Tsukasa Abe; Chiyo Takagi; Grau, Gordon E.; Tatsuya Sakamoto


    Objective: To examine the effects of fasting and refeeding on intestinal cell proliferation and apoptosis in an opportunistic predator, hammerhead shark (Sphyrna lewini) of elasmobranch fishes which are among the earliest known extant groups of vertebrates to have the valvular intestine typical for the primitive species. Methods: Animals were euthanized after 5-10 d of fasting or feeding, or after 10-day fasting and 5-day refeeding. Intestinal apoptosis and cell proliferation w...

  5. Isolation of novel ribozymes that ligate AMP-activated RNA substrates

    Hager, A. J.; Szostak, J. W.


    BACKGROUND: The protein enzymes RNA ligase and DNA ligase catalyze the ligation of nucleic acids via an adenosine-5'-5'-pyrophosphate 'capped' RNA or DNA intermediate. The activation of nucleic acid substrates by adenosine 5'-monophosphate (AMP) may be a vestige of 'RNA world' catalysis. AMP-activated ligation seems ideally suited for catalysis by ribozymes (RNA enzymes), because an RNA motif capable of tightly and specifically binding AMP has previously been isolated. RESULTS: We used in vitro selection and directed evolution to explore the ability of ribozymes to catalyze the template-directed ligation of AMP-activated RNAs. We subjected a pool of 10(15) RNA molecules, each consisting of long random sequences flanking a mutagenized adenosine triphosphate (ATP) aptamer, to ten rounds of in vitro selection, including three rounds involving mutagenic polymerase chain reaction. Selection was for the ligation of an oligonucleotide to the 5'-capped active pool RNA species. Many different ligase ribozymes were isolated; these ribozymes had rates of reaction up to 0.4 ligations per hour, corresponding to rate accelerations of approximately 5 x10(5) over the templated, but otherwise uncatalyzed, background reaction rate. Three characterized ribozymes catalyzed the formation of 3'-5'-phosphodiester bonds and were highly specific for activation by AMP at the ligation site. CONCLUSIONS: The existence of a new class of ligase ribozymes is consistent with the hypothesis that the unusual mechanism of the biological ligases resulted from a conservation of mechanism during an evolutionary replacement of a primordial ribozyme ligase by a more modern protein enzyme. The newly isolated ligase ribozymes may also provide a starting point for the isolation of ribozymes that catalyze the polymerization of AMP-activated oligonucleotides or mononucleotides, which might have been the prebiotic analogs of nucleoside triphosphates.

  6. An improved version of the hairpin ribozyme functions as a ribonucleoprotein complex.

    Sargueil, B; Pecchia, D B; Burke, J M


    Most RNA molecules that are endowed with catalytic activity function in the form of ribonucleoproteins within cells. These complexes are frequently large, poorly defined, and difficult to study. As a model system to study biological catalysis by ribonucleoproteins, we have modified the hairpin ribozyme by inserting an RNA structure that serves as a binding site for bacteriophage R17 coat protein in the form of an extension to ribozyme helix 4, which lies at the periphery of the catalytic domain. In the absence of protein, we find that incorporation of the protein-binding domain increases the catalytic efficiency of the hairpin ribozyme by 2-fold for the cleavage reaction and 16-fold for the ligation reaction. This increase in activity correlates with an increase in the proportion of molecules which fold into the active tertiary structure, as measured by a UV cross-linking assay. Mobility-shift and filter-binding assays of complex formation show that R17 coat protein binds to the chimeric ribozyme with a dissociation constant essentially identical to that of the isolated protein-binding domain; no binding of the protein to the unmodified ribozyme could be detected. The kinetics of cleavage and ligation reactions are not altered by the presence of saturating concentrations of coat protein, and competition studies demonstrate that the protein remains bound to the ribozyme throughout the catalytic cycle. These studies establish that the hairpin ribozyme can be engineered to function efficiently in the form of a ribonucleoprotein in vitro and will serve as the basis for future experimentation to understand mechanisms of protein modulation of catalytic RNA activity, and to introduce other protein-binding domains, for example, HIV-1 rev-binding and tar elements, which may be useful for influencing subcellular localization, regulating intracellular activity, or generating ribozymes that also function as "decoys" in antiviral applications. PMID:7779820

  7. Intracellular ribozyme-catalyzed trans-cleavage of RNA monitored by fluorescence resonance energy transfer.

    Vitiello, D; Pecchia, D B; Burke, J M


    Small catalytic RNAs like the hairpin ribozyme are proving to be useful intracellular tools; however, most attempts to demonstrate trans-cleavage of RNA by ribozymes in cells have been frustrated by rapid cellular degradation of the cleavage products. Here, we describe a fluorescence resonance energy transfer (FRET) assay that directly monitors cleavage of target RNA in tissue-culture cells. An oligoribonucleotide substrate was modified to inhibit cellular ribonuclease degradation without int...

  8. Putative intermediary stages for the molecular evolution from a ribozyme to a catalytic RNP

    IKAWA, YOSHIYA; Tsuda, Kentaro; Matsumura, Shigeyoshi; Atsumi, Shota; Inoue, Tan


    A hypothetical evolutionary pathway from a ribozyme to a catalytic RNA–protein complex (RNP) is proposed and examined. In this hypothesis for an early phase of molecular evolution, one RNA–RNA interaction in the starting ribozyme is replaced with an RNA–protein interaction via two intermediary stages. At each stage, the original RNA–RNA interaction and a newly introduced RNA–protein interaction are designed to coexist. The catalytic RNPs corresponding to the intermediary stages were construct...

  9. A comprehensive study of ribozyme-mediated nucleotide and sugar chemistries

    Lau, Matthew


    The ability of RNA catalysts (ribozymes) to synthesize nucleotides as basic building blocks for the assembly of larger RNA polymers is an important aspect of the 'RNA World' hypothesis. To examine the ability of RNAs to catalyze this chemistry, we performed an in vitro selection in my first project and successfully isolated ribozymes capable of synthesizing a purine nucleotide (6-thioguanosine, 6SG) from tethered 5-phosphoribosyl 1-pyrophosphate (PRPP) and 6-thioguanine (6SGua). Compared to t...

  10. Role of SLV in SLI substrate recognition by the Neurospora VS ribozyme

    Bouchard, Patricia; Lacroix-Labonté, Julie; Desjardins, Geneviève; Lampron, Philipe; Lisi, Véronique; Lemieux, Sébastien; Major, François; Legault, Pascale


    Substrate recognition by the VS ribozyme involves a magnesium-dependent loop/loop interaction between the SLI substrate and the SLV hairpin from the catalytic domain. Recent NMR studies of SLV demonstrated that magnesium ions stabilize a U-turn loop structure and trigger a conformational change for the extruded loop residue U700, suggesting a role for U700 in SLI recognition. Here, we kinetically characterized VS ribozyme mutants to evaluate the contribution of U700 and other SLV loop residue...

  11. Cleavage of an amide bond by a ribozyme

    Dai, X.; De Mesmaeker, A.; Joyce, G. F.; Miller, S. L. (Principal Investigator)


    A variant form of a group I ribozyme, optimized by in vitro evolution for its ability to catalyze magnesium-dependent phosphoester transfer reactions involving DNA substrates, also catalyzes the cleavage of an unactivated alkyl amide when that linkage is presented in the context of an oligodeoxynucleotide analog. Substrates containing an amide bond that joins either two DNA oligos, or a DNA oligo and a short peptide, are cleaved in a magnesium-dependent fashion to generate the expected products. The first-order rate constant, kcat, is 0.1 x 10(-5) min-1 to 1 x 10(-5) min-1 for the DNA-flanked substrates, which corresponds to a rate acceleration of more than 10(3) as compared with the uncatalyzed reaction.

  12. Maternal offloading of organochlorine contaminants in the yolk-sac placental scalloped hammerhead shark (Sphyrna lewini).

    Lyons, Kady; Adams, Douglas H


    Elasmobranchs are a group of animals that typically occupy upper trophic levels in food webs and have a propensity to accumulate high contaminant concentrations. To date, few studies have investigated maternal offloading processes in sharks, despite the fact that this process represents a substantial source of exposure for young sharks and is a significant pathway for contaminant redistribution within marine ecosystems. Comparable to mammalian systems, scalloped hammerhead sharks (Sphyrna lewini) utilize a yolk-sac placental strategy to nourish young in utero, which may allow females to transfer contaminants to young. Organic contaminants (PCBs and chlorinated pesticides) were measured in livers of both females and males from several age classes that were collected from U.S. Atlantic waters, including two near-term pregnant females and their embryos. Adult female hammerheads (n = 3) were found to have lower levels of PCBs compared to the younger, adult male (mean ± SD, 11.1 ± 1.0 vs. 22.8 μg g(-1) lw), but had substantially higher concentrations of pesticides (4.1 ± 0.9 vs. 1.9 μg g(-1) lw). Embryos from the two litters (n = 36) had similar levels of summed organic contaminant concentrations (4.6 ± 0.9 μg g(-1) lw) and pregnant females were estimated to offload approximately 0.03-2.3% of their hepatic contaminant load to offspring. While the potential health impacts of these transferred contaminants is unknown, this is the first study to demonstrate that scalloped hammerheads are exposed to a substantial amount of contaminants prior to birth and document maternal offloading of organochlorines in a pseudo-placental shark species. Therefore, future research should continue to investigate the potential adverse effects these contaminants have on elasmobranch physiology. PMID:25527298

  13. Vulnerability to longline fisheries of three hammerhead shark Sphyrna species in the south-western and equatorial Atlantic Ocean.

    Bezerra, N P A; Travassos, P; Hazin, F H V


    Catch and effort data from 29 418 longline sets from Brazilian tuna longline vessels operating in the south-western and equatorial Atlantic Ocean between 2004 and 2011 were analysed to investigate the distribution, catch rate and size of three species of hammerhead sharks (Sphyrna lewini, Sphyrna mokarran and Sphyrna zygaena). During that period, 6172 hammerhead sharks were caught. Among the elasmobranchs, the highest percentage of hammerhead sharks were caught in 2007, when they accounted for 3·90% of the group, while the lowest value of 0·40% was recorded in 2010. In general, the spatial distribution of the mean catch per unit effort (CPUE) by years and quarters showed a trend of higher catches near the equatorial region and in southern Brazil. The nominal mean CPUE was 0·12 Sphyrna spp. 1000(-1) hooks, with the highest value being recorded in 2007 (0·30 Sphyrna spp. 1000(-1) hooks). The standardized yearly CPUE estimated by a generalized linear model assuming a zero inflated negative binomial (ZINB) distribution were not much different from nominal values. Of the 205 sexed specimens, 117 were females and 88 were males, resulting in a sex ratio with a predominance of females (1·30:1·00), although not statistically significant. The total length of females ranged from 1200 to 2800 mm and of males from 1100 to 3100 mm. Juvenile hammerhead sharks represented 82 and 54% of the sexed female and male specimens, respectively. PMID:27349350

  14. Conservation Genetics of the Scalloped Hammerhead Shark in the Pacific Coast of Colombia.

    Quintanilla, Sonia; Gómez, Alberto; Mariño-Ramírez, Camila; Sorzano, Carolina; Bessudo, Sandra; Soler, German; Bernal, Jaime E; Caballero, Susana


    Previous investigations of the population genetics of the scalloped hammerhead sharks (Sphyrna lewini) in the Eastern Tropical Pacific have lacked information about nursery areas. Such areas are key to promoting conservation initiatives that can protect young sharks from threats such as overfishing. Here, we investigated the genetic diversity, phylogeography, and connectivity of S. lewini found in 3 areas of Colombia's Pacific coast: around Malpelo Island and in 2 National Natural Parks on the Colombian Pacific mainland (Sanquianga and Ensenada de Utría). We analyzed mtDNA control region (CR) sequences and genotyped 15 microsatellite loci in 137 samples of adults and juveniles. The mtDNA analyses showed haplotypes shared between the Colombian Pacific individuals sampled in this investigation and other areas in the Eastern Tropical Pacific, the Indo-Pacific, and with sequences previously reported in Colombia (Buenaventura Port), as well as 4 unique haplotypes. Population assignment and paternity analyses detected 3 parent-offspring pairs between Malpelo and Sanquianga and 1 between Malpelo and Utría. These results indicate high genetic connectivity between Malpelo Island and the Colombian Pacific coast, suggesting that these 2 areas are nurseries for S. lewini. This is, to our knowledge, the first evidence of nursery areas identified for the scalloped hammerhead shark anywhere in the world. Additional conservation planning may be required to protect these nursery habitats of this endangered shark species. PMID:26245780

  15. The complement system of elasmobranches revealed by liver transcriptome analysis of a hammerhead shark, Sphyrna zygaena.

    Goshima, Masayuki; Sekiguchi, Reo; Matsushita, Misao; Nonaka, Masaru


    Comprehensive studies of the complement genes in basal vertebrates have revealed that cyclostomes have apparently primitive complement systems whereas bony fish have well-developed complement systems comparable to those of mammals. Here we have performed liver transcriptome analysis of a hammerhead shark, Sphyrna zygaeana, to elucidate the early history of vertebrate complement evolution. Identified genes were; one C1qB, one C1r, one C1s, one MASP-1/-3, one MASP-2, two factor B/C2, one C3, three C4, one C5, one C6, one C7, one C8A, three C8B, one C8G, one C9, two factor I and one S protein. No MBL, ficolin, C1qA or C1qC were found. These results indicate that the lectin, classical, alternative and lytic pathways were established in the common ancestor of jawed vertebrates. In addition to the absence of MBL and ficolin, the MASP transcripts lacked the serine protease domain, suggesting that the lectin pathway was lost in the hammerhead shark lineage. PMID:26987526

  16. The Effect of Cytidine on the Structure and Function of an RNA Ligase Ribozyme

    Rogers, Jeff; Joyce, Gerald F.


    A cytidine-free ribozyme with RNA ligase activity was obtained by in vitro evolution, starting from a pool of random- sequence RNAs that contained only guanosine, adenosine, and uridine. This ribozyme contains 74 nt and catalyzes formation of a 3',5' -phosphodiester linkage with a catalytic rate of 0.016/min. The RNA adopts a simple secondary structure based on a three-way junction motif, with ligation occurring at the end of a stem region located several nucleotides away from the junction. Cytidine was introduced to the cytidine-free ribozyme in a combinatorial fashion and additional rounds of in vitro evolution were carried out to allow the molecule to adapt to this added component. The resulting cytidine-containing ribozyme formed a 3',5' linkage with a catalytic rate of 0.32/min. The improved rate of the cytidine-containing ribozyme was the result of 12 mutations, including seven added cytidines, that remodeled the internal bulge loops located adjacent to the three-way junction and stabilized the peripheral stem regions.

  17. Calibration Binaries

    Drummond, J.


    Two Excel Spreadsheet files are offered to help calibrate telescope or camera image scale and orientation with binary stars for any time. One is a personally selected list of fixed position binaries and binaries with well-determined orbits, and the other contains all binaries with published orbits. Both are derived from the web site of the Washington Double Star Library. The spreadsheets give the position angle and separation of the binaries for any entered time by taking advantage of Excel's built in iteration function to solve Kepler's transcendental equation.

  18. Investigating single and multiple species fisheries management: stock status evaluation of hammerhead (Sphyrna spp.) sharks in the western North Atlantic Ocean and Gulf of Mexico.

    Hayes, Christopher Glenn


    Three hammerhead sharks (Sphyrna spp.) are currently managed as part of the large coastal shark complex in the United States. Including multiple species in an assessment ignores the different stock dynamics of each individual species within the complex due to different life histories. This study completed individual assessments of scalloped (S. lewini), great (S. mokarran), and smooth (S. zygaena) hammerhead sharks in the U.S. Atlantic Ocean and Gulf of Mexico. Combined data for all three ...

  19. Application of Implicit Space Mapping in the Design of Hammerhead Filter in Millimeter-Wave Band

    Fuqun Zhong


    Full Text Available In this study, we present advances in microwave and millimeter-wave device modeling exploiting the Space Mapping (SM technology. New SM-based modeling techniques are used that are easy to implement entirely in the Agilent ADS framework. The implicit space mapping algorithm is applied to the design of hammerhead filter in millimeter-wave band. The validity of this method is confirmed by comparison with fullwave EM simulation result and measured data. Based on the proposed method, a filter was designed and fabricated on a substrate with thickness of 0.254 mm and dielectric constant of 2.2. The experimental results show good agreement with simulated results. It is proved that the accuracy can be achieved using the implicit space mapping algorithm, and the design efficiency can be greatly improved.

  20. Great hammerhead sharks swim on their side to reduce transport costs.

    Payne, Nicholas L; Iosilevskii, Gil; Barnett, Adam; Fischer, Chris; Graham, Rachel T; Gleiss, Adrian C; Watanabe, Yuuki Y


    Animals exhibit various physiological and behavioural strategies for minimizing travel costs. Fins of aquatic animals play key roles in efficient travel and, for sharks, the functions of dorsal and pectoral fins are considered well divided: the former assists propulsion and generates lateral hydrodynamic forces during turns and the latter generates vertical forces that offset sharks' negative buoyancy. Here we show that great hammerhead sharks drastically reconfigure the function of these structures, using an exaggerated dorsal fin to generate lift by swimming rolled on their side. Tagged wild sharks spend up to 90% of time swimming at roll angles between 50° and 75°, and hydrodynamic modelling shows that doing so reduces drag-and in turn, the cost of transport-by around 10% compared with traditional upright swimming. Employment of such a strongly selected feature for such a unique purpose raises interesting questions about evolutionary pathways to hydrodynamic adaptations, and our perception of form and function. PMID:27457414

  1. A novel strategy for selection of allosteric ribozymes yields RiboReporter™ sensors for caffeine and aspartame

    Ferguson, Alicia; Boomer, Ryan M.; Kurz, Markus; Keene, Sara C.; Diener, John L.; Keefe, Anthony D.; Wilson, Charles; Cload, Sharon T.


    We have utilized in vitro selection technology to develop allosteric ribozyme sensors that are specific for the small molecule analytes caffeine or aspartame. Caffeine- or aspartame-responsive ribozymes were converted into fluorescence-based RiboReporter™ sensor systems that were able to detect caffeine or aspartame in solution over a concentration range from 0.5 to 5 mM. With read-times as short as 5 min, these caffeine- or aspartame-dependent ribozymes function as highly specific and facile...

  2. Interacting binaries

    Shore, S N; van den Heuvel, EPJ


    This volume contains lecture notes presented at the 22nd Advanced Course of the Swiss Society for Astrophysics and Astronomy. The contributors deal with symbiotic stars, cataclysmic variables, massive binaries and X-ray binaries, in an attempt to provide a better understanding of stellar evolution.

  3. The emergence of ribozymes synthesizing membrane components in RNA-based protocells.

    Ma, Wentao; Yu, Chunwu; Zhang, Wentao; Zhou, Ping; Hu, Jiming


    A significant problem of the origin of life is the emergence of cellular self-replication. In the context of the "RNA world", a crucial concern is how the RNA-based protocells could achieve the ability to produce their own membrane. Here we show, with the aid of a computer simulation, that for these protocells, there would be "immediately" a selection pressure for the emergence of a ribozyme synthesizing membrane components. The ribozyme would promote the enlargement of cellular space and favor the incoming (by permeation) of RNA's precursors, thus benefit the replication of inner RNA, including itself. Via growth and division, protocells containing the ribozyme would achieve superiority and spread in the system, and meanwhile the ribozyme would spread in the system. The present work is inspiring because it suggests that the transition from molecular self-replication to cellular self-replication might have occurred naturally (and necessarily) in the origin of life, leading to the emergence of Darwinian evolution at the cellular level. PMID:19961895

  4. Ribozyme Activity of RNA Nonenzymatically Polymerized from 3 ',5 '-Cyclic GMP

    Pino, S.; Costanzo, G.; Giorgi, A.; Šponer, Jiří; Šponer, Judit E.; Di Mauro, E.


    Roč. 15, č. 12 (2013), s. 5362-5383. ISSN 1099-4300 R&D Projects: GA ČR(CZ) GAP208/10/2302; GA MŠk(CZ) ED1.1.00/02.0068 Institutional support: RVO:68081707 Keywords : RNA polymerization * RNA origin * ribozymes Subject RIV: BO - Biophysics Impact factor: 1.564, year: 2013

  5. Wobble pairs of the HDV ribozyme play specific roles in stabilization of active site dynamics

    Sripathi, K.N.; Banáš, P.; Réblová, K.; Šponer, Jiří; Otyepka, M.; Walter, Nils G.


    Roč. 17, č. 8 (2015), s. 5887-5900. ISSN 1463-9076 R&D Projects: GA ČR GAP208/12/1878 Institutional support: RVO:68081707 Keywords : HEPATITIS-DELTA-VIRUS * SELF-CLEAVING RIBOZYMES * ACID-BASE CATALYSIS Subject RIV: BO - Biophysics Impact factor: 4.493, year: 2014

  6. Feeding strategy of the night shark (Carcharhinus signatus) and scalloped hammerhead shark (Sphyrna lewini) near seamounts off northeastern Brazil

    Teodoro Vaske Júnior; Carolus Maria Vooren; Rosangela Paula Lessa


    A total of 425 stomachs of night shark (Carcharhinus signatus), and 98 stomachs of scalloped hammerhead shark (Sphyrna lewini), from longline and surface gillneters near seamounts off northeastern Brazil, were analysed between 1992 and 1999. Both predators prey upon reef and benthopelagic fishes, migrant cephalopods and deep water crustaceans, showing similar feeding niches (Schoener Index T=0.75). The great prey richness of the diets may reflect the fact that the marine food web for these sp...

  7. Stomach content analysis of juvenile, scalloped hammerhead shark Sphyrna lewini captured off the coast of Mazatlan, Mexico

    Torres Rojas, Yassir E.; Hernández Herrera, Agustin; Galván Magaña, Felipe; Alatorre Ramírez, Vanessa Guadalupe


    We quantified the diet of juvenile, scalloped hammerhead shark Sphyrna lewini in the area off Mazatlan, Sinaloa, Mexico, to understand their feeding ecology this shark. The prey species of Sphyrna lewini were identified and quantified from stomach content analysis. In addition, we determined the variations between genders. During two fishing seasons (2000–2001 and 2001–2002), we analyzed 232 stomachs, of which 85% contained food. The trophic spectrum was composed of three species of cephalopo...

  8. Structural and Chemical Basis for Glucosamine 6-Phosphate Binding and Activation of the glmS Ribozyme

    Cochrane, J.; Lipchock, S; Smith, K; Strobel, S


    The glmS ribozyme is the first naturally occurring catalytic RNA that relies on an exogenous, nonnucleotide cofactor for reactivity. From a biochemical perspective, the glmS ribozyme derived from Bacillus anthracis is the best characterized. However, much of the structural work to date has been done on a variant glmS ribozyme, derived from Thermoanaerobacter tengcongensis. Here we present structures of the B. anthracis glmS ribozyme in states before the activating sugar, glucosamine 6-phosphate (GlcN6P), has bound and after the reaction has occurred. These structures show an active site preorganized to bind GlcN6P that retains some affinity for the sugar even after cleavage of the RNA backbone. A structure of an inactive glmS ribozyme with a mutation distal from the ligand-binding pocket highlights a nucleotide critical to the reaction that does not affect GlcN6P binding. Structures of the glmS ribozyme bound to a naturally occurring inhibitor, glucose 6-phosphate (Glc6P), and a nonnatural activating sugar, mannosamine 6-phosphate (MaN6P), reveal a binding mode similar to that of GlcN6P. Kinetic analyses show a pH dependence of ligand binding that is consistent with titration of the cofactor's phosphate group and support a model in which the major determinant of activity is the sugar amine independent of its stereochemical presentation.

  9. Effects of fasting and refeeding on intestinal cell proliferation and apoptosis in hammerhead shark (Sphyrna lewini

    Hideya Takahashi


    Full Text Available Objective: To examine the effects of fasting and refeeding on intestinal cell proliferation and apoptosis in an opportunistic predator, hammerhead shark (Sphyrna lewini of elasmobranch fishes which are among the earliest known extant groups of vertebrates to have the valvular intestine typical for the primitive species. Methods: Animals were euthanized after 5-10 d of fasting or feeding, or after 10-day fasting and 5-day refeeding. Intestinal apoptosis and cell proliferation were assessed by using oligonucleotide detection assay, terminal deoxynucleotidyl transferase dUTP nick end labeling staining, and immunohistochemistry of proliferating cells nuclear antigen. Results: Plasma levels of cholesterol and glucose were reduced by fasting. Intestinal apoptosis generally decreased during fasting. Numerous apoptotic cells were observed around the tips of the villi, primarily in the epithelium in the fed sharks, whereas fewer labeled nuclei were detected in the epithelium of fasted sharks. Refeeding returned intestinal apoptosis to the level in the fed sharks. Proliferating cells were observed in the epithelium around the troughs of the villi and greater in number in fed sharks, whereas fewer labeled nuclei were detected in fasted sharks. Conclusions: The cell turnover is modified in both intestinal epithelia of the shark and the murines by fasting/feeding, but in opposite directions. The difference may reflect the feeding ecology of the elasmobranchs, primitive intermittent feeders.

  10. Effects of fasting and refeeding on intestinal cell proliferation and apoptosis in hammerhead shark (Sphyrna lewini)

    Hideya Takahashi; Susumu Hyodo; Tsukasa Abe; Chiyo Takagi; Gordon E Grau; Tatsuya Sakamoto


    Objective: To examine the effects of fasting and refeeding on intestinal cell proliferation and apoptosis in an opportunistic predator, hammerhead shark (Sphyrna lewini) of elasmobranch fishes which are among the earliest known extant groups of vertebrates to have the valvular intestine typical for the primitive species.Methods:5-day refeeding. Intestinal apoptosis and cell proliferation were assessed by using oligonucleotide detection assay, terminal deoxynucleotidyl transferase dUTP nick end labeling staining, and immunohistochemistry of proliferating cells nuclear antigen.Results:Animals were euthanized after 5-10 d of fasting or feeding, or after 10-day fasting and generally decreased during fasting. Numerous apoptotic cells were observed around the tips of the villi, primarily in the epithelium in the fed sharks, whereas fewer labeled nuclei were detected in the epithelium of fasted sharks. Refeeding returned intestinal apoptosis to the level in the fed sharks. Proliferating cells were observed in the epithelium around the troughs of the villi and greater in number in fed sharks, whereas fewer labeled nuclei were detected in fasted sharks. Plasma levels of cholesterol and glucose were reduced by fasting. Intestinal apoptosis Conclusions: The cell turnover is modified in both intestinal epithelia of the shark and the murines by fasting/feeding, but in opposite directions. The difference may reflect the feeding ecology of the elasmobranchs, primitive intermittent feeders.

  11. RNA-based networks: using RNA aptamers and ribozymes as synthetic genetic devices.

    Weigand, Julia E; Wittmann, Alexander; Suess, Beatrix


    Within the last few years, a set of synthetic riboswitches has been engineered, which expands the toolbox of genetic regulatory devices. Small molecule binding aptamers have been used for the design of such riboswitches by insertion into untranslated regions of mRNAs, exploiting the fact that upon ligand binding the RNA structure interferes either with translation initiation or pre-mRNA splicing in yeast. In combination with self-cleaving ribozymes, aptamers have been used to modulate RNA stability. In this chapter, we discuss the applicability of different aptamers, ways to identify novel genetic devices, the pros and cons of various insertion sites and the application of allosteric ribozymes. Our expertise help to apply synthetic riboswitches to engineer complex genetic circuits. PMID:22083741

  12. The Hairpin Ribozyme Substrate Binding-domain: A Highly Constrained D-shaped Conformation

    Pinard, Robert; Lambert, Dominic; Heckman, Joyce; Esteban, José A.; Gundlach IV, William; Hampel, Ken J.; Glick, Gary D.; Walter, Nils; Major, François; John M. Burke


    The two domains of the hairpin ribozyme-substrate complex, usually depicted as straight structural elements, must interact with one another in order to form an active conformation. Little is known about the internal geometry of the individual domains in an active docked complex. Using various crosslinking and structural approaches in conjunction with molecular modeling (constraint-satisfaction program MC-SYM), we have investigated the conformation of the substrate-binding do...

  13. Bacterial Riboswitches and Ribozymes Potently Activate the Human Innate Immune Sensor PKR.

    Hull, Chelsea M; Anmangandla, Ananya; Bevilacqua, Philip C


    The innate immune system provides the first line of defense against pathogens through the recognition of nonspecific patterns in RNA to protect the cell in a generalized way. The human RNA-activated protein kinase, PKR, is a dsRNA binding protein and an essential sensor in the innate immune response, which recognizes viral and bacterial pathogens through their RNAs. Upon activation via RNA-dependent autophosphorylation, PKR phosphorylates the eukaryotic initiation factor eIF2α, leading to termination of translation. PKR has a well-characterized role in recognizing viral RNA, where it binds long stretches of double-stranded RNA nonsequence specifically to promote activation; however, the mechanism by which bacterial RNA activates PKR and the mode by which self RNA avoids activating PKR are unknown. We characterized activation of PKR by three functional bacterial RNAs with pseudoknots and extensive tertiary structure: the cyclic di-GMP riboswitch, the glmS riboswitch-ribozyme, and the twister ribozyme, two of which are ligand-activated. These RNAs were found to activate PKR with comparable potency to long dsRNA. Enzymatic structure mapping in the absence and presence of PKR reveals a clear PKR footprint and provides a structural basis for how these bacterial RNAs activate PKR. In the case of the cyclic di-GMP riboswitch and the glmS riboswitch-ribozyme, PKR appears to dimerize on the peripheral double-stranded regions of the native RNA tertiary structure. Overall, these results provide new insights into how PKR acts as an innate immune signaling protein for the presence of bacteria and suggest a reason for the apparent absence of protein-free riboswitches and ribozymes in the human genome. PMID:27011290

  14. Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape

    Sripathi, K.N.; Tay, W.W.; Banáš, P.; Otyepka, M.; Šponer, Jiří; Walter, N. G.


    Roč. 20, č. 7 (2014), s. 1112-1128. ISSN 1355-8382 R&D Projects: GA MŠk(CZ) ED1.1.00/02.0068; GA ČR(CZ) GAP208/12/1878 Institutional support: RVO:68081707 Keywords : time-resolved FRET * steady-state FRET * small ribozyme Subject RIV: BO - Biophysics Impact factor: 4.936, year: 2014

  15. Nucleotide synthetase ribozymes may have emerged first in the RNA world

    Ma, Wentao; Yu, Chunwu; Zhang, Wentao; Hu, Jiming


    Though the “RNA world” hypothesis has gained a central role in ideas concerning the origin of life, the scenario concerning its emergence remains uncertain. It has been speculated that the first scene may have been the emergence of a template-dependent RNA synthetase ribozyme, which catalyzed its own replication: thus, “RNA replicase.” However, the speculation remains uncertain, primarily because of the large sequence length requirement of such a replicase and the lack of a convincing mechani...

  16. Gene silencing of HIV chemokine receptors using ribozymes and single-stranded antisense RNA.

    Qureshi, Amer; Zheng, Richard; Parlett, Terry; Shi, Xiaoju; Balaraman, Priyadhashini; Cheloufi, Sihem; Murphy, Brendan; Guntermann, Christine; Eagles, Peter


    The chemokine receptors CXCR4 and CCR5 are required for HIV-1 to enter cells, and the progression of HIV-1 infection to AIDS involves a switch in the co-receptor usage of the virus from CCR5 to CXCR4. These receptors therefore make attractive candidates for therapeutic intervention, and we have investigated the silencing of their genes by using ribozymes and single-stranded antisense RNAs. In the present study, we demonstrate using ribozymes that a depletion of CXCR4 and CCR5 mRNAs can be achieved simultaneously in human PBMCs (peripheral blood mononuclear cells), cells commonly used by the virus for infection and replication. Ribozyme activity leads to an inhibition of the cell-surface expression of both CCR5 and CXCR4, resulting in a significant inhibition of HIV-1 replication when PBMCs are challenged with the virus. In addition, we show that small single-stranded antisense RNAs can also be used to silence CCR5 and CXCR4 genes when delivered to PBMCs. This silencing is caused by selective degradation of receptor mRNAs. PMID:16293105

  17. Magnesium-Dependent Active-Site Conformational Selection in the Diels-Alderase Ribozyme

    Berezniak, Tomasz [University of Heidelberg; Zahran, Mai [ORNL; Imhof, Petra [University of Heidelberg; Jaeschke, Andres [Free University of Berlin; Smith, Jeremy C [ORNL


    The Diels-Alderase ribozyme, an in vitro-evolved ribonucleic acid enzyme, accelerates the formation of carbon-carbon bonds between an anthracene diene and a maleimide dienophile in a [4 + 2] cycloaddition, a reaction with broad application in organic chemistry. Here, the Diels-Alderase ribozyme is examined via molecular dynamics (MD) simulations in both crystalline and aqueous solution environments. The simulations indicate that the catalytic pocket is highly dynamic. At low Mg(2+) ion concentrations, inactive states with the catalytic pocket closed dominate. Stabilization of the enzymatically active, open state of the catalytic pocket requires a high concentration of Mg(2+) ions (e.g., 54 mM), with cations binding to specific phosphate sites on the backbone of the residues bridging the opposite strands of the pocket. The free energy profile for pocket opening at high Mg(2+) cation concentration exhibits a double minimum, with a barrier to opening of approximately 5.5 kJ/mol and the closed state approximately 3 kJ/mol lower than the open state. Selection of the open state on substrate binding leads to the catalytic activity of the ribozyme. The simulation results explain structurally the experimental observation that full catalytic activity depends on the Mg(2+) ion concentration

  18. The structure of the isolated, central hairpin of the HDV antigenomic ribozyme: novel structural features and similarity of the loop in the ribozyme and free in solution.

    Kolk, M H; Heus, H A; Hilbers, C W


    The structure of an RNA hairpin containing a seven-nucleotide loop that is present in the self-cleaving sequence of hepatitis delta virus antigenomic RNA was determined by high resolution NMR spectroscopy. The loop, which is composed of only one purine and six pyrimidines, has a suprisingly stable structure, mainly supported by sugar hydroxyl hydrogen bonds and base-base and base-phosphate stacking interactions. Compared with the structurally well-determined, seven-membered anticodon loop in tRNA, the sharp turn which affects the required 180 degrees change in direction of the sugar-phosphate backbone in the loop is shifted one nucleotide in the 3' direction. This change in direction can be characterized as a reversed U-turn. It is expected that the reversed U-turn may be found frequently in other molecules as well. There is evidence for a new non-Watson-Crick UC base pair formed between the first and the last residue in the loop, while most of the other bases in the loop are pointing outwards making them accessible to solvent. From chemical modification, mutational and photocrosslinking studies, a similar picture develops for the structure of the hairpin in the active ribozyme indicating that the loop structure in the isolated hairpin and in the ribozyme is very similar. PMID:9218809

  19. Inhibition of K562 cell growth and tumor angiogenesis in nude mice by transfection of anti-VEGF hairpin ribozyme gene into the cells



    Objective To explore the effect of anti-VEGF hairpin ribozyme gene on the tumor cell growth and tumor angiogenesis in nude mice. Methods The recombinant eukaryotic expression plasmid pcDNA-RZ containing anti-VEGF hairpin ribozyme gene and the empty vector plasmid pcDNA were introduced separately into K562 cells

  20. A conformational switch in the DiGIR1 ribozyme involved in release and folding of the downstream I-DirI mRNA

    Nielsen, Henrik; Einvik, Christer; Lentz, Thomas E;


    DiGIR1 is a group I-like cleavage ribozyme found as a structural domain within a nuclear twin-ribozyme group I intron. DiGIR1 catalyzes cleavage by branching at an Internal Processing Site (IPS) leading to formation of a lariat cap at the 5'-end of the 3'-cleavage product. The 3'-cleavage product...


    冯琦; 孙凯; 赵永同; 张涛; 尚振川; 王莎; 王玮; 赵宁; 颜真; 韩苇; 张英起; 孙秉中


    Objective: To investigate the in vitro cleavage ability and effects on apoptosis and cell growth of the bcr-abl fusion gene specific multi-unit ribozymes. Methods: Three fusion point specific ribozymes were designed and the multi-unit ribozymes' in vitro transcription vector and retroviral vector were constructed. The in vitro cleavage ability was tested. The retroviral vector was transfected into K562 cell and the effects on proliferation, apoptosis, cell cycle and cell structure were observed. Results: Multi-unit ribozymes had in vitro cleavage efficiency of 70.8%, which was more efficient than single-unit and double-unit ribozymes. Transfection of the retroviral vector of the ribozyme into K562 cells, induced inhibition of cell growth and apoptosis. The incorporation rate of DNA in ribozymes transfected K562 cells was greatly decreased along with time passed, with an inhibition rate of more than 50% after 96 h of transfection. Under FCM, 18.4% of the cells underwent apoptosis 72 h after transfection and more cells were blocked in G phase, with the ratio in S phase greatly decreased (41.9%). Under electron microscope, compaction of nuclear chromatin and apoptosis bodies were observed.Conclusion: Multi-unit ribozymes specific to bcr-abl fusion gene can be used to treat CML and to purge bone marrow for self-grafting.

  2. Binary Planets

    Ryan, Keegan; Nakajima, Miki; Stevenson, David J.


    Can a bound pair of similar mass terrestrial planets exist? We are interested here in bodies with a mass ratio of ~ 3:1 or less (so Pluto/Charon or Earth/Moon do not qualify) and we do not regard the absence of any such discoveries in the Kepler data set to be significant since the tidal decay and merger of a close binary is prohibitively fast well inside of 1AU. SPH simulations of equal mass “Earths” were carried out to seek an answer to this question, assuming encounters that were only slightly more energetic than parabolic (zero energy). We were interested in whether the collision or near collision of two similar mass bodies would lead to a binary in which the two bodies remain largely intact, effectively a tidal capture hypothesis though with the tidal distortion being very large. Necessarily, the angular momentum of such an encounter will lead to bodies separated by only a few planetary radii if capture occurs. Consistent with previous work, mostly by Canup, we find that most impacts are disruptive, leading to a dominant mass body surrounded by a disk from which a secondary forms whose mass is small compared to the primary, hence not a binary planet by our adopted definition. However, larger impact parameter “kissing” collisions were found to produce binaries because the dissipation upon first encounter was sufficient to provide a bound orbit that was then rung down by tides to an end state where the planets are only a few planetary radii apart. The long computational times for these simulation make it difficult to fully map the phase space of encounters for which this outcome is likely but the indications are that the probability is not vanishingly small and since planetary encounters are a plausible part of planet formation, we expect binary planets to exist and be a non-negligible fraction of the larger orbital radius exoplanets awaiting discovery.

  3. Demographic processes underlying subtle patterns of population structure in the scalloped hammerhead shark, Sphyrna lewini.

    Holly A Nance

    Full Text Available Genetic diversity (θ, effective population size (N(e, and contemporary levels of gene flow are important parameters to estimate for species of conservation concern, such as the globally endangered scalloped hammerhead shark, Sphyrna lewini. Therefore, we have reconstructed the demographic history of S. lewini across its Eastern Pacific (EP range by applying classical and coalescent population genetic methods to a combination of 15 microsatellite loci and mtDNA control region sequences. In addition to significant population genetic structure and isolation-by-distance among seven coastal sites between central Mexico and Ecuador, the analyses revealed that all populations have experienced a bottleneck and that all current values of θ are at least an order of magnitude smaller than ancestral θ, indicating large decreases in N(e (θ = 4N(eμ, where μ is the mutation rate. Application of the isolation-with-migration (IM model showed modest but significant genetic connectivity between most sampled sites (point estimates of Nm = 0.1-16.7, with divergence times (t among all populations significantly greater than zero. Using a conservative (i.e., slow fossil-based taxon-specific phylogenetic calibration for mtDNA mutation rates, posterior probability distributions (PPDs for the onset of the decline in N(e predate modern fishing in this region. The cause of decline over the last several thousand years is unknown but is highly atypical as a post-glacial demographic history. Regardless of the cause, our data and analyses suggest that S. lewini was far more abundant throughout the EP in the past than at present.

  4. Thiosulfate-Hydrogen Peroxide Redox Oscillator as pH Driver for Ribozyme Activity in the RNA World

    Ball, Rowena; Brindley, John


    The RNA world of more than 3.7 billion years ago may have drawn on thermal and pH oscillations set up by the oxidation of thiosulfate by hydrogen peroxide (the THP oscillator) as a power source to drive replication. Since this primordial RNA also must have developed enzyme functionalities, in this work we examine the responses of two simple ribozymes to a THP periodic drive, using experimental rate and thermochemical data in a dynamical model for the coupled, self-consistent evolution of all reactants and intermediates. The resulting time traces show that ribozyme performance can be enhanced under pH cycling, and that thermal cycling may have been necessary to achieve large performance gains. We discuss three important ways in which the dynamic hydrogen peroxide medium may have acted as an agent for development of the RNA world towards a cellular world: proton gradients, resolution of the ribozyme versus replication paradox, and vesicle formation.

  5. Short-term sequence evolution and vertical inheritance of the Naegleria twin-ribozyme group I intron

    De Jonckheere Johan F


    Full Text Available Abstract Background Ribosomal DNA of several species of the free-living Naegleria amoeba harbors an optional group I intron within the nuclear small subunit ribosomal RNA gene. The intron (Nae.S516 has a complex organization of two ribozyme domains (NaGIR1 and NaGIR2 and a homing endonuclease gene (NaHEG. NaGIR2 is responsible for intron excision, exon ligation, and full-length intron RNA circularization, reactions typical for nuclear group I intron ribozymes. NaGIR1, however, is essential for NaHEG expression by generating the 5' end of the homing endonuclease messenger RNA. Interestingly, this unusual class of ribozyme adds a lariat-cap at the mRNA. Results To elucidate the evolutionary history of the Nae.S516 twin-ribozyme introns we have analyzed 13 natural variants present in distinct Naegleria isolates. Structural variabilities were noted within both the ribozyme domains and provide strong comparative support to the intron secondary structure. One of the introns, present in N. martinezi NG872, contains hallmarks of a degenerated NaHEG. Phylogenetic analyses performed on separate data sets representing NaGIR1, NaGIR2, NaHEG, and ITS1-5.8S-ITS2 ribosomal DNA are consistent with an overall vertical inheritance pattern of the intron within the Naegleria genus. Conclusion The Nae.S516 twin-ribozyme intron was gained early in the Naegleria evolution with subsequent vertical inheritance. The intron was lost in the majority of isolates (70%, leaving a widespread but scattered distribution pattern. Why the apparent asexual Naegleria amoebae harbors active intron homing endonucleases, dependent on sexual reproduction for its function, remains a puzzle.

  6. Flanking sequences with an essential role in hydrolysis of a self-cleaving group I-like ribozyme

    Einvik, C; Nielsen, Henrik; Nour, R; Johansen, S


    that identify RNA elements critical for hydrolysis outside the DiGIR1 ribozyme core moiety. Results from deletion analysis, disruption/compensation mutagenesis and RNA structure probing analysis all support the existence of two new segments, named P2 and P2.1, involved in the hydrolysis of DiGIR1....... Significant decreases in the hydrolysis rate, k (obs), were observed in disruption mutants involving both segments. These effects were restored by compensatory base pairing mutants. The possible role of P2 is to tether the ribozyme core, whereas P2.1 appears to be more directly involved in catalysis....

  7. Molecular dynamics simulations of hepatitis delta virus and hairpin ribozymes: Distinct strategies to use pockets of deep electrostatic potential minima

    Šponer, Jiří; Krasovská, Maryna V.; Réblová, Kamila; Šefčíková, J.; Rhodes, M.M.; Walter, N.G.

    Albany, 2007. s. 693. ISSN 0739-1102. [The 15th Conversation. 19.06.2007-23.06.2007, Albany] Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : delta virus * ribozymes Subject RIV: BO - Biophysics

  8. Analysis of the tertiary structure of the ribonuclease P ribozyme-substrate complex by site-specific photoaffinity crosslinking.

    Harris, M E; Kazantsev, A V; Chen, J L; Pace, N R


    Bacterial ribonuclease P (RNase P), an endonuclease involved in tRNA maturation, is a ribonucleoprotein containing a catalytic RNA. The secondary structure of this ribozyme is well-established, and a low-resolution model of the three-dimensional structure of the ribozyme-substrate complex has been proposed based on site-specific crosslinking and phylogenetic comparative data [Harris ME et al., 1994 EMBO J 13:3953-3963]. However, several substructures of that model were poorly constrained by the available data. In the present analysis, additional constraints between elements within the Escherichia coli RNase P RNA-pre-tRNA complex were determined by intra- and intermolecular crosslinking experiments. Circularly permuted RNase P RNAs were used to position an azidophenacyl photoactive crosslinking agent specifically at strategic sites within the ribozyme-substrate complex. Crosslink sites were mapped by primer extension and confirmed by analysis of the mobility of the crosslinked RNA lariats on denaturing acrylamide gels relative to circular and linear RNA standards. Crosslinked species generally retained significant catalytic activity, indicating that the results reflect the native ribozyme structure. The crosslinking results support the general configuration of the structure model and predicate new positions and orientations for helices that were previously poorly constrained by the data set. The expanded library of crosslinking constraints was used, together with secondary and tertiary structure identified by phylogenetic sequence comparisons, to refine significantly the model of RNase P RNA with bound substrate pre-tRNA. The crosslinking results and data from chemical-modification and mutational studies are discussed in the context of the current structural perspective on this ribozyme. PMID:9174092

  9. 破碎机锤头铸造成型数值模拟%Numerical Simulation of Casting Process for Crusher Hammerhead

    易克传; 乔印虎


    锤击式破碎机锤头在使用中受交变力的作用,极易磨损乃至失效破坏.在有限元应力分析基础上,找出极易发生破坏的部位.通过材料的合理选择,铸造工艺的合理设计,并进行锤头铸造模拟,确保了铸件质量,以便延长锤头使用寿命,提高设计效率.%Crusher hammerhead is exerted force of alternate change in working. Fatigue loads can lead to damage and eventually to failures of hammer. Based on the finite element stress analysis, the site of easy damage was identified. Through the choice of proper material, the design of rational casting process and simulation of casting process for hammerhead, the quality of castings was ensured to extend the hammerhead life and to improve design efficiency.

  10. Dynamic signal processing by ribozyme-mediated RNA circuits to control gene expression

    Shen, Shensi; Rodrigo, Guillermo; Prakash, Satya; Majer, Eszter; Landrain, Thomas E.; Kirov, Boris; Daròs, José-Antonio; Jaramillo, Alfonso


    Organisms have different circuitries that allow converting signal molecule levels to changes in gene expression. An important challenge in synthetic biology involves the de novo design of RNA modules enabling dynamic signal processing in live cells. This requires a scalable methodology for sensing, transmission, and actuation, which could be assembled into larger signaling networks. Here, we present a biochemical strategy to design RNA-mediated signal transduction cascades able to sense small molecules and small RNAs. We design switchable functional RNA domains by using strand-displacement techniques. We experimentally characterize the molecular mechanism underlying our synthetic RNA signaling cascades, show the ability to regulate gene expression with transduced RNA signals, and describe the signal processing response of our systems to periodic forcing in single live cells. The engineered systems integrate RNA–RNA interaction with available ribozyme and aptamer elements, providing new ways to engineer arbitrary complex gene circuits. PMID:25916845

  11. Inducible Expression and Splicing of Candida Group Ⅰ Ribozyme in E.coli

    SHANG Yuan; WANG Chen; ZHANG Yi


    The Ca. LSU intron flanking a 129 bp exon upstream and a 100 bp exon downstream was inserted into the lacZ gene on pRS426 to transform E. coli. Northern blot analysis and RT-PCR showed that splicing of Ca. LSU in E.coli is efficient upon inducible expression of the precursor RNA. In contrast, co-transcriptional self-splicing of the intron in vitro is much less active. Therefore, this E. coli splicing system can be used as a better model to investigate the effect of the ribozyme inhibitors on Ca. LSU splicing in living cell. We examined the effects of neomycin sulfate and pentamidine on Ca. LSU splicing in E. coli, and found that these drugs does-dependently inhibit the intron splicing.However, heomycin is more potent than pentamidine in this action.

  12. Chemical Feasibility of the General Acid/Base Mechanism of glmS Ribozyme Self-Cleavage

    Dubecký, M.; Walter, Nils G.; Šponer, Jiří; Otyepka, M.; Banáš, Pavel


    Roč. 103, č. 10 (2015), s. 550-562. ISSN 0006-3525 R&D Projects: GA MŠk(CZ) ED1.1.00/02.0068; GA ČR(CZ) GAP208/12/1878 Institutional support: RVO:68081707 Keywords : MOLECULAR-DYNAMICS SIMULATIONS * ACTIVE-SITE GUANINE * HAIRPIN RIBOZYME Subject RIV: BO - Biophysics Impact factor: 2.385, year: 2014

  13. Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme

    Mlýnský, V.; Banáš, P.; Šponer, Jiří; van der Kamp, M.W.; Mulholland, A.J.; Otyepka, M.


    Roč. 10, č. 4 (2014), s. 1608-1622. ISSN 1549-9618 R&D Projects: GA ČR(CZ) GAP208/12/1878; GA ČR(CZ) GBP301/11/P558; GA MŠk(CZ) ED1.1.00/02.0068 Institutional support: RVO:68081707 Keywords : MOLECULAR-DYNAMICS SIMULATIONS * DELTA-VIRUS RIBOZYME * ACID- BASE CATALYSIS Subject RIV: BO - Biophysics Impact factor: 5.498, year: 2014

  14. Induction of wild-type p53 activity in human cancer cells by ribozymes that repair mutant p53 transcripts

    Watanabe, Takashi; Sullenger, Bruce A


    Several groups have attempted to develop gene therapy strategies to treat cancer via introduction of the wild-type (wt) p53 cDNA into cancer cells. Unfortunately, these approaches do not result in regulated expression of the p53 gene and do not reduce expression of the mutant p53 that is overexpressed in cancerous cells. These shortcomings may greatly limit the utility of this gene replacement approach. We describe an alternative strategy with trans-splicing ribozymes that can simultaneously ...

  15. Tailing cDNAs with terminal deoxynucleotidyl transferase in RT-PCR assays to identify ribozyme cleavage products.

    Albuquerque-Silva, J; Houard, S.; Bollen, A.


    Polytailing a cDNA with terminal deoxynucleotidyltransferase (TdT) results in the addition of a homopolymeric sequence at its 3'-end. Here we describe the use of tailing in competitive RT-PCR assays to evaluate cleavage efficiency of ribozymes. Using a system that perfectly mimics intracellular cleavage, we were able to detect as few as 1% of cleaved moieties. Furthermore, employing primers overlapping the junction between tails and the cleaved RNA moiety in non-competitive assays, the sensit...

  16. Chemical feasibility of the general acid/base mechanism of glmS ribozyme self-cleavage.

    Dubecký, Matúš; Walter, Nils G; Šponer, Jiří; Otyepka, Michal; Banáš, Pavel


    In numerous Gram-positive bacteria, the glmS ribozyme or catalytic riboswitch regulates the expression of glucosamine-6-phosphate (GlcN6P) synthase via site-specific cleavage of its sugar-phosphate backbone in response to GlcN6P ligand binding. Biochemical data have suggested a crucial catalytic role for an active site guanine (G40 in Thermoanaerobacter tengcongensis, G33 in Bacillus anthracis). We used hybrid quantum chemical/molecular mechanical (QM/MM) calculations to probe the mechanism where G40 is deprotonated and acts as a general base. The calculations suggest that the deprotonated guanine G40(-) is sufficiently reactive to overcome the thermodynamic penalty arising from its rare protonation state, and thus is able to activate the A-1(2'-OH) group toward nucleophilic attack on the adjacent backbone. Furthermore, deprotonation of A-1(2'-OH) and nucleophilic attack are predicted to occur as separate steps, where activation of A-1(2'-OH) precedes nucleophilic attack. Conversely, the transition state associated with the rate-determining step corresponds to concurrent nucleophilic attack and protonation of the G1(O5') leaving group by the ammonium moiety of the GlcN6P cofactor. Overall, our calculations help to explain the crucial roles of G40 (as a general base) and GlcN6P (as a general acid) during glmS ribozyme self-cleavage. In addition, we show that the QM/MM description of the glmS ribozyme self-cleavage reaction is significantly more sensitive to the size of the QM region and the quality of the QM-MM coupling than that of other small ribozymes. PMID:25858644

  17. Binary effectivity rules

    Keiding, Hans; Peleg, Bezalel


    Abstract  A social choice rule (SCR) is a collection of social choice correspondences, one for each agenda. An effectivity rule is a collection of effectivity functions, one for each agenda. We prove that every monotonic and superadditive effectivity rule is the effectivity rule of some SCR. A SCR...... is binary if it is rationalized by an acyclic binary relation. The foregoing result motivates our definition of a binary effectivity rule as the effectivity rule of some binary SCR. A binary SCR is regular if it satisfies unanimity, monotonicity, and independence of infeasible alternatives. A binary...... effectivity rule is regular if it is the effectivity rule of some regular binary SCR. We characterize completely the family of regular binary effectivity rules. Quite surprisingly, intrinsically defined von Neumann-Morgenstern solutions play an important role in this characterization...

  18. Eclipsing binaries in open clusters

    Southworth, John; Clausen, J.V.

    Stars: fundamental parameters - Stars : binaries : eclipsing - Stars: Binaries: spectroscopic - Open clusters and ass. : general Udgivelsesdato: 5 August......Stars: fundamental parameters - Stars : binaries : eclipsing - Stars: Binaries: spectroscopic - Open clusters and ass. : general Udgivelsesdato: 5 August...

  19. PHOEBE: PHysics Of Eclipsing BinariEs

    Prsa, Andrej; Matijevic, Gal; Latkovic, Olivera; Vilardell, Francesc; Wils, Patrick


    PHOEBE (PHysics Of Eclipsing BinariEs) is a modeling package for eclipsing binary stars, built on top of the widely used WD program (Wilson & Devinney 1971). This introductory paper overviews most important scientific extensions (incorporating observational spectra of eclipsing binaries into the solution-seeking process, extracting individual temperatures from observed color indices, main-sequence constraining and proper treatment of the reddening), numerical innovations (suggested improvements to WD's Differential Corrections method, the new Nelder & Mead's downhill Simplex method) and technical aspects (back-end scripter structure, graphical user interface). While PHOEBE retains 100% WD compatibility, its add-ons are a powerful way to enhance WD by encompassing even more physics and solution reliability.

  20. Crystallization and preliminary diffraction analysis of a group I ribozyme from bacteriophage Twort

    A group I self-splicing RNA has been synthesized and cocrystallized with a four-nucleotide product RNA. Iodination of the product RNA produces a heavy-atom derivative suitable for structure determination. Group I introns are catalytic RNAs that are capable of performing a variety of phosphotransesterification reactions including self-splicing and RNA cleavage. The reactions are efficient, accurate and dependent only on the presence of guanosine-nucleotide substrate and sufficient magnesium ion to stabilize the structure of the RNA. To understand how the group I intron active-site facilitates catalysis, crystals of a 242-nucleotide ribozyme bound to a four-nucleotide product RNA have been produced that diffract to 3.6 Å resolution. The space group of these crystals is I212121 and the unit-cell parameters are a = 94.6, b = 141.0, c = 210.9 Å. A single heavy-atom derivative has been synthesized by covalent modification of the product RNA with iodine

  1. Encounters of binaries

    Numerical integrations of encounters of pairs of binaries have been used to study the class of interactions, called fly-bys, in which the two-binary configuration survives. It is shown that these typically weak interactions can be treated by means of a first-order perturbation theory. A simple simulation model for obtaining the energy transfer rate between various degrees of freedom has been constructed. The model was employed to estimate the additional energy transfer arising from impact parameters larger than those used in the numerical experiments. In the hard binary limit the total energy transfer caused by binary-binary encounters is dominated by the collisional interactions in which the two-binary configuration is destroyed. (author)

  2. Global phylogeography with mixed-marker analysis reveals male-mediated dispersal in the endangered scalloped hammerhead shark (Sphyrna lewini.

    Toby S Daly-Engel

    Full Text Available BACKGROUND: The scalloped hammerhead shark, Sphyrna lewini, is a large endangered predator with a circumglobal distribution, observed in the open ocean but linked ontogenetically to coastal embayments for parturition and juvenile development. A previous survey of maternal (mtDNA markers demonstrated strong genetic partitioning overall (global Φ(ST = 0.749 and significant population separations across oceans and between discontinuous continental coastlines. METHODOLOGY/PRINCIPAL FINDINGS: We surveyed the same global range with increased sample coverage (N = 403 and 13 microsatellite loci to assess the male contribution to dispersal and population structure. Biparentally inherited microsatellites reveal low or absent genetic structure across ocean basins and global genetic differentiation (F(ST = 0.035 over an order of magnitude lower than the corresponding measures for maternal mtDNA lineages (Φ(ST = 0.749. Nuclear allelic richness and heterozygosity are high throughout the Indo-Pacific, while genetic structure is low. In contrast, allelic diversity is low while population structure is higher for populations at the ends of the range in the West Atlantic and East Pacific. CONCLUSIONS/SIGNIFICANCE: These data are consistent with the proposed Indo-Pacific center of origin for S. lewini, and indicate that females are philopatric or adhere to coastal habitats while males facilitate gene flow across oceanic expanses. This study includes the largest sampling effort and the most molecular loci ever used to survey the complete range of a large oceanic predator, and findings emphasize the importance of incorporating mixed-marker analysis into stock assessments of threatened and endangered shark species.

  3. Feeding strategy of the night shark (Carcharhinus signatus and scalloped hammerhead shark (Sphyrna lewini near seamounts off northeastern Brazil

    Teodoro Vaske Júnior


    Full Text Available A total of 425 stomachs of night shark (Carcharhinus signatus, and 98 stomachs of scalloped hammerhead shark (Sphyrna lewini, from longline and surface gillneters near seamounts off northeastern Brazil, were analysed between 1992 and 1999. Both predators prey upon reef and benthopelagic fishes, migrant cephalopods and deep water crustaceans, showing similar feeding niches (Schoener Index T=0.75. The great prey richness of the diets may reflect the fact that the marine food web for these species is very extensive in this region. Due to the concentration for feeding of both predators in the seamounts, intense fisheries should be monitored to avoid localised depletions.Um total de 425 estômagos de tubarão-toninha (Carcharhinus signatus e 98 estômagos de tubarão-martelo-entalhado (Sphyrna lewini, oriundos da pesca de espinhel e pesca com rede de emalhe nas adjacências dos bancos oceânicos do nordeste do Brasil, foi analisado entre 1992 e 1999. Ambas as espécies predam sobre peixes bento-pelágicos e recifais, cefalópodes migradores, e crustáceos de águas profundas, apresentando nichos alimentares similares (Índice de Schoener T=0.75. A alta riqueza de presas nas dietas deve ser um reflexo de que as teias alimentares para estas espécies são consideravelmente longas nessa região. Devido à concentração alimentar de ambos predadores nos bancos oceânicos, a pescaria intensa deve ser monitorada para evitar depleções locais.

  4. The wide expansion of hepatitis delta virus-like ribozymes throughout trypanosomatid genomes is linked to the spreading of L1Tc/ingi clade mobile elements

    Francisco J. Sánchez-Luque; López López, Manuel Carlos; Carreira, Patricia E; Alonso, Carlos; Thomas, María Carmen


    Background Hepatitis Delta Virus (HDV)-like ribozymes have recently been found in many mobile elements in which they take part in a mechanism that releases intermediate RNAs from cellular co-transcripts. L1Tc in Trypanosoma cruzi is one of the elements in which such a ribozyme is located. It lies in the so-called Pr77-hallmark, a conserved region shared by retrotransposons belonging to the trypanosomatid L1Tc/ingi clade. The wide distribution of the Pr77-hallmark detected in trypanosomatid re...

  5. Interacting binary stars

    Sahade, Jorge; Ter Haar, D


    Interacting Binary Stars deals with the development, ideas, and problems in the study of interacting binary stars. The book consolidates the information that is scattered over many publications and papers and gives an account of important discoveries with relevant historical background. Chapters are devoted to the presentation and discussion of the different facets of the field, such as historical account of the development in the field of study of binary stars; the Roche equipotential surfaces; methods and techniques in space astronomy; and enumeration of binary star systems that are studied

  6. Stabilization of ribozyme-like cis-noncoding rRNAs induces apoptotic and nonapoptotic death in lung cells

    Gee, M; Gu, Y.; Fields, J R; Shiao, Y-H


    Bidirectional non-protein-coding RNAs are ubiquitously transcribed from the genome. Convergent sense and antisense transcripts may regulate each other. Here, we examined the convergent cis-noncoding rRNAs (nc-rRNAs) in A5 and E9 lung cancer models. Sense nc-rRNAs extending from rDNA intergenic region to internal transcribed spacer of around 10 kb in length were identified. nc-rRNAs in sense direction exhibited in vitro characteristics of ribozymes, namely, degradation upon incubation with MgC...

  7. A Novel Vector for Abundant Expression of Antisense RNA, Triplex-forming RNA and Ribozyme in vivo


    For abundant expression of antisense RNA, triplex-forming RNA and Ribozyme in vivo, a novel vector pBSKneorU6' was constructed by PCR cloning. This vector contains the intact human snRNA U6 gene expression unit, yet replacing the 61-nt-sequence in the middle of U6 snRNA coding region with three restriction enzyme sites. Hela nuclear extract in vitro transcription experiments demonstrated that this vector can effectively express U6 mutant RNA. Containing neor at the same time, stably transfected pBSKneorU6' can be selected easily.

  8. Studies of viomycin, an anti-tuberculosis antibiotic: copper(ii) coordination, DNA degradation and the impact on delta ribozyme cleavage activity.

    Stokowa-Sołtys, K; Barbosa, N A; Kasprowicz, A; Wieczorek, R; Gaggelli, N; Gaggelli, E; Valensin, G; Wrzesiński, J; Ciesiołka, J; Kuliński, T; Szczepanik, W; Jeżowska-Bojczuk, M


    Viomycin is a basic peptide antibiotic, which is among the most effective agents against multidrug-resistant tuberculosis. In this paper we provide the characteristics of its acid base properties, coordination preferences towards the Cu(ii) ions, as well as the reactivity of the resulting complexes against plasmid DNA and HDV ribozyme. Careful coordination studies throughout the wide pH range allow for the characterisation of all the Cu(ii)-viomycin complex species. The assignment of proton chemical shifts was achieved by NMR experiments, while the DTF level of theory was applied to support molecular structures of the studied complexes. The experiments with the plasmid DNA reveal that at the physiological levels of hydrogen peroxide the Cu(ii)-viomycin complex is more aggressive against DNA than uncomplexed metal ions. Moreover, the degradation of DNA by viomycin can be carried out without the presence of transition metal ions. In the studies of antigenomic delta ribozyme catalytic activity, viomycin and its complex are shown to modulate the ribozyme functioning. The molecular modelling approach allows the indication of two different locations of viomycin binding sites to the ribozyme. PMID:27143296

  9. Activating the branch-forming splicing pathway by reengineering the ribozyme component of a natural group II intron.

    Monachello, Dario; Michel, François; Costa, Maria


    When assayed in vitro, group IIC self-splicing introns, which target bacterial Rho-independent transcription terminators, generally fail to yield branched products during splicing despite their possessing a seemingly normal branchpoint. Starting with intron O.i.I1 from Oceanobacillus iheyensis, whose crystallographically determined structure lacks branchpoint-containing domain VI, we attempted to determine what makes this intron unfit for in vitro branch formation. A major factor was found to be the length of the helix at the base of domain VI: 4 base pairs (bp) are required for efficient branching, even though a majority of group IIC introns have a 3-bp helix. Equally important for lariat formation is the removal of interactions between ribozyme domains II and VI, which are specific to the second step of splicing. Conversely, mismatching of domain VI and its proposed first-step receptor in subdomain IC1 was found to be detrimental; these data suggest that the intron-encoded protein may promote branch formation partly by modulating the equilibrium between conformations specific to the first and second steps of splicing. As a practical application, we show that by making just two changes to the O.i.I1 ribozyme, it is possible to generate sufficient amounts of lariat intron for the latter to be purified and used in kinetic assays in which folding and reaction are uncoupled. PMID:26769855

  10. Molecular Dynamics Study of Twister Ribozyme: Role of Mg(2+) Ions and the Hydrogen-Bonding Network in the Active Site.

    Ucisik, Melek N; Bevilacqua, Philip C; Hammes-Schiffer, Sharon


    The recently discovered twister ribozyme is thought to utilize general acid-base catalysis in its self-cleavage mechanism, but the roles of nucleobases and metal ions in the mechanism are unclear. Herein, molecular dynamics simulations of the env22 twister ribozyme are performed to elucidate the structural and equilibrium dynamical properties, as well as to examine the role of Mg(2+) ions and possible candidates for the general base and acid in the self-cleavage mechanism. The active site region and the ends of the pseudoknots were found to be less mobile than other regions of the ribozyme, most likely providing structural stability and possibly facilitating catalysis. A purported catalytic Mg(2+) ion and the closest neighboring Mg(2+) ion remained chelated and relatively immobile throughout the microsecond trajectories, although removal of these Mg(2+) ions did not lead to any significant changes in the structure or equilibrium motions of the ribozyme on the microsecond time scale. In addition, a third metal ion, a Na(+) ion remained close to A1(O5'), the leaving group atom, during the majority of the microsecond trajectories, suggesting that it might stabilize the negative charge on A1(O5') during self-cleavage. The locations of these cations and their interactions with key nucleotides in the active site suggest that they may be catalytically relevant. The P1 stem is partially melted at its top and bottom in the crystal structure and further unwinds in the trajectories. The simulations also revealed an interconnected network comprised of hydrogen-bonding and π-stacking interactions that create a relatively rigid network around the self-cleavage site. The nucleotides involved in this network are among the highly conserved nucleotides in twister ribozymes, suggesting that this interaction network may be important to structure and function. PMID:27295275

  11. The binary proletariat

    Bolt, Nate


    In the endless quest to transform itself, capitalism has spawned a new working class. The proletariat was an essential product of the industrial revolution, and the lighter, more efficient capitalism of the digital revolution has created the Binary Proletariat.

  12. Eclipsing Binary Pulsars

    Freire, P C C


    The first eclipsing binary pulsar, PSR B1957+20, was discovered in 1987. Since then, 13 other eclipsing low-mass binary pulsars have been found, 12 of these are in globular clusters. In this paper we list the known eclipsing binary pulsars and their properties, with special attention to the eclipsing systems in 47 Tuc. We find that there are two fundamentally different groups of eclipsing binary pulsars; separated by their companion masses. The less massive systems (M_c ~ 0.02 M_sun) are a product of predictable stellar evolution in binary pulsars. The systems with more massive companions (M_c ~ 0.2 M_sun) were formed by exchange encounters in globular clusters, and for that reason are exclusive to those environments. This class of systems can be used to learn about the neutron star recycling fraction in the globular clusters actively forming pulsars. We suggest that most of these binary systems are undetectable at radio wavelengths.

  13. Binary Evolutionary Models

    Han, Z


    In this talk, we present the general principles of binary evolution and give two examples. The first example is the formation of subdwarf B stars (sdBs) and their application to the long-standing problem of ultraviolet excess (also known as UV-upturn) in elliptical galaxies. The second is for the progenitors of type Ia supernovae (SNe Ia). We discuss the main binary interactions, i.e., stable Roche lobe overflow (RLOF) and common envelope (CE) evolution, and show evolutionary channels leading to the formation of various binary-related objects. In the first example, we show that the binary model of sdB stars of Han et al. (2002, 2003) can reproduce field sdB stars and their counterparts, extreme horizontal branch (EHB) stars, in globular clusters. By applying the binary model to the study of evolutionary population synthesis, we have obtained an ``a priori'' model for the UV-upturn of elliptical galaxies and showed that the UV-upturn is most likely resulted from binary interactions. This has major implications...

  14. Binary Neutron Star Mergers

    Joshua A. Faber


    Full Text Available We review the current status of studies of the coalescence of binary neutron star systems. We begin with a discussion of the formation channels of merging binaries and we discuss the most recent theoretical predictions for merger rates. Next, we turn to the quasi-equilibrium formalisms that are used to study binaries prior to the merger phase and to generate initial data for fully dynamical simulations. The quasi-equilibrium approximation has played a key role in developing our understanding of the physics of binary coalescence and, in particular, of the orbital instability processes that can drive binaries to merger at the end of their lifetimes. We then turn to the numerical techniques used in dynamical simulations, including relativistic formalisms, (magneto-hydrodynamics, gravitational-wave extraction techniques, and nuclear microphysics treatments. This is followed by a summary of the simulations performed across the field to date, including the most recent results from both fully relativistic and microphysically detailed simulations. Finally, we discuss the likely directions for the field as we transition from the first to the second generation of gravitational-wave interferometers and while supercomputers reach the petascale frontier.

  15. Skewed Binary Search Trees

    Brodal, Gerth Stølting; Moruz, Gabriel


    It is well-known that to minimize the number of comparisons a binary search tree should be perfectly balanced. Previous work has shown that a dominating factor over the running time for a search is the number of cache faults performed, and that an appropriate memory layout of a binary search tree...... can reduce the number of cache faults by several hundred percent. Motivated by the fact that during a search branching to the left or right at a node does not necessarily have the same cost, e.g. because of branch prediction schemes, we in this paper study the class of skewed binary search trees. For...... all nodes in a skewed binary search tree the ratio between the size of the left subtree and the size of the tree is a fixed constant (a ratio of 1/2 gives perfect balanced trees). In this paper we present an experimental study of various memory layouts of static skewed binary search trees, where each...

  16. Synthesis of a bifunctional cytidine derivative and its conjugation to RNA for in vitro selection of a cytidine deaminase ribozyme

    Nico Rublack


    Full Text Available Over the past 20 years, the generation of functional RNAs by in vitro selection has become a standard technique. Apart from aptamers for simple binding of defined ligands, also RNAs for catalysis of chemical reactions have been selected. In the latter case, a key step often is the conjugation of one of the two reactants to the library, requiring suitable strategies for terminal or internal RNA functionalization. With the aim of selecting a ribozyme for deamination of cytidine, we have set up a selection scheme involving the attachment of the cytidine acting as deamination substrate to the 3'-terminus of the RNAs in the library, and library immobilization. Here, we report the synthesis of a bifunctional cytidine derivative suitable for conjugation to RNA and linkage of the conjugated library to a streptavidine-coated surface. Successful conjugation of the cytidine derivative to the 3'-terminus of a model RNA is demonstrated.

  17. 发夹核酶的研究与应用%Study and Application of the Hairpin Ribozyme

    姚杰; 杨克恭; 陈松森


    @@核酶(ribozyme)是既能特异识别又能特异切割小分子RNA的核酸内切酶,其本身也是RNA,主要包括发夹核酶、锤头核酶、丁肝病毒、链孢霉属VS和铅依赖性RNA,共同特点是可逆地切割底物RNA的磷酸二酯键,生成5′-OH和2′,3′-环磷酸末端。虽然催化产物相似,但它们的结构和催化机制却是很不相同的。 发夹核酶(hairpin ribozyme)发现于三种不同植物RNA病毒,即烟草环点病毒(to-bacco ringspot virus),菊苣黄色斑点病毒型(chicory yellowmottle virus type)和筷子芥花叶病毒(arabis mosaic virus)。三种发夹核酶分别是这些RNA病毒卫星RNA(satelliteRNA)的负链,它们的英文缩写分别是sTRSV、sCYMVT和sARMV,均为单链RNA,以滚环方式复制[1,2]。目前针对AIDS而人工合成的发夹核酶已成为第一个进入基因治疗临床试验阶段的核酶。

  18. Quantum mechanical/molecular mechanical free energy simulations of the self-cleavage reaction in the hepatitis delta virus ribozyme.

    Ganguly, Abir; Thaplyal, Pallavi; Rosta, Edina; Bevilacqua, Philip C; Hammes-Schiffer, Sharon


    The hepatitis delta virus (HDV) ribozyme catalyzes a self-cleavage reaction using a combination of nucleobase and metal ion catalysis. Both divalent and monovalent ions can catalyze this reaction, although the rate is slower with monovalent ions alone. Herein, we use quantum mechanical/molecular mechanical (QM/MM) free energy simulations to investigate the mechanism of this ribozyme and to elucidate the roles of the catalytic metal ion. With Mg(2+) at the catalytic site, the self-cleavage mechanism is observed to be concerted with a phosphorane-like transition state and a free energy barrier of ∼13 kcal/mol, consistent with free energy barrier values extrapolated from experimental studies. With Na(+) at the catalytic site, the mechanism is observed to be sequential, passing through a phosphorane intermediate, with free energy barriers of 2-4 kcal/mol for both steps; moreover, proton transfer from the exocyclic amine of protonated C75 to the nonbridging oxygen of the scissile phosphate occurs to stabilize the phosphorane intermediate in the sequential mechanism. To explain the slower rate observed experimentally with monovalent ions, we hypothesize that the activation of the O2' nucleophile by deprotonation and orientation is less favorable with Na(+) ions than with Mg(2+) ions. To explore this hypothesis, we experimentally measure the pKa of O2' by kinetic and NMR methods and find it to be lower in the presence of divalent ions rather than only monovalent ions. The combined theoretical and experimental results indicate that the catalytic Mg(2+) ion may play three key roles: assisting in the activation of the O2' nucleophile, acidifying the general acid C75, and stabilizing the nonbridging oxygen to prevent proton transfer to it. PMID:24383543

  19. Binary Popldation Synthcsis Study

    HAN Zhanwen


    Binary population synthesis (BPS), an approach to evolving millions of stars (including binaries) simultaneously, plays a crucial role in our understanding of stellar physics, the structure and evolution of galaxies, and cosmology. We proposed and developed a BPS approach, and used it to investigate the formation of many peculiar stars such as hot subdwarf stars, progenitors of type la supernovae, barium stars, CH stars, planetary nebulae, double white dwarfs, blue stragglers, contact binaries, etc. We also established an evolution population synthesis (EPS) model, the Yunnan Model, which takes into account binary interactions for the first time. We applied our model for the origin of hot subdwarf stars in the study of elliptical galaxies and explained their far-UV radiation.

  20. Binary and Millisecond Pulsars

    Lorimer Duncan R.


    Full Text Available We review the main properties, demographics and applications of binary and millisecond radio pulsars. Our knowledge of these exciting objects has greatly increased in recent years, mainly due to successful surveys which have brought the known pulsar population to over 1800. There are now 83 binary and millisecond pulsars associated with the disk of our Galaxy, and a further 140 pulsars in 26 of the Galactic globular clusters. Recent highlights include the discovery of the young relativistic binary system PSR J1906+0746, a rejuvination in globular cluster pulsar research including growing numbers of pulsars with masses in excess of 1.5M_⊙, a precise measurement of relativistic spin precession in the double pulsar system and a Galactic millisecond pulsar in an eccentric (e = 0.44 orbit around an unevolved companion.

  1. Binary and Millisecond Pulsars

    Lorimer, D R


    We review the main properties, demographics and applications of binary and millisecond radio pulsars. Our knowledge of these exciting objects has greatly increased in recent years, mainly due to successful surveys which have brought the known pulsar population to over 1800. There are now 83 binary and millisecond pulsars associated with the disk of our Galaxy, and a further 140 pulsars in 26 of the Galactic globular clusters. Recent highlights include the discovery of the young relativistic binary system PSR J1906+0746, a rejuvination in globular cluster pulsar research including growing numbers of pulsars with masses in excess of 1.5 solar masses, a precise measurement of relativistic spin precession in the double pulsar system and a Galactic millisecond pulsar in an eccentric (e=0.44) orbit around an unevolved companion.

  2. Hypervelocity binary stars: smoking gun of massive binary black holes

    Lu, Youjun; Lin, D N C


    The hypervelocity stars recently found in the Galactic halo are expelled from the Galactic center through interactions between binary stars and the central massive black hole or between single stars and a hypothetical massive binary black hole. In this paper, we demonstrate that binary stars can be ejected out of the Galactic center with velocities up to 10^3 km/s, while preserving their integrity, through interactions with a massive binary black hole. Binary stars are unlikely to attain such high velocities via scattering by a single massive black hole or through any other mechanisms. Based on the above theoretical prediction, we propose a search for binary systems among the hypervelocity stars. Discovery of hypervelocity binary stars, even one, is a definitive evidence of the existence of a massive binary black hole in the Galactic center.

  3. Milli-arcsecond Binaries

    Torres, R M; Mioduszewki, A; Rodríguez, L F


    As part of an astrometric program, we have used the Very Long Baseline Array to measure the trigonometric parallax of several young stars in the Taurus and Ophiuchus star-forming regions with great accuracy. Additionally, we have obtained an unprecedented sample of high-resolution (~ 1 mas) images of several young stellar systems. These images revealed that about 70% of the stars in our sample are very tight binary stars (with separations of a few mas). Since it is highly unlikely that 70% of all stars are such tight binaries, we argue that selection effects are at work.

  4. Binary Cumulant Varieties

    Sturmfels, Bernd


    Algebraic statistics for binary random variables is concerned with highly structured algebraic varieties in the space of 2x2x...x2-tensors. We demonstrate the advantages of representing such varieties in the coordinate system of binary cumulants. Our primary focus lies on hidden subset models. Parametrizations and implicit equations in cumulants are derived for hyperdeterminants, for secant and tangential varieties of Segre varieties, and for certain context-specific independence models. Extending work of Rota and collaborators, we explore the polynomial inequalities satisfied by cumulants.

  5. Lentiviral transduction of Tar Decoy and CCR5 ribozyme into CD34+ progenitor cells and derivation of HIV-1 resistant T cells and macrophages

    Rossi John


    Full Text Available Abstract Background RNA based antiviral approaches against HIV-1 are among the most promising for long-term gene therapy. These include ribozymes, aptamers (decoys, and small interfering RNAs (siRNAs. Lentiviral vectors are ideal for transduction of such inhibitory RNAs into hematopoietic stem cells due to their ability to transduce non-dividing cells and their relative refractiveness to gene silencing. The objective of this study is to introduce an HIV-1 Tar aptamer either alone or in combination with an anti-CCR5 ribozyme into CD34+ hematopoietic progenitor cells via an HIV-based lentiviral vector to derive viral resistant progeny T cells and macrophages. Results High efficiency and sustained gene transfer into CD34+ cells were achieved with lentiviral vector constructs harboring either Tar decoy or Tar decoy in combination with CCR5 ribozyme. Cells transduced with these constructs differentiated normally into T-lymphocytes in vivo in thy/liv grafts of SCID-hu mice, and into macrophages in vitro in the presence of appropriate growth factors. When challenged in vitro, the differentiated T lymphocytes and macrophages showed marked resistance against HIV-1 infection. Conclusions Viral resistant transgenic T cells and macrophages that express HIV-1 Tar aptamer either alone or in combination with an anti-CCR5 ribozyme could be obtained by lentiviral gene transduction of CD34+ progenitor cells. These results showed for the first time that expression of these anti-HIV-1 transgenes in combination do not interfere with normal thymopoiesis and thus have set the stage for their application in stem cell based gene therapy for HIV/AIDS.

  6. Formation of binary radio pulsars

    In the framework of the standard scenario of the evolution of massive binary stars a study is made of the formation of final binary systems in which at least one of the components is a neutron star. It is found that about every fortieth radio pulsar must be a member of a close binary system. This is confirmed by observations. Radio pulsars are not formed in wide binary systems, possibly because of the very slow rotation of the presupernova stars

  7. Compressing Binary Decision Diagrams

    Hansen, Esben Rune; Satti, Srinivasa Rao; Tiedemann, Peter

    The paper introduces a new technique for compressing Binary Decision Diagrams in those cases where random access is not required. Using this technique, compression and decompression can be done in linear time in the size of the BDD and compression will in many cases reduce the size of the BDD to 1...

  8. Equational binary decision diagrams

    Groote, J.F.; Pol, J.C. van de


    We incorporate equations in binary decision diagrams (BDD). The resulting objects are called EQ-BDDs. A straightforward notion of ordered EQ-BDDs (EQ-OBDD) is defined, and it is proved that each EQ-BDD is logically equivalent to an EQ-OBDD. Moreover, on EQ-OBDDs satisfiability and tautology checkin

  9. Non-Watson Crick base pairs might stabilize RNA structural motifs in ribozymes – A comparative study of group-I intron structures

    K Chandrasekhar; R Malathi


    In recent decades studies on RNA structure and function have gained significance due to discoveries on diversified functions of RNA. A common element for RNA secondary structure formed by series of non-Watson/Watson Crick base pairs, internal loops and pseudoknots have been the highlighting feature of recent structural determination of RNAs. The recent crystal structure of group-I introns has demonstrated that these might constitute RNA structural motifs in ribozymes, playing a crucial role in their enzymatic activity. To understand the functional significance of these non-canonical base pairs in catalytic RNA, we analysed the sequences of group-I introns from nuclear genes. The results suggest that they might form the building blocks of folded RNA motifs which are crucial to the catalytic activity of the ribozyme. The conservation of these, as observed from divergent organisms, argues for the presence of non-canonical base pairs as an important requisite for the structure and enzymatic property of ribozymes by enabling them to carry out functions such as replication, polymerase activity etc. in primordial conditions in the absence of proteins.

  10. Binary MEMS gas sensors

    A novel sensing mechanism for electrostatic MEMS that employs static bifurcation-based sensing and binary detection is demonstrated. It is implemented as an ethanol vapour sensor that exploits the static pull-in bifurcation. Sensor detection of 5 ppm of ethanol vapour in dry nitrogen, equivalent to a detectable mass of 165 pg, is experimentally demonstrated. Sensor robustness to external disturbances is also demonstrated. A closed-form expression for the sensitivity of statically detected electrostatic MEMS sensors is derived. It is shown that the sensitivity of static bifurcation-based binary electrostatic MEMS sensors represents an upper bound on the sensitivity of static detection for given sensor dimensions and material properties. (paper)

  11. Binary Tetrahedral Flavor Symmetry

    Eby, David A


    A study of the T' Model and its variants utilizing Binary Tetrahedral Flavor Symmetry. We begin with a description of the historical context and motivations for this theory, together with some conceptual background for added clarity, and an account of our theory's inception in previous works. Our model endeavors to bridge two categories of particles, leptons and quarks, a unification made possible by the inclusion of additional Higgs particles, shared between the two fermion sectors and creating a single coherent system. This is achieved through the use of the Binary Tetrahedral symmetry group and an investigation of the Tribimaximal symmetry evidenced by neutrinos. Our work details perturbations and extensions of this T' Model as we apply our framework to neutrino mixing, quark mixing, unification, and dark matter. Where possible, we evaluate model predictions against experimental results and find excellent matching with the atmospheric and reactor neutrino mixing angles, an accurate prediction of the Cabibb...

  12. Compressing Binary Decision Diagrams

    Hansen, Esben Rune; Tiedemann, Peter


    The paper introduces a new technique for compressing Binary Decision Diagrams in those cases where random access is not required. Using this technique, compression and decompression can be done in linear time in the size of the BDD and compression will in many cases reduce the size of the BDD to 1-2 bits per node. Empirical results for our compression technique are presented, including comparisons with previously introduced techniques, showing that the new technique dominate on all tested instances.

  13. Knocking on FXR's door: the "hammerhead"-structure series of FXR agonists - amphiphilic isoxazoles with potent in vitro and in vivo activities.

    Gege, Christian; Kinzel, Olaf; Steeneck, Christoph; Schulz, Andreas; Kremoser, Claus


    The Farnesoid X Receptor (FXR) was recently validated in clinical studies using the bile acid analogue Obeticholic Acid (OCA) as an attractive drug target for liver diseases such as Primary Biliary Cirrhosis (PBC) or Non-alcoholic Steatohepatitis (NASH). OCA, however, turned out to induce cholesterol- related side effects upon prolonged treatment and it shows bile acid like pharmacokinetics. The quest for synthetic non-steroidal FXR agonists with general drug likeliness and improved pharmacokinetic and - dynamic properties has started more than a decade ago: The first non-steroidal and selective FXR agonist with decent submicromolar potency, GW4064, was patented in 1998 and published in 2000. Since then, many pharmaceutical companies have taken GW4064 as a structural template for their efforts in identifying novel patentable FXR agonists with the GW-derived trisubstituted isoxazole general structure. However, so far only one compound out of these different series has made it into the early stages of clinical development: The Px-102/Px-104 from Phenex is currently tested in a phase IIa study in patients with Non-Alcoholic Fatty Liver Disease (NAFLD). In this review we try to summarize from the patent and scientific literature the attempts to improve the GW4064 structure into different directions. Furthermore, we suggest directions for further improvements of this special class of synthetic FXR agonists which all display the typical "hammerhead"-conformation in the FXR ligand binding pocket that provides the basis for their impressive in vitro and in vivo potencies. PMID:25388536

  14. Binary-Signal Recovery

    Griebeler, Elmer L.


    Binary communication through long cables, opto-isolators, isolating transformers, or repeaters can become distorted in characteristic ways. The usual solution is to slow the communication rate, change to a different method, or improve the communication media. It would help if the characteristic distortions could be accommodated at the receiving end to ease the communication problem. The distortions come from loss of the high-frequency content, which adds slopes to the transitions from ones to zeroes and zeroes to ones. This weakens the definition of the ones and zeroes in the time domain. The other major distortion is the reduction of low frequency, which causes the voltage that defines the ones or zeroes to drift out of recognizable range. This development describes a method for recovering a binary data stream from a signal that has been subjected to a loss of both higher-frequency content and low-frequency content that is essential to define the difference between ones and zeroes. The method makes use of the frequency structure of the waveform created by the data stream, and then enhances the characteristics related to the data to reconstruct the binary switching pattern. A major issue is simplicity. The approach taken here is to take the first derivative of the signal and then feed it to a hysteresis switch. This is equivalent in practice to using a non-resonant band pass filter feeding a Schmitt trigger. Obviously, the derivative signal needs to be offset to halfway between the thresholds of the hysteresis switch, and amplified so that the derivatives reliably exceed the thresholds. A transition from a zero to a one is the most substantial, fastest plus movement of voltage, and therefore will create the largest plus first derivative pulse. Since the quiet state of the derivative is sitting between the hysteresis thresholds, the plus pulse exceeds the plus threshold, switching the hysteresis switch plus, which re-establishes the data zero to one transition

  15. Massive Black Hole Binary Evolution

    Merritt David


    Full Text Available Coalescence of binary supermassive black holes (SBHs would constitute the strongest sources of gravitational waves to be observed by LISA. While the formation of binary SBHs during galaxy mergers is almost inevitable, coalescence requires that the separation between binary components first drop by a few orders of magnitude, due presumably to interaction of the binary with stars and gas in a galactic nucleus. This article reviews the observational evidence for binary SBHs and discusses how they would evolve. No completely convincing case of a bound, binary SBH has yet been found, although a handful of systems (e.g. interacting galaxies; remnants of galaxy mergers are now believed to contain two SBHs at projected separations of <~ 1kpc. N-body studies of binary evolution in gas-free galaxies have reached large enough particle numbers to reproduce the slow, “diffusive” refilling of the binary’s loss cone that is believed to characterize binary evolution in real galactic nuclei. While some of the results of these simulations - e.g. the binary hardening rate and eccentricity evolution - are strongly N-dependent, others - e.g. the “damage” inflicted by the binary on the nucleus - are not. Luminous early-type galaxies often exhibit depleted cores with masses of ~ 1-2 times the mass of their nuclear SBHs, consistent with the predictions of the binary model. Studies of the interaction of massive binaries with gas are still in their infancy, although much progress is expected in the near future. Binary coalescence has a large influence on the spins of SBHs, even for mass ratios as extreme as 10:1, and evidence of spin-flips may have been observed.

  16. Biclustering Sparse Binary Genomic Data

    Van Uitert, M.; Meuleman, W.; Wessels, L. F. A.


    Genomic datasets often consist of large, binary, sparse data matrices. In such a dataset, one is often interested in finding contiguous blocks that (mostly) contain ones. This is a biclustering problem, and while many algorithms have been proposed to deal with gene expression data, only two algorithms have been proposed that specifically deal with binary matrices. None of the gene expression biclustering algorithms can handle the large number of zeros in sparse binary matrices. The two propos...

  17. Evolution of Close Binary Systems

    Yakut, K; Eggleton, P


    We collected data on the masses, radii, etc. of three classes of close binary stars: low-temperature contact binaries (LTCBs), near-contact binaries (NCBs), and detached close binaries (DCBs). They restrict themselves to systems where (1) both components are, at least arguably, near the Main Sequence, (2) the periods are less than a day, and (3) there is both spectroscopic and photometric analysis leading to reasonably reliable data. They discuss the possible evolutionary connections between these three classes, emphasizing the roles played by mass loss and angular momentum loss in rapidly-rotating cool stars.

  18. Report IAU Comm. 42, Close Binary Stars

    Ribas, Ignasi; Scarfe, Colin D.; Torres, Guillermo; Rucinski, Slavek M.; Sion, Edward M.; Richards, Mercedes T.; Niarchos, Panayiotis; Olah, Katalin


    Brief summaries are given about (1) close binary research from the perspective of the Bibliography of Close Binaries, (2) low-mass binaries and model discrepancies, (3) W UMa-type binaries, (4) cataclysmic variables, (5) Algol binaries, (6) the oEA stars, (7) effects of binarity on stellar activity.

  19. Low autocorrelation binary sequences

    Packebusch, Tom; Mertens, Stephan


    Binary sequences with minimal autocorrelations have applications in communication engineering, mathematics and computer science. In statistical physics they appear as groundstates of the Bernasconi model. Finding these sequences is a notoriously hard problem, that so far can be solved only by exhaustive search. We review recent algorithms and present a new algorithm that finds optimal sequences of length N in time O(N {1.73}N). We computed all optimal sequences for N≤slant 66 and all optimal skewsymmetric sequences for N≤slant 119.

  20. Magnetic binary nanofillers

    Magnetic binary nanofillers containing multiwall carbon nanotubes (MWCNT) and hercynite were synthesized by Chemical Vapor Deposition (CVD) on Fe/AlOOH prepared by the sol-gel method. The catalyst precursor was fired at 450 °C, ground and sifted through different meshes. Two powders were obtained with different particle sizes: sample A (50-75 μm) and sample B (smaller than 50 μm). These powders are composed of iron oxide particles widely dispersed in the non-crystalline matrix of aluminum oxide and they are not ferromagnetic. After reduction process the powders are composed of α-Fe nanoparticles inside hercynite matrix. These nanofillers are composed of hercynite containing α-Fe nanoparticles and MWCNT. The binary magnetic nanofillers were slightly ferromagnetic. The saturation magnetization of the nanofillers depended on the powder particle size. The nanofiller obtained from powder particles in the range 50-75 μm showed a saturation magnetization 36% higher than the one formed from powder particles smaller than 50 μm. The phenomenon is explained in terms of changes in the magnetic environment of the particles as consequence of the presence of MWCNT.

  1. Computing on Binary Strings

    Bu, Tian-Ming; Zhang, Peng


    Many problems in Computer Science can be abstracted to the following question: given a set of objects and rules respectively, which new objects can be produced? In the paper, we consider a succinct version of the question: given a set of binary strings and several operations like conjunction and disjunction, which new binary strings can be generated? Although it is a fundamental problem, to the best of our knowledge, the problem hasn't been studied yet. In this paper, an O(m^2n) algorithm is presented to determine whether a string s is representable by a set W, where n is the number of strings in W and each string has the same length m. However, looking for the minimum subset from a set to represent a given string is shown to be NP-hard. In addition, we prove that counting the number of strings representable is #P-complete. But if the operator negation can be used, the number is some power of 2. This di?erence maybe help us understand the problem more profoundly.

  2. General base catalysis for cleavage by the active-site cytosine of the hepatitis delta virus ribozyme: QM/MM calculations establish chemical feasibility

    Banáš, Pavel; Rulíšek, Lubomír; Hánošová, V.; Svozil, Daniel; Walter, N.G.; Šponer, Jiří; Otyepka, Michal


    Roč. 112, č. 35 (2008), s. 11177-11187. ISSN 1520-6106 R&D Projects: GA MŠk LC512; GA MŠk(CZ) LC06030; GA AV ČR(CZ) IAA400040802; GA AV ČR 1QS500040581 Grant ostatní: NIH(US) GM62357 Institutional research plan: CEZ:AV0Z40550506; CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : HDV ribozyme * catalysis * QM/MM calculations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.189, year: 2008

  3. Relativistic Binaries in Globular Clusters

    Benacquista Matthew J.


    Full Text Available The galactic population of globular clusters are old, dense star systems, with a typical cluster containing 10^4 - 10^7 stars. As an old population of stars, globular clusters contain many collapsed and degenerate objects. As a dense population of stars, globular clusters are the scene of many interesting close dynamical interactions between stars. These dynamical interactions can alter the evolution of individual stars and can produce tight binary systems containing one or two compact objects. In this review, we discuss the theoretical models of globular cluster evolution and binary evolution, techniques for simulating this evolution which lead to relativistic binaries, and current and possible future observational evidence for this population. Globular cluster evolution will focus on the properties that boost the production of hard binary systems and on the tidal interactions of the galaxy with the cluster, which tend to alter the structure of the globular cluster with time. The interaction of the components of hard binary systems alters the evolution of both bodies and can lead to exotic objects. Direct N-body integrations and Fokker-Planck simulations of the evolution of globular clusters that incorporate tidal interactions and lead to predictions of relativistic binary populations are also discussed. We discuss the current observational evidence for cataclysmic variables, millisecond pulsars, and low-mass X-ray binaries as well as possible future detection of relativistic binaries with gravitational radiation.

  4. Relativistic Binaries in Globular Clusters

    Matthew J. Benacquista


    Full Text Available Galactic globular clusters are old, dense star systems typically containing 10^4 – 10^6 stars. As an old population of stars, globular clusters contain many collapsed and degenerate objects. As a dense population of stars, globular clusters are the scene of many interesting close dynamical interactions between stars. These dynamical interactions can alter the evolution of individual stars and can produce tight binary systems containing one or two compact objects. In this review, we discuss theoretical models of globular cluster evolution and binary evolution, techniques for simulating this evolution that leads to relativistic binaries, and current and possible future observational evidence for this population. Our discussion of globular cluster evolution will focus on the processes that boost the production of tight binary systems and the subsequent interaction of these binaries that can alter the properties of both bodies and can lead to exotic objects. Direct N-body integrations and Fokker–Planck simulations of the evolution of globular clusters that incorporate tidal interactions and lead to predictions of relativistic binary populations are also discussed. We discuss the current observational evidence for cataclysmic variables, millisecond pulsars, and low-mass X-ray binaries as well as possible future detection of relativistic binaries with gravitational radiation.


    XuChengqian; ZhaoXiaoqun


    A new set of binary sequences-Periodic Complementary Binary Sequence Pair (PCSP)is proposed .A new class of block design-Difference Family Pair (DFP)is also proposed .The relationship between PCSP and DFP,the properties and exising conditions of PCSP and the recursive constructions for PCSP are given.


    Xu Chengqian; Zhao Xiaoqun


    A new set of binary sequences-Periodic Complementary Binary Sequence Pair (PCSP) is proposed. A new class of block design-Difference Family Pair (DFP) is also proposed.The relationship between PCSP and DFP, the properties and existing conditions of PCSP and the recursive constructions for PCSP are given.

  7. Pairing mechanisms for binary stars

    Kouwenhoven, M B N; Goodwin, S P; Zwart, S F Portegies; Kaper, L; 10.1002/asna.200811061


    Knowledge of the binary population in stellar groupings provides important information about the outcome of the star forming process in different environments. Binarity is also a key ingredient in stellar population studies and is a prerequisite to calibrate the binary evolution channels. In these proceedings we present an overview of several commonly used methods to pair individual stars into binary systems, which we refer to as the pairing function. Many pairing functions are frequently used by observers and computational astronomers, either for the mathematical convenience, or because they roughly describe the expected outcome of the star forming process. We discuss the consequences of each pairing function for the interpretation of observations and numerical simulations. The binary fraction and mass ratio distribution generally depend strongly on the selection of the range in primary spectral type in a sample. These quantities, when derived from a binary survey with a mass-limited sample of target stars, ...

  8. Planets in Binary Star Systems

    Haghighipour, Nader


    The discovery of extrasolar planets over the past decade has had major impacts on our understanding of the formation and dynamical evolution of planetary systems. There are features and characteristics unseen in our solar system and unexplainable by the current theories of planet formation and dynamics. Among these new surprises is the discovery of planets in binary and multiple-star systems. The discovery of such "binary-planetary" systems has confronted astrodynamicists with many new challenges, and has led them to re-examine the theories of planet formation and dynamics. Among these challenges are: How are planets formed in binary star systems? What would be the notion of habitability in such systems? Under what conditions can binary star systems have habitable planets? How will volatiles necessary for life appear on such planets? This volume seeks to gather the current research in the area of planets in binary and multistar systems and to familiarize readers with its associated theoretical and observation...

  9. Towards Physarum Binary Adders

    Jones, Jeff; 10.1016/j.biosystems.2010.04.005


    Plasmodium of \\emph{Physarum polycephalum} is a single cell visible by unaided eye. The plasmodium's foraging behaviour is interpreted in terms of computation. Input data is a configuration of nutrients, result of computation is a network of plasmodium's cytoplasmic tubes spanning sources of nutrients. Tsuda et al (2004) experimentally demonstrated that basic logical gates can be implemented in foraging behaviour of the plasmodium. We simplify the original designs of the gates and show --- in computer models --- that the plasmodium is capable for computation of two-input two-output gate $ \\to $ and three-input two-output $ \\to $. We assemble the gates in a binary one-bit adder and demonstrate validity of the design using computer simulation.

  10. Eccentric Binary Millisecond Pulsars

    Freire, Paulo C C


    In this paper we review the recent discovery of several millisecond pulsars (MSPs) in eccentric binary systems. Timing these MSPs we were able to estimate (and in one case precisely measure) their masses. These results suggest that, as a class, MSPs have a much wider range of masses (1.3 to > 2 solar masses) than the normal and mildly recycled pulsars found in double neutron star (DNS) systems (1.25 < Mp < 1.44 solar masses). This is very likely to be due to the prolonged accretion episode that is thought to be required to form a MSP. The likely existence of massive MSPs makes them a powerful probe for understanding the behavior of matter at densities larger than that of the atomic nucleus; in particular, the precise measurement of the mass of PSR J1903+0327 ($1.67 +/- 0.01 solar masses) excludes several "soft" equations of state for dense matter.

  11. Binaries and distances

    Pourbaix, D.; Arenou, F.; Halbwachs, J.-L.; Siopis, C.


    Gaia's five-year observation baseline might naively lead to the expectation that it will be possible to fit the parallax of any sufficiently nearby object with the default five-parameter model (position at a reference epoch, parallax and proper motion). However, simulated Gaia observations of a `model Universe' composed of nearly 107 objects, 50% of which turn out to be multiple stars, show that the single-star hypothesis can severely affect parallax estimation and that more sophisticated models must be adopted. In principle, screening these spurious single-star solutions is rather straightforward, for example by evaluating the quality of the fits. However, the simulated Gaia observations also reveal that some seemingly acceptable single-star solutions can nonetheless lead to erroneous distances. These solutions turn out to be binaries with an orbital period close to one year. Without auxiliary (e.g., spectroscopic) data, they will remain unnoticed.

  12. Binary black hole spectroscopy

    We study parameter estimation with post-Newtonian (PN) gravitational waveforms for the quasi-circular, adiabatic inspiral of spinning binary compact objects. In particular, the performance of amplitude-corrected waveforms is compared with that of the more commonly used restricted waveforms, in Advanced LIGO and EGO. With restricted waveforms, the properties of the source can only be extracted from the phasing. In the case of amplitude-corrected waveforms, the spectrum encodes a wealth of additional information, which leads to dramatic improvements in parameter estimation. At distances of ∼100 Mpc, the full PN waveforms allow for high-accuracy parameter extraction for total mass up to several hundred solar masses, while with the restricted ones the errors are steep functions of mass, and accurate parameter estimation is only possible for relatively light stellar mass binaries. At the low-mass end, the inclusion of amplitude corrections reduces the error on the time of coalescence by an order of magnitude in Advanced LIGO and a factor of 5 in EGO compared to the restricted waveforms; at higher masses these differences are much larger. The individual component masses, which are very poorly determined with restricted waveforms, become measurable with high accuracy if amplitude-corrected waveforms are used, with errors as low as a few per cent in Advanced LIGO and a few tenths of a per cent in EGO. The usual spin-orbit parameter β is also poorly determined with restricted waveforms (except for low-mass systems in EGO), but the full waveforms give errors that are small compared to the largest possible value consistent with the Kerr bound. This suggests a way of finding out if one or both of the component objects violate this bound. On the other hand, we find that the spin-spin parameter σ remains poorly determined even when the full waveform is used. Generally, all errors have but a weak dependence on the magnitudes and orientations of the spins. We also briefly

  13. Strong Lensing by Binary Galaxies

    Shin, E M


    We study the problem of gravitational lensing by binary galaxies, idealized as two isothermal spheres. In a wide binary, each galaxy possesses individual tangential, nearly astroidal, caustics and roundish radial caustics. As the separation of the binary is made smaller, the caustics undergo a sequence of metamorphoses. The first metamorphosis occurs when the tangential caustics merge to form a single six-cusped caustic, lying interior to the radial caustics. At still smaller separations, the six-cusped caustic undergoes the second metamorphosis and splits into a four-cusped caustic and two three-cusped caustics, which shrink to zero size (an elliptic umbilic catastrophe) before they enlarge again and move away from the origin perpendicular to the binary axis. Finally, a third metamorphosis occurs as the three-cusp caustics join the radial caustics, leaving an inner distorted astroid caustic enclosed by two outer caustics. The maximum number of images possible is 7. Classifying the multiple imaging according ...

  14. Magnetic braking in ultracompact binaries

    Farmer, Alison


    Angular momentum loss in ultracompact binaries, such as the AM Canum Venaticorum stars, is usually assumed to be due entirely to gravitational radiation. Motivated by the outflows observed in ultracompact binaries, we investigate whether magnetically coupled winds could in fact lead to substantial additional angular momentum losses. We remark that the scaling relations often invoked for the relative importance of gravitational and magnetic braking do not apply, and instead use simple non-empirical expressions for the braking rates. In order to remove significant angular momentum, the wind must be tied to field lines anchored in one of the binary's component stars; uncertainties remain as to the driving mechanism for such a wind. In the case of white dwarf accretors, we find that magnetic braking can potentially remove angular momentum on comparable or even shorter timescales than gravitational waves over a large range in orbital period. We present such a solution for the 17-minute binary AM CVn itself which a...

  15. Discs in misaligned binary systems

    Rawiraswattana, Krisada; Goodwin, Simon P


    We perform SPH simulations to study precession and changes in alignment between the circumprimary disc and the binary orbit in misaligned binary systems. We find that the precession process can be described by the rigid-disc approximation, where the disc is considered as a rigid body interacting with the binary companion only gravitationally. Precession also causes change in alignment between the rotational axis of the disc and the spin axis of the primary star. This type of alignment is of great important for explaining the origin of spin-orbit misaligned planetary systems. However, we find that the rigid-disc approximation fails to describe changes in alignment between the disc and the binary orbit. This is because the alignment process is a consequence of interactions that involve the fluidity of the disc, such as the tidal interaction and the encounter interaction. Furthermore, simulation results show that there are not only alignment processes, which bring the components towards alignment, but also anti-...

  16. Cryptography with DNA binary strands.

    Leier, A; Richter, C; Banzhaf, W; Rauhe, H


    Biotechnological methods can be used for cryptography. Here two different cryptographic approaches based on DNA binary strands are shown. The first approach shows how DNA binary strands can be used for steganography, a technique of encryption by information hiding, to provide rapid encryption and decryption. It is shown that DNA steganography based on DNA binary strands is secure under the assumption that an interceptor has the same technological capabilities as sender and receiver of encrypted messages. The second approach shown here is based on steganography and a method of graphical subtraction of binary gel-images. It can be used to constitute a molecular checksum and can be combined with the first approach to support encryption. DNA cryptography might become of practical relevance in the context of labelling organic and inorganic materials with DNA 'barcodes'. PMID:10963862


    Praveena Murugesan


    Full Text Available Reversible logic gates under ideal conditions produce zero power dissipation. This factor highlights the usage of these gates in optical computing, low power CMOS design, quantum optics and quantum computing. The growth of decimal arithmetic in various applications as stressed the need to propose the study on reversible binary to BCD converter which plays a greater role in decimal multiplication for providing faster results. The different parameters such as gate count,garbage output and constant input are more optimized in the proposed fixed bit binary to binary coded decimal converter than the existing design.

  18. Transient Black Hole Binaries

    Belloni, T M


    The last two decades have seen a great improvement in our understand- ing of the complex phenomenology observed in transient black-hole binary systems, especially thanks to the activity of the Rossi X-Ray Timing Explorer satellite, com- plemented by observations from many other X-ray observatories and ground-based radio, optical and infrared facilities. Accretion alone cannot describe accurately the intricate behavior associated with black-hole transients and it is now clear that the role played by different kinds of (often massive) outflows seen at different phases of the outburst evolution of these systems is as fundamental as the one played by the accretion process itself. The spectral-timing states originally identified in the X-rays and fundamentally based on the observed effect of accretion, have acquired new importance as they now allow to describe within a coherent picture the phenomenology observed at other wave- length, where the effects of ejection processes are most evident. With a particular focu...

  19. Binary nucleation beyond capillarity approximation

    Kalikmanov, V.I.


    Large discrepancies between binary classical nucleation theory (BCNT) and experiments result from adsorption effects and inability of BCNT, based on the phenomenological capillarity approximation, to treat small clusters. We propose a model aimed at eliminating both of these deficiencies. Adsorption is taken into account within Gibbsian approximation. Binary clusters are treated by means of statistical-mechanical considerations: tracing out the molecular degrees of freedom of the more volatil...

  20. Clostridium difficile binary toxin CDT

    Gerding, Dale N.; Johnson, Stuart; Rupnik, Maja; Aktories, Klaus


    Binary toxin (CDT) is frequently observed in Clostridium difficile strains associated with increased severity of C. difficile infection (CDI). CDT belongs to the family of binary ADP-ribosylating toxins consisting of two separate toxin components: CDTa, the enzymatic ADP-ribosyltransferase which modifies actin, and CDTb which binds to host cells and translocates CDTa into the cytosol. CDTb is activated by serine proteases and binds to lipolysis stimulated lipoprotein receptor. ADP-ribosylatio...

  1. Coalescence of Binary Neutron Stars

    Oohara, Ken-ichi; Namamura, Takashi


    The most important sources for laser-interferometric gravitational-wave detectors like LIGO or VIRGO are catastrophic events such as coalescence of a neutron-star binary. The final phase, or the last three milliseconds, of coalescence is considered. We describe results of numerical simulations of coalescing binary neutron stars using Newtonian and post-Newtonian hydrodynamics code and then discuss recent development of our 3D GR code.

  2. Binary Encodings of Non-binary Constraint Satisfaction Problems: Algorithms and Experimental Results

    Samaras, N; 10.1613/jair.1776


    A non-binary Constraint Satisfaction Problem (CSP) can be solved directly using extended versions of binary techniques. Alternatively, the non-binary problem can be translated into an equivalent binary one. In this case, it is generally accepted that the translated problem can be solved by applying well-established techniques for binary CSPs. In this paper we evaluate the applicability of the latter approach. We demonstrate that the use of standard techniques for binary CSPs in the encodings of non-binary problems is problematic and results in models that are very rarely competitive with the non-binary representation. To overcome this, we propose specialized arc consistency and search algorithms for binary encodings, and we evaluate them theoretically and empirically. We consider three binary representations; the hidden variable encoding, the dual encoding, and the double encoding. Theoretical and empirical results show that, for certain classes of non-binary constraints, binary encodings are a competitive op...

  3. Transfection with the ribozyme targeting HPVE6 mRNA results in growth inhibition of E6-expressing cervical carcinoma cells

    郑燕芳; 张积仁


    Objective: To acquire a ribozyme against the E6 gene of human papillomaviruses type 16 (HPV16E6) and investigate its effects on the phenotypes and gene expression of cervical cancer cell line. Methods: Anti-HPV16E6 ribozyme (HRz) was designed by computer programs and its activity identified by cleavage experiment in vitro before its transfection via lipofectin into CaSKi cells with the empty eucaryotic expression plasmid transfection of the cells also performed, the resultant cells designated as CaSKi-R, CaSKi-P respectively. The morphology and the soft agar forming ability were studied in CaSKi cells and the transfected cells, and the expression of E6, proliferating cell nuclear antigen (PCNA) and C-erbB-2 genes assayed by flow cytometry. The tumorgenicity of each cell line was evaluated in nude mice receiving inoculations of CaSKi, CaSKi-R and CaSKi-P cells separately, while in one group, both CaSKi and CaSKi-R cells were inoculated on different sides of the mice. Results: HRz was able to cleave HPV16E6 mRNA in a site-specific manner and could be expressed stably in transfected CaSKi cells. Northern blot analysis showed that E6 mRNA was less in CaSKi-R than in CaSKi cells, and no significant difference in the morphology and growth rate was observed between CaSKi and CaSKi-P cells, but the growth rate CaSKi-R was lowered. The colony-forming rate of CaSKi-P in soft agar was similar to that of CaSKi cells, while that of CaSKi-R was decreased. Flow cytometry showed that anti-HPV16E6 ribozyme reduced the expression of E6, PCNA and C-erbB-2 genes in CaSKi-R cells, but not in CaSKi-P cells. The tumorgenicity of CaSKi-R in nude mice was decreased compared with CaSKi cells. Conclusion: HRz can partially reverse the malignant phenotype of CaSKi cells, possibly due to decreased E6 gene expression, and the consequent decrease of PCNA and C-erbB-2 gene expressions.

  4. Binaries and Globular Cluster Dynamics

    Rasio, F A; Joshi, K J; Rasio, Frederic A.; Fregeau, John M.; Joshi, Kriten J.


    We summarize the results of recent theoretical work on the dynamical evolution of globular clusters containing primordial binaries. Even a very small initial binary fraction (e.g., 10%) can play a key role in supporting a cluster against gravothermal collapse for many relaxation times. Inelastic encounters between binaries and single stars or other binaries provide a very significant energy source for the cluster. These dynamical interactions also lead to the production of large numbers of exotic systems such as ultracompact X-ray binaries, recycled radio pulsars, double degenerate systems, and blue stragglers. Our work is based on a new parallel supercomputer code implementing Henon's Monte Carlo method for simulating the dynamical evolution of dense stellar systems in the Fokker-Planck approximation. This new code allows us to calculate very accurately the evolution of a cluster containing a realistic number of stars (N ~ 10^5 - 10^6) in typically a few hours to a few days of computing time. The discrete, s...

  5. Exoplanets Bouncing Between Binary Stars

    Moeckel, Nickolas


    Exoplanetary systems are found not only among single stars, but also binaries of widely varying parameters. Binaries with separations of 100--1000 au are prevalent in the Solar neighborhood; at these separations planet formation around a binary member may largely proceed as if around a single star. During the early dynamical evolution of a planetary system, planet--planet scattering can eject planets from a star's grasp. In a binary, the motion of a planet ejected from one star has effectively entered a restricted three-body system consisting of itself and the two stars, and the equations of motion of the three body problem will apply as long as the ejected planet remains far from the remaining planets. Depending on its energy, escape from the binary as a whole may be impossible or delayed until the three-body approximation breaks down, and further close interactions with its planetary siblings boost its energy when it passes close to its parent star. Until then this planet may be able to transition from the ...

  6. Using Binary Code Instrumentation in Computer Security

    Marius POPA


    Full Text Available The paper approaches the low-level details of the code generated by compilers whose format permits outside actions. Binary code modifications are manually done when the internal format is known and understood, or automatically by certain tools developed to process the binary code. The binary code instrumentation goals may be various from security increasing and bug fixing to development of malicious software. The paper highlights the binary code instrumentation techniques by code injection to increase the security and reliability of a software application. Also, the paper offers examples for binary code formats understanding and how the binary code injection may be applied.

  7. The structure of contact binaries

    Kaehler, H


    In radiative layers of rotating stars the luminosity carried by circulation currents through a surface of constant entropy (circulation luminosity) is shown to be positive. The corresponding decrease in the temperature gradient is important in the secondary of contact binaries. This result removes the deadlock in the theory of contact binaries. The resulting treatment of contact binaries is investigated, assuming thermal equilibrium. If the circulation luminosity is adjusted to give a prescribed temperature difference between the components, details turn out to be unimportant. The temperature difference is bound to be positive. The fractional extent of radiative regions is larger in the secondary than in the primary. In the course of evolution the period increases and the mass ratio decreases. A survey of unevolved and evolved contact configurations is presented. Observational tests are passed. In stable systems the degree of contact is small. Stable systems in the period-colour diagram, unevolved and evolved...

  8. Practical Binary Adaptive Block Coder

    Reznik, Yuriy A


    This paper describes design of a low-complexity algorithm for adaptive encoding/ decoding of binary sequences produced by memoryless sources. The algorithm implements universal block codes constructed for a set of contexts identified by the numbers of non-zero bits in previous bits in a sequence. We derive a precise formula for asymptotic redundancy of such codes, which refines previous well-known estimate by Krichevsky and Trofimov, and provide experimental verification of this result. In our experimental study we also compare our implementation with existing binary adaptive encoders, such as JBIG's Q-coder, and MPEG AVC (ITU-T H.264)'s CABAC algorithms.

  9. Coalescing binaries and Doppler experiments

    Vecchio, A.; Bertotti, B.; Iess, L.


    We discuss the sensitivity of the CASSINI experiments to gravitational waves emitted by the in-spiral of compact binaries. We show that the maximum distance reachable by the instrument is $\\sim 100$ Mpc. In particular, CASSINI can detect massive black hole binaries with chirp mass $\\simgt 10^6 \\Ms$ in the Virgo Cluster with signal-to-noise ratio between 5 and 30 and possible compact objects of mass $\\simgt 30 \\Ms$ orbiting the massive black hole that our Galactic Centre is likely to harbour.

  10. Rectangular Decomposition of Binary Images

    Suk, Tomáš; Höschl, Cyril; Flusser, Jan

    Berlin : Springer, 2012 - (Blanc-Talon, J.; Popescu, D.; Philips, W.; Scheunders, P.), s. 213-224 ISBN 978-3-642-33139-8. - (Lecture Notes in Computer Science. 7517). [Advanced Concepts for Intelligent Vision Systems (Acivs 2012). Brno (CZ), 04.09.2012-07.09.2012] R&D Projects: GA ČR GAP103/11/1552 Institutional support: RVO:67985556 Keywords : binary image decomposition * generalized delta-method * distance transformation * quadtree * bipartite graph * image compression * fast convolution Subject RIV: IN - Informatics, Computer Science decomposition of binary images.pdf

  11. Kepler Eclipsing Binaries with Stellar Companions

    Gies, D R; Guo, Z; Lester, K V; Orosz, J A; Peters, G J


    Many short-period binary stars have distant orbiting companions that have played a role in driving the binary components into close separation. Indirect detection of a tertiary star is possible by measuring apparent changes in eclipse times of eclipsing binaries as the binary orbits the common center of mass. Here we present an analysis of the eclipse timings of 41 eclipsing binaries observed throughout the NASA Kepler mission of long duration and precise photometry. This subset of binaries is characterized by relatively deep and frequent eclipses of both stellar components. We present preliminary orbital elements for seven probable triple stars among this sample, and we discuss apparent period changes in seven additional eclipsing binaries that may be related to motion about a tertiary in a long period orbit. The results will be used in ongoing investigations of the spectra and light curves of these binaries for further evidence of the presence of third stars.

  12. Frame theory for binary vector spaces

    Bodmann, Bernhard G.; Le, My; Reza, Letty; Tobin, Matthew; Tomforde, Mark


    We develop the theory of frames and Parseval frames for finite-dimensional vector spaces over the binary numbers. This includes characterizations which are similar to frames and Parseval frames for real or complex Hilbert spaces, and the discussion of conceptual differences caused by the lack of a proper inner product on binary vector spaces. We also define switching equivalence for binary frames, and list all equivalence classes of binary Parseval frames in lowest dimensions, excluding cases...

  13. Using Binary Code Instrumentation in Computer Security

    Marius POPA; Sergiu Marin CAPISIZU


    The paper approaches the low-level details of the code generated by compilers whose format permits outside actions. Binary code modifications are manually done when the internal format is known and understood, or automatically by certain tools developed to process the binary code. The binary code instrumentation goals may be various from security increasing and bug fixing to development of malicious software. The paper highlights the binary code instrumentation techniques by code injection to...

  14. Discs in misaligned binary systems

    Rawiraswattana, Krisada; Hubber, David A.; Goodwin, Simon P.


    We perform SPH simulations to study precession and changes in alignment between the circumprimary disc and the binary orbit in misaligned binary systems. We find that the precession process can be described by the rigid-disc approximation, where the disc is considered as a rigid body interacting with the binary companion only gravitationally. Precession also causes change in alignment between the rotational axis of the disc and the spin axis of the primary star. This type of alignment is of great important for explaining the origin of spin-orbit misaligned planetary systems. However, we find that the rigid-disc approximation fails to describe changes in alignment between the disc and the binary orbit. This is because the alignment process is a consequence of interactions that involve the fluidity of the disc, such as the tidal interaction and the encounter interaction. Furthermore, simulation results show that there are not only alignment processes, which bring the components towards alignment, but also anti-alignment processes, which tend to misalign the components. The alignment process dominates in systems with misalignment angle near 90°, while the anti-alignment process dominates in systems with the misalignment angle near 0° or 180°. This means that highly misaligned systems will become more aligned but slightly misaligned systems will become more misaligned.

  15. A Galactic Binary Detection Pipeline

    Littenberg, Tyson B.


    The Galaxy is suspected to contain hundreds of millions of binary white dwarf systems, a large fraction of which will have sufficiently small orbital period to emit gravitational radiation in band for space-based gravitational wave detectors such as the Laser Interferometer Space Antenna (LISA). LISA's main science goal is the detection of cosmological events (supermassive black hole mergers, etc.) however the gravitational signal from the galaxy will be the dominant contribution to the data - including instrumental noise over approximately two decades in frequency. The catalogue of detectable binary systems will serve as an unparalleled means of studying the Galaxy. Furthermore, to maximize the scientific return from the mission, the data must be "cleansed" of the galactic foreground. We will present an algorithm that can accurately resolve and subtract 2:: 10000 of these sources from simulated data supplied by the Mock LISA Data Challenge Task Force. Using the time evolution of the gravitational wave frequency, we will reconstruct the position of the recovered binaries and show how LISA will sample the entire compact binary population in the Galaxy.

  16. CFD Simulations of Binary Nucleation

    Herrmann, E.; Brus, David; Hyvärinen, A-P.; Kulmala, M.

    Helsinki : -, 2010, P3U16. ISBN N. [International Aerosol Conference IAC 2010. Helsinki (FI), 29.08.2010-03.09.2010] Grant ostatní: FCR(FI) 1118615 Institutional research plan: CEZ:AV0Z40720504 Keywords : nucleation * binary * parameterization Subject RIV: CF - Physical ; Theoretical Chemistry

  17. Eccentricity distribution of wide binaries

    Tokovinin, Andrei


    A sample of 477 solar-type binaries within 67pc with projected separations larger than 50AU is studied by a new statistical method. Speed and direction of the relative motion are determined from the short observed arcs or known orbits, and their joint distribution is compared to the numerical simulations. By inverting the observed distribution with the help of simulations, we find that average eccentricity of wide binaries is 0.59+-0.02 and the eccentricity distribution can be modeled as f(e) ~= 1.2 e + 0.4. However, wide binaries containing inner subsystems, i.e. triple or higher-order multiples, have significantly smaller eccentricities with the average e = 0.52+-0.05 and the peak at e ~ 0.5. We find that the catalog of visual orbits is strongly biased against large eccentricities. A marginal evidence of eccentricity increasing with separation (or period) is found for this sample. Comparison with spectroscopic binaries proves the reality of the controversial period-eccentricity relation. The average eccentr...

  18. A Redundant Binary Algorithm for RSA



    The normal form and modified normal form for binary redundant representation are defined.A redundant binary algorithm to compute modular exponentiation for very large integers is proposed.It is shown that the proposed algorithm requires the minimum number of basic operations(modular multiplications)among all possible binary redundant representations.

  19. Competitive learning for binary valued data

    Leisch, Friedrich; Weingessel, Andreas; Dimitriadou, Evgenia


    We propose a new approach for using online competitive learning on binary data. The usual Euclidean distance is replaced by binary distance measures, which take possible asymmetries of binary data into account and therefore provide a "different point of view" for looking at the data. The method is demonstrated on two artificial examples and applied on tourist marketing research data. (author's abstract)

  20. Permutation Entropy for Random Binary Sequences

    Lingfeng Liu


    Full Text Available In this paper, we generalize the permutation entropy (PE measure to binary sequences, which is based on Shannon’s entropy, and theoretically analyze this measure for random binary sequences. We deduce the theoretical value of PE for random binary sequences, which can be used to measure the randomness of binary sequences. We also reveal the relationship between this PE measure with other randomness measures, such as Shannon’s entropy and Lempel–Ziv complexity. The results show that PE is consistent with these two measures. Furthermore, we use PE as one of the randomness measures to evaluate the randomness of chaotic binary sequences.

  1. Remnants of compact binary mergers

    Domainko, W


    We investigate the long-term evolution and observability of remnants originating from the merger of compact binary systems and discuss the differences to supernova remnants. Compact binary mergers expel much smaller amounts of mass at much higher velocities, as compared to supernovae, which will affect the dynamical evolution of their remnants. The ejecta of mergers consist of very neutron rich nuclei. Some of these neutron rich nuclei will produce observational signatures in form of gamma ray lines during their decay. The composition of the ejecta might even give interesting constraints about the internal structure of the neutron star. We further discuss the possibility that merger remnants appear as recently discovered 'dark accelerators' which are extended TeV sources which lack emission in other bands.

  2. Event Rates for Binary Inspiral

    Kalogera, V


    Double compact objects (neutron stars and black holes) found in binaries with small orbital separations are known to spiral in and are expected to coalesce eventually because of the emission of gravitational waves. Such inspiral and merger events are thought to be primary sources for ground based gravitational-wave interferometric detectors (such as LIGO). Here, we present a brief review of estimates of coalescence rates and we examine the origin and relative importance of uncertainties associated with the rate estimates. For the case of double neutron star systems, we compare the most recent rate estimates to upper limits derived in a number of different ways. We also discuss the implications of the formation of close binaries with two non-recycled pulsars.

  3. Modified binary particle swam optimization

    Sangwook Lee; Sangmoon Soak; Sanghoun Oh; Witold Pedrycz; Moongu Jeon


    This paper presents a modified binary particle swarm optimization(BPSO)which adopts concepts of the genotype-phenotype rep-resentation and the mutation operator of genetic algorithms.Its main feature is that the BPSO can be treated as a continuous PSO.The proposed BPSO algorithm is tested on various benchmark functions,and its performance is compared with that of the original BPSO.Experimental results show that the modified BPSO outperforms the original BPSO algorithm.

  4. Tides in asynchronous binary systems

    Toledano, Oswaldo; Moreno, Edmundo; Koenigsberger, Gloria; Detmers, R.; Langer, Norbert


    Stellar oscillations are excited in non-synchronously rotating stars in binary systems due to the tidal forces. Tangential components of the tides can drive a shear flow which behaves as a differentially forced rotating structure in a stratified outer medium. In this paper we show that our single-layer approximation for the calculation of the forced oscillations yields results that are consistent with the predictions for the synchronization timescales in circular orbits. In addition, calibrat...

  5. Galaxy Rotation and Rapid Supermassive Binary Coalescence

    Holley-Bockelmann, Kelly; Khan, Fazeel Mahmood


    Galaxy mergers usher the supermassive black hole (SMBH) in each galaxy to the center of the potential, where they form an SMBH binary. The binary orbit shrinks by ejecting stars via three-body scattering, but ample work has shown that in spherical galaxy models, the binary separation stalls after ejecting all the stars in its loss cone—this is the well-known final parsec problem. However, it has been shown that SMBH binaries in non-spherical galactic nuclei harden at a nearly constant rate until reaching the gravitational wave regime. Here we use a suite of direct N-body simulations to follow SMBH binary evolution in both corotating and counterrotating flattened galaxy models. For N > 500 K, we find that the evolution of the SMBH binary is convergent and is independent of the particle number. Rotation in general increases the hardening rate of SMBH binaries even more effectively than galaxy geometry alone. SMBH binary hardening rates are similar for co- and counterrotating galaxies. In the corotating case, the center of mass of the SMBH binary settles into an orbit that is in corotation resonance with the background rotating model, and the coalescence time is roughly a few 100 Myr faster than a non-rotating flattened model. We find that counterrotation drives SMBHs to coalesce on a nearly radial orbit promptly after forming a hard binary. We discuss the implications for gravitational wave astronomy, hypervelocity star production, and the effect on the structure of the host galaxy.

  6. Visual Binaries in the Orion Nebula Cluster

    Reipurth, Bo; Connelley, Michael S; Bally, John


    We have carried out a major survey for visual binaries towards the Orion Nebula Cluster using HST images obtained with an H-alpha filter. Among 781 likely ONC members more than 60" from theta-1 Ori C, we find 78 multiple systems (75 binaries and 3 triples), of which 55 are new discoveries, in the range from 0.1" to 1.5". About 9 binaries are likely line-of-sight associations. We find a binary fraction of 8.8%+-1.1% within the limited separation range from 67.5 to 675 AU. The field binary fraction in the same range is a factor 1.5 higher. Within the range 150 AU to 675 AU we find that T Tauri associations have a factor 2.2 more binaries than the ONC. The binary separation distribution function of the ONC shows unusual structure, with a sudden steep decrease in the number of binaries as the separation increases beyond 0.5", corresponding to 225 AU. We have measured the ratio of binaries wider than 0.5" to binaries closer than 0.5" as a function of distance from the Trapezium, and find that this ratio is signifi...

  7. Evolution of binary stars in multiple-population globular clusters - II. Compact binaries

    Hong, Jongsuk; Vesperini, Enrico; Sollima, Antonio; McMillan, Stephen L. W.; D'Antona, Franca; D'Ercole, Annibale


    We present the results of a survey of N-body simulations aimed at exploring the evolution of compact binaries in multiple-population globular clusters. We show that as a consequence of the initial differences in the structural properties of the first-generation (FG) and the second-generation (SG) populations and the effects of dynamical processes on binary stars, the SG binary fraction decreases more rapidly than that of the FG population. The difference between the FG and SG binary fraction is qualitatively similar to but quantitatively smaller than that found for wider binaries in our previous investigations. The evolution of the radial variation of the binary fraction is driven by the interplay between binary segregation, ionization and ejection. Ionization and ejection counteract in part the effects of mass segregation but for compact binaries the effects of segregation dominate and the inner binary fraction increases during the cluster evolution. We explore the variation of the difference between the FG and the SG binary fraction with the distance from the cluster centre and its dependence on the binary binding energy and cluster structural parameters. The difference between the binary fraction in the FG and the SG populations found in our simulations is consistent with the results of observational studies finding a smaller binary fraction in the SG population.

  8. Orbital eccentricities in primordial black holes binaries

    Cholis, Ilias; Kovetz, Ely D.; Ali-Haïmoud, Yacine; Bird, Simeon; Kamionkowski, Marc; Muñoz, Julian B.; Raccanelli, Alvise


    It was recently suggested that the merger of $\\sim30\\,M_\\odot$ primordial black holes (PBHs) may provide a significant number of events in gravitational-wave observatories over the next decade, if they make up an appreciable fraction of the dark matter. Here we show that measurement of the eccentricities of the inspiralling binary black holes can be used to distinguish these binaries from those produced by more traditional astrophysical mechanisms. These PBH binaries are formed on highly ecce...

  9. Asteroid Systems: Binaries, Triples, and Pairs

    Margot, Jean-Luc; Taylor, Patrick; Carry, Benoît; Jacobson, Seth


    In the past decade, the number of known binary near-Earth asteroids has more than quadrupled and the number of known large main belt asteroids with satellites has doubled. Half a dozen triple asteroids have been discovered, and the previously unrecognized populations of asteroid pairs and small main belt binaries have been identified. The current observational evidence confirms that small (20 km) binaries with small satellites are most likely created during large collisions.

  10. Relativistic Gravity and Binary Radio Pulsars

    Kaspi, V. M.


    Following a summary of the basic principles of pulsar timing, we present a review of recent results from timing observations of relativistic binary pulsars. In particular, we summarize the status of timing observations of the much celebrated original binary pulsar PSR B1913+16, draw attention to the recent confirmation of strong evidence for geodetic precession in this system, review the recent measurement of multiple post-Keplerian binary parameters for PSR B1534+12, and describe the Parkes ...

  11. Microlensing Signature of Binary Black Holes

    Schnittman, Jeremy; Sahu, Kailash; Littenberg, Tyson


    We calculate the light curves of galactic bulge stars magnified via microlensing by stellar-mass binary black holes along the line-of-sight. We show the sensitivity to measuring various lens parameters for a range of survey cadences and photometric precision. Using public data from the OGLE collaboration, we identify two candidates for massive binary systems, and discuss implications for theories of star formation and binary evolution.

  12. Detection of unresolved binaries with multicolor photometry

    Chulkov, D; Malkov, O; Sichevskij, S; Krussanova, N; Mironov, A; Zakharov, A; Kniazev, A


    The principal goal of this paper is to specify conditions of detection of unresolved binaries by multicolor photometry. We have developed a method for estimating the critical distance at which an unresolved binary of given mass and age can be detected. The method is applied to the photometric system of the planned Lyra-B spaceborne experiment. We have shown that some types of unresolved binary stars can be discovered and distinguished from single stars solely by means of photometric observations.

  13. Relativistic Gravity and Binary Radio Pulsars

    Kaspi, V M


    Following a summary of the basic principles of pulsar timing, we present a review of recent results from timing observations of relativistic binary pulsars. In particular, we summarize the status of timing observations of the much celebrated original binary pulsar PSR B1913+16, draw attention to the recent confirmation of strong evidence for geodetic precession in this system, review the recent measurement of multiple post-Keplerian binary parameters for PSR B1534+12, and describe the Parkes Multibeam survey, a major survey of the Galactic Plane which promises to discover new relativistic binary pulsar systems.

  14. Speech perception of noise with binary gains

    Wang, DeLiang; Kjems, Ulrik; Pedersen, Michael Syskind;


    For a given mixture of speech and noise, an ideal binary time-frequency mask is constructed by comparing speech energy and noise energy within local time-frequency units. It is observed that listeners achieve nearly perfect speech recognition from gated noise with binary gains prescribed by the i...... by the ideal binary mask. Only 16 filter channels and a frame rate of 100 Hz are sufficient for high intelligibility. The results show that, despite a dramatic reduction of speech information, a pattern of binary gains provides an adequate basis for speech perception....

  15. The equations for binary density and the binary stream of particles of electro conducting magnetic liquids

    In work on the basis of a method of the kinetic equations it is output the differential equations for binary density and a binary stream of particles of electro conducting magnetic liquids. These equations are the nonuniform equations of parabolic type. The solution of these equations completely feature existential behaviour of binary density and a binary stream of particles of electro conducting magnetic liquids, i.e. process of a structural relaxation. (author)

  16. Massive Stars in Interactive Binaries

    St.-Louis, Nicole; Moffat, Anthony F. J.

    Massive stars start their lives above a mass of ~8 time solar, finally exploding after a few million years as core-collapse or pair-production supernovae. Above ~15 solar masses, they also spend most of their lives driving especially strong, hot winds due to their extreme luminosities. All of these aspects dominate the ecology of the Universe, from element enrichment to stirring up and ionizing the interstellar medium. But when they occur in close pairs or groups separated by less than a parsec, the interaction of massive stars can lead to various exotic phenomena which would not be seen if there were no binaries. These depend on the actual separation, and going from wie to close including colliding winds (with non-thermal radio emission and Wolf-Rayet dust spirals), cluster dynamics, X-ray binaries, Roche-lobe overflow (with inverse mass-ratios and rapid spin up), collisions, merging, rejuventation and massive blue stragglers, black-hole formation, runaways and gamma-ray bursts. Also, one wonders whether the fact that a massive star is in a binary affects its parameters compared to its isolated equivalent. These proceedings deal with all of these phenomena, plus binary statistics and determination of general physical properties of massive stars, that would not be possible with their single cousins. The 77 articles published in these proceedings, all based on oral talks, vary from broad revies to the lates developments in the field. About a third of the time was spent in open discussion of all participants, both for ~5 minutes after each talk and 8 half-hour long general dialogues, all audio-recorded, transcribed and only moderately edited to yield a real flavour of the meeting. The candid information in these discussions is sometimes more revealing than the article(s) that preceded them and also provide entertaining reading. The book is suitable for researchers and graduate students interested in stellar astrophysics and in various physical processes involved when

  17. Young and Waltzing Binary Stars


    ADONIS Observes Low-mass Eclipsing System in Orion Summary A series of very detailed images of a binary system of two young stars have been combined into a movie . In merely 3 days, the stars swing around each other. As seen from the earth, they pass in front of each other twice during a full revolution, producing eclipses during which their combined brightness diminishes . A careful analysis of the orbital motions has now made it possible to deduce the masses of the two dancing stars . Both turn out to be about as heavy as our Sun. But while the Sun is about 4500 million years old, these two stars are still in their infancy. They are located some 1500 light-years away in the Orion star-forming region and they probably formed just 10 million years ago . This is the first time such an accurate determination of the stellar masses could be achieved for a young binary system of low-mass stars . The new result provides an important piece of information for our current understanding of how young stars evolve. The observations were obtained by a team of astronomers from Italy and ESO [1] using the ADaptive Optics Near Infrared System (ADONIS) on the 3.6-m telescope at the ESO La Silla Observatory. PR Photo 29a/01 : The RXJ 0529.4+0041 system before primary eclipse PR Photo 29b/01 : The RXJ 0529.4+0041 system at mid-primary eclipse PR Photo 29c/01 : The RXJ 0529.4+0041 system after primary eclipse PR Photo 29d/01 : The RXJ 0529.4+0041 system before secondary eclipse PR Photo 29e/01 : The RXJ 0529.4+0041 system at mid-secondary eclipse PR Photo 29f/01 : The RXJ 0529.4+0041 system after secondary eclipse PR Video Clip 06/01 : Video of the RXJ 0529.4+0041 system Binary stars and stellar masses Since some time, astronomers have noted that most stars seem to form in binary or multiple systems. This is quite fortunate, as the study of binary stars is the only way in which it is possible to measure directly one of the most fundamental quantities of a star, its mass. The mass of a

  18. The structures of binary compounds

    Hafner, J; Jensen, WB; Majewski, JA; Mathis, K; Villars, P; Vogl, P; de Boer, FR


    - Up-to-date compilation of the experimental data on the structures of binary compounds by Villars and colleagues. - Coloured structure maps which order the compounds into their respective structural domains and present for the first time the local co-ordination polyhedra for the 150 most frequently occurring structure types, pedagogically very helpful and useful in the search for new materials with a required crystal structure. - Crystal co-ordination formulas: a flexible notation for the interpretation of solid-state structures by chemist Bill Jensen. - Recent important advances in unders

  19. R144 : a very massive binary likely ejected from R136 through a binary-binary encounter

    Oh, Seungkyung; Banerjee, Sambaran


    R144 is a recently confirmed very massive, spectroscopic binary which appears isolated from the core of the massive young star cluster R136. The dynamical ejection hypothesis as an origin for its location is claimed improbable by Sana et al. due to its binary nature and high mass. We demonstrate here by means of direct N-body calculations that a very massive binary system can be readily dynamically ejected from a R136-like cluster, through a close encounter with a very massive system. One out of four N-body cluster models produces a dynamically ejected very massive binary system with a mass comparable to R144. The system has a system mass of $\\approx$ 355 Msun and is located at 36.8 pc from the centre of its parent cluster, moving away from the cluster with a velocity of 57 km/s at 2 Myr as a result of a binary-binary interaction. This implies that R144 could have been ejected from R136 through a strong encounter with an other massive binary or single star. In addition, we discuss all massive binaries and sin...

  20. Mercury and Selenium in Muscle and Target Organs of Scalloped Hammerhead Sharks Sphyrna lewini of the SE Gulf of California: Dietary Intake, Molar Ratios, Loads, and Human Health Risks.

    Bergés-Tiznado, Magdalena E; Márquez-Farías, Fernando; Lara-Mendoza, Raúl E; Torres-Rojas, Yassir E; Galván-Magaña, Felipe; Bojórquez-Leyva, Humberto; Páez-Osuna, Federico


    Selenium and mercury were evaluated in muscle, liver, kidney, brain, and the stomach contents of juvenile scalloped hammerhead shark Sphyrna lewini. Se:Hg molar ratios were calculated. The average Hg levels in muscle ranged from 0.12 to 1.17 μg/g (wet weight); Hg was 1. Correlations were found for Hg in muscle with size, age, and weight, and also for Hg in liver with size, age, and weight. Hg in muscle was significantly positive correlated to Hg in brain as well as Hg in liver was correlated to Hg in kidney. The highest Hg in preys was for carangid fishes; scombrid and carangid fishes contributed with the highest Se levels. Results suggest that more than 98 % of the total Hg and 62 % of Se end up in muscle and might be affected by factors, such as geographical area, age, size, and feeding habits. The muscle of S. lewini should be consumed by people cautiously so as not to exceed the recommended intake per week. PMID:26369650

  1. Millisecond Pulsars in Close Binaries

    Tauris, Thomas M


    In this Habilitationsschrift (Habilitation thesis) I present my research carried out over the last four years at the Argelander Institute for Astronomy (AIfA) and the Max Planck Institute for Radio Astronomy (MPIfR). The thesis summarizes my main findings and has been written to fulfill the requirements for the Habilitation qualification at the University of Bonn. Although my work is mainly focused on the topic of millisecond pulsars (MSPs), there is a fairly broad spread of research areas ranging from the formation of neutron stars (NSs) in various supernova (SN) events, to their evolution, for example, via accretion processes in binary and triple systems, and finally to their possible destruction in merger events. The thesis is organized in the following manner: A general introduction to neutron stars and millisecond pulsars is given in Chapter 1. A selection of key papers published in 2011-2014 are presented in Chapters 2-10, ordered within five main research areas (ultra-stripped SNe in close binaries, ma...

  2. Polarization in binary microlensing events

    The light received by source stars in microlensing events may be significantly polarized if both an efficient photon-scattering mechanism is active in the source stellar atmosphere and a differential magnification is therein induced by the lensing system. The best candidate events for observing polarization are highly magnified events with source stars belonging to the class of cool, giant stars in which the stellar light is polarized by photon scattering on dust grains contained in their envelopes. The presence in the stellar atmosphere of an internal cavity devoid of dust produces polarization profiles with a two peaks structure. Hence, the time interval between them gives an important observable quantity directly related to the size of the internal cavity and to the model parameters of the lens system. We show that, during a microlensing event, the expected polarization variability can solve an ambiguity that arises in some cases, related to the binary or planetary lensing interpretation of the perturbations observed near the maximum of the event light-curve. We consider a specific event case for which the parameter values corresponding to the two solutions are given. Then, assuming a polarization model for the source star, we compute the two expected polarization profiles. The position of the two peaks appearing in the polarization curves and the characteristic time interval between them allow us to distinguish between the binary and planetary lens solutions. (paper)

  3. Pulsating Components in Binary and Multiple Stellar Systems --- A Catalog of Oscillating Binaries

    Zhou, A. -Y.


    We present an up-to-date catalog of pulsating binaries, i.e. the binary and multiple stellar systems containing pulsating components, along with a statistics on them. Compared to the earlier compilation by Soydugan et al.(2006a) of 25 delta Scuti-type `oscillating Algol-type eclipsing binaries' (oEA), the recent collection of 74 oEA by Liakos et al.(2012), and the collection of Cepheids in binaries by Szabados (2003a), the numbers and types of pulsating variables in binaries are now extended....

  4. The Evolution of Compact Binary Star Systems

    Yungelson, Lev R.


    Full Text Available We review the formation and evolution of compact binary stars consisting of white dwarfs (WDs, neutron stars (NSs, and black holes (BHs. Binary NSs and BHs are thought to be the primary astrophysical sources of gravitational waves (GWs within the frequency band of ground-based detectors, while compact binaries of WDs are important sources of GWs at lower frequencies to be covered by space interferometers (LISA. Major uncertainties in the current understanding of properties of NSs and BHs most relevant to the GW studies are discussed, including the treatment of the natal kicks which compact stellar remnants acquire during the core collapse of massive stars and the common envelope phase of binary evolution. We discuss the coalescence rates of binary NSs and BHs and prospects for their detections, the formation and evolution of binary WDs and their observational manifestations. Special attention is given to AM CVn-stars -- compact binaries in which the Roche lobe is filled by another WD or a low-mass partially degenerate helium-star, as these stars are thought to be the best LISA verification binary GW sources.

  5. The Evolution of Compact Binary Star Systems

    Konstantin A. Postnov


    Full Text Available We review the formation and evolution of compact binary stars consisting of white dwarfs (WDs, neutron stars (NSs, and black holes (BHs. Mergings of compact-star binaries are expected to be the most important sources for forthcoming gravitational-wave (GW astronomy. In the first part of the review, we discuss observational manifestations of close binaries with NS and/or BH components and their merger rate, crucial points in the formation and evolution of compact stars in binary systems, including the treatment of the natal kicks, which NSs and BHs acquire during the core collapse of massive stars and the common envelope phase of binary evolution, which are most relevant to the merging rates of NS-NS, NS-BH and BH-BH binaries. The second part of the review is devoted mainly to the formation and evolution of binary WDs and their observational manifestations, including their role as progenitors of cosmologically-important thermonuclear SN Ia. We also consider AM CVn-stars, which are thought to be the best verification binary GW sources for future low-frequency GW space interferometers.

  6. Eliciting Subjective Probabilities with Binary Lotteries

    Harrison, Glenn W.; Martínez-Correa, Jimmy; Swarthout, J. Todd

    We evaluate the binary lottery procedure for inducing risk neutral behavior in a subjective belief elicitation task. Harrison, Martínez-Correa and Swarthout [2013] found that the binary lottery procedure works robustly to induce risk neutrality when subjects are given one risk task defined over o...

  7. Pulsed Accretion onto Eccentric and Circular Binaries

    Muñoz, Diego J


    We present numerical simulations of circumbinary accretion onto eccentric and circular binaries using the moving-mesh code AREPO. This is the first set of simulations to tackle the problem of binary accretion using a finite-volume scheme on a freely moving mesh, which allows for accurate measurements of accretion onto individual stars for arbitrary binary eccentricity. While accretion onto a circular binary shows bursts with period of ~5 times the binary period P_b,accretion onto an eccentric binary is predominantly modulated at the period ~1P_b. For an equal-mass circular binary, the accretion rates onto individual stars are quite similar to each other, following the same variable pattern in time. By contrast, for eccentric binaries, one of the stars can accrete at a rate 10-20 times larger than its companion. This "symmetry breaking" between the stars, however, alternates over timescales of order 200 P_b, and can be attributed to a slowly precessing, eccentric circumbinary disk. Over longer timescales, the ...


    In recent numerical simulations, it has been found that the eccentricity of supermassive black hole (SMBH)-intermediate black hole (IMBH) binaries grows toward unity through interactions with the stellar background. This increase of eccentricity reduces the merging timescale of the binary through the gravitational radiation to a value well below the Hubble time. It also gives a theoretical explanation of the existence of eccentric binaries such as that in OJ287. In self-consistent N-body simulations, this increase of eccentricity is always observed. On the other hand, the result of the scattering experiment between SMBH binaries and field stars indicated that the eccentricity dose not change significantly. This discrepancy leaves the high eccentricity of the SMBH binaries in N-body simulations unexplained. Here, we present a stellar-dynamical mechanism that drives the increase of the eccentricity of an SMBH binary with a large mass ratio. There are two key processes involved. The first one is the Kozai mechanism under a non-axisymmetric potential, which effectively randomizes the angular momenta of surrounding stars. The other is the selective ejection of stars with prograde orbits. Through these two mechanisms, field stars extract the orbital angular momentum of the SMBH binary. Our proposed mechanism causes the increase in the eccentricity of most of SMBH binaries, resulting in the rapid merger through gravitational wave radiation. Our result has given a definite solution to the 'last-parsec problem'.

  9. Microlensing Binaries with Candidate Brown Dwarf Companions

    Shin, I.-G; Han, C.; Gould, A.;


    Brown dwarfs are important objects because they may provide a missing link between stars and planets, two populations that have dramatically different formation histories. In this paper, we present the candidate binaries with brown dwarf companions that are found by analyzing binary microlensing ...

  10. Gravitational radiation, inspiraling binaries, and cosmology

    Chernoff, David F.; Finn, Lee S.


    We show how to measure cosmological parameters using observations of inspiraling binary neutron star or black hole systems in one or more gravitational wave detectors. To illustrate, we focus on the case of fixed mass binary systems observed in a single Laser Interferometer Gravitational-wave Observatory (LIGO)-like detector. Using realistic detector noise estimates, we characterize the rate of detections as a function of a threshold SNR Rho(0), H0, and the binary 'chirp' mass. For Rho(0) = 8, H0 = 100 km/s/Mpc, and 1.4 solar mass neutron star binaries, the sample has a median redshift of 0.22. Under the same assumptions but independent of H0, a conservative rate density of coalescing binaries implies LIGO will observe about 50/yr binary inspiral events. The precision with which H0 and the deceleration parameter q0 may be determined depends on the number of observed inspirals. For fixed mass binary systems, about 100 observations with Rho(0) = 10 in the LIGO will give H0 to 10 percent in an Einstein-DeSitter cosmology, and 3000 will give q0 to 20 percent. For the conservative rate density of coalescing binaries, 100 detections with Rho(0) = 10 will require about 4 yrs.

  11. Gravitational waves from inspiralling binary black holes

    Binary black holes are the most promising candidate sources for the first generation of earth-based interferometric gravitational-wave detectors. We summarize and discuss the state-of-the-art analytical techniques developed during the last few years to better describe the late dynamical evolution of binary black holes of comparable masses

  12. Bayesian analysis of exoplanet and binary orbits

    Schulze-Hartung, Tim; Henning, Thomas


    We introduce BASE (Bayesian astrometric and spectroscopic exoplanet detection and characterisation tool), a novel program for the combined or separate Bayesian analysis of astrometric and radial-velocity measurements of potential exoplanet hosts and binary stars. The capabilities of BASE are demonstrated using all publicly available data of the binary Mizar A.

  13. Planet Scattering Around Binaries: Ejections, Not Collisions

    Smullen, Rachel A; Shannon, Andrew


    Transiting circumbinary planets discovered by Kepler provide unique insight into binary and planet formation. Several features of this new found population, for example the apparent pile-up of planets near the innermost stable orbit, may distinguish between formation theories. In this work, we determine how planet-planet scattering shapes planetary systems around binaries as compared to single stars. In particular, we look for signatures that arise due to differences in dynamical evolution in binary systems. We carry out a parameter study of N-body scattering simulations for four distinct planet populations around both binary and single stars. While binarity has little influence on the final system multiplicity or orbital distribution, the presence of a binary dramatically effects the means by which planets are lost from the system. Most circumbinary planets are lost due to ejections rather than planet-planet or planet-star collisions. The most massive planet in the system tends to control the evolution. Asid...

  14. Orbital dynamics of binary boson star systems

    We extend our previous studies of head-on collisions of boson stars by considering orbiting binary boson stars. We concentrate on equal-mass binaries and study the dynamical behavior of boson/boson and boson/antiboson pairs. We examine the gravitational wave output of these binaries and compare with other compact binaries. Such a comparison lets us probe the apparent simplicity observed in gravitational waves produced by black hole binary systems. In our system of interest however, there is an additional internal freedom which plays a significant role in the system's dynamics, namely, the phase of each star. Our evolutions show rather simple behavior at early times, but large differences occur at late times for the various initial configurations

  15. Logistic chaotic maps for binary numbers generations

    Two pseudorandom binary sequence generators, based on logistic chaotic maps intended for stream cipher applications, are proposed. The first is based on a single one-dimensional logistic map which exhibits random, noise-like properties at given certain parameter values, and the second is based on a combination of two logistic maps. The encryption step proposed in both algorithms consists of a simple bitwise XOR operation of the plaintext binary sequence with the keystream binary sequence to produce the ciphertext binary sequence. A threshold function is applied to convert the floating-point iterates into binary form. Experimental results show that the produced sequences possess high linear complexity and very good statistical properties. The systems are put forward for security evaluation by the cryptographic committees.

  16. Polarization in binary microlensing events

    Ingrosso, G; Nucita, A A; Strafella, F; Novati, S Calchi; Jetzer, Ph; Liuzzi, G; Zakharov, A


    The light received by source stars in microlensing events may be significantly polarized if both an efficient photon scattering mechanism is active in the source stellar atmosphere and a differential magnification is therein induced by the lensing system. The best candidate events for observing polarization are highly magnified events with source stars belonging to the class of cool, giant stars {in which the stellar light is polarized by photon scattering on dust grains contained in their envelopes. The presence in the stellar atmosphere of an internal cavity devoid of dust produces polarization profiles with a two peaks structure. Hence, the time interval between them gives an important observable quantity directly related to the size of the internal cavity and to the model parameters of the lens system.} We show that {during a microlensing event} the expected polarization variability can solve an ambiguity, that arises in some cases, related to the binary or planetary lensing interpretation of the perturba...

  17. Binary Cepheids from optical interferometry

    Gallenne, A; Mérand, A; Monnier, J D; Pietrzyński, J Breitfelder G; Gieren, W


    Classical Cepheid stars have been considered since more than a century as reliable tools to estimate distances in the universe thanks to their Period-Luminosity (P-L) relationship. Moreover, they are also powerful astrophysical laboratories, providing fundamental clues for studying the pulsation and evolution of intermediate-mass stars. When in binary systems, we can investigate the age and evolution of the Cepheid, estimate the mass and distance, and constrain theoretical models. However, most of the companions are located too close to the Cepheid (1-40 mas) to be spatially resolved with a 10-meter class telescope. The only way to spatially resolve such systems is to use long-baseline interferometry. Recently, we have started a unique and long-term interferometric program that aims at detecting and characterizing physical parameters of the Cepheid companions, with as main objectives the determination of accurate masses and geometric distances.

  18. Binary theory of electronic stopping

    Sigmund, P


    Binary stopping theory has been developed to characterize the electronic stopping of swift heavy ions in matter. It is an extension of Bohr's classical theory of 1913 incorporating screening, higher-order-Z sub 1 and shell corrections, high-speed quantum and relativity corrections as well as projectile excitation and ionization. The main numerical input comes from optical properties. The computation of shell corrections involves orbital velocity distributions of target and projectile electrons. Calculated stopping parameters depend on ion charge. Equilibrium stopping forces may be computed by adoption of a suitable model for the equilibrium charge state. This paper summarizes the current status of the theory, in particular the sensitivity of its predictions to pertinent input. Charge-dependent stopping forces have been calculated for selected systems and compared to experimental results. Equilibrium stopping forces calculated for a wide variety of ion-target combinations are compared with experimental data fr...

  19. Binary mixtures of chiral gases

    Presilla, Carlo


    A possible solution of the well known paradox of chiral molecules is based on the idea of spontaneous symmetry breaking. At low pressure the molecules are delocalized between the two minima of a given molecular potential while at higher pressure they become localized in one minimum due to the intermolecular dipole-dipole interactions. Evidence for such a phase transition is provided by measurements of the inversion spectrum of ammonia and deuterated ammonia at different pressures. In particular, at pressure greater than a critical value no inversion line is observed. These data are well accounted for by a model previously developed and recently extended to mixtures. In the present paper, we discuss the variation of the critical pressure in binary mixtures as a function of the fractions of the constituents.

  20. Age and growth of the scalloped hammerhead shark, Sphyrna lewini (Griffith & Smith, 1834) from the Southern coast of Sinaloa, México Edad y crecimiento del tiburón martillo, Sphyrna lewini (Griffith & Smith, 1834) de la costa sur de Sinaloa, México

    Vicente Anislado-Tolentino; Manuel Gallardo Cabello; Felipe Amezcua Linares; Carlos Robinson Mendoza


    Age and growth for the scalloped hammerhead shark (Sphyrna lewini) were determined from opaque bands (OBs) on postcephalic vertebrae from 109 organisms (44 females, 52 cm to 276 cm total length (TL) and 65 males, 47 cm to 245 cm TL) obtained bimonthly from commercial fisheries off the southern coast of Sinaloa state (23°45'25"N and 106°05'15"W to 21°52'N and 105°54'W) from January 2003 to February 2005. The Bowker test of symmetry and the Index of Average Percent Error, suggest that this agei...

  1. Gamma-ray binaries and related systems

    Dubus, Guillaume


    After initial claims and a long hiatus, it is now established that several binary stars emit high (0.1-100 GeV) and very high energy (>100 GeV) gamma rays. A new class has emerged called 'gamma-ray binaries', since most of their radiated power is emitted beyond 1 MeV. Accreting X-ray binaries, novae and a colliding wind binary (eta Car) have also been detected - 'related systems' that confirm the ubiquity of particle acceleration in astrophysical sources. Do these systems have anything in common ? What drives their high-energy emission ? How do the processes involved compare to those in other sources of gamma rays: pulsars, active galactic nuclei, supernova remnants ? I review the wealth of observational and theoretical work that have followed these detections, with an emphasis on gamma-ray binaries. I present the current evidence that gamma-ray binaries are driven by rotation-powered pulsars. Binaries are laboratories giving access to different vantage points or physical conditions on a regular timescale as ...

  2. Interrupted Binary Mass Transfer in Star Clusters

    Leigh, Nathan W C; Toonen, Silvia


    Binary mass transfer is at the forefront of some of the most exciting puzzles of modern astrophysics, including Type Ia supernovae, gamma-ray bursts, and the formation of most observed exotic stellar populations. Typically, the evolution is assumed to proceed in isolation, even in dense stellar environments such as star clusters. In this paper, we test the validity of this assumption via the analysis of a large grid of binary evolution models simulated with the SeBa code. For every binary, we calculate analytically the mean time until another single or binary star comes within the mean separation of the mass-transferring binary, and compare this time-scale to the mean time for stable mass transfer to occur. We then derive the probability for each respective binary to experience a direct dynamical interruption. The resulting probability distribution can be integrated to give an estimate for the fraction of binaries undergoing mass transfer that are expected to be disrupted as a function of the host cluster pro...

  3. Pd-Si binary bulk metallic glass

    YAO KeFu; CHEN Na


    Pd80+xSi20-x (x=0, 1, and 2) binary metallic glasses with the diameter ranging from 7 to 8 mm were prepared by a combination of fluxing and water quenching or air cooling. Thermal analysis results show that with increasing Si content, the glass transition temperature Tg, the initial crystallization temperature Tx and the onset crystalliza-tion temperature Tp of Pd-Si binary glassy alloys increase. Moreover, the super-cooled liquid region reaches 61 K. It indicates that Pd-Si binary alloys possess large glass forming ability, which can be greatly improved by fluxing treatment.

  4. Pd-Si binary bulk metallic glass


    Pd80+xSi20-x (x=0,1,and 2) binary metallic glasses with the diameter ranging from 7 to 8 mm were prepared by a combination of fluxing and water quenching or air cooling. Thermal analysis results show that with increasing Si content,the glass transition temperature Tg,the initial crystallization temperature Tx and the onset crystalliza-tion temperature Tp of Pd-Si binary glassy alloys increase. Moreover,the super-cooled liquid region reaches 61 K. It indicates that Pd-Si binary alloys possess large glass forming ability,which can be greatly improved by fluxing treatment.

  5. Eliciting Subjective Probabilities with Binary Lotteries

    Harrison, Glenn W.; Martínez-Correa, Jimmy; Swarthout, J. Todd


    We evaluate a binary lottery procedure for inducing risk neutral behavior in a subjective belief elicitation task. Prior research has shown this procedure to robustly induce risk neutrality when subjects are given a single risk task defined over objective probabilities. Drawing a sample from the...... same subject population, we find evidence that the binary lottery procedure also induces linear utility in a subjective probability elicitation task using the Quadratic Scoring Rule. We also show that the binary lottery procedure can induce direct revelation of subjective probabilities in subjects with...

  6. Cassini states for black hole binaries

    Correia, Alexandre C. M.


    Cassini states correspond to the equilibria of the spin axis of a body when its orbit is perturbed. They were initially described for planetary satellites, but the spin axes of black hole binaries also present this kind of equilibria. In previous works, Cassini states were reported as spin-orbit resonances, but actually the spin of black hole binaries is in circulation and there is no resonant motion. Here we provide a general description of the spin dynamics of black hole binary systems base...

  7. Fast algorithms for generating binary holograms

    Stuart, Dustin; Kuhn, Axel


    We describe three algorithms for generating binary-valued holograms. Our methods are optimised for producing large arrays of tightly focussed optical tweezers for trapping particles. Binary-valued holograms allow us to use a digital mirror device (DMD) as the display element, which is much faster than other alternatives. We describe how our binary amplitude holograms can be used to correct for phase errors caused by optical aberrations. Furthermore, we compare the speed and accuracy of the algorithms for both periodic and arbitrary arrangements of traps, which allows one to choose the ideal scheme depending on the circumstances.

  8. Potato spindle tuber viroid: the simplicity paradox resolved?

    Taxonomy: Potato spindle tuber viroid (PSTVd) is the type species of the genus Posipiviroid, family Pospiviroidae. An absence of hammerhead ribozymes and the presence of a 'central conserved region' distinguish PSTVd and related viroids from members of a second viroid family, the Avsunviroidae. ...


    We have developed a comprehensive methodology for calculating the circumbinary habitable zone (HZ) in planet-hosting P-type binary star systems. We present a general formalism for determining the contribution of each star of the binary to the total flux received at the top of the atmosphere of an Earth-like planet and use the Sun's HZ to calculate the inner and outer boundaries of the HZ around a binary star system. We apply our calculations to the Kepler's currently known circumbinary planetary systems and show the combined stellar flux that determines the boundaries of their HZs. We also show that the HZ in P-type systems is dynamic and, depending on the luminosity of the binary stars, their spectral types, and the binary eccentricity, its boundaries vary as the stars of the binary undergo their orbital motion. We present the details of our calculations and discuss the implications of the results


    Haghighipour, Nader [Institute for Astronomy and NASA Astrobiology Institute, University of Hawaii-Manoa, Honolulu, HI 96822 (United States); Kaltenegger, Lisa [MPIA, Koenigstuhl 17, Heidelberg, D-69117 (Germany)


    We have developed a comprehensive methodology for calculating the circumbinary habitable zone (HZ) in planet-hosting P-type binary star systems. We present a general formalism for determining the contribution of each star of the binary to the total flux received at the top of the atmosphere of an Earth-like planet and use the Sun's HZ to calculate the inner and outer boundaries of the HZ around a binary star system. We apply our calculations to the Kepler's currently known circumbinary planetary systems and show the combined stellar flux that determines the boundaries of their HZs. We also show that the HZ in P-type systems is dynamic and, depending on the luminosity of the binary stars, their spectral types, and the binary eccentricity, its boundaries vary as the stars of the binary undergo their orbital motion. We present the details of our calculations and discuss the implications of the results.