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Sample records for helicases multiple structures

  1. Crystal structure of Middle East respiratory syndrome coronavirus helicase.

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    Wei Hao

    2017-06-01

    Full Text Available Middle East respiratory syndrome coronavirus (MERS-CoV remains a threat to public health worldwide; however, effective vaccine or drug against CoVs remains unavailable. CoV helicase is one of the three evolutionary most conserved proteins in nidoviruses, thus making it an important target for drug development. We report here the first structure of full-length coronavirus helicase, MERS-CoV nsp13. MERS-CoV helicase has multiple domains, including an N-terminal Cys/His rich domain (CH with three zinc atoms, a beta-barrel domain and a C-terminal SF1 helicase core with two RecA-like subdomains. Our structural analyses show that while the domain organization of nsp13 is conserved throughout nidoviruses, the individual domains of nsp13 are closely related to the equivalent eukaryotic domains of Upf1 helicases. The most distinctive feature differentiating CoV helicases from eukaryotic Upf1 helicases is the interaction between CH domain and helicase core.

  2. Structural basis of Zika virus helicase in recognizing its substrates

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    Hongliang Tian

    2016-07-01

    Full Text Available Abstract The recent explosive outbreak of Zika virus (ZIKV infection has been reported in South and Central America and the Caribbean. Neonatal microcephaly associated with ZIKV infection has already caused a public health emergency of international concern. No specific vaccines or drugs are currently available to treat ZIKV infection. The ZIKV helicase, which plays a pivotal role in viral RNA replication, is an attractive target for therapy. We determined the crystal structures of ZIKV helicase-ATP-Mn2+ and ZIKV helicase-RNA. This is the first structure of any flavivirus helicase bound to ATP. Comparisons with related flavivirus helicases have shown that although the critical P-loop in the active site has variable conformations among different species, it adopts an identical mode to recognize ATP/Mn2+. The structure of ZIKV helicase-RNA has revealed that upon RNA binding, rotations of the motor domains can cause significant conformational changes. Strikingly, although ZIKV and dengue virus (DENV apo-helicases share conserved residues for RNA binding, their different manners of motor domain rotations result in distinct individual modes for RNA recognition. It suggests that flavivirus helicases could have evolved a conserved engine to convert chemical energy from nucleoside triphosphate to mechanical energy for RNA unwinding, but different motor domain rotations result in variable RNA recognition modes to adapt to individual viral replication.

  3. Structural basis for the function of DEAH helicases

    DEFF Research Database (Denmark)

    He, Yangzi; Andersen, Gregers Rom; Nielsen, Klaus Hvid

    2010-01-01

    DEAH helicases participate in pre‐messenger RNA splicing and ribosome biogenesis. The structure of yeast Prp43p‐ADP reveals the homology of DEAH helicases to DNA helicases and the presence of an oligonucleotide‐binding motif. A β‐hairpin from the second RecA domain is wedged between two carboxy......‐terminal domains and blocks access to the occluded RNA binding site formed by the RecA domains and a C‐terminal domain. ATP binding and hydrolysis are likely to induce conformational changes in the hairpin that are important for RNA unwinding or ribonucleoprotein remodelling. The structure of Prp43p provides...

  4. The Arabidopsis thaliana homolog of the helicase RTEL1 plays multiple roles in preserving genome stability.

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    Recker, Julia; Knoll, Alexander; Puchta, Holger

    2014-12-01

    In humans, mutations in the DNA helicase Regulator of Telomere Elongation Helicase1 (RTEL1) lead to Hoyeraal-Hreidarsson syndrome, a severe, multisystem disorder. Here, we demonstrate that the RTEL1 homolog in Arabidopsis thaliana plays multiple roles in preserving genome stability. RTEL1 suppresses homologous recombination in a pathway parallel to that of the DNA translocase FANCM. Cytological analyses of root meristems indicate that RTEL1 is involved in processing DNA replication intermediates independently from FANCM and the nuclease MUS81. Moreover, RTEL1 is involved in interstrand and intrastrand DNA cross-link repair independently from FANCM and (in intrastrand cross-link repair) parallel to MUS81. RTEL1 contributes to telomere homeostasis; the concurrent loss of RTEL1 and the telomerase TERT leads to rapid, severe telomere shortening, which occurs much more rapidly than it does in the single-mutant line tert, resulting in developmental arrest after four generations. The double mutant rtel1-1 recq4A-4 exhibits massive growth defects, indicating that this RecQ family helicase, which is also involved in the suppression of homologous recombination and the repair of DNA lesions, can partially replace RTEL1 in the processing of DNA intermediates. The requirement for RTEL1 in multiple pathways to preserve genome stability in plants can be explained by its putative role in the destabilization of DNA loop structures, such as D-loops and T-loops. © 2014 American Society of Plant Biologists. All rights reserved.

  5. Three-dimensional structure of N-terminal domain of DnaB helicase and helicase-primase interactions in Helicobacter pylori.

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    Tara Kashav

    2009-10-01

    Full Text Available Replication initiation is a crucial step in genome duplication and homohexameric DnaB helicase plays a central role in the replication initiation process by unwinding the duplex DNA and interacting with several other proteins during the process of replication. N-terminal domain of DnaB is critical for helicase activity and for DnaG primase interactions. We present here the crystal structure of the N-terminal domain (NTD of H. pylori DnaB (HpDnaB helicase at 2.2 A resolution and compare the structural differences among helicases and correlate with the functional differences. The structural details of NTD suggest that the linker region between NTD and C-terminal helicase domain plays a vital role in accurate assembly of NTD dimers. The sequence analysis of the linker regions from several helicases reveals that they should form four helix bundles. We also report the characterization of H. pylori DnaG primase and study the helicase-primase interactions, where HpDnaG primase stimulates DNA unwinding activity of HpDnaB suggesting presence of helicase-primase cohort at the replication fork. The protein-protein interaction study of C-terminal domain of primase and different deletion constructs of helicase suggests that linker is essential for proper conformation of NTD to interact strongly with HpDnaG. The surface charge distribution on the primase binding surface of NTDs of various helicases suggests that DnaB-DnaG interaction and stability of the complex is most probably charge dependent. Structure of the linker and helicase-primase interactions indicate that HpDnaB differs greatly from E.coli DnaB despite both belong to gram negative bacteria.

  6. Comparative structural analysis of human DEAD-box RNA helicases.

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    Patrick Schütz

    2010-09-01

    Full Text Available DEAD-box RNA helicases play various, often critical, roles in all processes where RNAs are involved. Members of this family of proteins are linked to human disease, including cancer and viral infections. DEAD-box proteins contain two conserved domains that both contribute to RNA and ATP binding. Despite recent advances the molecular details of how these enzymes convert chemical energy into RNA remodeling is unknown. We present crystal structures of the isolated DEAD-domains of human DDX2A/eIF4A1, DDX2B/eIF4A2, DDX5, DDX10/DBP4, DDX18/myc-regulated DEAD-box protein, DDX20, DDX47, DDX52/ROK1, and DDX53/CAGE, and of the helicase domains of DDX25 and DDX41. Together with prior knowledge this enables a family-wide comparative structural analysis. We propose a general mechanism for opening of the RNA binding site. This analysis also provides insights into the diversity of DExD/H- proteins, with implications for understanding the functions of individual family members.

  7. The Drosophila Helicase MLE Targets Hairpin Structures in Genomic Transcripts.

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    Simona Cugusi

    2016-01-01

    Full Text Available RNA hairpins are a common type of secondary structures that play a role in every aspect of RNA biochemistry including RNA editing, mRNA stability, localization and translation of transcripts, and in the activation of the RNA interference (RNAi and microRNA (miRNA pathways. Participation in these functions often requires restructuring the RNA molecules by the association of single-strand (ss RNA-binding proteins or by the action of helicases. The Drosophila MLE helicase has long been identified as a member of the MSL complex responsible for dosage compensation. The complex includes one of two long non-coding RNAs and MLE was shown to remodel the roX RNA hairpin structures in order to initiate assembly of the complex. Here we report that this function of MLE may apply to the hairpins present in the primary RNA transcripts that generate the small molecules responsible for RNA interference. Using stocks from the Transgenic RNAi Project and the Vienna Drosophila Research Center, we show that MLE specifically targets hairpin RNAs at their site of transcription. The association of MLE at these sites is independent of sequence and chromosome location. We use two functional assays to test the biological relevance of this association and determine that MLE participates in the RNAi pathway.

  8. Comparative structural analysis of human DEAD-box RNA helicases.

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    Schütz, Patrick; Karlberg, Tobias; van den Berg, Susanne; Collins, Ruairi; Lehtiö, Lari; Högbom, Martin; Holmberg-Schiavone, Lovisa; Tempel, Wolfram; Park, Hee-Won; Hammarström, Martin; Moche, Martin; Thorsell, Ann-Gerd; Schüler, Herwig

    2010-09-30

    DEAD-box RNA helicases play various, often critical, roles in all processes where RNAs are involved. Members of this family of proteins are linked to human disease, including cancer and viral infections. DEAD-box proteins contain two conserved domains that both contribute to RNA and ATP binding. Despite recent advances the molecular details of how these enzymes convert chemical energy into RNA remodeling is unknown. We present crystal structures of the isolated DEAD-domains of human DDX2A/eIF4A1, DDX2B/eIF4A2, DDX5, DDX10/DBP4, DDX18/myc-regulated DEAD-box protein, DDX20, DDX47, DDX52/ROK1, and DDX53/CAGE, and of the helicase domains of DDX25 and DDX41. Together with prior knowledge this enables a family-wide comparative structural analysis. We propose a general mechanism for opening of the RNA binding site. This analysis also provides insights into the diversity of DExD/H- proteins, with implications for understanding the functions of individual family members.

  9. The Arabidopsis thaliana Homolog of the Helicase RTEL1 Plays Multiple Roles in Preserving Genome Stability[C][W

    Science.gov (United States)

    Recker, Julia; Knoll, Alexander; Puchta, Holger

    2014-01-01

    In humans, mutations in the DNA helicase Regulator of Telomere Elongation Helicase1 (RTEL1) lead to Hoyeraal-Hreidarsson syndrome, a severe, multisystem disorder. Here, we demonstrate that the RTEL1 homolog in Arabidopsis thaliana plays multiple roles in preserving genome stability. RTEL1 suppresses homologous recombination in a pathway parallel to that of the DNA translocase FANCM. Cytological analyses of root meristems indicate that RTEL1 is involved in processing DNA replication intermediates independently from FANCM and the nuclease MUS81. Moreover, RTEL1 is involved in interstrand and intrastrand DNA cross-link repair independently from FANCM and (in intrastrand cross-link repair) parallel to MUS81. RTEL1 contributes to telomere homeostasis; the concurrent loss of RTEL1 and the telomerase TERT leads to rapid, severe telomere shortening, which occurs much more rapidly than it does in the single-mutant line tert, resulting in developmental arrest after four generations. The double mutant rtel1-1 recq4A-4 exhibits massive growth defects, indicating that this RecQ family helicase, which is also involved in the suppression of homologous recombination and the repair of DNA lesions, can partially replace RTEL1 in the processing of DNA intermediates. The requirement for RTEL1 in multiple pathways to preserve genome stability in plants can be explained by its putative role in the destabilization of DNA loop structures, such as D-loops and T-loops. PMID:25516598

  10. PBDE: Structure-Activity Studies for the Inhibition of Hepatitis C Virus NS3 Helicase

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    Kazi Abdus Salam

    2014-04-01

    Full Text Available The helicase portion of the hepatitis C virus nonstructural protein 3 (NS3 is considered one of the most validated targets for developing direct acting antiviral agents. We isolated polybrominated diphenyl ether (PBDE 1 from a marine sponge as an NS3 helicase inhibitor. In this study, we evaluated the inhibitory effects of PBDE (1 on the essential activities of NS3 protein such as RNA helicase, ATPase, and RNA binding activities. The structure-activity relationship analysis of PBDE (1 against the HCV ATPase revealed that the biphenyl ring, bromine, and phenolic hydroxyl group on the benzene backbone might be a basic scaffold for the inhibitory potency.

  11. Crystal structures of the methyltransferase and helicase from the ZIKA 1947 MR766 Uganda strain

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    Bukrejewska, Malgorzata; Derewenda, Urszula; Radwanska, Malwina; Engel, Daniel A.; Derewenda, Zygmunt S.

    2017-08-15

    Two nonstructural proteins encoded byZika virusstrain MR766 RNA, a methyltransferase and a helicase, were crystallized and their structures were solved and refined at 2.10 and 2.01 Å resolution, respectively. The NS5 methyltransferase contains a boundS-adenosyl-L-methionine (SAM) co-substrate. The NS3 helicase is in the apo form. Comparison with published crystal structures of the helicase in the apo, nucleotide-bound and single-stranded RNA (ssRNA)-bound states suggests that binding of ssRNA to the helicase may occur through conformational selection rather than induced fit.

  12. Targeting Dengue Virus NS-3 Helicase by Ligand based Pharmacophore Modeling and Structure based Virtual Screening

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    Halim, Sobia A.; Khan, Shanza; Khan, Ajmal; Wadood, Abdul; Mabood, Fazal; Hussain, Javid; Al-Harrasi, Ahmed

    2017-10-01

    Dengue fever is an emerging public health concern, with several million viral infections occur annually, for which no effective therapy currently exist. Non-structural protein 3 (NS-3) Helicase encoded by the dengue virus (DENV) is considered as a potential drug target to design new and effective drugs against dengue. Helicase is involved in unwinding of dengue RNA. This study was conducted to design new NS-3 Helicase inhibitor by in silico ligand- and structure based approaches. Initially ligand-based pharmacophore model was generated that was used to screen a set of 1201474 compounds collected from ZINC Database. The compounds matched with the pharmacophore model were docked into the active site of NS-3 helicase. Based on docking scores and binding interactions, twenty five compounds are suggested to be potential inhibitors of NS3 Helicase. The pharmacokinetic properties of these hits were predicted. The selected hits revealed acceptable ADMET properties. This study identified potential inhibitors of NS-3 Helicase in silico, and can be helpful in the treatment of Dengue.

  13. XPD Helicase Structures and Activities: Insights into the Cancer and Aging Phenotypes from XPD Mutations

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    Tainer, John; Fan, Li; Fuss, Jill O.; Cheng, Quen J.; Arvai, Andrew S.; Hammel, Michal; Roberts, Victoria A.; Cooper, Priscilla K.; Tainer, John A.

    2008-06-02

    Mutations in XPD helicase, required for nucleotide excision repair (NER) as part of the transcription/repair complex TFIIH, cause three distinct phenotypes: cancer-prone xeroderma pigmentosum (XP), or aging disorders Cockayne syndrome (CS), and trichothiodystrophy (TTD). To clarify molecular differences underlying these diseases, we determined crystal structures of the XPD catalytic core from Sulfolobus acidocaldarius and measured mutant enzyme activities. Substrate-binding grooves separate adjacent Rad51/RecA-like helicase domains (HD1, HD2) and an arch formed by 4FeS and Arch domains. XP mutations map along the HD1 ATP-binding edge and HD2 DNA-binding channel and impair helicase activity essential for NER. XP/CS mutations both impair helicase activity and likely affect HD2 functional movement. TTD mutants lose or retain helicase activity but map to sites in all four domains expected to cause framework defects impacting TFIIH integrity. These results provide a foundation for understanding disease consequences of mutations in XPD and related 4Fe-4S helicases including FancJ.

  14. XPD Helicase Structures And Activities: Insights Into the Cancer And Aging Phenotypes From XPD Mutations

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    Fan, L.; Fuss, J.O.; Cheng, Q.J.; Arvai, A.S.; Hammel, M.; Roberts, V.A.; Cooper, P.K.; Tainer, J.A.

    2009-05-18

    Mutations in XPD helicase, required for nucleotide excision repair (NER) as part of the transcription/repair complex TFIIH, cause three distinct phenotypes: cancer-prone xeroderma pigmentosum (XP), or aging disorders Cockayne syndrome (CS), and trichothiodystrophy (TTD). To clarify molecular differences underlying these diseases, we determined crystal structures of the XPD catalytic core from Sulfolobus acidocaldarius and measured mutant enzyme activities. Substrate-binding grooves separate adjacent Rad51/RecA-like helicase domains (HD1, HD2) and an arch formed by 4FeS and Arch domains. XP mutations map along the HD1 ATP-binding edge and HD2 DNA-binding channel and impair helicase activity essential for NER. XP/CS mutations both impair helicase activity and likely affect HD2 functional movement. TTD mutants lose or retain helicase activity but map to sites in all four domains expected to cause framework defects impacting TFIIH integrity. These results provide a foundation for understanding disease consequences of mutations in XPD and related 4Fe-4S helicases including FancJ.

  15. Unzippers, Resolvers and Sensors: A Structural and Functional Biochemistry Tale of RNA Helicases

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    Ana Lúcia Leitão

    2015-01-01

    Full Text Available The centrality of RNA within the biological world is an irrefutable fact that currently attracts increasing attention from the scientific community. The panoply of functional RNAs requires the existence of specific biological caretakers, RNA helicases, devoted to maintain the proper folding of those molecules, resolving unstable structures. However, evolution has taken advantage of the specific position and characteristics of RNA helicases to develop new functions for these proteins, which are at the interface of the basic processes for transference of information from DNA to proteins. RNA helicases are involved in many biologically relevant processes, not only as RNA chaperones, but also as signal transducers, scaffolds of molecular complexes, and regulatory elements. Structural biology studies during the last decade, founded in X-ray crystallography, have characterized in detail several RNA-helicases. This comprehensive review summarizes the structural knowledge accumulated in the last two decades within this family of proteins, with special emphasis on the structure-function relationships of the most widely-studied families of RNA helicases: the DEAD-box, RIG-I-like and viral NS3 classes.

  16. Structural view of the helicase reveals that Zika virus uses a conserved mechanism for unwinding RNA.

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    Li, Lei; Wang, Jin; Jia, Zhihui; Shaw, Neil

    2018-04-01

    Recent studies suggest a link between infection by Zika virus (ZIKV) and the development of neurological complications. The lack of ZIKV-specific therapeutics has alarmed healthcare professionals worldwide. Here, crystal structures of apo and AMPPNP- and Mn 2+ -bound forms of the essential helicase of ZIKV refined to 1.78 and 1.3 Å resolution, respectively, are reported. The structures reveal a conserved trimodular topology of the helicase. ATP and Mn 2+ are tethered between two RecA-like domains by conserved hydrogen-bonding interactions. The binding of ligands induces the movement of backbone Cα and side-chain atoms. Numerous solvent molecules are observed in the vicinity of the AMPPNP, suggesting a role in catalysis. These high-resolution structures could be useful for the design of inhibitors targeting the helicase of ZIKV for the treatment of infections caused by ZIKV.

  17. Structure-Based Mutational Analysis of the Hepatitis C Virus NS3 Helicase

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    Tai, Chun-Ling; Pan, Wen-Ching; Liaw, Shwu-Huey; Yang, Ueng-Cheng; Hwang, Lih-Hwa; Chen, Ding-Shinn

    2001-01-01

    The carboxyl terminus of the hepatitis C virus (HCV) nonstructural protein 3 (NS3) possesses ATP-dependent RNA helicase activity. Based on the conserved sequence motifs and the crystal structures of the helicase domain, 17 mutants of the HCV NS3 helicase were generated. The ATP hydrolysis, RNA binding, and RNA unwinding activities of the mutant proteins were examined in vitro to determine the functional role of the mutated residues. The data revealed that Lys-210 in the Walker A motif and Asp-290, Glu-291, and His-293 in the Walker B motif were crucial to ATPase activity and that Thr-322 and Thr-324 in motif III and Arg-461 in motif VI significantly influenced ATPase activity. When the pairing between His-293 and Gln-460, referred to as gatekeepers, was replaced with the Asp-293/His-460 pair, which makes the NS3 helicase more like the DEAD helicase subgroup, ATPase activity was not restored. It thus indicated that the whole microenvironment surrounding the gatekeepers, rather than the residues per se, was important to the enzymatic activities. Arg-461 and Trp-501 are important residues for RNA binding, while Val-432 may only play a coadjutant role. The data demonstrated that RNA helicase activity was possibly abolished by the loss of ATPase activity or by reduced RNA binding activity. Nevertheless, a low threshold level of ATPase activity was found sufficient for helicase activity. Results in this study provide a valuable reference for efforts under way to develop anti-HCV therapeutic drugs targeting NS3. PMID:11483774

  18. Crystal structure of the FeS cluster-containing nucleotide excision repair helicase XPD.

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    Stefanie C Wolski

    2008-06-01

    Full Text Available DNA damage recognition by the nucleotide excision repair pathway requires an initial step identifying helical distortions in the DNA and a proofreading step verifying the presence of a lesion. This proofreading step is accomplished in eukaryotes by the TFIIH complex. The critical damage recognition component of TFIIH is the XPD protein, a DNA helicase that unwinds DNA and identifies the damage. Here, we describe the crystal structure of an archaeal XPD protein with high sequence identity to the human XPD protein that reveals how the structural helicase framework is combined with additional elements for strand separation and DNA scanning. Two RecA-like helicase domains are complemented by a 4Fe4S cluster domain, which has been implicated in damage recognition, and an alpha-helical domain. The first helicase domain together with the helical and 4Fe4S-cluster-containing domains form a central hole with a diameter sufficient in size to allow passage of a single stranded DNA. Based on our results, we suggest a model of how DNA is bound to the XPD protein, and can rationalize several of the mutations in the human XPD gene that lead to one of three severe diseases, xeroderma pigmentosum, Cockayne syndrome, and trichothiodystrophy.

  19. Non-B DNA Secondary Structures and Their Resolution by RecQ Helicases

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    Sudha Sharma

    2011-01-01

    Full Text Available In addition to the canonical B-form structure first described by Watson and Crick, DNA can adopt a number of alternative structures. These non-B-form DNA secondary structures form spontaneously on tracts of repeat sequences that are abundant in genomes. In addition, structured forms of DNA with intrastrand pairing may arise on single-stranded DNA produced transiently during various cellular processes. Such secondary structures have a range of biological functions but also induce genetic instability. Increasing evidence suggests that genomic instabilities induced by non-B DNA secondary structures result in predisposition to diseases. Secondary DNA structures also represent a new class of molecular targets for DNA-interactive compounds that might be useful for targeting telomeres and transcriptional control. The equilibrium between the duplex DNA and formation of multistranded non-B-form structures is partly dependent upon the helicases that unwind (resolve these alternate DNA structures. With special focus on tetraplex, triplex, and cruciform, this paper summarizes the incidence of non-B DNA structures and their association with genomic instability and emphasizes the roles of RecQ-like DNA helicases in genome maintenance by resolution of DNA secondary structures. In future, RecQ helicases are anticipated to be additional molecular targets for cancer chemotherapeutics.

  20. Escherichia coli and Neisseria gonorrhoeae UvrD helicase unwinds G4 DNA structures.

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    Shukla, Kaustubh; Thakur, Roshan Singh; Ganguli, Debayan; Rao, Desirazu Narasimha; Nagaraju, Ganesh

    2017-10-18

    G-quadruplex (G4) secondary structures have been implicated in various biological processes, including gene expression, DNA replication and telomere maintenance. However, unresolved G4 structures impede replication progression which can lead to the generation of DNA double-strand breaks and genome instability. Helicases have been shown to resolve G4 structures to facilitate faithful duplication of the genome. Escherichia coli UvrD (EcUvrD) helicase plays a crucial role in nucleotide excision repair, mismatch repair and in the regulation of homologous recombination. Here, we demonstrate a novel role of E. coli and Neisseria gonorrhoeae UvrD in resolving G4 tetraplexes. EcUvrD and N gonorrhoeae UvrD were proficient in unwinding previously characterized tetramolecular G4 structures. Notably, EcUvrD was equally efficient in resolving tetramolecular and bimolecular G4 DNA that were derived from the potential G4-forming sequences from the genome of E. coli Interestingly, in addition to resolving intermolecular G4 structures, EcUvrD was robust in unwinding intramolecular G4 structures. These data for the first time provide evidence for the role of UvrD in the resolution of G4 structures, which has implications for the in vivo role of UvrD helicase in G4 DNA resolution and genome maintenance. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

  1. Structural mechanisms of human RecQ helicases WRN and BLM

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    Ken eKitano

    2014-10-01

    Full Text Available The RecQ family DNA helicases WRN (Werner syndrome protein and BLM (Bloom syndrome protein play a key role in protecting the genome against deleterious changes. In humans, mutations in these proteins lead to rare genetic diseases associated with cancer predisposition and accelerated aging. WRN and BLM are distinguished from other helicases by possessing signature tandem domains toward the C terminus, referred to as the RecQ C-terminal (RQC and helicase-and-ribonuclease D-C-terminal (HRDC domains. Although the precise function of the HRDC domain remains unclear, the previous crystal structure of a WRN RQC-DNA complex visualized a central role for the RQC domain in recognizing, binding and unwinding DNA at branch points. In particular, a prominent hairpin structure (the β-wing within the RQC winged-helix motif acts as a scalpel to induce the unpairing of a Watson-Crick base pair at the DNA duplex terminus. A similar RQC-DNA interaction was also observed in the recent crystal structure of a BLM-DNA complex. I review the latest structures of WRN and BLM, and then provide a docking simulation of BLM with a Holliday junction. The model offers an explanation for the efficient branch migration activity of the RecQ family toward recombination and repair intermediates.

  2. DNA secondary structure of the released strand stimulates WRN helicase action on forked duplexes without coordinate action of WRN exonuclease

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    Ahn, Byungchan, E-mail: bbccahn@mail.ulsan.ac.kr [Department of Life Sciences, University of Ulsan, Ulsan (Korea, Republic of); Bohr, Vilhelm A. [Laboratory of Molecular Gerontology, Biomedical Research Center, National Institute on Aging, Baltimore, MD (United States)

    2011-08-12

    Highlights: {yields} In this study, we investigated the effect of a DNA secondary structure on the two WRN activities. {yields} We found that a DNA secondary structure of the displaced strand during unwinding stimulates WRN helicase without coordinate action of WRN exonuclease. {yields} These results imply that WRN helicase and exonuclease activities can act independently. -- Abstract: Werner syndrome (WS) is an autosomal recessive premature aging disorder characterized by aging-related phenotypes and genomic instability. WS is caused by mutations in a gene encoding a nuclear protein, Werner syndrome protein (WRN), a member of the RecQ helicase family, that interestingly possesses both helicase and exonuclease activities. Previous studies have shown that the two activities act in concert on a single substrate. We investigated the effect of a DNA secondary structure on the two WRN activities and found that a DNA secondary structure of the displaced strand during unwinding stimulates WRN helicase without coordinate action of WRN exonuclease. These results imply that WRN helicase and exonuclease activities can act independently, and we propose that the uncoordinated action may be relevant to the in vivo activity of WRN.

  3. Emerging Importance of Helicases in Plant Stress Tolerance: Characterization of Oryza sativa Repair Helicase XPB2 Promoter and Its Functional Validation in Tobacco under Multiple Stresses.

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    Raikwar, Shailendra; Srivastava, Vineet K; Gill, Sarvajeet S; Tuteja, Renu; Tuteja, Narendra

    2015-01-01

    Genetic material always remains at the risk of spontaneous or induced damage which challenges the normal functioning of DNA molecule, thus, DNA repair is vital to protect the organisms against genetic damage. Helicases, the unique molecular motors, are emerged as prospective molecules to engineer stress tolerance in plants and are involved in nucleic acid metabolism including DNA repair. The repair helicase, XPB is an evolutionary conserved protein present in different organisms, including plants. Availability of few efficient promoters for gene expression in plants provoked us to study the promoter of XPB for better understanding of gene regulation under stress conditions. Here, we report the in silico analysis of novel stress inducible promoter of Oryza sativa XPB2 (OsXPB2). The in vivo validation of functionality/activity of OsXPB2 promoter under abiotic and hormonal stress conditions was performed by Agrobacterium-mediated transient assay in tobacco leaves using OsXPB2::GUS chimeric construct. The present research revealed that OsXPB2 promoter contains cis-elements accounting for various abiotic stresses (salt, dehydration, or cold) and hormone (Auxin, ABA, or MeJA) induced GUS expression/activity in the promoter-reporter assay. The promoter region of OsXPB2 contains CACG, GTAACG, CACGTG, CGTCA CCGCCGCGCT cis acting-elements which are reported to be salt, dehydration, cold, MeJA, or ABA responsive, respectively. Functional analysis was done by Agrobacterium-mediated transient assay using agroinfiltration in tobacco leaves, followed by GUS staining and fluorescence quantitative analyses. The results revealed high induction of GUS activity under multiple abiotic stresses as compared to mock treated control. The present findings suggest that OsXPB2 promoter is a multi-stress inducible promoter and has potential applications in sustainable crop production under abiotic stresses by regulating desirable pattern of gene expression.

  4. X-ray structure of the pestivirus NS3 helicase and its conformation in solution.

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    Tortorici, M Alejandra; Duquerroy, Stéphane; Kwok, Jane; Vonrhein, Clemens; Perez, Javier; Lamp, Benjamin; Bricogne, Gerard; Rümenapf, Till; Vachette, Patrice; Rey, Félix A

    2015-04-01

    Pestiviruses form a genus in the Flaviviridae family of small enveloped viruses with a positive-sense single-stranded RNA genome. Viral replication in this family requires the activity of a superfamily 2 RNA helicase contained in the C-terminal domain of nonstructural protein 3 (NS3). NS3 features two conserved RecA-like domains (D1 and D2) with ATPase activity, plus a third domain (D3) that is important for unwinding nucleic acid duplexes. We report here the X-ray structure of the pestivirus NS3 helicase domain (pNS3h) at a 2.5-Å resolution. The structure deviates significantly from that of NS3 of other genera in the Flaviviridae family in D3, as it contains two important insertions that result in a narrower nucleic acid binding groove. We also show that mutations in pNS3h that rescue viruses from which the core protein is deleted map to D3, suggesting that this domain may be involved in interactions that facilitate particle assembly. Finally, structural comparisons of the enzyme in different crystalline environments, together with the findings of small-angle X-ray-scattering studies in solution, show that D2 is mobile with respect to the rest of the enzyme, oscillating between closed and open conformations. Binding of a nonhydrolyzable ATP analog locks pNS3h in a conformation that is more compact than the closest apo-form in our crystals. Together, our results provide new insight and bring up new questions about pNS3h function during pestivirus replication. Although pestivirus infections impose an important toll on the livestock industry worldwide, little information is available about the nonstructural proteins essential for viral replication, such as the NS3 helicase. We provide here a comparative structural and functional analysis of pNS3h with respect to its orthologs in other viruses of the same family, the flaviviruses and hepatitis C virus. Our studies reveal differences in the nucleic acid binding groove that could have implications for understanding the

  5. A holistic evolutionary and structural study of flaviviridae provides insights into the function and inhibition of HCV helicase

    Directory of Open Access Journals (Sweden)

    Dimitrios Vlachakis

    2013-05-01

    Full Text Available Viral RNA helicases are involved in duplex unwinding during the RNA replication of the virus. It is suggested that these helicases represent very promising antiviral targets. Viruses of the flaviviridae family are the causative agents of many common and devastating diseases, including hepatitis, yellow fever and dengue fever. As there is currently no available anti-Flaviviridae therapy, there is urgent need for the development of efficient anti-viral pharmaceutical strategies. Herein, we report the complete phylogenetic analysis across flaviviridae alongside a more in-depth evolutionary study that revealed a series of conserved and invariant amino acids that are predicted to be key to the function of the helicase. Structural molecular modelling analysis revealed the strategic significance of these residues based on their relative positioning on the 3D structures of the helicase enzymes, which may be used as pharmacological targets. We previously reported a novel series of highly potent HCV helicase inhibitors, and we now re-assess their antiviral potential using the 3D structural model of the invariant helicase residues. It was found that the most active compound of the series, compound C4, exhibited an IC50 in the submicromolar range, whereas its stereoisomer (compound C12 was completely inactive. Useful insights were obtained from molecular modelling and conformational search studies via molecular dynamics simulations. C12 tends to bend and lock in an almost “U” shape conformation, failing to establish vital interactions with the active site of HCV. On the contrary, C4 spends most of its conformational time in a straight, more rigid formation that allows it to successfully block the passage of the oligonucleotide in the ssRNA channel of the HCV helicase. This study paves the way and provides the necessary framework for the in-depth analysis required to enable the future design of new and potent anti-viral agents.

  6. Structural and functional analysis of the human spliceosomal DEAD-box helicase Prp28

    Energy Technology Data Exchange (ETDEWEB)

    Möhlmann, Sina [Georg-August-University Göttingen, Justus-von-Liebig Weg 11, 37077 Göttingen (Germany); Mathew, Rebecca [Max-Planck-Institute for Biophysical Chemistry, Am Fassberg, 37077 Göttingen (Germany); Neumann, Piotr; Schmitt, Andreas [Georg-August-University Göttingen, Justus-von-Liebig Weg 11, 37077 Göttingen (Germany); Lührmann, Reinhard [Max-Planck-Institute for Biophysical Chemistry, Am Fassberg, 37077 Göttingen (Germany); Ficner, Ralf, E-mail: rficner@uni-goettingen.de [Georg-August-University Göttingen, Justus-von-Liebig Weg 11, 37077 Göttingen (Germany)

    2014-06-01

    The crystal structure of the helicase domain of the human spliceosomal DEAD-box protein Prp28 was solved by SAD. The binding of ADP and ATP by Prp28 was studied biochemically and analysed with regard to the crystal structure. The DEAD-box protein Prp28 is essential for pre-mRNA splicing as it plays a key role in the formation of an active spliceosome. Prp28 participates in the release of the U1 snRNP from the 5′-splice site during association of the U5·U4/U6 tri-snRNP, which is a crucial step in the transition from a pre-catalytic spliceosome to an activated spliceosome. Here, it is demonstrated that the purified helicase domain of human Prp28 (hPrp28ΔN) binds ADP, whereas binding of ATP and ATPase activity could not be detected. ATP binding could not be observed for purified full-length hPrp28 either, but within an assembled spliceosomal complex hPrp28 gains ATP-binding activity. In order to understand the structural basis for the ATP-binding deficiency of isolated hPrp28, the crystal structure of hPrp28ΔN was determined at 2.0 Å resolution. In the crystal the helicase domain adopts a wide-open conformation, as the two RecA-like domains are extraordinarily displaced from the productive ATPase conformation. Binding of ATP is hindered by a closed conformation of the P-loop, which occupies the space required for the γ-phosphate of ATP.

  7. Emerging Importance of Helicases in Plant Stress Tolerance: Characterization of Oryza sativa Repair Helicase XPB2 Promoter and Its Functional Validation in Tobacco under Multiple Stresses

    OpenAIRE

    Raikwar, Shailendra; Srivastava, Vineet K.; Gill, Sarvajeet S.; Tuteja, Renu; Tuteja, Narendra

    2015-01-01

    Genetic material always remains at the risk of spontaneous or induced damage which challenges the normal functioning of DNA molecule, thus, DNA repair is vital to protect the organisms against genetic damage. Helicases, the unique molecular motors, are emerged as prospective molecules to engineer stress tolerance in plants and are involved in nucleic acid metabolism including DNA repair. The repair helicase, XPB is an evolutionary conserved protein present in different organisms, including pl...

  8. Emerging importance of helicases in plant stress tolerance: characterization of Oryza sativa repair helicase XPB2 promoter and its functional validation in tobacco under multiple stresses

    OpenAIRE

    Shailendra eRaikwar; Vineet Kumar Shrivastava; Sarvajeet Singh Gill; Renu eTuteja; Narendra eTuteja; Narendra eTuteja

    2015-01-01

    Genetic material always remains at the risk of spontaneous or induced damage which challenges the normal functioning of DNA molecule, thus, DNA repair is vital to protect the organisms against genetic damage. DNA hHelicases, the unique molecular motors, are emerged as potentialprospective molecules to engineer stress tolerance in plants and are involved in a variety of DNA nucleic acid metabolismc processes including DNA repair. The DNA repair helicase, OsXPB2 is an evolutionary conserved pr...

  9. Emerging importance of helicases in plant stress tolerance: characterization of Oryza sativa repair helicase XPB2 promoter and its functional validation in tobacco under multiple stresses

    Directory of Open Access Journals (Sweden)

    Shailendra eRaikwar

    2015-12-01

    Full Text Available Genetic material always remains at the risk of spontaneous or induced damage which challenges the normal functioning of DNA molecule, thus, DNA repair is vital to protect the organisms against genetic damage. DNA hHelicases, the unique molecular motors, are emerged as potentialprospective molecules to engineer stress tolerance in plants and are involved in a variety of DNA nucleic acid metabolismc processes including DNA repair. The DNA repair helicase, OsXPB2 is an evolutionary conserved protein present in different organisms, including plants. Availability of few efficient promoters for gene expression in plants provoked us to study the promoter of XPB for better understanding of gene regulation under stress The analysis of promoter sequence from plant genome is important in understanding the gene regulation. Hereconditions. Here, we report the in silico analysis of novel stress inducible promoter of rice Oryza sativa OsXPB2 (OsXPB2. gene is reported. The in vivo validation of functionality/activity of novel stress inducible promoter of rice OsXPB2 gene promoter under abiotic and hormonal stress conditions was performed by Agrobacterium-mediated transient assay in tobacco leaves using OsXPB2::GUS chimeric construct. Our resultsThe present research revealed that OsXPB2 promoter contains cis-elements accounting for various abiotic stresses (salt, dehydration or cold and hormone (Auxin, ABA or MeJA induced GUS expression/activity in the promoter-reporter assay. The promoter region of OsXPB2 contains CACG, GTAACG, CACGTG, CGTCA CCGCCGCGCT cis acting-elements which are reported to be salt, dehydration, cold, MeJA or ABA responsive, respectively. Functional analysis was done by Agrobacterium-transient assays using agroinfiltration in tobacco leaves, followed by GUS staining and fluorescence quantitative analyses. The results revealed high induction of GUS activity under multiple abiotic stresses as compared to mock treated control. The present

  10. Archaeal MCM Proteins as an Analog for the Eukaryotic Mcm2–7 Helicase to Reveal Essential Features of Structure and Function

    Science.gov (United States)

    Miller, Justin M.; Enemark, Eric J.

    2015-01-01

    In eukaryotes, the replicative helicase is the large multisubunit CMG complex consisting of the Mcm2–7 hexameric ring, Cdc45, and the tetrameric GINS complex. The Mcm2–7 ring assembles from six different, related proteins and forms the core of this complex. In archaea, a homologous MCM hexameric ring functions as the replicative helicase at the replication fork. Archaeal MCM proteins form thermostable homohexamers, facilitating their use as models of the eukaryotic Mcm2–7 helicase. Here we review archaeal MCM helicase structure and function and how the archaeal findings relate to the eukaryotic Mcm2–7 ring. PMID:26539061

  11. Dna2 nuclease-helicase structure, mechanism and regulation by Rpa.

    Science.gov (United States)

    Zhou, Chun; Pourmal, Sergei; Pavletich, Nikola P

    2015-11-02

    The Dna2 nuclease-helicase maintains genomic integrity by processing DNA double-strand breaks, Okazaki fragments and stalled replication forks. Dna2 requires ssDNA ends, and is dependent on the ssDNA-binding protein Rpa, which controls cleavage polarity. Here we present the 2.3 Å structure of intact mouse Dna2 bound to a 15-nucleotide ssDNA. The nuclease active site is embedded in a long, narrow tunnel through which the DNA has to thread. The helicase domain is required for DNA binding but not threading. We also present the structure of a flexibly-tethered Dna2-Rpa interaction that recruits Dna2 to Rpa-coated DNA. We establish that a second Dna2-Rpa interaction is mutually exclusive with Rpa-DNA interactions and mediates the displacement of Rpa from ssDNA. This interaction occurs at the nuclease tunnel entrance and the 5' end of the Rpa-DNA complex. Hence, it only displaces Rpa from the 5' but not 3' end, explaining how Rpa regulates cleavage polarity.

  12. EM structure of a helicase-loader complex depicting a 6:2 binding sub-stoichiometry from Geobacillus kaustophilus HTA426

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Yen-Chen [Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan (China); Naveen, Vankadari [Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan (China); Molecular Cell Biology, Taiwan International Graduate Program, Institute of Molecular Biology, Academia Sinica, and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan (China); Hsiao, Chwan-Deng, E-mail: hsiao@gate.sinica.edu.tw [Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan (China); Molecular Cell Biology, Taiwan International Graduate Program, Institute of Molecular Biology, Academia Sinica, and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan (China)

    2016-04-22

    During DNA replication, bacterial helicase is recruited as a complex in association with loader proteins to unwind the parental duplex. Previous structural studies have reported saturated 6:6 helicase-loader complexes with different conformations. However, structural information on the sub-stoichiometric conformations of these previously-documented helicase-loader complexes remains elusive. Here, with the aid of single particle electron-microscopy (EM) image reconstruction, we present the Geobacillus kaustophilus HTA426 helicase-loader (DnaC-DnaI) complex with a 6:2 binding stoichiometry in the presence of ATPγS. In the 19 Å resolution EM map, the undistorted and unopened helicase ring holds a robust loader density above the C-terminal RecA-like domain. Meanwhile, the path of the central DNA binding channel appears to be obstructed by the reconstructed loader density, implying its potential role as a checkpoint conformation to prevent the loading of immature complex onto DNA. Our data also reveals that the bound nucleotides and the consequently induced conformational changes in the helicase hexamer are essential for active association with loader proteins. These observations provide fundamental insights into the formation of the helicase-loader complex in bacteria that regulates the DNA replication process. - Highlights: • Helicase-loader complex structure with 6:2 sub-stoichiometry is resolved by EM. • Helicase hexamer in 6:2 sub-stoichiometry is constricted and un-opened. • 6:2 binding ratio of helicase-loader complex could act as a DNA loading checkpoint. • Nucleotides stabilize helicase-loader complex at low protein concentrations.

  13. EM structure of a helicase-loader complex depicting a 6:2 binding sub-stoichiometry from Geobacillus kaustophilus HTA426

    International Nuclear Information System (INIS)

    Lin, Yen-Chen; Naveen, Vankadari; Hsiao, Chwan-Deng

    2016-01-01

    During DNA replication, bacterial helicase is recruited as a complex in association with loader proteins to unwind the parental duplex. Previous structural studies have reported saturated 6:6 helicase-loader complexes with different conformations. However, structural information on the sub-stoichiometric conformations of these previously-documented helicase-loader complexes remains elusive. Here, with the aid of single particle electron-microscopy (EM) image reconstruction, we present the Geobacillus kaustophilus HTA426 helicase-loader (DnaC-DnaI) complex with a 6:2 binding stoichiometry in the presence of ATPγS. In the 19 Å resolution EM map, the undistorted and unopened helicase ring holds a robust loader density above the C-terminal RecA-like domain. Meanwhile, the path of the central DNA binding channel appears to be obstructed by the reconstructed loader density, implying its potential role as a checkpoint conformation to prevent the loading of immature complex onto DNA. Our data also reveals that the bound nucleotides and the consequently induced conformational changes in the helicase hexamer are essential for active association with loader proteins. These observations provide fundamental insights into the formation of the helicase-loader complex in bacteria that regulates the DNA replication process. - Highlights: • Helicase-loader complex structure with 6:2 sub-stoichiometry is resolved by EM. • Helicase hexamer in 6:2 sub-stoichiometry is constricted and un-opened. • 6:2 binding ratio of helicase-loader complex could act as a DNA loading checkpoint. • Nucleotides stabilize helicase-loader complex at low protein concentrations.

  14. Structural Studies of RNA Helicases Involved in Eukaryotic Pre-mRNA Splicing, Ribosome Biogenesis, and Translation Initiation

    DEFF Research Database (Denmark)

    He, Yangzi

    and ligates the neighbouring exons to generate mature mRNAs. Prp43 is an RNA helicase of the DEAH/RHA family. In yeast, once mRNAs are released, Prp43 catalyzes the disassembly of spliceosomes. The 18S, 5.8S and 25S rRNAs are transcribed as a single polycistronic transcript—the 35S pre......-rRNA. It is nucleolytically cleaved and chemically modified to generate mature rRNAs, which assemble with ribosomal proteins to form the ribosome. Prp43 is required for the processing of the 18S rRNA. Using X-ray crystallography, I determined a high resolution structure of Prp43 bound to ADP, the first structure of a DEAH....../RHA helicase. It defined the conserved structural features of all DEAH/RHA helicases, and unveiled a novel nucleotide binding site. Additionally a preliminary low resolution structure of a ternary complex comprising Prp43, a non-hydrolyzable ATP analogue, and a single-stranded RNA, was obtained. The ribosome...

  15. Preliminary crystallographic characterization of an RNA helicase from Kunjin virus

    International Nuclear Information System (INIS)

    Mastrangelo, Eloise; Bollati, Michela; Milani, Mario; Brisbarre, Nadège; Lamballerie, Xavier de; Coutard, Bruno; Canard, Bruno; Khromykh, Alexander; Bolognesi, Martino

    2006-01-01

    The C-terminal 440 amino acids of the NS3 protein from Kunjin virus (Flaviviridae) code for a helicase. The protein has been overexpressed and crystallized. Characterization of the isolated monoclinic crystal form and diffraction data (at 3.0 Å resolution) are presented, together with a preliminary molecular-replacement solution. Kunjin virus is a member of the Flavivirus genus and is an Australian variant of West Nile virus. The C-terminal domain of the Kunjin virus NS3 protein displays helicase activity. The protein is thought to separate daughter and template RNA strands, assisting the initiation of replication by unwinding RNA secondary structure in the 3′ nontranslated region. Expression, purification and preliminary crystallographic characterization of the NS3 helicase domain are reported. It is shown that Kunjin virus helicase may adopt a dimeric assembly in absence of nucleic acids, oligomerization being a means to provide the helicases with multiple nucleic acid-binding capability, facilitating translocation along the RNA strands. Kunjin virus NS3 helicase domain is an attractive model for studying the molecular mechanisms of flavivirus replication, while simultaneously providing a new basis for the rational development of anti-flaviviral compounds

  16. Mycobacterium tuberculosis DinG is a structure-specific helicase that unwinds G4 DNA: implications for targeting G4 DNA as a novel therapeutic approach.

    Science.gov (United States)

    Thakur, Roshan Singh; Desingu, Ambika; Basavaraju, Shivakumar; Subramanya, Shreelakshmi; Rao, Desirazu N; Nagaraju, Ganesh

    2014-09-05

    The significance of G-quadruplexes and the helicases that resolve G4 structures in prokaryotes is poorly understood. The Mycobacterium tuberculosis genome is GC-rich and contains >10,000 sequences that have the potential to form G4 structures. In Escherichia coli, RecQ helicase unwinds G4 structures. However, RecQ is absent in M. tuberculosis, and the helicase that participates in G4 resolution in M. tuberculosis is obscure. Here, we show that M. tuberculosis DinG (MtDinG) exhibits high affinity for ssDNA and ssDNA translocation with a 5' → 3' polarity. Interestingly, MtDinG unwinds overhangs, flap structures, and forked duplexes but fails to unwind linear duplex DNA. Our data with DNase I footprinting provide mechanistic insights and suggest that MtDinG is a 5' → 3' polarity helicase. Notably, in contrast to E. coli DinG, MtDinG catalyzes unwinding of replication fork and Holliday junction structures. Strikingly, we find that MtDinG resolves intermolecular G4 structures. These data suggest that MtDinG is a multifunctional structure-specific helicase that unwinds model structures of DNA replication, repair, and recombination as well as G4 structures. We finally demonstrate that promoter sequences of M. tuberculosis PE_PGRS2, mce1R, and moeB1 genes contain G4 structures, implying that G4 structures may regulate gene expression in M. tuberculosis. We discuss these data and implicate targeting G4 structures and DinG helicase in M. tuberculosis could be a novel therapeutic strategy for culminating the infection with this pathogen. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  17. Structural insights into RISC assembly facilitated by dsRNA-binding domains of human RNA helicase A (DHX9).

    Science.gov (United States)

    Fu, Qinqin; Yuan, Y Adam

    2013-03-01

    Intensive research interest has focused on small RNA-processing machinery and the RNA-induced silencing complex (RISC), key cellular machines in RNAi pathways. However, the structural mechanism regarding RISC assembly, the primary step linking small RNA processing and RNA-mediated gene silencing, is largely unknown. Human RNA helicase A (DHX9) was reported to function as an RISC-loading factor, and such function is mediated mainly by its dsRNA-binding domains (dsRBDs). Here, we report the crystal structures of human RNA helicase A (RHA) dsRBD1 and dsRBD2 domains in complex with dsRNAs, respectively. Structural analysis not only reveals higher siRNA duplex-binding affinity displayed by dsRBD1, but also identifies a crystallographic dsRBD1 pair of physiological significance in cooperatively recognizing dsRNAs. Structural observations are further validated by isothermal titration calorimetric (ITC) assay. Moreover, co-immunoprecipitation (co-IP) assay coupled with mutagenesis demonstrated that both dsRBDs are required for RISC association, and such association is mediated by dsRNA. Hence, our structural and functional efforts have revealed a potential working model for siRNA recognition by RHA tandem dsRBDs, and together they provide direct structural insights into RISC assembly facilitated by RHA.

  18. Insights into the Structure of Dimeric RNA Helicase CsdA and Indispensable Role of Its C-Terminal Regions.

    Science.gov (United States)

    Xu, Ling; Wang, Lijun; Peng, Junhui; Li, Fudong; Wu, Lijie; Zhang, Beibei; Lv, Mengqi; Zhang, Jiahai; Gong, Qingguo; Zhang, Rongguang; Zuo, Xiaobing; Zhang, Zhiyong; Wu, Jihui; Tang, Yajun; Shi, Yunyu

    2017-12-05

    CsdA has been proposed to be essential for the biogenesis of ribosome and gene regulation after cold shock. However, the structure of CsdA and the function of its long C-terminal regions are still unclear. Here, we solved all of the domain structures of CsdA and found two previously uncharacterized auxiliary domains: a dimerization domain (DD) and an RNA-binding domain (RBD). Small-angle X-ray scattering experiments helped to track the conformational flexibilities of the helicase core domains and C-terminal regions. Biochemical assays revealed that DD is indispensable for stabilizing the CsdA dimeric structure. We also demonstrate for the first time that CsdA functions as a stable dimer at low temperature. The C-terminal regions are critical for RNA binding and efficient enzymatic activities. CsdA_RBD could specifically bind to the regions with a preference for single-stranded G-rich RNA, which may help to bring the helicase core to unwind the adjacent duplex. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Disintegration of cruciform and G-quadruplex structures during the course of helicase-dependent amplification (HDA).

    Science.gov (United States)

    Li, Dawei; Lv, Bei; Zhang, Hao; Lee, Jasmine Yiqin; Li, Tianhu

    2015-04-15

    Unlike chemical damages on DNA, physical alterations of B-form of DNA occur commonly in organisms that serve as signals for specified cellular events. Although the modes of action for repairing of chemically damaged DNA have been well studied nowadays, the repairing mechanisms for physically altered DNA structures have not yet been understood. Our current in vitro studies show that both breakdown of stable non-B DNA structures and resumption of canonical B-conformation of DNA can take place during the courses of isothermal helicase-dependent amplification (HDA). The pathway that makes the non-B DNA structures repairable is presumably the relieving of the accumulated torsional stress that was caused by the positive supercoiling. Our new findings suggest that living organisms might have evolved this distinct and economical pathway for repairing their physically altered DNA structures. Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. Authentic interdomain communication in an RNA helicase reconstituted by expressed protein ligation of two helicase domains.

    Science.gov (United States)

    Karow, Anne R; Theissen, Bettina; Klostermeier, Dagmar

    2007-01-01

    RNA helicases mediate structural rearrangements of RNA or RNA-protein complexes at the expense of ATP hydrolysis. Members of the DEAD box helicase family consist of two flexibly connected helicase domains. They share nine conserved sequence motifs that are involved in nucleotide binding and hydrolysis, RNA binding, and helicase activity. Most of these motifs line the cleft between the two helicase domains, and extensive communication between them is required for RNA unwinding. The two helicase domains of the Bacillus subtilis RNA helicase YxiN were produced separately as intein fusions, and a functional RNA helicase was generated by expressed protein ligation. The ligated helicase binds adenine nucleotides with very similar affinities to the wild-type protein. Importantly, its intrinsically low ATPase activity is stimulated by RNA, and the Michaelis-Menten parameters are similar to those of the wild-type. Finally, ligated YxiN unwinds a minimal RNA substrate to an extent comparable to that of the wild-type helicase, confirming authentic interdomain communication.

  1. DHX9 helicase is involved in preventing genomic instability induced by alternatively structured DNA in human cells.

    Science.gov (United States)

    Jain, Aklank; Bacolla, Albino; Del Mundo, Imee M; Zhao, Junhua; Wang, Guliang; Vasquez, Karen M

    2013-12-01

    Sequences that have the capacity to adopt alternative (i.e. non-B) DNA structures in the human genome have been implicated in stimulating genomic instability. Previously, we found that a naturally occurring intra-molecular triplex (H-DNA) caused genetic instability in mammals largely in the form of DNA double-strand breaks. Thus, it is of interest to determine the mechanism(s) involved in processing H-DNA. Recently, we demonstrated that human DHX9 helicase preferentially unwinds inter-molecular triplex DNA in vitro. Herein, we used a mutation-reporter system containing H-DNA to examine the relevance of DHX9 activity on naturally occurring H-DNA structures in human cells. We found that H-DNA significantly increased mutagenesis in small-interfering siRNA-treated, DHX9-depleted cells, affecting mostly deletions. Moreover, DHX9 associated with H-DNA in the context of supercoiled plasmids. To further investigate the role of DHX9 in the recognition/processing of H-DNA, we performed binding assays in vitro and chromatin immunoprecipitation assays in U2OS cells. DHX9 recognized H-DNA, as evidenced by its binding to the H-DNA structure and enrichment at the H-DNA region compared with a control region in human cells. These composite data implicate DHX9 in processing H-DNA structures in vivo and support its role in the overall maintenance of genomic stability at sites of alternatively structured DNA.

  2. Structure based modification of Bluetongue virus helicase protein VP6 to produce a viable VP6-truncated BTV

    Energy Technology Data Exchange (ETDEWEB)

    Matsuo, Eiko [Microbiology and Immunology, Division of Animal Science, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1, Rokkodai, Nada-ku, Kobe-City 657-8501 (Japan); Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT (United Kingdom); Leon, Esther; Matthews, Steve J. [Division of Molecular Biosciences, Centre for Structural Biology, Imperial College London, South Kensington, London SW7 2AZ (United Kingdom); Roy, Polly, E-mail: polly.roy@lshtm.ac.uk [Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT (United Kingdom)

    2014-09-05

    Highlights: • NMR analysis on BTV VP6 reveals two large loop regions. • The loss of a loop (aa 34–130) does not affect the overall fold of the protein. • A region of VP6 (aa 34–92) is not required for BTV replication. • A region of VP6 (aa 93–130) plays an essential role in the virus replication. - Abstract: Bluetongue virus core protein VP6 is an ATP hydrolysis dependent RNA helicase. However, despite much study, the precise role of VP6 within the viral capsid and its structure remain unclear. To investigate the requirement of VP6 in BTV replication, we initiated a structural and biological study. Multinuclear nuclear magnetic resonance spectra were assigned on his-tagged full-length VP6 (329 amino acid residues) as well as several truncated VP6 variants. The analysis revealed a large structured domain with two large loop regions that exhibit significant conformational exchange. One of the loops (amino acid position 34–130) could be removed without affecting the overall fold of the protein. Moreover, using a BTV reverse genetics system, it was possible to demonstrate that the VP6-truncated BTV was viable in BHK cells in the absence of any helper VP6 protein, suggesting that a large portion of this loop region is not absolutely required for BTV replication.

  3. Structure of the SPRY domain of the human RNA helicase DDX1, a putative interaction platform within a DEAD-box protein

    Energy Technology Data Exchange (ETDEWEB)

    Kellner, Julian N.; Meinhart, Anton, E-mail: anton.meinhart@mpimf-heidelberg.mpg.de [Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg (Germany)

    2015-08-25

    The structure of the SPRY domain of the human RNA helicase DDX1 was determined at 2.0 Å resolution. The SPRY domain provides a putative protein–protein interaction platform within DDX1 that differs from other SPRY domains in its structure and conserved regions. The human RNA helicase DDX1 in the DEAD-box family plays an important role in RNA processing and has been associated with HIV-1 replication and tumour progression. Whereas previously described DEAD-box proteins have a structurally conserved core, DDX1 shows a unique structural feature: a large SPRY-domain insertion in its RecA-like consensus fold. SPRY domains are known to function as protein–protein interaction platforms. Here, the crystal structure of the SPRY domain of human DDX1 (hDSPRY) is reported at 2.0 Å resolution. The structure reveals two layers of concave, antiparallel β-sheets that stack onto each other and a third β-sheet beneath the β-sandwich. A comparison with SPRY-domain structures from other eukaryotic proteins showed that the general β-sandwich fold is conserved; however, differences were detected in the loop regions, which were identified in other SPRY domains to be essential for interaction with cognate partners. In contrast, in hDSPRY these loop regions are not strictly conserved across species. Interestingly, though, a conserved patch of positive surface charge is found that may replace the connecting loops as a protein–protein interaction surface. The data presented here comprise the first structural information on DDX1 and provide insights into the unique domain architecture of this DEAD-box protein. By providing the structure of a putative interaction domain of DDX1, this work will serve as a basis for further studies of the interaction network within the hetero-oligomeric complexes of DDX1 and of its recruitment to the HIV-1 Rev protein as a viral replication factor.

  4. Purification and crystallization of Kokobera virus helicase

    International Nuclear Information System (INIS)

    De Colibus, Luigi; Speroni, Silvia; Coutard, Bruno; Forrester, Naomi L.; Gould, Ernest; Canard, Bruno; Mattevi, Andrea

    2007-01-01

    Kokobera virus is a mosquito-borne flavivirus belonging, like West Nile virus, to the Japanese encephalitis virus serocomplex. Crystals of the Kokobera virus helicase domain were obtained by the hanging-drop vapour-diffusion method and exhibit a diffraction limit of 2.3 Å. Kokobera virus is a mosquito-borne flavivirus belonging, like West Nile virus, to the Japanese encephalitis virus serocomplex. The flavivirus genus is characterized by a positive-sense single-stranded RNA genome. The unique open reading frame of the viral RNA is transcribed and translated as a single polyprotein which is post-translationally cleaved to yield three structural and seven nonstructural proteins, one of which is the NS3 gene that encodes a C-terminal helicase domain consisting of 431 amino acids. Helicase inhibitors are potential antiviral drugs as the helicase is essential to viral replication. Crystals of the Kokobera virus helicase domain were obtained by the hanging-drop vapour-diffusion method. The crystals belong to space group P3 1 21 (or P3 2 21), with unit-cell parameters a = 88.6, c = 138.6 Å, and exhibit a diffraction limit of 2.3 Å

  5. Purification and crystallization of Kokobera virus helicase

    Energy Technology Data Exchange (ETDEWEB)

    De Colibus, Luigi; Speroni, Silvia [Department of Genetics and Microbiology, University of Pavia, Via Ferrata 1, 27100 Pavia (Italy); Coutard, Bruno [Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS et Université Aix-Marseille I et II, ESIL, Campus de Luminy, 13288 Marseille CEDEX 09 (France); Forrester, Naomi L.; Gould, Ernest [Centre for Ecology and Hydrology (formerly Institute of Virology), Mansfield Road, Oxford OX1 3SR (United Kingdom); Canard, Bruno [Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS et Université Aix-Marseille I et II, ESIL, Campus de Luminy, 13288 Marseille CEDEX 09 (France); Mattevi, Andrea, E-mail: mattevi@ipvgen.unipv.it [Department of Genetics and Microbiology, University of Pavia, Via Ferrata 1, 27100 Pavia (Italy)

    2007-03-01

    Kokobera virus is a mosquito-borne flavivirus belonging, like West Nile virus, to the Japanese encephalitis virus serocomplex. Crystals of the Kokobera virus helicase domain were obtained by the hanging-drop vapour-diffusion method and exhibit a diffraction limit of 2.3 Å. Kokobera virus is a mosquito-borne flavivirus belonging, like West Nile virus, to the Japanese encephalitis virus serocomplex. The flavivirus genus is characterized by a positive-sense single-stranded RNA genome. The unique open reading frame of the viral RNA is transcribed and translated as a single polyprotein which is post-translationally cleaved to yield three structural and seven nonstructural proteins, one of which is the NS3 gene that encodes a C-terminal helicase domain consisting of 431 amino acids. Helicase inhibitors are potential antiviral drugs as the helicase is essential to viral replication. Crystals of the Kokobera virus helicase domain were obtained by the hanging-drop vapour-diffusion method. The crystals belong to space group P3{sub 1}21 (or P3{sub 2}21), with unit-cell parameters a = 88.6, c = 138.6 Å, and exhibit a diffraction limit of 2.3 Å.

  6. Identification of multiple distinct Snf2 subfamilies with conserved structural motifs.

    Science.gov (United States)

    Flaus, Andrew; Martin, David M A; Barton, Geoffrey J; Owen-Hughes, Tom

    2006-01-01

    The Snf2 family of helicase-related proteins includes the catalytic subunits of ATP-dependent chromatin remodelling complexes found in all eukaryotes. These act to regulate the structure and dynamic properties of chromatin and so influence a broad range of nuclear processes. We have exploited progress in genome sequencing to assemble a comprehensive catalogue of over 1300 Snf2 family members. Multiple sequence alignment of the helicase-related regions enables 24 distinct subfamilies to be identified, a considerable expansion over earlier surveys. Where information is known, there is a good correlation between biological or biochemical function and these assignments, suggesting Snf2 family motor domains are tuned for specific tasks. Scanning of complete genomes reveals all eukaryotes contain members of multiple subfamilies, whereas they are less common and not ubiquitous in eubacteria or archaea. The large sample of Snf2 proteins enables additional distinguishing conserved sequence blocks within the helicase-like motor to be identified. The establishment of a phylogeny for Snf2 proteins provides an opportunity to make informed assignments of function, and the identification of conserved motifs provides a framework for understanding the mechanisms by which these proteins function.

  7. The Crystal Structure of the Drosophila Germline Inducer Oskar Identifies Two Domains with Distinct Vasa Helicase- and RNA-Binding Activities

    Directory of Open Access Journals (Sweden)

    Mandy Jeske

    2015-07-01

    Full Text Available In many animals, the germ plasm segregates germline from soma during early development. Oskar protein is known for its ability to induce germ plasm formation and germ cells in Drosophila. However, the molecular basis of germ plasm formation remains unclear. Here, we show that Oskar is an RNA-binding protein in vivo, crosslinking to nanos, polar granule component, and germ cell-less mRNAs, each of which has a role in germline formation. Furthermore, we present high-resolution crystal structures of the two Oskar domains. RNA-binding maps in vitro to the C-terminal domain, which shows structural similarity to SGNH hydrolases. The highly conserved N-terminal LOTUS domain forms dimers and mediates Oskar interaction with the germline-specific RNA helicase Vasa in vitro. Our findings suggest a dual function of Oskar in RNA and Vasa binding, providing molecular clues to its germ plasm function.

  8. Structure of a Novel DNA-binding Domain of Helicase-like Transcription Factor (HLTF) and Its Functional Implication in DNA Damage Tolerance.

    Science.gov (United States)

    Hishiki, Asami; Hara, Kodai; Ikegaya, Yuzu; Yokoyama, Hideshi; Shimizu, Toshiyuki; Sato, Mamoru; Hashimoto, Hiroshi

    2015-05-22

    HLTF (helicase-like transcription factor) is a yeast RAD5 homolog found in mammals. HLTF has E3 ubiquitin ligase and DNA helicase activities, and plays a pivotal role in the template-switching pathway of DNA damage tolerance. HLTF has an N-terminal domain that has been designated the HIRAN (HIP116 and RAD5 N-terminal) domain. The HIRAN domain has been hypothesized to play a role in DNA binding; however, the structural basis of, and functional evidence for, the HIRAN domain in DNA binding has remained unclear. Here we show for the first time the crystal structure of the HIRAN domain of human HLTF in complex with DNA. The HIRAN domain is composed of six β-strands and two α-helices, forming an OB-fold structure frequently found in ssDNA-binding proteins, including in replication factor A (RPA). Interestingly, this study reveals that the HIRAN domain interacts with not only with a single-stranded DNA but also with a duplex DNA. Furthermore, the structure unexpectedly clarifies that the HIRAN domain specifically recognizes the 3'-end of DNA. These results suggest that the HIRAN domain functions as a sensor to the 3'-end of the primer strand at the stalled replication fork and that the domain facilitates fork regression. HLTF is recruited to a damaged site through the HIRAN domain at the stalled replication fork. Furthermore, our results have implications for the mechanism of template switching. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  9. Overcoming natural replication barriers: differential helicase requirements.

    Science.gov (United States)

    Anand, Ranjith P; Shah, Kartik A; Niu, Hengyao; Sung, Patrick; Mirkin, Sergei M; Freudenreich, Catherine H

    2012-02-01

    DNA sequences that form secondary structures or bind protein complexes are known barriers to replication and potential inducers of genome instability. In order to determine which helicases facilitate DNA replication across these barriers, we analyzed fork progression through them in wild-type and mutant yeast cells, using 2-dimensional gel-electrophoretic analysis of the replication intermediates. We show that the Srs2 protein facilitates replication of hairpin-forming CGG/CCG repeats and prevents chromosome fragility at the repeat, whereas it does not affect replication of G-quadruplex forming sequences or a protein-bound repeat. Srs2 helicase activity is required for hairpin unwinding and fork progression. Also, the PCNA binding domain of Srs2 is required for its in vivo role of replication through hairpins. In contrast, the absence of Sgs1 or Pif1 helicases did not inhibit replication through structural barriers, though Pif1 did facilitate replication of a telomeric protein barrier. Interestingly, replication through a protein barrier but not a DNA structure barrier was modulated by nucleotide pool levels, illuminating a different mechanism by which cells can regulate fork progression through protein-mediated stall sites. Our analyses reveal fundamental differences in the replication of DNA structural versus protein barriers, with Srs2 helicase activity exclusively required for fork progression through hairpin structures.

  10. RecQ Helicases

    DEFF Research Database (Denmark)

    Larsen, Nicolai Balle; Hickson, Ian D

    2013-01-01

    The RecQ family of DNA helicases is highly conserved throughout -evolution, and is important for the maintenance of genome stability. In humans, five RecQ family members have been identified: BLM, WRN, RECQ4, RECQ1 and RECQ5. Defects in three of these give rise to Bloom's syndrome (BLM), Werner...

  11. Multiplicative Galois module structure

    CERN Document Server

    Weiss, A

    1996-01-01

    This book is the result of a short course on the Galois structure of S-units that was given at The Fields Institute in the fall of 1993. Offering a new angle on an old problem, the main theme is that this structure should be determined by class field theory, in its cohomological form, and by the behavior of Artin L-functions at s=0. A proof of this-or even a precise formulation-is still far away, but the available evidence all points in this direction. The work brings together the current evidence that the Galois structure of S-units can be described.

  12. Mycobacterium tuberculosis UvrB Is a Robust DNA-Stimulated ATPase That Also Possesses Structure-Specific ATP-Dependent DNA Helicase Activity.

    Science.gov (United States)

    Thakur, Manoj; Kumar, Mohan B J; Muniyappa, K

    2016-10-18

    Much is known about the Escherichia coli nucleotide excision repair (NER) pathway; however, very little is understood about the proteins involved and the molecular mechanism of NER in mycobacteria. In this study, we show that Mycobacterium tuberculosis UvrB (MtUvrB), which exists in solution as a monomer, binds to DNA in a structure-dependent manner. A systematic examination of MtUvrB substrate specificity reveals that it associates preferentially with single-stranded DNA, duplexes with 3' or 5' overhangs, and linear duplex DNA with splayed arms. Whereas E. coli UvrB (EcUvrB) binds weakly to undamaged DNA and has no ATPase activity, MtUvrB possesses intrinsic ATPase activity that is greatly stimulated by both single- and double-stranded DNA. Strikingly, we found that MtUvrB, but not EcUvrB, possesses the DNA unwinding activity characteristic of an ATP-dependent DNA helicase. The helicase activity of MtUvrB proceeds in the 3' to 5' direction and is strongly modulated by a nontranslocating 5' single-stranded tail, indicating that in addition to the translocating strand it also interacts with the 5' end of the substrate. The fraction of DNA unwound by MtUvrB decreases significantly as the length of the duplex increases: it fails to unwind duplexes longer than 70 bp. These results, on one hand, reveal significant mechanistic differences between MtUvrB and EcUvrB and, on the other, support an alternative role for UvrB in the processing of key DNA replication intermediates. Altogether, our findings provide insights into the catalytic functions of UvrB and lay the foundation for further understanding of the NER pathway in M. tuberculosis.

  13. Interplay of cis- and trans-regulatory mechanisms in the spliceosomal RNA helicase Brr2.

    Science.gov (United States)

    Absmeier, Eva; Becke, Christian; Wollenhaupt, Jan; Santos, Karine F; Wahl, Markus C

    2017-01-02

    RNA helicase Brr2 is implicated in multiple phases of pre-mRNA splicing and thus requires tight regulation. Brr2 can be auto-inhibited via a large N-terminal region folding back onto its helicase core and auto-activated by a catalytically inactive C-terminal helicase cassette. Furthermore, it can be regulated in trans by the Jab1 domain of the Prp8 protein, which can inhibit Brr2 by intermittently inserting a C-terminal tail in the enzyme's RNA-binding tunnel or activate the helicase after removal of this tail. Presently it is unclear, whether these regulatory mechanisms functionally interact and to which extent they are evolutionarily conserved. Here, we report crystal structures of Saccharomyces cerevisiae and Chaetomium thermophilum Brr2-Jab1 complexes, demonstrating that Jab1-based inhibition of Brr2 presumably takes effect in all eukaryotes but is implemented via organism-specific molecular contacts. Moreover, the structures show that Brr2 auto-inhibition can act in concert with Jab1-mediated inhibition, and suggest that the N-terminal region influences how the Jab1 C-terminal tail interacts at the RNA-binding tunnel. Systematic RNA binding and unwinding studies revealed that the N-terminal region and the Jab1 C-terminal tail specifically interfere with accommodation of double-stranded and single-stranded regions of an RNA substrate, respectively, mutually reinforcing each other. Additionally, such analyses show that regulation based on the N-terminal region requires the presence of the inactive C-terminal helicase cassette. Together, our results outline an intricate system of regulatory mechanisms, which control Brr2 activities during snRNP assembly and splicing.

  14. Crystal Structure of the Phage T4 Recombinase UvsX and Its Functional Interaction with the T4 SF2 Helicase UvsW

    Energy Technology Data Exchange (ETDEWEB)

    Gajewski, Stefan; Webb, Michael R.; Galkin, Vitold; Egelman, Edward H.; Kreuzer, Kenneth N.; White, Stephen W. (Duke); (UV); (SJCH)

    2012-07-11

    Bacteriophage T4 provides an important model system for studying the mechanism of homologous recombination. We have determined the crystal structure of the T4 UvsX recombinase, and the overall architecture and fold closely resemble those of RecA, including a highly conserved ATP binding site. Based on this new structure, we reanalyzed electron microscopy reconstructions of UvsX-DNA filaments and docked the UvsX crystal structure into two different filament forms: a compressed filament generated in the presence of ADP and an elongated filament generated in the presence of ATP and aluminum fluoride. In these reconstructions, the ATP binding site sits at the protomer interface, as in the RecA filament crystal structure. However, the environment of the ATP binding site is altered in the two filament reconstructions, suggesting that nucleotide cannot be as easily accommodated at the protomer interface of the compressed filament. Finally, we show that the phage helicase UvsW completes the UvsX-promoted strand-exchange reaction, allowing the generation of a simple nicked circular product rather than complex networks of partially exchanged substrates.

  15. Mycobacterial UvrD1 is a Ku-dependent DNA helicase that plays a role in multiple DNA repair events, including double-strand break repair.

    Science.gov (United States)

    Sinha, Krishna Murari; Stephanou, Nicolas C; Gao, Feng; Glickman, Michael S; Shuman, Stewart

    2007-05-18

    Mycobacterium tuberculosis and other bacterial pathogens have a Ku-dependent nonhomologous end joining pathway of DNA double-strand break repair. Here we identify mycobacterial UvrD1 as a novel interaction partner for Ku in a genome-wide yeast two-hybrid screen. UvrD1 per se is a vigorous DNA-dependent ATPase but a feeble DNA helicase. Ku stimulates UvrD1 to catalyze ATP-dependent unwinding of 3'-tailed DNAs. UvrD1, Ku, and DNA form a stable ternary complex in the absence of ATP. The Ku binding determinants are located in the distinctive C-terminal segment of UvrD1. A second mycobacterial paralog, UvrD2, is a vigorous Ku-independent DNA helicase. Ablation of UvrD1 sensitizes Mycobacterium smegmatis to killing by ultraviolet and ionizing radiation and to a single chromosomal break generated by I-SceI endonuclease. The physical and functional interactions of bacterial Ku and UvrD1 highlight the potential for cross-talk between components of nonhomologous end joining and nucleotide excision repair pathways.

  16. Balancing Structure for Multiple Generator

    Directory of Open Access Journals (Sweden)

    LUPU Ciprian

    2014-05-01

    Full Text Available This paper presents a strategy to (rebalance a multiple generator control system structure on maintaining the global output in case of load and functioning disturbances. Applicability is proved on a control structure of the two and three sources connected in parallel to produce energy, a situation that has been encountered more and more these days especially in the renewable energy industry (wind, solar and small generators etc.

  17. Structure and reconstitution of yeast Mpp6-nuclear exosome complexes reveals that Mpp6 stimulates RNA decay and recruits the Mtr4 helicase

    Energy Technology Data Exchange (ETDEWEB)

    Wasmuth, Elizabeth V. [Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States; Zinder, John C. [Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States; Tri-Institutional Training Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, United States; Zattas, Dimitrios [Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States; Das, Mom [Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States; Lima, Christopher D. [Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States; Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, United States

    2017-07-25

    Nuclear RNA exosomes catalyze a range of RNA processing and decay activities that are coordinated in part by cofactors, including Mpp6, Rrp47, and the Mtr4 RNA helicase. Mpp6 interacts with the nine-subunit exosome core, while Rrp47 stabilizes the exoribonuclease Rrp6 and recruits Mtr4, but it is less clear if these cofactors work together. Using biochemistry with Saccharomyces cerevisiae proteins, we show that Rrp47 and Mpp6 stimulate exosome-mediated RNA decay, albeit with unique dependencies on elements within the nuclear exosome. Mpp6-exosomes can recruit Mtr4, while Mpp6 and Rrp47 each contribute to Mtr4-dependent RNA decay, with maximal Mtr4-dependent decay observed with both cofactors. The 3.3 Å structure of a twelve-subunit nuclear Mpp6 exosome bound to RNA shows the central region of Mpp6 bound to the exosome core, positioning its Mtr4 recruitment domain next to Rrp6 and the exosome central channel. Genetic analysis reveals interactions that are largely consistent with our model.

  18. Saccharomyces cerevisiae Hrq1 requires a long 3′-tailed DNA substrate for helicase activity

    International Nuclear Information System (INIS)

    Kwon, Sung-Hun; Choi, Do-Hee; Lee, Rina; Bae, Sung-Ho

    2012-01-01

    Highlights: ► Hrq1 has intrinsic 3′–5′ helicase and DNA strand annealing activities. ► Hrq1 requires a long 3′-tail for efficient DNA unwinding. ► Helicase activity of Hrq1 is stimulated by a fork structure. ► Hrq1 is a moderately processive helicase. -- Abstract: RecQ helicases are well conserved proteins from bacteria to human and function in various DNA metabolism for maintenance of genome stability. Five RecQ helicases are found in humans, whereas only one RecQ helicase has been described in lower eukaryotes. However, recent studies predicted the presence of a second RecQ helicase, Hrq1, in fungal genomes and verified it as a functional gene in fission yeast. Here we show that 3′–5′ helicase activity is intrinsically associated with Hrq1 of Saccharomyces cerevisiae. We also determined several biochemical properties of Hrq1 helicase distinguishable from those of other RecQ helicase members. Hrq1 is able to unwind relatively long duplex DNA up to 120-bp and is significantly stimulated by a preexisting fork structure. Further, the most striking feature of Hrq1 is its absolute requirement for a long 3′-tail (⩾70-nt) for efficient unwinding of duplex DNA. We also found that Hrq1 has potent DNA strand annealing activity. Our results indicate that Hrq1 has vigorous helicase activity that deserves further characterization to expand our understanding of RecQ helicases.

  19. Saccharomyces cerevisiae Hrq1 requires a long 3'-tailed DNA substrate for helicase activity.

    Science.gov (United States)

    Kwon, Sung-Hun; Choi, Do-Hee; Lee, Rina; Bae, Sung-Ho

    2012-10-26

    RecQ helicases are well conserved proteins from bacteria to human and function in various DNA metabolism for maintenance of genome stability. Five RecQ helicases are found in humans, whereas only one RecQ helicase has been described in lower eukaryotes. However, recent studies predicted the presence of a second RecQ helicase, Hrq1, in fungal genomes and verified it as a functional gene in fission yeast. Here we show that 3'-5' helicase activity is intrinsically associated with Hrq1 of Saccharomyces cerevisiae. We also determined several biochemical properties of Hrq1 helicase distinguishable from those of other RecQ helicase members. Hrq1 is able to unwind relatively long duplex DNA up to 120-bp and is significantly stimulated by a preexisting fork structure. Further, the most striking feature of Hrq1 is its absolute requirement for a long 3'-tail (⩾70-nt) for efficient unwinding of duplex DNA. We also found that Hrq1 has potent DNA strand annealing activity. Our results indicate that Hrq1 has vigorous helicase activity that deserves further characterization to expand our understanding of RecQ helicases. Copyright © 2012 Elsevier Inc. All rights reserved.

  20. The RecQ helicase-topoisomerase III-Rmi1 complex: a DNA structure-specific 'dissolvasome'?

    DEFF Research Database (Denmark)

    Mankouri, Hocine W; Hickson, Ian D

    2007-01-01

    structures, and we propose here that it functions in a coordinated fashion as a DNA structure-specific 'dissolvasome'. Little is known about how the RTR complex might be regulated or targeted to various DNA structures in vivo. Recent findings indicate that the components of the RTR complex might activate...... the cell cycle checkpoint machinery as well as be a target of checkpoint kinases, suggesting that these events are crucial to ensure faithful DNA replication and chromosome segregation....

  1. A mechanical mechanism for translocation of ring-shaped helicases on DNA and its demonstration in a macroscopic simulation system

    Science.gov (United States)

    Chou, Y. C.

    2018-04-01

    The asymmetry in the two-layered ring structure of helicases and the random thermal fluctuations of the helicase and DNA molecules are considered as the bases for the generation of the force required for translocation of the ring-shaped helicase on DNA. The helicase comprises a channel at its center with two unequal ends, through which strands of DNA can pass. The random collisions between the portion of the DNA strand in the central channel and the wall of the channel generate an impulsive force toward the small end. This impulsive force is the starting point for the helicase to translocate along the DNA with the small end in front. Such a physical mechanism may serve as a complementary for the chemomechanical mechanism of the translocation of helicase on DNA. When the helicase arrives at the junction of ssDNA and dsDNA (a fork), the collision between the helicase and the closest base pair may produce a sufficient impulsive force to break the weak hydrogen bond of the base pair. Thus, the helicase may advance and repeat the process of unwinding the dsDNA strand. This mechanism was tested in a macroscopic simulation system where the helicase was simulated using a truncated-cone structure and DNA was simulated with bead chains. Many features of translocation and unwinding such as translocation on ssDNA and dsDNA, unwinding of dsDNA, rewinding, strand switching, and Holliday junction resolution were reproduced.

  2. Identification of Hydroxyanthraquinones as Novel Inhibitors of Hepatitis C Virus NS3 Helicase

    Science.gov (United States)

    Furuta, Atsushi; Tsubuki, Masayoshi; Endoh, Miduki; Miyamoto, Tatsuki; Tanaka, Junichi; Abdus Salam, Kazi; Akimitsu, Nobuyoshi; Tani, Hidenori; Yamashita, Atsuya; Moriishi, Kohji; Nakakoshi, Masamichi; Sekiguchi, Yuji; Tsuneda, Satoshi; Noda, Naohiro

    2015-01-01

    Hepatitis C virus (HCV) is an important etiological agent of severe liver diseases, including cirrhosis and hepatocellular carcinoma. The HCV genome encodes nonstructural protein 3 (NS3) helicase, which is a potential anti-HCV drug target because its enzymatic activity is essential for viral replication. Some anthracyclines are known to be NS3 helicase inhibitors and have a hydroxyanthraquinone moiety in their structures; mitoxantrone, a hydroxyanthraquinone analogue, is also known to inhibit NS3 helicase. Therefore, we hypothesized that the hydroxyanthraquinone moiety alone could also inhibit NS3 helicase. Here, we performed a structure–activity relationship study on a series of hydroxyanthraquinones by using a fluorescence-based helicase assay. Hydroxyanthraquinones inhibited NS3 helicase with IC50 values in the micromolar range. The inhibitory activity varied depending on the number and position of the phenolic hydroxyl groups, and among different hydroxyanthraquinones examined, 1,4,5,8-tetrahydroxyanthraquinone strongly inhibited NS3 helicase with an IC50 value of 6 µM. Furthermore, hypericin and sennidin A, which both have two hydroxyanthraquinone-like moieties, were found to exert even stronger inhibition with IC50 values of 3 and 0.8 µM, respectively. These results indicate that the hydroxyanthraquinone moiety can inhibit NS3 helicase and suggest that several key chemical structures are important for the inhibition. PMID:26262613

  3. Identification of Hydroxyanthraquinones as Novel Inhibitors of Hepatitis C Virus NS3 Helicase

    Directory of Open Access Journals (Sweden)

    Atsushi Furuta

    2015-08-01

    Full Text Available Hepatitis C virus (HCV is an important etiological agent of severe liver diseases, including cirrhosis and hepatocellular carcinoma. The HCV genome encodes nonstructural protein 3 (NS3 helicase, which is a potential anti-HCV drug target because its enzymatic activity is essential for viral replication. Some anthracyclines are known to be NS3 helicase inhibitors and have a hydroxyanthraquinone moiety in their structures; mitoxantrone, a hydroxyanthraquinone analogue, is also known to inhibit NS3 helicase. Therefore, we hypothesized that the hydroxyanthraquinone moiety alone could also inhibit NS3 helicase. Here, we performed a structure–activity relationship study on a series of hydroxyanthraquinones by using a fluorescence-based helicase assay. Hydroxyanthraquinones inhibited NS3 helicase with IC50 values in the micromolar range. The inhibitory activity varied depending on the number and position of the phenolic hydroxyl groups, and among different hydroxyanthraquinones examined, 1,4,5,8-tetrahydroxyanthraquinone strongly inhibited NS3 helicase with an IC50 value of 6 µM. Furthermore, hypericin and sennidin A, which both have two hydroxyanthraquinone-like moieties, were found to exert even stronger inhibition with IC50 values of 3 and 0.8 µM, respectively. These results indicate that the hydroxyanthraquinone moiety can inhibit NS3 helicase and suggest that several key chemical structures are important for the inhibition.

  4. Mitochondrial helicases and mitochondrial genome maintenance

    DEFF Research Database (Denmark)

    de Souza-Pinto, Nadja C; Aamann, Maria Diget; Kulikowicz, Tomasz

    2010-01-01

    Helicases are essential enzymes that utilize the energy of nucleotide hydrolysis to drive unwinding of nucleic acid duplexes. Helicases play roles in all aspects of DNA metabolism including DNA repair, DNA replication and transcription. The subcellular locations and functions of several helicases...

  5. Toric Codes, Multiplicative Structure and Decoding

    DEFF Research Database (Denmark)

    Hansen, Johan Peder

    2017-01-01

    Long linear codes constructed from toric varieties over finite fields, their multiplicative structure and decoding. The main theme is the inherent multiplicative structure on toric codes. The multiplicative structure allows for \\emph{decoding}, resembling the decoding of Reed-Solomon codes and al...

  6. Uncoupling of Protease trans-Cleavage and Helicase Activities in Pestivirus NS3.

    Science.gov (United States)

    Zheng, Fengwei; Lu, Guoliang; Li, Ling; Gong, Peng; Pan, Zishu

    2017-11-01

    The nonstructural protein NS3 from the Flaviviridae family is a multifunctional protein that contains an N-terminal protease and a C-terminal helicase, playing essential roles in viral polyprotein processing and genome replication. Here we report a full-length crystal structure of the classical swine fever virus (CSFV) NS3 in complex with its NS4A protease cofactor segment (PCS) at a 2.35-Å resolution. The structure reveals a previously unidentified ∼2,200-Å 2 intramolecular protease-helicase interface comprising three clusters of interactions, representing a "closed" global conformation related to the NS3-NS4A cis -cleavage event. Although this conformation is incompatible with protease trans -cleavage, it appears to be functionally important and beneficial to the helicase activity, as the mutations designed to perturb this conformation impaired both the helicase activities in vitro and virus production in vivo Our work reveals important features of protease-helicase coordination in pestivirus NS3 and provides a key basis for how different conformational states may explicitly contribute to certain functions of this natural protease-helicase fusion protein. IMPORTANCE Many RNA viruses encode helicases to aid their RNA genome replication and transcription by unwinding structured RNA. Being naturally fused to a protease participating in viral polyprotein processing, the NS3 helicases encoded by the Flaviviridae family viruses are unique. Therefore, how these two enzyme modules coordinate in a single polypeptide is of particular interest. Here we report a previously unidentified conformation of pestivirus NS3 in complex with its NS4A protease cofactor segment (PCS). This conformational state is related to the protease cis -cleavage event and is optimal for the function of helicase. This work provides an important basis to understand how different enzymatic activities of NS3 may be achieved by the coordination between the protease and helicase through different

  7. Viral hijacking of a replicative helicase loader and its implications for helicase loading control and phage replication

    Energy Technology Data Exchange (ETDEWEB)

    Hood, Iris V.; Berger, James M.

    2016-05-31

    Replisome assembly requires the loading of replicative hexameric helicases onto origins by AAA+ ATPases. How loader activity is appropriately controlled remains unclear. Here, we use structural and biochemical analyses to establish how an antimicrobial phage protein interferes with the function of theStaphylococcus aureusreplicative helicase loader, DnaI. The viral protein binds to the loader’s AAA+ ATPase domain, allowing binding of the host replicative helicase but impeding loader self-assembly and ATPase activity. Close inspection of the complex highlights an unexpected locus for the binding of an interdomain linker element in DnaI/DnaC-family proteins. We find that the inhibitor protein is genetically coupled to a phage-encoded homolog of the bacterial helicase loader, which we show binds to the host helicase but not to the inhibitor itself. These findings establish a new approach by which viruses can hijack host replication processes and explain how loader activity is internally regulated to prevent aberrant auto-association.

  8. Genome-Wide Analysis of the RNA Helicase Gene Family in Gossypium raimondii

    Directory of Open Access Journals (Sweden)

    Jie Chen

    2014-03-01

    Full Text Available The RNA helicases, which help to unwind stable RNA duplexes, and have important roles in RNA metabolism, belong to a class of motor proteins that play important roles in plant development and responses to stress. Although this family of genes has been the subject of systematic investigation in Arabidopsis, rice, and tomato, it has not yet been characterized in cotton. In this study, we identified 161 putative RNA helicase genes in the genome of the diploid cotton species Gossypium raimondii. We classified these genes into three subfamilies, based on the presence of either a DEAD-box (51 genes, DEAH-box (52 genes, or DExD/H-box (58 genes in their coding regions. Chromosome location analysis showed that the genes that encode RNA helicases are distributed across all 13 chromosomes of G. raimondii. Syntenic analysis revealed that 62 of the 161 G. raimondii helicase genes (38.5% are within the identified syntenic blocks. Sixty-six (40.99% helicase genes from G. raimondii have one or several putative orthologs in tomato. Additionally, GrDEADs have more conserved gene structures and more simple domains than GrDEAHs and GrDExD/Hs. Transcriptome sequencing data demonstrated that many of these helicases, especially GrDEADs, are highly expressed at the fiber initiation stage and in mature leaves. To our knowledge, this is the first report of a genome-wide analysis of the RNA helicase gene family in cotton.

  9. DNA Sequences Proximal to Human Mitochondrial DNA Deletion Breakpoints Prevalent in Human Disease Form G-quadruplexes, a Class of DNA Structures Inefficiently Unwound by the Mitochondrial Replicative Twinkle Helicase*

    Science.gov (United States)

    Bharti, Sanjay Kumar; Sommers, Joshua A.; Zhou, Jun; Kaplan, Daniel L.; Spelbrink, Johannes N.; Mergny, Jean-Louis; Brosh, Robert M.

    2014-01-01

    Mitochondrial DNA deletions are prominent in human genetic disorders, cancer, and aging. It is thought that stalling of the mitochondrial replication machinery during DNA synthesis is a prominent source of mitochondrial genome instability; however, the precise molecular determinants of defective mitochondrial replication are not well understood. In this work, we performed a computational analysis of the human mitochondrial genome using the “Pattern Finder” G-quadruplex (G4) predictor algorithm to assess whether G4-forming sequences reside in close proximity (within 20 base pairs) to known mitochondrial DNA deletion breakpoints. We then used this information to map G4P sequences with deletions characteristic of representative mitochondrial genetic disorders and also those identified in various cancers and aging. Circular dichroism and UV spectral analysis demonstrated that mitochondrial G-rich sequences near deletion breakpoints prevalent in human disease form G-quadruplex DNA structures. A biochemical analysis of purified recombinant human Twinkle protein (gene product of c10orf2) showed that the mitochondrial replicative helicase inefficiently unwinds well characterized intermolecular and intramolecular G-quadruplex DNA substrates, as well as a unimolecular G4 substrate derived from a mitochondrial sequence that nests a deletion breakpoint described in human renal cell carcinoma. Although G4 has been implicated in the initiation of mitochondrial DNA replication, our current findings suggest that mitochondrial G-quadruplexes are also likely to be a source of instability for the mitochondrial genome by perturbing the normal progression of the mitochondrial replication machinery, including DNA unwinding by Twinkle helicase. PMID:25193669

  10. Multiple Blockholder Structures and Family Firm Performance

    DEFF Research Database (Denmark)

    Fattoum-Guedri, Asma; Guedri, Zied; Delmar, Frédéric

    2018-01-01

    This study examines how multiple blockholder structures affect family firm performance. Building on arguments from both principal–principal agency and familiness perspectives, we suggest that asymmetrical distribution of voting power among family and nonfamily blockholders hurts firm performance....

  11. Ebselen inhibits hepatitis C virus NS3 helicase binding to nucleic acid and prevents viral replication.

    Science.gov (United States)

    Mukherjee, Sourav; Weiner, Warren S; Schroeder, Chad E; Simpson, Denise S; Hanson, Alicia M; Sweeney, Noreena L; Marvin, Rachel K; Ndjomou, Jean; Kolli, Rajesh; Isailovic, Dragan; Schoenen, Frank J; Frick, David N

    2014-10-17

    The hepatitis C virus (HCV) nonstructural protein 3 (NS3) is both a protease, which cleaves viral and host proteins, and a helicase that separates nucleic acid strands, using ATP hydrolysis to fuel the reaction. Many antiviral drugs, and compounds in clinical trials, target the NS3 protease, but few helicase inhibitors that function as antivirals have been reported. This study focuses on the analysis of the mechanism by which ebselen (2-phenyl-1,2-benzisoselenazol-3-one), a compound previously shown to be a HCV antiviral agent, inhibits the NS3 helicase. Ebselen inhibited the abilities of NS3 to unwind nucleic acids, to bind nucleic acids, and to hydrolyze ATP, and about 1 μM ebselen was sufficient to inhibit each of these activities by 50%. However, ebselen had no effect on the activity of the NS3 protease, even at 100 times higher ebselen concentrations. At concentrations below 10 μM, the ability of ebselen to inhibit HCV helicase was reversible, but prolonged incubation of HCV helicase with higher ebselen concentrations led to irreversible inhibition and the formation of covalent adducts between ebselen and all 14 cysteines present in HCV helicase. Ebselen analogues with sulfur replacing the selenium were just as potent HCV helicase inhibitors as ebselen, but the length of the linker between the phenyl and benzisoselenazol rings was critical. Modifications of the phenyl ring also affected compound potency over 30-fold, and ebselen was a far more potent helicase inhibitor than other, structurally unrelated, thiol-modifying agents. Ebselen analogues were also more effective antiviral agents, and they were less toxic to hepatocytes than ebselen. Although the above structure-activity relationship studies suggest that ebselen targets a specific site on NS3, we were unable to confirm binding to either the NS3 ATP binding site or nucleic acid binding cleft by examining the effects of ebselen on NS3 proteins lacking key cysteines.

  12. Close encounters for the first time: Helicase interactions with DNA damage.

    Science.gov (United States)

    Khan, Irfan; Sommers, Joshua A; Brosh, Robert M

    2015-09-01

    DNA helicases are molecular motors that harness the energy of nucleoside triphosphate hydrolysis to unwinding structured DNA molecules that must be resolved during cellular replication, DNA repair, recombination, and transcription. In vivo, DNA helicases are expected to encounter a wide spectrum of covalent DNA modifications to the sugar phosphate backbone or the nitrogenous bases; these modifications can be induced by endogenous biochemical processes or exposure to environmental agents. The frequency of lesion abundance can vary depending on the lesion type. Certain adducts such as oxidative base modifications can be quite numerous, and their effects can be helix-distorting or subtle perturbations to DNA structure. Helicase encounters with specific DNA lesions and more novel forms of DNA damage will be discussed. We will also review the battery of assays that have been used to characterize helicase-catalyzed unwinding of damaged DNA substrates. Characterization of the effects of specific DNA adducts on unwinding by various DNA repair and replication helicases has proven to be insightful for understanding mechanistic and biological aspects of helicase function in cellular DNA metabolism. Published by Elsevier B.V.

  13. Mycobacterium smegmatis SftH exemplifies a distinctive clade of superfamily II DNA-dependent ATPases with 3′ to 5′ translocase and helicase activities

    OpenAIRE

    Yakovleva, Lyudmila; Shuman, Stewart

    2012-01-01

    Bacterial DNA helicases are nucleic acid-dependent NTPases that play important roles in DNA replication, recombination and repair. We are interested in the DNA helicases of Mycobacteria, a genus of the phylum Actinobacteria, which includes the human pathogen Mycobacterium tuberculosis and its avirulent relative Mycobacterium smegmatis. Here, we identify and characterize M. smegmatis SftH, a superfamily II helicase with a distinctive domain structure, comprising an N-terminal NTPase domain and...

  14. The MCM Helicase Motor of the Eukaryotic Replisome.

    Science.gov (United States)

    Abid Ali, Ferdos; Costa, Alessandro

    2016-05-08

    The MCM motor of the CMG helicase powers ahead of the eukaryotic replication machinery to unwind DNA, in a process that requires ATP hydrolysis. The reconstitution of DNA replication in vitro has established the succession of events that lead to replication origin activation by the MCM and recent studies have started to elucidate the structural basis of duplex DNA unwinding. Despite the exciting progress, how the MCM translocates on DNA remains a matter of debate. Copyright © 2016. Published by Elsevier Ltd.

  15. ARCPHdb: A comprehensive protein database for SF1 and SF2 helicase from archaea.

    Science.gov (United States)

    Moukhtar, Mirna; Chaar, Wafi; Abdel-Razzak, Ziad; Khalil, Mohamad; Taha, Samir; Chamieh, Hala

    2017-01-01

    Superfamily 1 and Superfamily 2 helicases, two of the largest helicase protein families, play vital roles in many biological processes including replication, transcription and translation. Study of helicase proteins in the model microorganisms of archaea have largely contributed to the understanding of their function, architecture and assembly. Based on a large phylogenomics approach, we have identified and classified all SF1 and SF2 protein families in ninety five sequenced archaea genomes. Here we developed an online webserver linked to a specialized protein database named ARCPHdb to provide access for SF1 and SF2 helicase families from archaea. ARCPHdb was implemented using MySQL relational database. Web interfaces were developed using Netbeans. Data were stored according to UniProt accession numbers, NCBI Ref Seq ID, PDB IDs and Entrez Databases. A user-friendly interactive web interface has been developed to browse, search and download archaeal helicase protein sequences, their available 3D structure models, and related documentation available in the literature provided by ARCPHdb. The database provides direct links to matching external databases. The ARCPHdb is the first online database to compile all protein information on SF1 and SF2 helicase from archaea in one platform. This database provides essential resource information for all researchers interested in the field. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. Multiplicity Control in Structural Equation Modeling

    Science.gov (United States)

    Cribbie, Robert A.

    2007-01-01

    Researchers conducting structural equation modeling analyses rarely, if ever, control for the inflated probability of Type I errors when evaluating the statistical significance of multiple parameters in a model. In this study, the Type I error control, power and true model rates of famsilywise and false discovery rate controlling procedures were…

  17. In TFIIH, XPD helicase is exclusively devoted to DNA repair.

    Directory of Open Access Journals (Sweden)

    Jochen Kuper

    2014-09-01

    Full Text Available The eukaryotic XPD helicase is an essential subunit of TFIIH involved in both transcription and nucleotide excision repair (NER. Mutations in human XPD are associated with several inherited diseases such as xeroderma pigmentosum, Cockayne syndrome, and trichothiodystrophy. We performed a comparative analysis of XPD from Homo sapiens and Chaetomium thermophilum (a closely related thermostable fungal orthologue to decipher the different molecular prerequisites necessary for either transcription or DNA repair. In vitro and in vivo assays demonstrate that mutations in the 4Fe4S cluster domain of XPD abrogate the NER function of TFIIH and do not affect its transcriptional activity. We show that the p44-dependent activation of XPD is promoted by the stimulation of its ATPase activity. Furthermore, we clearly demonstrate that XPD requires DNA binding, ATPase, and helicase activity to function in NER. In contrast, these enzymatic properties are dispensable for transcription initiation. XPD helicase is thus exclusively devoted to NER and merely acts as a structural scaffold to maintain TFIIH integrity during transcription.

  18. Requirement for the E1 Helicase C-Terminal Domain in Papillomavirus DNA Replication In Vivo.

    Science.gov (United States)

    Bergvall, Monika; Gagnon, David; Titolo, Steve; Lehoux, Michaël; D'Abramo, Claudia M; Melendy, Thomas; Archambault, Jacques

    2016-01-06

    The papillomavirus (PV) E1 helicase contains a conserved C-terminal domain (CTD), located next to its ATP-binding site, whose function in vivo is still poorly understood. The CTD is comprised of an alpha helix followed by an acidic region (AR) and a C-terminal extension termed the C-tail. Recent biochemical studies on bovine papillomavirus 1 (BPV1) E1 showed that the AR and C-tail regulate the oligomerization of the protein into a double hexamer at the origin. In this study, we assessed the importance of the CTD of human papillomavirus 11 (HPV11) E1 in vivo, using a cell-based DNA replication assay. Our results indicate that combined deletion of the AR and C-tail drastically reduces DNA replication, by 85%, and that further truncation into the alpha-helical region compromises the structural integrity of the E1 helicase domain and its interaction with E2. Surprisingly, removal of the C-tail alone or mutation of highly conserved residues within the domain still allows significant levels of DNA replication (55%). This is in contrast to the absolute requirement for the C-tail reported for BPV1 E1 in vitro and confirmed here in vivo. Characterization of chimeric proteins in which the AR and C-tail from HPV11 E1 were replaced by those of BPV1 indicated that while the function of the AR is transferable, that of the C-tail is not. Collectively, these findings define the contribution of the three CTD subdomains to the DNA replication activity of E1 in vivo and suggest that the function of the C-tail has evolved in a PV type-specific manner. While much is known about hexameric DNA helicases from superfamily 3, the papillomavirus E1 helicase contains a unique C-terminal domain (CTD) adjacent to its ATP-binding site. We show here that this CTD is important for the DNA replication activity of HPV11 E1 in vivo and that it can be divided into three functional subdomains that roughly correspond to the three conserved regions of the CTD: an alpha helix, needed for the structural

  19. Requirement for the E1 Helicase C-Terminal Domain in Papillomavirus DNA Replication In Vivo

    Science.gov (United States)

    Bergvall, Monika; Gagnon, David; Titolo, Steve; Lehoux, Michaël; D'Abramo, Claudia M.

    2016-01-01

    for the structural integrity of the helicase domain, followed by an acidic region (AR) and a C-terminal tail (C-tail) that have been shown to regulate the oligomerization of BPV1 E1 in vitro. Characterization of E1 chimeras revealed that, while the function of the AR could be transferred from BPV1 E1 to HPV11 E1, that of the C-tail could not. These results suggest that the E1 CTD performs multiple functions in DNA replication, some of them in a virus type-specific manner. PMID:26739052

  20. Genome-wide comparative in silico analysis of the RNA helicase gene family in Zea mays and Glycine max: a comparison with Arabidopsis and Oryza sativa.

    Science.gov (United States)

    Xu, Ruirui; Zhang, Shizhong; Huang, Jinguang; Zheng, Chengchao

    2013-01-01

    RNA helicases are enzymes that are thought to unwind double-stranded RNA molecules in an energy-dependent fashion through the hydrolysis of NTP. RNA helicases are associated with all processes involving RNA molecules, including nuclear transcription, editing, splicing, ribosome biogenesis, RNA export, and organelle gene expression. The involvement of RNA helicase in response to stress and in plant growth and development has been reported previously. While their importance in Arabidopsis and Oryza sativa has been partially studied, the function of RNA helicase proteins is poorly understood in Zea mays and Glycine max. In this study, we identified a total of RNA helicase genes in Arabidopsis and other crop species genome by genome-wide comparative in silico analysis. We classified the RNA helicase genes into three subfamilies according to the structural features of the motif II region, such as DEAD-box, DEAH-box and DExD/H-box, and different species showed different patterns of alternative splicing. Secondly, chromosome location analysis showed that the RNA helicase protein genes were distributed across all chromosomes with different densities in the four species. Thirdly, phylogenetic tree analyses identified the relevant homologs of DEAD-box, DEAH-box and DExD/H-box RNA helicase proteins in each of the four species. Fourthly, microarray expression data showed that many of these predicted RNA helicase genes were expressed in different developmental stages and different tissues under normal growth conditions. Finally, real-time quantitative PCR analysis showed that the expression levels of 10 genes in Arabidopsis and 13 genes in Zea mays were in close agreement with the microarray expression data. To our knowledge, this is the first report of a comparative genome-wide analysis of the RNA helicase gene family in Arabidopsis, Oryza sativa, Zea mays and Glycine max. This study provides valuable information for understanding the classification and putative functions of

  1. Helicase-dependent amplification of nucleic acids.

    Science.gov (United States)

    Cao, Yun; Kim, Hyun-Jin; Li, Ying; Kong, Huimin; Lemieux, Bertrand

    2013-10-11

    Helicase-dependent amplification (HDA) is a novel method for the isothermal in vitro amplification of nucleic acids. The HDA reaction selectively amplifies a target sequence by extension of two oligonucleotide primers. Unlike the polymerase chain reaction (PCR), HDA uses a helicase enzyme to separate the deoxyribonucleic acid (DNA) strands, rather than heat denaturation. This allows DNA amplification without the need for thermal cycling. The helicase used in HDA is a helicase super family II protein obtained from a thermophilic organism, Thermoanaerobacter tengcongensis (TteUvrD). This thermostable helicase is capable of unwinding blunt-end nucleic acid substrates at elevated temperatures (60° to 65°C). The HDA reaction can also be coupled with reverse transcription for ribonucleic acid (RNA) amplification. The products of this reaction can be detected during the reaction using fluorescent probes when incubations are conducted in a fluorimeter. Alternatively, products can be detected after amplification using a disposable amplicon containment device that contains an embedded lateral flow strip. Copyright © 2013 John Wiley & Sons, Inc.

  2. Distinct functions of human RecQ helicases during DNA replication.

    Science.gov (United States)

    Urban, Vaclav; Dobrovolna, Jana; Janscak, Pavel

    2017-06-01

    DNA replication is the most vulnerable process of DNA metabolism in proliferating cells and therefore it is tightly controlled and coordinated with processes that maintain genomic stability. Human RecQ helicases are among the most important factors involved in the maintenance of replication fork integrity, especially under conditions of replication stress. RecQ helicases promote recovery of replication forks being stalled due to different replication roadblocks of either exogenous or endogenous source. They prevent generation of aberrant replication fork structures and replication fork collapse, and are involved in proper checkpoint signaling. The essential role of human RecQ helicases in the genome maintenance during DNA replication is underlined by association of defects in their function with cancer predisposition. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Parallel magnetotransport in multiple quantum well structures

    International Nuclear Information System (INIS)

    Sheregii, E.M.; Ploch, D.; Marchewka, M.; Tomaka, G.; Kolek, A.; Stadler, A.; Mleczko, K.; Strupinski, W.; Jasik, A.; Jakiela, R.

    2004-01-01

    The results of investigations of parallel magnetotransport in AlGaAs/GaAs and InGaAs/InAlAs/InP multiple quantum wells structures (MQW's) are presented in this paper. The MQW's were obtained by metalorganic vapour phase epitaxy with different shapes of QW, numbers of QW and levels of doping. The magnetotransport measurements were performed in wide region of temperatures (0.5-300 K) and at high magnetic fields up to 30 T (B is perpendicular and current is parallel to the plane of the QW). Three types of observed effects are analyzed: quantum Hall effect and Shubnikov-de Haas oscillations at low temperatures (0.5-6 K) as well as magnetophonon resonance at higher temperatures (77-300 K)

  4. DNA binding and unwinding by Hel308 helicase requires dual functions of a winged helix domain.

    Science.gov (United States)

    Northall, Sarah J; Buckley, Ryan; Jones, Nathan; Penedo, J Carlos; Soultanas, Panos; Bolt, Edward L

    2017-09-01

    Hel308 helicases promote genome stability linked to DNA replication in archaea, and have homologues in metazoans. In the crystal structure of archaeal Hel308 bound to a tailed DNA duplex, core helicase domains encircle single-stranded DNA (ssDNA) in a "ratchet" for directional translocation. A winged helix domain (WHD) is also present, but its function is mysterious. We investigated the WHD in full-length Hel308, identifying that mutations in a solvent exposed α-helix resulted in reduced DNA binding and unwinding activities. When isolated from the rest of Hel308, the WHD protein alone bound to duplex DNA but not ssDNA, and DNA binding by WHD protein was abolished by the same mutations as were analyzed in full-length Hel308. Isolated WHD from a human Hel308 homologue (HelQ) also bound to duplex DNA. By disrupting the interface between the Hel308 WHD and a RecA-like domain, a topology typical of Ski2 helicases, we show that this is crucial for ATPase and helicase activities. The data suggest a model in which the WHD promotes activity of Hel308 directly, through binding to duplex DNA that is distinct from ssDNA binding by core helicase, and indirectly through interaction with the RecA-like domain. We propose how the WHD may contribute to ssDNA translocation, resulting in DNA helicase activity or in removal of other DNA bound proteins by "reeling" ssDNA. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Unwinding after high salinity stress: Pea DNA helicase 45 over- expression in tobacco confers high salinity tolerance without affecting yield (abstract)

    International Nuclear Information System (INIS)

    Tuteja, N.

    2005-01-01

    Soil salinity is an increasing threat for agriculture and is a major factor in reducing plant productivity; therefore, it is necessary to obtain salinity-tolerant varieties. A typical characteristic of soil salinity is the induction of multiple stress- inducible genes. Some of the genes encoding osmolytes, ion channels or enzymes are able to confer salinity-tolerant phenotypes when transferred to sensitive plants. As salinity stress affects the cellular gene-expression machinery, it is evident that molecules involved in nucleic acid processing including helicases, are likely to be affected as well. DNA helicases unwind duplex DNA and are involved in replication, repair, recombination and transcription while RNA helicases unfold the secondary structures in RNA and are involved in transcription, ribosome biogenesis and translation initiation. We have earlier reported the isolation of a pea DNA helicase 45 (PDH45) that exhibits striking homology with eIF-4A (Plant J. 24:219-230,2000). Here we report that PDH45 mRNA is induced in pea seedlings in response to high salt and its over- expression driven by a constitutive CAMV-355-promoter in tobacco plants confers salinity tolerance, thus suggesting a new pathway for manipulating stress tolerance in crop plants. The T0 transgenic plants showed high-levels of PDH45 protein in normal and stress conditions, as compared to wild type (WT) plants. The T0 transgenics also showed tolerance to high salinity as tested by a leaf disc senescence assay. The T1 transgenics were able to grow to maturity and set normal viable seeds under continuous salinity stress, without any reduction in plant yield, in terms of seed weight. Measurement of Na/sup +/ ions in different parts of the plant showed higher accumulation in the old leaves and negligible in seeds of T1 transgenic lines as compared with the WT plants. The possible mechanism of salinity tolerance will be discussed. Over-expression of PDH45 provides a possible example of the

  6. Molecular determinants of nucleolar translocation of RNA helicase A

    International Nuclear Information System (INIS)

    Liu Zhe; Kenworthy, Rachael; Green, Christopher; Tang, Hengli

    2007-01-01

    RNA helicase A (RHA) is a member of the DEAH-box family of DNA/RNA helicases involved in multiple cellular processes and the life cycles of many viruses. The subcellular localization of RHA is dynamic despite its steady-state concentration in the nucleoplasm. We have previously shown that it shuttles rapidly between the nucleus and the cytoplasm by virtue of a bidirectional nuclear transport domain (NTD) located in its carboxyl terminus. Here, we investigate the molecular determinants for its translocation within the nucleus and, more specifically, its redistribution from the nucleoplasm to nucleolus or the perinucleolar region. We found that low temperature treatment, transcription inhibition or replication of hepatitis C virus caused the intranuclear redistribution of the protein, suggesting that RHA shuttles between the nucleolus and nucleoplasm and becomes trapped in the nucleolus or the perinucleolar region upon blockade of transport to the nucleoplasm. Both the NTD and ATPase activity were essential for RHA's transport to the nucleolus or perinucleolar region. One of the double-stranded RNA binding domains (dsRBD II) was also required for this nucleolar translocation (NoT) phenotype. RNA interference studies revealed that RHA is essential for survival of cultured hepatoma cells and the ATPase activity appears to be important for this critical role

  7. Molecular Dynamics of the ZIKA Virus NS3 Helicase

    Science.gov (United States)

    Raubenolt, Bryan; Rick, Steven; The Rick Group Team

    The recent outbreaks of the ZIKA virus (ZIKV) and its connection to microcephaly in newborns has raised its awareness as a global threat and many scientific research efforts are currently underway in attempt to create a vaccine. Molecular Dynamics is a powerful method of investigating the physical behavior of protein complexes. ZIKV is comprised of 3 structural and 7 nonstructural proteins. The NS3 helicase protein appears to play a significant role in the replication complex and its inhibition could be a crucial source of antiviral drug design. This research primarily focuses on studying the structural dynamics, over the course of few hundred nanoseconds, of NS3 helicase in the free state, as well as in complex form with human ssRNA, ATP, and an analogue of GTP. RMSD and RMSF plots of each simulation will provide details on the forces involved in the overall stability of the active and inactive states. Furthermore, free energy calculations on a per residue level will reveal the most interactive residues between states and ultimately the primary driving force behind these interactions. Together these analyses will provide highly relevant information on the binding surface chemistry and thus serve as the basis for potential drug design.

  8. DNA binding polarity, dimerization, and ATPase ring remodeling in the CMG helicase of the eukaryotic replisome

    Science.gov (United States)

    Costa, Alessandro; Renault, Ludovic; Swuec, Paolo; Petojevic, Tatjana; Pesavento, James J; Ilves, Ivar; MacLellan-Gibson, Kirsty; Fleck, Roland A; Botchan, Michael R; Berger, James M

    2014-01-01

    The Cdc45/Mcm2-7/GINS (CMG) helicase separates DNA strands during replication in eukaryotes. How the CMG is assembled and engages DNA substrates remains unclear. Using electron microscopy, we have determined the structure of the CMG in the presence of ATPγS and a DNA duplex bearing a 3′ single-stranded tail. The structure shows that the MCM subunits of the CMG bind preferentially to single-stranded DNA, establishes the polarity by which DNA enters into the Mcm2-7 pore, and explains how Cdc45 helps prevent DNA from dissociating from the helicase. The Mcm2-7 subcomplex forms a cracked-ring, right-handed spiral when DNA and nucleotide are bound, revealing unexpected congruencies between the CMG and both bacterial DnaB helicases and the AAA+ motor of the eukaryotic proteasome. The existence of a subpopulation of dimeric CMGs establishes the subunit register of Mcm2-7 double hexamers and together with the spiral form highlights how Mcm2-7 transitions through different conformational and assembly states as it matures into a functional helicase. DOI: http://dx.doi.org/10.7554/eLife.03273.001 PMID:25117490

  9. DNA unwinding by ring-shaped T4 helicase gp41 is hindered by tension on the occluded strand.

    Science.gov (United States)

    Ribeck, Noah; Saleh, Omar A

    2013-01-01

    The replicative helicase for bacteriophage T4 is gp41, which is a ring-shaped hexameric motor protein that achieves unwinding of dsDNA by translocating along one strand of ssDNA while forcing the opposite strand to the outside of the ring. While much study has been dedicated to the mechanism of binding and translocation along the ssDNA strand encircled by ring-shaped helicases, relatively little is known about the nature of the interaction with the opposite, 'occluded' strand. Here, we investigate the interplay between the bacteriophage T4 helicase gp41 and the ss/dsDNA fork by measuring, at the single-molecule level, DNA unwinding events on stretched DNA tethers in multiple geometries. We find that gp41 activity is significantly dependent on the geometry and tension of the occluded strand, suggesting an interaction between gp41 and the occluded strand that stimulates the helicase. However, the geometry dependence of gp41 activity is the opposite of that found previously for the E. coli hexameric helicase DnaB. Namely, tension applied between the occluded strand and dsDNA stem inhibits unwinding activity by gp41, while tension pulling apart the two ssDNA tails does not hinder its activity. This implies a distinct variation in helicase-occluded strand interactions among superfamily IV helicases, and we propose a speculative model for this interaction that is consistent with both the data presented here on gp41 and the data that had been previously reported for DnaB.

  10. Human Enterovirus Nonstructural Protein 2CATPase Functions as Both an RNA Helicase and ATP-Independent RNA Chaperone

    Science.gov (United States)

    Xia, Hongjie; Wang, Peipei; Wang, Guang-Chuan; Yang, Jie; Sun, Xianlin; Wu, Wenzhe; Qiu, Yang; Shu, Ting; Zhao, Xiaolu; Yin, Lei; Qin, Cheng-Feng; Hu, Yuanyang; Zhou, Xi

    2015-01-01

    RNA helicases and chaperones are the two major classes of RNA remodeling proteins, which function to remodel RNA structures and/or RNA-protein interactions, and are required for all aspects of RNA metabolism. Although some virus-encoded RNA helicases/chaperones have been predicted or identified, their RNA remodeling activities in vitro and functions in the viral life cycle remain largely elusive. Enteroviruses are a large group of positive-stranded RNA viruses in the Picornaviridae family, which includes numerous important human pathogens. Herein, we report that the nonstructural protein 2CATPase of enterovirus 71 (EV71), which is the major causative pathogen of hand-foot-and-mouth disease and has been regarded as the most important neurotropic enterovirus after poliovirus eradication, functions not only as an RNA helicase that 3′-to-5′ unwinds RNA helices in an adenosine triphosphate (ATP)-dependent manner, but also as an RNA chaperone that destabilizes helices bidirectionally and facilitates strand annealing and complex RNA structure formation independently of ATP. We also determined that the helicase activity is based on the EV71 2CATPase middle domain, whereas the C-terminus is indispensable for its RNA chaperoning activity. By promoting RNA template recycling, 2CATPase facilitated EV71 RNA synthesis in vitro; when 2CATPase helicase activity was impaired, EV71 RNA replication and virion production were mostly abolished in cells, indicating that 2CATPase-mediated RNA remodeling plays a critical role in the enteroviral life cycle. Furthermore, the RNA helicase and chaperoning activities of 2CATPase are also conserved in coxsackie A virus 16 (CAV16), another important enterovirus. Altogether, our findings are the first to demonstrate the RNA helicase and chaperoning activities associated with enterovirus 2CATPase, and our study provides both in vitro and cellular evidence for their potential roles during viral RNA replication. These findings increase our

  11. RTEL1: functions of a disease-associated helicase.

    Science.gov (United States)

    Vannier, Jean-Baptiste; Sarek, Grzegorz; Boulton, Simon J

    2014-07-01

    DNA secondary structures that arise during DNA replication, repair, and recombination (3R) must be processed correctly to prevent genetic instability. Regulator of telomere length 1 (RTEL1) is an essential DNA helicase that disassembles a variety of DNA secondary structures to facilitate 3R processes and to maintain telomere integrity. The past few years have witnessed the emergence of RTEL1 variants that confer increased susceptibility to high-grade glioma, astrocytomas, and glioblastomas. Mutations in RTEL1 have also been implicated in Hoyeraal-Hreidarsson syndrome, a severe form of the bone-marrow failure and cancer predisposition disorder, dyskeratosis congenita. We review these recent findings and highlight its crucial link between DNA secondary-structure metabolism and human disease. Copyright © 2014 Elsevier Ltd. All rights reserved.

  12. Mms1 is an assistant for regulating G-quadruplex DNA structures.

    Science.gov (United States)

    Schwindt, Eike; Paeschke, Katrin

    2017-11-02

    The preservation of genome stability is fundamental for every cell. Genomic integrity is constantly challenged. Among those challenges are also non-canonical nucleic acid structures. In recent years, scientists became aware of the impact of G-quadruplex (G4) structures on genome stability. It has been shown that folded G4-DNA structures cause changes in the cell, such as transcriptional up/down-regulation, replication stalling, or enhanced genome instability. Multiple helicases have been identified to regulate G4 structures and by this preserve genome stability. Interestingly, although these helicases are mostly ubiquitous expressed, they show specificity for G4 regulation in certain cellular processes (e.g., DNA replication). To this date, it is not clear how this process and target specificity of helicases are achieved. Recently, Mms1, an ubiquitin ligase complex protein, was identified as a novel G4-DNA-binding protein that supports genome stability by aiding Pif1 helicase binding to these regions. In this perspective review, we discuss the question if G4-DNA interacting proteins are fundamental for helicase function and specificity at G4-DNA structures.

  13. MOV10 RNA helicase is a potent inhibitor of retrotransposition in cells.

    Directory of Open Access Journals (Sweden)

    John L Goodier

    Full Text Available MOV10 protein, a putative RNA helicase and component of the RNA-induced silencing complex (RISC, inhibits retrovirus replication. We show that MOV10 also severely restricts human LINE1 (L1, Alu, and SVA retrotransposons. MOV10 associates with the L1 ribonucleoprotein particle, along with other RNA helicases including DDX5, DHX9, DDX17, DDX21, and DDX39A. However, unlike MOV10, these other helicases do not strongly inhibit retrotransposition, an activity dependent upon intact helicase domains. MOV10 association with retrotransposons is further supported by its colocalization with L1 ORF1 protein in stress granules, by cytoplasmic structures associated with RNA silencing, and by the ability of MOV10 to reduce endogenous and ectopic L1 expression. The majority of the human genome is repetitive DNA, most of which is the detritus of millions of years of accumulated retrotransposition. Retrotransposons remain active mutagens, and their insertion can disrupt gene function. Therefore, the host has evolved defense mechanisms to protect against retrotransposition, an arsenal we are only beginning to understand. With homologs in other vertebrates, insects, and plants, MOV10 may represent an ancient and innate form of immunity against both infective viruses and endogenous retroelements.

  14. [RTEL1 (regulator of telomere elongation helicase 1), a DNA helicase essential for genome stability].

    Science.gov (United States)

    Le Guen, Tangui; Jullien, Laurent; Schertzer, Mike; Lefebvre, Axelle; Kermasson, Laetitia; de Villartay, Jean-Pierre; Londoño-Vallejo, Arturo; Revy, Patrick

    2013-12-01

    RTEL1 (regulator of telomere length helicase 1) is a DNA helicase that has been identified more than 10 years ago. Many works since, mainly in the nematode Caenorhabditis elegans and the mouse, have highlighted its role in chromosomal stability, maintenance of telomere length, and DNA repair. Recently, four laboratories have characterized RTEL1 mutations in patients with dyskeratosis congenita (DC) and Hoyeraal-Hreidarsson (HH) syndrome, a rare and severe variant of DC. We here summarize the current knowledge on RTEL1 and discuss the possible other functions that RTEL1 could play. © 2013 médecine/sciences – Inserm.

  15. Interactive Roles of DNA Helicases and Translocases with the Single-Stranded DNA Binding Protein RPA in Nucleic Acid Metabolism.

    Science.gov (United States)

    Awate, Sanket; Brosh, Robert M

    2017-06-08

    Helicases and translocases use the energy of nucleoside triphosphate binding and hydrolysis to unwind/resolve structured nucleic acids or move along a single-stranded or double-stranded polynucleotide chain, respectively. These molecular motors facilitate a variety of transactions including replication, DNA repair, recombination, and transcription. A key partner of eukaryotic DNA helicases/translocases is the single-stranded DNA binding protein Replication Protein A (RPA). Biochemical, genetic, and cell biological assays have demonstrated that RPA interacts with these human molecular motors physically and functionally, and their association is enriched in cells undergoing replication stress. The roles of DNA helicases/translocases are orchestrated with RPA in pathways of nucleic acid metabolism. RPA stimulates helicase-catalyzed DNA unwinding, enlists translocases to sites of action, and modulates their activities in DNA repair, fork remodeling, checkpoint activation, and telomere maintenance. The dynamic interplay between DNA helicases/translocases and RPA is just beginning to be understood at the molecular and cellular levels, and there is still much to be learned, which may inform potential therapeutic strategies.

  16. Multiplant strategy under core-periphery structure

    OpenAIRE

    Tsubota, Kenmei

    2012-01-01

    A typical implicit assumption on monopolistic competition models for trade and economic geography is that firms can produce and sell only at one place. This paper fallows endogenous determination of the number of plants in a new economic geography model and examine the stable outcomes of organization choice between single-plant and multi-plant in two regions. We explicitly consider the firms' trade-off between larger economies of scale under single plant configuration and the saving in interr...

  17. Effects of multiple bursts on structural response

    International Nuclear Information System (INIS)

    Mohammadi, J.; Longinow, A.; Napandensky, H.S.

    1983-01-01

    A method was formulated for studying the probability of failure of structures when subjected to repeated blast loads. It was applied to the analysis of a structure subjected to a series of identical blast loads and several different ranges from ground zero. Results indicate that even as few as three repeated blast loads can significantly increase the probability of failure even for cases with a relatively high R/F. (The R/F ratio can be looked at as indicating the relative strength of the structure or as an indication of its range from the point of detonation)

  18. Mutational analysis of an archaeal minichromosome maintenance protein exterior hairpin reveals critical residues for helicase activity and DNA binding

    Directory of Open Access Journals (Sweden)

    Brewster Aaron S

    2010-08-01

    Full Text Available Abstract Background The mini-chromosome maintenance protein (MCM complex is an essential replicative helicase for DNA replication in Archaea and Eukaryotes. While the eukaryotic complex consists of six homologous proteins (MCM2-7, the archaeon Sulfolobus solfataricus has only one MCM protein (ssoMCM, six subunits of which form a homohexamer. We have recently reported a 4.35Å crystal structure of the near full-length ssoMCM. The structure reveals a total of four β-hairpins per subunit, three of which are located within the main channel or side channels of the ssoMCM hexamer model generated based on the symmetry of the N-terminal Methanothermobacter thermautotrophicus (mtMCM structure. The fourth β-hairpin, however, is located on the exterior of the hexamer, near the exit of the putative side channels and next to the ATP binding pocket. Results In order to better understand this hairpin's role in DNA binding and helicase activity, we performed a detailed mutational and biochemical analysis of nine residues on this exterior β-hairpin (EXT-hp. We examined the activities of the mutants related to their helicase function, including hexamerization, ATPase, DNA binding and helicase activities. The assays showed that some of the residues on this EXT-hp play a role for DNA binding as well as for helicase activity. Conclusions These results implicate several current theories regarding helicase activity by this critical hexameric enzyme. As the data suggest that EXT-hp is involved in DNA binding, the results reported here imply that the EXT-hp located near the exterior exit of the side channels may play a role in contacting DNA substrate in a manner that affects DNA unwinding.

  19. The Q Motif Is Involved in DNA Binding but Not ATP Binding in ChlR1 Helicase.

    Directory of Open Access Journals (Sweden)

    Hao Ding

    Full Text Available Helicases are molecular motors that couple the energy of ATP hydrolysis to the unwinding of structured DNA or RNA and chromatin remodeling. The conversion of energy derived from ATP hydrolysis into unwinding and remodeling is coordinated by seven sequence motifs (I, Ia, II, III, IV, V, and VI. The Q motif, consisting of nine amino acids (GFXXPXPIQ with an invariant glutamine (Q residue, has been identified in some, but not all helicases. Compared to the seven well-recognized conserved helicase motifs, the role of the Q motif is less acknowledged. Mutations in the human ChlR1 (DDX11 gene are associated with a unique genetic disorder known as Warsaw Breakage Syndrome, which is characterized by cellular defects in genome maintenance. To examine the roles of the Q motif in ChlR1 helicase, we performed site directed mutagenesis of glutamine to alanine at residue 23 in the Q motif of ChlR1. ChlR1 recombinant protein was overexpressed and purified from HEK293T cells. ChlR1-Q23A mutant abolished the helicase activity of ChlR1 and displayed reduced DNA binding ability. The mutant showed impaired ATPase activity but normal ATP binding. A thermal shift assay revealed that ChlR1-Q23A has a melting point value similar to ChlR1-WT. Partial proteolysis mapping demonstrated that ChlR1-WT and Q23A have a similar globular structure, although some subtle conformational differences in these two proteins are evident. Finally, we found ChlR1 exists and functions as a monomer in solution, which is different from FANCJ, in which the Q motif is involved in protein dimerization. Taken together, our results suggest that the Q motif is involved in DNA binding but not ATP binding in ChlR1 helicase.

  20. Structural model analysis of multiple quantitative traits.

    Directory of Open Access Journals (Sweden)

    Renhua Li

    2006-07-01

    Full Text Available We introduce a method for the analysis of multilocus, multitrait genetic data that provides an intuitive and precise characterization of genetic architecture. We show that it is possible to infer the magnitude and direction of causal relationships among multiple correlated phenotypes and illustrate the technique using body composition and bone density data from mouse intercross populations. Using these techniques we are able to distinguish genetic loci that affect adiposity from those that affect overall body size and thus reveal a shortcoming of standardized measures such as body mass index that are widely used in obesity research. The identification of causal networks sheds light on the nature of genetic heterogeneity and pleiotropy in complex genetic systems.

  1. On multiple crack detection in beam structures

    Energy Technology Data Exchange (ETDEWEB)

    Moradi, Shapour; Kargozarfard, Mohammad [Shahid Chamran University, Ahvaz (Iran, Islamic Republic of)

    2013-01-15

    This study presents an inverse procedure to identify multiple cracks in beams using an evolutionary algorithm. By considering the crack detection procedure as an optimization problem, an objective function can be constructed based on the change of the eigenfrequencies and some strain energy parameters. Each crack is modeled by a rotational spring. The changes in natural frequencies due to the presence of the cracks are related to a damage index vector. Then, the bees algorithm, a swarm-based evolutionary optimization technique, is used to optimize the objective function and find the damage index vector, whose positive components show the number and position of the cracks. A second objective function is also optimized to find the crack depths. Several experimental studies on cracked cantilever beams are conducted to ensure the integrity of the proposed method. The results show that the number of cracks as well as their sizes and locations can be predicted well through this method.

  2. Nucleolin inhibits G4 oligonucleotide unwinding by Werner helicase.

    Directory of Open Access Journals (Sweden)

    Fred E Indig

    Full Text Available The Werner protein (WRNp, a member of the RecQ helicase family, is strongly associated with the nucleolus, as is nucleolin (NCL, an important nucleolar constituent protein. Both WRNp and NCL respond to the effects of DNA damaging agents. Therefore, we have investigated if these nuclear proteins interact and if this interaction has a possible functional significance in DNA damage repair.Here we report that WRNp interacts with the RNA-binding protein, NCL, based on immunoprecipitation, immunofluorescent co-localization in live and fixed cells, and direct binding of purified WRNp to nucleolin. We also map the binding region to the C-terminal domains of both proteins. Furthermore, treatment of U2OS cells with 15 µM of the Topoisomerase I inhibitor, camptothecin, causes the dissociation of the nucleolin-Werner complex in the nucleolus, followed by partial re-association in the nucleoplasm. Other DNA damaging agents, such as hydroxyurea, Mitomycin C, and aphidicolin do not have these effects. Nucleolin or its C-terminal fragment affected the helicase, but not the exonuclease activity of WRNp, by inhibiting WRN unwinding of G4 tetraplex DNA structures, as seen in activity assays and electrophoretic mobility shift assays (EMSA.These data suggest that nucleolin may regulate G4 DNA unwinding by WRNp, possibly in response to certain DNA damaging agents. We postulate that the NCL-WRNp complex may contain an inactive form of WRNp, which is released from the nucleolus upon DNA damage. Then, when required, WRNp is released from inhibition and can participate in the DNA repair processes.

  3. MultiSETTER: web server for multiple RNA structure comparison.

    Science.gov (United States)

    Čech, Petr; Hoksza, David; Svozil, Daniel

    2015-08-12

    Understanding the architecture and function of RNA molecules requires methods for comparing and analyzing their tertiary and quaternary structures. While structural superposition of short RNAs is achievable in a reasonable time, large structures represent much bigger challenge. Therefore, we have developed a fast and accurate algorithm for RNA pairwise structure superposition called SETTER and implemented it in the SETTER web server. However, though biological relationships can be inferred by a pairwise structure alignment, key features preserved by evolution can be identified only from a multiple structure alignment. Thus, we extended the SETTER algorithm to the alignment of multiple RNA structures and developed the MultiSETTER algorithm. In this paper, we present the updated version of the SETTER web server that implements a user friendly interface to the MultiSETTER algorithm. The server accepts RNA structures either as the list of PDB IDs or as user-defined PDB files. After the superposition is computed, structures are visualized in 3D and several reports and statistics are generated. To the best of our knowledge, the MultiSETTER web server is the first publicly available tool for a multiple RNA structure alignment. The MultiSETTER server offers the visual inspection of an alignment in 3D space which may reveal structural and functional relationships not captured by other multiple alignment methods based either on a sequence or on secondary structure motifs.

  4. Multiple-lesion track-structure model

    International Nuclear Information System (INIS)

    Wilson, J.W.; Cucinotta, F.A.; Shinn, J.L.

    1992-03-01

    A multilesion cell kinetic model is derived, and radiation kinetic coefficients are related to the Katz track structure model. The repair-related coefficients are determined from the delayed plating experiments of Yang et al. for the C3H10T1/2 cell system. The model agrees well with the x ray and heavy ion experiments of Yang et al. for the immediate plating, delaying plating, and fractionated exposure protocols employed by Yang. A study is made of the effects of target fragments in energetic proton exposures and of the repair-deficient target-fragment-induced lesions

  5. Novel benzoxazole inhibitor of dengue virus replication that targets the NS3 helicase.

    Science.gov (United States)

    Byrd, Chelsea M; Grosenbach, Douglas W; Berhanu, Aklile; Dai, Dongcheng; Jones, Kevin F; Cardwell, Kara B; Schneider, Christine; Yang, Guang; Tyavanagimatt, Shanthakumar; Harver, Chris; Wineinger, Kristin A; Page, Jessica; Stavale, Eric; Stone, Melialani A; Fuller, Kathleen P; Lovejoy, Candace; Leeds, Janet M; Hruby, Dennis E; Jordan, Robert

    2013-04-01

    Dengue virus (DENV) is the predominant mosquito-borne viral pathogen that infects humans with an estimated 50 to 100 million infections per year worldwide. Over the past 50 years, the incidence of dengue disease has increased dramatically and the virus is now endemic in more than 100 countries. Moreover, multiple serotypes of DENV are now found in the same geographic region, increasing the likelihood of more severe forms of disease. Despite extensive research, there are still no approved vaccines or therapeutics commercially available to treat DENV infection. Here we report the results of a high-throughput screen of a chemical compound library using a whole-virus assay that identified a novel small-molecule inhibitor of DENV, ST-610, that potently and selectively inhibits all four serotypes of DENV replication in vitro. Sequence analysis of drug-resistant virus isolates has identified a single point mutation, A263T, in the NS3 helicase domain that confers resistance to this compound. ST-610 inhibits DENV NS3 helicase RNA unwinding activity in a molecular-beacon-based helicase assay but does not inhibit nucleoside triphosphatase activity based on a malachite green ATPase assay. ST-610 is nonmutagenic, is well tolerated (nontoxic) in mice, and has shown efficacy in a sublethal murine model of DENV infection with the ability to significantly reduce viremia and viral load compared to vehicle controls.

  6. Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment

    Directory of Open Access Journals (Sweden)

    Daniels Noah M

    2012-10-01

    Full Text Available Abstract Background The quality of multiple protein structure alignments are usually computed and assessed based on geometric functions of the coordinates of the backbone atoms from the protein chains. These purely geometric methods do not utilize directly protein sequence similarity, and in fact, determining the proper way to incorporate sequence similarity measures into the construction and assessment of protein multiple structure alignments has proved surprisingly difficult. Results We present Formatt, a multiple structure alignment based on the Matt purely geometric multiple structure alignment program, that also takes into account sequence similarity when constructing alignments. We show that Formatt outperforms Matt and other popular structure alignment programs on the popular HOMSTRAD benchmark. For the SABMark twilight zone benchmark set that captures more remote homology, Formatt and Matt outperform other programs; depending on choice of embedded sequence aligner, Formatt produces either better sequence and structural alignments with a smaller core size than Matt, or similarly sized alignments with better sequence similarity, for a small cost in average RMSD. Conclusions Considering sequence information as well as purely geometric information seems to improve quality of multiple structure alignments, though defining what constitutes the best alignment when sequence and structural measures would suggest different alignments remains a difficult open question.

  7. Reconstruction of ancestral RNA sequences under multiple structural constraints

    OpenAIRE

    Tremblay-Savard, Olivier; Reinharz, Vladimir; Waldisp?hl, J?r?me

    2016-01-01

    Background Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA) families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors. Methods In this paper, we introduce achARNement, a maximum parsimony approach that, given...

  8. Helicase properties of the Escherichia coli UvrAb protein complex

    International Nuclear Information System (INIS)

    Oh, E.Y.; Grossman, L.

    1987-01-01

    The Escherichia coli UvrA protein has an associated ATPase activity with a turnover number affected by the presence of UvrB protein as well as by DNA. Specifically, the structure of DNA significantly influences the turnover rate of the UvrAB ATPase activity. Double-stranded DNA maximally activates the turnover rate 10-fold whereas single-stranded DNA maximally activates the turnover rate 20-fold, suggesting that the mode of interaction of UvrAB protein with different DNAs is distinctive. We have previously shown that the UvrAB protein complex, driven by the binding energy of ATP, can locally unwind supercoiled DNA. The nature of the DNA unwinding activity and single-stranded DNA activation of ATPase activity suggest potential helicase activity. In the presence of a number of helicase substrates, the UvrAB complex, indeed, manifests a strand-displacement activity-unwinding short duplexes and D-loop DNA, thereby generating component DNA structures. The energy for the activity is derived from ATP or dATP hydrolysis. Unlike the E. coli DnaB, the UvrAB helicase is sensitive to UV-induced photoproducts

  9. A Co-Opted DEAD-Box RNA helicase enhances tombusvirus plus-strand synthesis.

    Directory of Open Access Journals (Sweden)

    Nikolay Kovalev

    2012-02-01

    Full Text Available Replication of plus-strand RNA viruses depends on recruited host factors that aid several critical steps during replication. In this paper, we show that an essential translation factor, Ded1p DEAD-box RNA helicase of yeast, directly affects replication of Tomato bushy stunt virus (TBSV. To separate the role of Ded1p in viral protein translation from its putative replication function, we utilized a cell-free TBSV replication assay and recombinant Ded1p. The in vitro data show that Ded1p plays a role in enhancing plus-strand synthesis by the viral replicase. We also find that Ded1p is a component of the tombusvirus replicase complex and Ded1p binds to the 3'-end of the viral minus-stranded RNA. The data obtained with wt and ATPase deficient Ded1p mutants support the model that Ded1p unwinds local structures at the 3'-end of the TBSV (-RNA, rendering the RNA compatible for initiation of (+-strand synthesis. Interestingly, we find that Ded1p and glyceraldehyde-3-phosphate dehydrogenase (GAPDH, which is another host factor for TBSV, play non-overlapping functions to enhance (+-strand synthesis. Altogether, the two host factors enhance TBSV replication synergistically by interacting with the viral (-RNA and the replication proteins. In addition, we have developed an in vitro assay for Flock house virus (FHV, a small RNA virus of insects, that also demonstrated positive effect on FHV replicase activity by the added Ded1p helicase. Thus, two small RNA viruses, which do not code for their own helicases, seems to recruit a host RNA helicase to aid their replication in infected cells.

  10. The helicase domain of Polθ counteracts RPA to promote alt-NHEJ.

    Science.gov (United States)

    Mateos-Gomez, Pedro A; Kent, Tatiana; Deng, Sarah K; McDevitt, Shane; Kashkina, Ekaterina; Hoang, Trung M; Pomerantz, Richard T; Sfeir, Agnel

    2017-12-01

    Mammalian polymerase theta (Polθ) is a multifunctional enzyme that promotes error-prone DNA repair by alternative nonhomologous end joining (alt-NHEJ). Here we present structure-function analyses that reveal that, in addition to the polymerase domain, Polθ-helicase activity plays a central role during double-strand break (DSB) repair. Our results show that the helicase domain promotes chromosomal translocations by alt-NHEJ in mouse embryonic stem cells and also suppresses CRISPR-Cas9- mediated gene targeting by homologous recombination (HR). In vitro assays demonstrate that Polθ-helicase activity facilitates the removal of RPA from resected DSBs to allow their annealing and subsequent joining by alt-NHEJ. Consistent with an antagonistic role for RPA during alt-NHEJ, inhibition of RPA1 enhances end joining and suppresses recombination. Taken together, our results reveal that the balance between HR and alt-NHEJ is controlled by opposing activities of Polθ and RPA, providing further insight into the regulation of repair-pathway choice in mammalian cells.

  11. Staphylococcal SCCmec elements encode an active MCM-like helicase and thus may be replicative

    Energy Technology Data Exchange (ETDEWEB)

    Mir-Sanchis, Ignacio; Roman, Christina A.; Misiura, Agnieszka; Pigli, Ying Z.; Boyle-Vavra, Susan; Rice , Phoebe A. (UC)

    2016-08-29

    Methicillin-resistant Staphylococcus aureus (MRSA) is a public-health threat worldwide. Although the mobile genomic island responsible for this phenotype, staphylococcal cassette chromosome (SCC), has been thought to be nonreplicative, we predicted DNA-replication-related functions for some of the conserved proteins encoded by SCC. We show that one of these, Cch, is homologous to the self-loading initiator helicases of an unrelated family of genomic islands, that it is an active 3'-to-5' helicase and that the adjacent ORF encodes a single-stranded DNA–binding protein. Our 2.9-Å crystal structure of intact Cch shows that it forms a hexameric ring. Cch, like the archaeal and eukaryotic MCM-family replicative helicases, belongs to the pre–sensor II insert clade of AAA+ ATPases. Additionally, we found that SCC elements are part of a broader family of mobile elements, all of which encode a replication initiator upstream of their recombinases. Replication after excision would enhance the efficiency of horizontal gene transfer.

  12. SOLAR MULTIPLE ERUPTIONS FROM A CONFINED MAGNETIC STRUCTURE

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Jeongwoo; Chae, Jongchul [Department of Physics and Astronomy, Seoul National University, Seoul 08826 (Korea, Republic of); Liu, Chang; Jing, Ju [Space Weather Research Laboratory, New Jersey Institute of Technology, Newark, NJ 07102 (United States)

    2016-09-20

    How eruption can recur from a confined magnetic structure is discussed based on the Solar Dynamics Observatory observations of the NOAA active region 11444, which produced three eruptions within 1.5 hr on 2012 March 27. The active region (AR) had the positive-polarity magnetic fields in the center surrounded by the negative-polarity fields around. Since such a distribution of magnetic polarity tends to form a dome-like magnetic fan structure confined over the AR, the multiple eruptions were puzzling. Our investigation reveals that this event exhibits several properties distinct from other eruptions associated with magnetic fan structures: (i) a long filament encircling the AR was present before the eruptions; (ii) expansion of the open–closed boundary (OCB) of the field lines after each eruption was suggestive of the growing fan-dome structure, and (iii) the ribbons inside the closed magnetic polarity inversion line evolved in response to the expanding OCB. It thus appears that in spite of multiple eruptions the fan-dome structure remained undamaged, and the closing back field lines after each eruption rather reinforced the fan-dome structure. We argue that the multiple eruptions could occur in this AR in spite of its confined magnetic structure because the filament encircling the AR was adequate for slipping through the magnetic separatrix to minimize the damage to its overlying fan-dome structure. The result of this study provides a new insight into the productivity of eruptions from a confined magnetic structure.

  13. SOLAR MULTIPLE ERUPTIONS FROM A CONFINED MAGNETIC STRUCTURE

    International Nuclear Information System (INIS)

    Lee, Jeongwoo; Chae, Jongchul; Liu, Chang; Jing, Ju

    2016-01-01

    How eruption can recur from a confined magnetic structure is discussed based on the Solar Dynamics Observatory observations of the NOAA active region 11444, which produced three eruptions within 1.5 hr on 2012 March 27. The active region (AR) had the positive-polarity magnetic fields in the center surrounded by the negative-polarity fields around. Since such a distribution of magnetic polarity tends to form a dome-like magnetic fan structure confined over the AR, the multiple eruptions were puzzling. Our investigation reveals that this event exhibits several properties distinct from other eruptions associated with magnetic fan structures: (i) a long filament encircling the AR was present before the eruptions; (ii) expansion of the open–closed boundary (OCB) of the field lines after each eruption was suggestive of the growing fan-dome structure, and (iii) the ribbons inside the closed magnetic polarity inversion line evolved in response to the expanding OCB. It thus appears that in spite of multiple eruptions the fan-dome structure remained undamaged, and the closing back field lines after each eruption rather reinforced the fan-dome structure. We argue that the multiple eruptions could occur in this AR in spite of its confined magnetic structure because the filament encircling the AR was adequate for slipping through the magnetic separatrix to minimize the damage to its overlying fan-dome structure. The result of this study provides a new insight into the productivity of eruptions from a confined magnetic structure.

  14. Dynamical simulation of structural multiplicity in grain boundaries

    International Nuclear Information System (INIS)

    Majid, I.; Bristowe, P.D.

    1987-06-01

    Work on a computer simulation study of a low-energy high-angle boundary structure which is not periodic have been recently reported. This result is of interest since grain boundary structures are usually assumed to have a periodicity corresponding to the appropriate coincidence site lattice (CSL) and many experimental observations of the structure of grain boundaries performed using conventional and high-resolution electron microscopy, electron diffraction and x-ray diffraction appear to support this work. However, this work, using empirical interatomic pair potentials and the relaxation method of molecular statics, have simulated a Σ = 5 36.87 0 (001) twist boundary and found a low energy structure having a larger repeat cell than the CSL and is composed of two different types of structural unit that are randomly distributed in the boundary plane. This result, which has been termed the multiplicity of grain boundary structures, has also been found in the simulation of tilt boundaries. The multiplicity phenomenon is of special interest in twist boundaries since it is used as a structural model to explain the x-ray scattering from a Σ = 5 boundary in gold. These scattering patterns had previously remained unexplained using stable structures that had simple CSL periodicity. Also, the effect of having a multiple number of low energy structural units coexisting in the grain boundary is of more general interest since it implies that the boundary structures may be quasi-periodic and, in some circumstances, may even result in a roughening of the boundary plane. This paper extends this work by showing, using molecular dynamics, that a multiplicity of structural units can actually nucleate spontaneously in a high-angle grain boundary at finite temperatures

  15. Negative binomial properties and clan structure in multiplicity distributions

    International Nuclear Information System (INIS)

    Giovannini, A.; Van Hove, L.

    1988-01-01

    We review the negative binomial properties measured recently for many multiplicity distributions of high energy hadronic, semi-leptonic reactions in selected rapidity intervals. We analyse them in terms of the ''clan'' structure which can be defined for any negative binomial distribution. By comparing reactions we exhibit a number of regularities for the average number N-bar of clans and the average charged multiplicity (n-bar) c per clan. 22 refs., 6 figs. (author)

  16. Joint Estimation of Multiple Precision Matrices with Common Structures.

    Science.gov (United States)

    Lee, Wonyul; Liu, Yufeng

    Estimation of inverse covariance matrices, known as precision matrices, is important in various areas of statistical analysis. In this article, we consider estimation of multiple precision matrices sharing some common structures. In this setting, estimating each precision matrix separately can be suboptimal as it ignores potential common structures. This article proposes a new approach to parameterize each precision matrix as a sum of common and unique components and estimate multiple precision matrices in a constrained l 1 minimization framework. We establish both estimation and selection consistency of the proposed estimator in the high dimensional setting. The proposed estimator achieves a faster convergence rate for the common structure in certain cases. Our numerical examples demonstrate that our new estimator can perform better than several existing methods in terms of the entropy loss and Frobenius loss. An application to a glioblastoma cancer data set reveals some interesting gene networks across multiple cancer subtypes.

  17. Structured diagnostic imaging in patients with multiple trauma

    International Nuclear Information System (INIS)

    Linsenmaier, U.; Rieger, J.; Rock, C.; Pfeifer, K.J.; Reiser, M.; Kanz, K.G.

    2002-01-01

    Purpose. Development of a concept for structured diagnostic imaging in patients with multiple trauma.Material and methods. Evaluation of data from a prospective trial with over 2400 documented patients with multiple trauma. All diagnostic and therapeutic steps, primary and secondary death and the 90 days lethality were documented.Structured diagnostic imaging of multiple injured patients requires the integration of an experienced radiologist in an interdisciplinary trauma team consisting of anesthesia, radiology and trauma surgery. Radiology itself deserves standardized concepts for equipment, personnel and logistics to perform diagnostic imaging for a 24-h-coverage with constant quality.Results. This paper describes criteria for initiation of a shock room or emergency room treatment, strategies for documentation and interdisciplinary algorithms for the early clinical care coordinating diagnostic imaging and therapeutic procedures following standardized guidelines. Diagnostic imaging consists of basic diagnosis, radiological ABC-rule, radiological follow-up and structured organ diagnosis using CT. Radiological trauma scoring allows improved quality control of diagnosis and therapy of multiple injured patients.Conclusion. Structured diagnostic imaging of multiple injured patients leads to a standardization of diagnosis and therapy and ensures constant process quality. (orig.) [de

  18. DNA-conjugated gold nanoparticles based colorimetric assay to assess helicase activity: a novel route to screen potential helicase inhibitors

    Science.gov (United States)

    Deka, Jashmini; Mojumdar, Aditya; Parisse, Pietro; Onesti, Silvia; Casalis, Loredana

    2017-03-01

    Helicase are essential enzymes which are widespread in all life-forms. Due to their central role in nucleic acid metabolism, they are emerging as important targets for anti-viral, antibacterial and anti-cancer drugs. The development of easy, cheap, fast and robust biochemical assays to measure helicase activity, overcoming the limitations of the current methods, is a pre-requisite for the discovery of helicase inhibitors through high-throughput screenings. We have developed a method which exploits the optical properties of DNA-conjugated gold nanoparticles (AuNP) and meets the required criteria. The method was tested with the catalytic domain of the human RecQ4 helicase and compared with a conventional FRET-based assay. The AuNP-based assay produced similar results but is simpler, more robust and cheaper than FRET. Therefore, our nanotechnology-based platform shows the potential to provide a useful alternative to the existing conventional methods for following helicase activity and to screen small-molecule libraries as potential helicase inhibitors.

  19. Effects of multiple scattering and target structure on photon emission

    International Nuclear Information System (INIS)

    Blankenbecler, R.

    1996-05-01

    The Landau-Pomeranchuk-Migdal effect is the suppression of Bethe-Heitler radiation caused by multiple scattering in the target medium. The quantum treatment given by S.D. Drell and the author for homogeneous targets of finite thickness will be reviewed. It will then be extended to structured targets. In brief, it is shown that radiators composed of separated plates or of a medium with a spatially varying radiation length can exhibit unexpected structure, even coherence maxima and minima, in their photon spectra. Finally, a functional integral method for performing the averaging implicit in multiple scattering will be briefly discussed and the leading corrections to previous results evaluated

  20. Structure D'Ensemble, Multiple Classification, Multiple Seriation and Amount of Irrelevant Information

    Science.gov (United States)

    Hamel, B. Remmo; Van Der Veer, M. A. A.

    1972-01-01

    A significant positive correlation between multiple classification was found, in testing 65 children aged 6 to 8 years, at the stage of concrete operations. This is interpreted as support for the existence of a structure d'ensemble of operational schemes in the period of concrete operations. (Authors)

  1. Cdt1 stabilizes an open MCM ring for helicase loading.

    Science.gov (United States)

    Frigola, Jordi; He, Jun; Kinkelin, Kerstin; Pye, Valerie E; Renault, Ludovic; Douglas, Max E; Remus, Dirk; Cherepanov, Peter; Costa, Alessandro; Diffley, John F X

    2017-06-23

    ORC, Cdc6 and Cdt1 act together to load hexameric MCM, the motor of the eukaryotic replicative helicase, into double hexamers at replication origins. Here we show that Cdt1 interacts with MCM subunits Mcm2, 4 and 6, which both destabilizes the Mcm2-5 interface and inhibits MCM ATPase activity. Using X-ray crystallography, we show that Cdt1 contains two winged-helix domains in the C-terminal half of the protein and a catalytically inactive dioxygenase-related N-terminal domain, which is important for MCM loading, but not for subsequent replication. We used these structures together with single-particle electron microscopy to generate three-dimensional models of MCM complexes. These show that Cdt1 stabilizes MCM in a left-handed spiral open at the Mcm2-5 gate. We propose that Cdt1 acts as a brace, holding MCM open for DNA entry and bound to ATP until ORC-Cdc6 triggers ATP hydrolysis by MCM, promoting both Cdt1 ejection and MCM ring closure.

  2. Protein Structure Classification and Loop Modeling Using Multiple Ramachandran Distributions

    KAUST Repository

    Najibi, Seyed Morteza

    2017-02-08

    Recently, the study of protein structures using angular representations has attracted much attention among structural biologists. The main challenge is how to efficiently model the continuous conformational space of the protein structures based on the differences and similarities between different Ramachandran plots. Despite the presence of statistical methods for modeling angular data of proteins, there is still a substantial need for more sophisticated and faster statistical tools to model the large-scale circular datasets. To address this need, we have developed a nonparametric method for collective estimation of multiple bivariate density functions for a collection of populations of protein backbone angles. The proposed method takes into account the circular nature of the angular data using trigonometric spline which is more efficient compared to existing methods. This collective density estimation approach is widely applicable when there is a need to estimate multiple density functions from different populations with common features. Moreover, the coefficients of adaptive basis expansion for the fitted densities provide a low-dimensional representation that is useful for visualization, clustering, and classification of the densities. The proposed method provides a novel and unique perspective to two important and challenging problems in protein structure research: structure-based protein classification and angular-sampling-based protein loop structure prediction.

  3. Protein Structure Classification and Loop Modeling Using Multiple Ramachandran Distributions

    KAUST Repository

    Najibi, Seyed Morteza; Maadooliat, Mehdi; Zhou, Lan; Huang, Jianhua Z.; Gao, Xin

    2017-01-01

    Recently, the study of protein structures using angular representations has attracted much attention among structural biologists. The main challenge is how to efficiently model the continuous conformational space of the protein structures based on the differences and similarities between different Ramachandran plots. Despite the presence of statistical methods for modeling angular data of proteins, there is still a substantial need for more sophisticated and faster statistical tools to model the large-scale circular datasets. To address this need, we have developed a nonparametric method for collective estimation of multiple bivariate density functions for a collection of populations of protein backbone angles. The proposed method takes into account the circular nature of the angular data using trigonometric spline which is more efficient compared to existing methods. This collective density estimation approach is widely applicable when there is a need to estimate multiple density functions from different populations with common features. Moreover, the coefficients of adaptive basis expansion for the fitted densities provide a low-dimensional representation that is useful for visualization, clustering, and classification of the densities. The proposed method provides a novel and unique perspective to two important and challenging problems in protein structure research: structure-based protein classification and angular-sampling-based protein loop structure prediction.

  4. Multifractal structure of multiplicity distributions and negative binomials

    International Nuclear Information System (INIS)

    Malik, S.; Delhi, Univ.

    1997-01-01

    The paper presents experimental results of the multifractal structure analysis in proton-emulsion interactions at 800 GeV. The multiplicity moments have a power law dependence on the mean multiplicity in varying bin sizes of pseudorapidity. The values of generalised dimensions are calculated from the slope value. The multifractal characteristics are also examined in the light of negative binomials. The observed multiplicity moments and those derived from the negative-binomial fits agree well with each other. Also the values of D q , both observed and derived from the negative-binomial fits not only decrease with q typifying multifractality but also agree well each other showing consistency with the negative-binomial form

  5. RecQ helicases and cellular responses to DNA damage

    International Nuclear Information System (INIS)

    Wu, Leonard; Hickson, Ian D.

    2002-01-01

    The faithful replication of the genome is essential for the survival of all organisms. It is not surprising therefore that numerous mechanisms have evolved to ensure that duplication of the genome occurs with only minimal risk of mutation induction. One mechanism of genome destabilization is replication fork demise, which can occur when a translocating fork meets a lesion or adduct in the template. Indeed, the collapse of replication forks has been suggested to occur in every replicative cell cycle making this a potentially significant problem for all proliferating cells. The RecQ helicases, which are essential for the maintenance of genome stability, are thought to function during DNA replication. In particular, RecQ helicase mutants display replication defects and have phenotypes consistent with an inability to efficiently reinitiate replication following replication fork demise. Here, we review some current models for how replication fork repair might be effected, and discuss potential roles for RecQ helicases in this process

  6. Detection of electromagnetic radiation using micromechanical multiple quantum wells structures

    Science.gov (United States)

    Datskos, Panagiotis G [Knoxville, TN; Rajic, Slobodan [Knoxville, TN; Datskou, Irene [Knoxville, TN

    2007-07-17

    An apparatus and method for detecting electromagnetic radiation employs a deflectable micromechanical apparatus incorporating multiple quantum wells structures. When photons strike the quantum-well structure, physical stresses are created within the sensor, similar to a "bimetallic effect." The stresses cause the sensor to bend. The extent of deflection of the sensor can be measured through any of a variety of conventional means to provide a measurement of the photons striking the sensor. A large number of such sensors can be arranged in a two-dimensional array to provide imaging capability.

  7. Multiple piece turbine engine airfoil with a structural spar

    Science.gov (United States)

    Vance, Steven J [Orlando, FL

    2011-10-11

    A multiple piece turbine airfoil having an outer shell with an airfoil tip that is attached to a root with an internal structural spar is disclosed. The root may be formed from first and second sections that include an internal cavity configured to receive and secure the one or more components forming the generally elongated airfoil. The internal structural spar may be attached to an airfoil tip and place the generally elongated airfoil in compression. The configuration enables each component to be formed from different materials to reduce the cost of the materials and to optimize the choice of material for each component.

  8. Efficient cascade multiple heterojunction organic solar cells with inverted structure

    Science.gov (United States)

    Guo, Tingting; Li, Mingtao; Qiao, Zhenfang; Yu, Leiming; Zhao, Jianhong; Feng, Nianjun; Shi, Peiguang; Wang, Xiaoyan; Pu, Xiaoyun; Wang, Hai

    2018-05-01

    In this work, we demonstrate an efficient cascade multiple heterojunction organic solar cell with inverted structure. By using two donor materials, poly(3-hexylthiosphene) (P3HT) and titanyl phthalocyanine (TiOPc), as well as two acceptor materials, [6,6]-phenyl C61 butyric acid methyl ester (PCBM) and C60, the cascade multiple heterojunctions of P3HT:PCBM/TiOPc:C60/C60 have been constructed. Applying the optimized inverted configuration of FTO/Zinc Tin Oxide (ZTO)/C60 (30 nm)/TiOPc:C60 (1:1.5, 25 nm)/P3HT:PCBM (1:0.8, 100 nm)/MoO3 (4 nm)/Ag, the considerably enhanced open circuit voltage (VOC) and short circuit current (JSC) can be harvested together, and the power conversion efficiency (PCE) is three times higher than that of the control cell with conventional structure. The significant improvements of the inverted cell are mostly due to the broadened spectral absorption and high efficient multi-interface exciton dissociation in the cascade multiple heterojunctions, indicating that the optimized cascade heterojunctions match the inverted structure well.

  9. Dealing with Multiple Solutions in Structural Vector Autoregressive Models.

    Science.gov (United States)

    Beltz, Adriene M; Molenaar, Peter C M

    2016-01-01

    Structural vector autoregressive models (VARs) hold great potential for psychological science, particularly for time series data analysis. They capture the magnitude, direction of influence, and temporal (lagged and contemporaneous) nature of relations among variables. Unified structural equation modeling (uSEM) is an optimal structural VAR instantiation, according to large-scale simulation studies, and it is implemented within an SEM framework. However, little is known about the uniqueness of uSEM results. Thus, the goal of this study was to investigate whether multiple solutions result from uSEM analysis and, if so, to demonstrate ways to select an optimal solution. This was accomplished with two simulated data sets, an empirical data set concerning children's dyadic play, and modifications to the group iterative multiple model estimation (GIMME) program, which implements uSEMs with group- and individual-level relations in a data-driven manner. Results revealed multiple solutions when there were large contemporaneous relations among variables. Results also verified several ways to select the correct solution when the complete solution set was generated, such as the use of cross-validation, maximum standardized residuals, and information criteria. This work has immediate and direct implications for the analysis of time series data and for the inferences drawn from those data concerning human behavior.

  10. Identification of multiple modes of axisymmetric or circularly repetitive structures

    International Nuclear Information System (INIS)

    Kopff, P.

    1983-01-01

    The axisymmetric structures, or those composed with circularly repetitive elements, often display multiple modes, which are not easy to separate by modal identification of experimental responses. To be able to solve in situ some problems related to the vibrational behaviour of reactor vessels or other such huge structures, ELECTRICITY DE FRANCE developed a few years ago, experimental capabilities providing heavy harmonic driving forces, and elaborate data acquisition, signal processing and modal identification software, self-contained in an integrated mobile test facility. The modal analysis techniques we have developed with the LABORATOIRE DE MECANIQUE Appliquee of University of BESANCON (FRANCE) were especially suited for identification of multiple or separation of quasi-multiple modes, i.e. very close and strongly coupled resonances. Besides, the curve fitting methods involved, compute the same complex eigen-frequencies for all the vibration pick-ups, for better accuracy of the related eigen-vector components. Moreover, the latest extensions of these algorithms give us the means to deal with non-linear behaviour. The performances of these programs are drawn from some experimental results on axisymmetric or circularly repetitive structure, we tested in our laboratory to validate the computational hypothesis used in models for seismic responses of breeder reactor vessels. (orig.)

  11. Comparison of reconfigurable structures for flexible word-length multiplication

    Directory of Open Access Journals (Sweden)

    O. A. Pfänder

    2008-05-01

    Full Text Available Binary multiplication continues to be one of the essential arithmetic operations in digital circuits. Even though field-programmable gate arrays (FPGAs are becoming more and more powerful these days, the vendors cannot avoid implementing multiplications with high word-lengths using embedded blocks instead of configurable logic. But on the other hand, the circuit's efficiency decreases if the provided word-length of the hard-wired multipliers exceeds the precision requirements of the algorithm mapped into the FPGA. Thus it is beneficial to use multiplier blocks with configurable word-length, optimized for area, speed and power dissipation, e.g. regarding digital signal processing (DSP applications.

    In this contribution, we present different approaches and structures for the realization of a multiplication with variable precision and perform an objective comparison. This includes one approach based on a modified Baugh and Wooley algorithm and three structures using Booth's arithmetic operand recoding with different array structures. All modules have the option to compute signed two's complement fix-point numbers either as an individual computing unit or interconnected to a superior array. Therefore, a high throughput at low precision through parallelism, or a high precision through concatenation can be achieved.

  12. Automated Localization of Multiple Pelvic Bone Structures on MRI.

    Science.gov (United States)

    Onal, Sinan; Lai-Yuen, Susana; Bao, Paul; Weitzenfeld, Alfredo; Hart, Stuart

    2016-01-01

    In this paper, we present a fully automated localization method for multiple pelvic bone structures on magnetic resonance images (MRI). Pelvic bone structures are at present identified manually on MRI to locate reference points for measurement and evaluation of pelvic organ prolapse (POP). Given that this is a time-consuming and subjective procedure, there is a need to localize pelvic bone structures automatically. However, bone structures are not easily differentiable from soft tissue on MRI as their pixel intensities tend to be very similar. In this paper, we present a model that combines support vector machines and nonlinear regression capturing global and local information to automatically identify the bounding boxes of bone structures on MRI. The model identifies the location of the pelvic bone structures by establishing the association between their relative locations and using local information such as texture features. Results show that the proposed method is able to locate the bone structures of interest accurately (dice similarity index >0.75) in 87-91% of the images. This research aims to enable accurate, consistent, and fully automated localization of bone structures on MRI to facilitate and improve the diagnosis of health conditions such as female POP.

  13. G-quadruplexes Significantly Stimulate Pif1 Helicase-catalyzed Duplex DNA Unwinding*

    Science.gov (United States)

    Duan, Xiao-Lei; Liu, Na-Nv; Yang, Yan-Tao; Li, Hai-Hong; Li, Ming; Dou, Shuo-Xing; Xi, Xu-Guang

    2015-01-01

    The evolutionarily conserved G-quadruplexes (G4s) are faithfully inherited and serve a variety of cellular functions such as telomere maintenance, gene regulation, DNA replication initiation, and epigenetic regulation. Different from the Watson-Crick base-pairing found in duplex DNA, G4s are formed via Hoogsteen base pairing and are very stable and compact DNA structures. Failure of untangling them in the cell impedes DNA-based transactions and leads to genome instability. Cells have evolved highly specific helicases to resolve G4 structures. We used a recombinant nuclear form of Saccharomyces cerevisiae Pif1 to characterize Pif1-mediated DNA unwinding with a substrate mimicking an ongoing lagging strand synthesis stalled by G4s, which resembles a replication origin and a G4-structured flap in Okazaki fragment maturation. We find that the presence of G4 may greatly stimulate the Pif1 helicase to unwind duplex DNA. Further studies reveal that this stimulation results from G4-enhanced Pif1 dimerization, which is required for duplex DNA unwinding. This finding provides new insights into the properties and functions of G4s. We discuss the observed activation phenomenon in relation to the possible regulatory role of G4s in the rapid rescue of the stalled lagging strand synthesis by helping the replicator recognize and activate the replication origin as well as by quickly removing the G4-structured flap during Okazaki fragment maturation. PMID:25627683

  14. Seismic structural response analysis for multiple support excitation

    International Nuclear Information System (INIS)

    Shaw, D.E.

    1975-01-01

    In the seismic analysis of nuclear power plant equipment such as piping systems situations often arise in which piping systems span between adjacent structures or between different elevations in the same structure. Owing to the differences in the seismic time history response of different structures or different elevations of the same structure, the input support motion will differ for different supports. The concept of a frequency dependent participation factor and rotational response spectra accounting for phase differences between support excitations is developed by using classical equations of motion to formulate the seismic response of a structure subjected to multiple support excitation. The essence of the method lies in describing the seismic excitation of a multiply excited structure in terms of translational and rotational spectra used at every support and a frequency dependent spatial distribution function derived from the phase relationships of the different support time histories. In this manner it is shown that frequency dependent participation factors can be derived from the frequency dependent distribution functions. Examples are shown and discussed relative to closed form solutions and the state-of-the-art techniques presently being used for the solution of problems of multiply excited structures

  15. Angle-resolved photoemission extended fine structure: Multiple layers of emitters and multiple initial states

    International Nuclear Information System (INIS)

    Huff, W.R.A.; Kellar, S.A.; Moler, E.J.; California Univ., Berkeley, CA; Chen, Y.; Wu, H.; Shirley, D.A.; Hussain, Z.

    1995-01-01

    Recently, angle-resolved photoemission extended fine structure (ARPEFS) has been applied to experimental systems involving multiple layers of emitters and non-s core-level photoemission in an effort to broaden the utility of the technique. Most of the previous systems have been comprised of atomic or molecular overlayers adsorbed onto a single-crystal, metal surface and the photoemission data were taken from an s atomic core-level in the overlayer. For such a system, the acquired ARPEFS data is dominated by the p o final state wave backscattering from the substrate atoms and is well understood. In this study, we investigate ARPEFS as a surface-region structure determination technique when applied to experimental systems comprised of multiple layers of photoemitters and arbitrary initial state core-level photoemission. Understanding the data acquired from multiple layers of photoemitters is useful for studying multilayer interfaces, ''buried'' surfaces, and clean crystals in ultra- high vacuum. The ability to apply ARPEFS to arbitrary initial state core-level photoemission obviously opens up many systems to analysis. Efforts have been ongoing to understand such data in depth. We present clean Cu(111) 3s, 3p, and 3d core-level, normal photoemission data taken on a high resolution soft x-ray beamline 9.3.2 at the Advanced Light Source in Berkeley, California and clean Ni(111) 3p normal photoemission data taken at the National Synchrotron Light Source in Upton, New York, USA

  16. Multiple regression and beyond an introduction to multiple regression and structural equation modeling

    CERN Document Server

    Keith, Timothy Z

    2014-01-01

    Multiple Regression and Beyond offers a conceptually oriented introduction to multiple regression (MR) analysis and structural equation modeling (SEM), along with analyses that flow naturally from those methods. By focusing on the concepts and purposes of MR and related methods, rather than the derivation and calculation of formulae, this book introduces material to students more clearly, and in a less threatening way. In addition to illuminating content necessary for coursework, the accessibility of this approach means students are more likely to be able to conduct research using MR or SEM--and more likely to use the methods wisely. Covers both MR and SEM, while explaining their relevance to one another Also includes path analysis, confirmatory factor analysis, and latent growth modeling Figures and tables throughout provide examples and illustrate key concepts and techniques For additional resources, please visit: http://tzkeith.com/.

  17. Reconstruction of ancestral RNA sequences under multiple structural constraints

    Directory of Open Access Journals (Sweden)

    Olivier Tremblay-Savard

    2016-11-01

    Full Text Available Abstract Background Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors. Methods In this paper, we introduce achARNement, a maximum parsimony approach that, given two alignments of homologous ncRNA families with consensus secondary structures and a phylogenetic tree, simultaneously calculates ancestral RNA sequences for these two families. Results We test our methodology on simulated data sets, and show that achARNement outperforms classical maximum parsimony approaches in terms of accuracy, but also reduces by several orders of magnitude the number of candidate sequences. To conclude this study, we apply our algorithms on the Glm clan and the FinP-traJ clan from the Rfam database. Conclusions Our results show that our methods reconstruct small sets of high-quality candidate ancestors with better agreement to the two target structures than with classical approaches. Our program is freely available at: http://csb.cs.mcgill.ca/acharnement .

  18. Reconstruction of ancestral RNA sequences under multiple structural constraints.

    Science.gov (United States)

    Tremblay-Savard, Olivier; Reinharz, Vladimir; Waldispühl, Jérôme

    2016-11-11

    Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA) families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors. In this paper, we introduce achARNement, a maximum parsimony approach that, given two alignments of homologous ncRNA families with consensus secondary structures and a phylogenetic tree, simultaneously calculates ancestral RNA sequences for these two families. We test our methodology on simulated data sets, and show that achARNement outperforms classical maximum parsimony approaches in terms of accuracy, but also reduces by several orders of magnitude the number of candidate sequences. To conclude this study, we apply our algorithms on the Glm clan and the FinP-traJ clan from the Rfam database. Our results show that our methods reconstruct small sets of high-quality candidate ancestors with better agreement to the two target structures than with classical approaches. Our program is freely available at: http://csb.cs.mcgill.ca/acharnement .

  19. MCM Paradox: Abundance of Eukaryotic Replicative Helicases and Genomic Integrity.

    Science.gov (United States)

    Das, Mitali; Singh, Sunita; Pradhan, Satyajit; Narayan, Gopeshwar

    2014-01-01

    As a crucial component of DNA replication licensing system, minichromosome maintenance (MCM) 2-7 complex acts as the eukaryotic DNA replicative helicase. The six related MCM proteins form a heterohexamer and bind with ORC, CDC6, and Cdt1 to form the prereplication complex. Although the MCMs are well known as replicative helicases, their overabundance and distribution patterns on chromatin present a paradox called the "MCM paradox." Several approaches had been taken to solve the MCM paradox and describe the purpose of excess MCMs distributed beyond the replication origins. Alternative functions of these MCMs rather than a helicase had also been proposed. This review focuses on several models and concepts generated to solve the MCM paradox coinciding with their helicase function and provides insight into the concept that excess MCMs are meant for licensing dormant origins as a backup during replication stress. Finally, we extend our view towards the effect of alteration of MCM level. Though an excess MCM constituent is needed for normal cells to withstand stress, there must be a delineation of the threshold level in normal and malignant cells. This review also outlooks the future prospects to better understand the MCM biology.

  20. Bloom syndrome helicase in meiosis: Pro-crossover functions of an anti-crossover protein.

    Science.gov (United States)

    Hatkevich, Talia; Sekelsky, Jeff

    2017-09-01

    The functions of the Bloom syndrome helicase (BLM) and its orthologs are well characterized in mitotic DNA damage repair, but their roles within the context of meiotic recombination are less clear. In meiotic recombination, multiple repair pathways are used to repair meiotic DSBs, and current studies suggest that BLM may regulate the use of these pathways. Based on literature from Saccharomyces cerevisiae, Arabidopsis thaliana, Mus musculus, Drosophila melanogaster, and Caenorhabditis elegans, we present a unified model for a critical meiotic role of BLM and its orthologs. In this model, BLM and its orthologs utilize helicase activity to regulate the use of various pathways in meiotic recombination by continuously disassembling recombination intermediates. This unwinding activity provides the meiotic program with a steady pool of early recombination substrates, increasing the probability for a DSB to be processed by the appropriate pathway. As a result of BLM activity, crossovers are properly placed throughout the genome, promoting proper chromosomal disjunction at the end of meiosis. This unified model can be used to further refine the complex role of BLM and its orthologs in meiotic recombination. © 2017 WILEY Periodicals, Inc.

  1. Mutations of the RTEL1 Helicase in a Hoyeraal-Hreidarsson Syndrome Patient Highlight the Importance of the ARCH Domain.

    Science.gov (United States)

    Jullien, Laurent; Kannengiesser, Caroline; Kermasson, Laetitia; Cormier-Daire, Valérie; Leblanc, Thierry; Soulier, Jean; Londono-Vallejo, Arturo; de Villartay, Jean-Pierre; Callebaut, Isabelle; Revy, Patrick

    2016-05-01

    The DNA helicase RTEL1 participates in telomere maintenance and genome stability. Biallelic mutations in the RTEL1 gene account for the severe telomere biology disorder characteristic of the Hoyeraal-Hreidarsson syndrome (HH). Here, we report a HH patient (P4) carrying two novel compound heterozygous mutations in RTEL1: a premature stop codon (c.949A>T, p.Lys317*) and an intronic deletion leading to an exon skipping and an in-frame deletion of 25 amino-acids (p.Ile398_Lys422). P4's cells exhibit short and dysfunctional telomeres similarly to other RTEL1-deficient patients. 3D structure predictions indicated that the p.Ile398_Lys422 deletion affects a part of the helicase ARCH domain, which lines the pore formed with the core HD and the iron-sulfur cluster domains and is highly specific of sequences from the eukaryotic XPD family members. © 2016 WILEY PERIODICALS, INC.

  2. Classification of Farmland Landscape Structure in Multiple Scales

    Science.gov (United States)

    Jiang, P.; Cheng, Q.; Li, M.

    2017-12-01

    Farmland is one of the basic terrestrial resources that support the development and survival of human beings and thus plays a crucial role in the national security of every country. Pattern change is the intuitively spatial representation of the scale and quality variation of farmland. Through the characteristic development of spatial shapes as well as through changes in system structures, functions and so on, farmland landscape patterns may indicate the landscape health level. Currently, it is still difficult to perform positioning analyses of landscape pattern changes that reflect the landscape structure variations of farmland with an index model. Depending on a number of spatial properties such as locations and adjacency relations, distance decay, fringe effect, and on the model of patch-corridor-matrix that is applied, this study defines a type system of farmland landscape structure on the national, provincial, and city levels. According to such a definition, the classification model of farmland landscape-structure type at the pixel scale is developed and validated based on mathematical-morphology concepts and on spatial-analysis methods. Then, the laws that govern farmland landscape-pattern change in multiple scales are analyzed from the perspectives of spatial heterogeneity, spatio-temporal evolution, and function transformation. The result shows that the classification model of farmland landscape-structure type can reflect farmland landscape-pattern change and its effects on farmland production function. Moreover, farmland landscape change in different scales displayed significant disparity in zonality, both within specific regions and in urban-rural areas.

  3. Financial crisis and market risk premium: Identifying multiple structural changes

    Directory of Open Access Journals (Sweden)

    Juan J. García-Machado

    2011-03-01

    Full Text Available The relationship between macroeconomic variables and stock market returns is, by now, well-documented in the literature. However, in this article we examine the long-run relationship between stock and bond markets returns over the period from 1991:11 to 2009:11, using Bai and Perron’s multiple structural change approach. Findings indicate that while the market risk premium is usually positive, periods with negative values appear only in three periods (1991:1-1993:2, 1998:3-2002:2 and from 2007:1-2009:11 leading to changes in the GDP evolution. Thereby, the study shows the presence of structural breaks in the Spanish market risk premium and its relationship with business cycle. These findings contribute to a better understanding of close linkages between the financial markets and the macroeconomic variables such as GDP. Implications of the study and suggestions for future research are provided.

  4. Characterization of the Caenorhabditis elegans HIM-6/BLM helicase: unwinding recombination intermediates.

    Science.gov (United States)

    Jung, Hana; Lee, Jin A; Choi, Seoyoon; Lee, Hyunwoo; Ahn, Byungchan

    2014-01-01

    Mutations in three human RecQ genes are implicated in heritable human syndromes. Mutations in BLM, a RecQ gene, cause Bloom syndrome (BS), which is characterized by short stature, cancer predisposition, and sensitivity to sunlight. BLM is a RecQ DNA helicase that, with interacting proteins, is able to dissolve various DNA structures including double Holliday junctions. A BLM ortholog, him-6, has been identified in Caenorhabditis elegans, but little is known about its enzymatic activities or its in vivo roles. By purifying recombinant HIM-6 and performing biochemical assays, we determined that the HIM-6 has DNA-dependent ATPase activity HIM-6 and helicase activity that proceeds in the 3'-5' direction and needs at least five 3' overhanging nucleotides. HIM-6 is also able to unwind DNA structures including D-loops and Holliday junctions. Worms with him-6 mutations were defective in recovering the cell cycle arrest after HU treatment. These activities strongly support in vivo roles for HIM-6 in processing recombination intermediates.

  5. Feedback structure based entropy approach for multiple-model estimation

    Institute of Scientific and Technical Information of China (English)

    Shen-tu Han; Xue Anke; Guo Yunfei

    2013-01-01

    The variable-structure multiple-model (VSMM) approach, one of the multiple-model (MM) methods, is a popular and effective approach in handling problems with mode uncertainties. The model sequence set adaptation (MSA) is the key to design a better VSMM. However, MSA methods in the literature have big room to improve both theoretically and practically. To this end, we propose a feedback structure based entropy approach that could find the model sequence sets with the smallest size under certain conditions. The filtered data are fed back in real time and can be used by the minimum entropy (ME) based VSMM algorithms, i.e., MEVSMM. Firstly, the full Markov chains are used to achieve optimal solutions. Secondly, the myopic method together with particle filter (PF) and the challenge match algorithm are also used to achieve sub-optimal solutions, a trade-off between practicability and optimality. The numerical results show that the proposed algorithm provides not only refined model sets but also a good robustness margin and very high accuracy.

  6. Velocity and processivity of helicase unwinding of double-stranded nucleic acids

    International Nuclear Information System (INIS)

    Betterton, M D; Juelicher, F

    2005-01-01

    Helicases are molecular motors which unwind double-stranded nucleic acids (dsNA) in cells. Many helicases move with directional bias on single-stranded (ss) nucleic acids, and couple their directional translocation to strand separation. A model of the coupling between translocation and unwinding uses an interaction potential to represent passive and active helicase mechanisms. A passive helicase must wait for thermal fluctuations to open dsNA base pairs before it can advance and inhibit NA closing. An active helicase directly destabilizes dsNA base pairs, accelerating the opening rate. Here we extend this model to include helicase unbinding from the nucleic-acid strand. The helicase processivity depends on the form of the interaction potential. A passive helicase has a mean attachment time which does not change between ss translocation and ds unwinding, while an active helicase in general shows a decrease in attachment time during unwinding relative to ss translocation. In addition, we describe how helicase unwinding velocity and processivity vary if the base-pair binding free energy is changed

  7. Mcm10 regulates DNA replication elongation by stimulating the CMG replicative helicase.

    Science.gov (United States)

    Lõoke, Marko; Maloney, Michael F; Bell, Stephen P

    2017-02-01

    Activation of the Mcm2-7 replicative DNA helicase is the committed step in eukaryotic DNA replication initiation. Although Mcm2-7 activation requires binding of the helicase-activating proteins Cdc45 and GINS (forming the CMG complex), an additional protein, Mcm10, drives initial origin DNA unwinding by an unknown mechanism. We show that Mcm10 binds a conserved motif located between the oligonucleotide/oligosaccharide fold (OB-fold) and A subdomain of Mcm2. Although buried in the interface between these domains in Mcm2-7 structures, mutations predicted to separate the domains and expose this motif restore growth to conditional-lethal MCM10 mutant cells. We found that, in addition to stimulating initial DNA unwinding, Mcm10 stabilizes Cdc45 and GINS association with Mcm2-7 and stimulates replication elongation in vivo and in vitro. Furthermore, we identified a lethal allele of MCM10 that stimulates initial DNA unwinding but is defective in replication elongation and CMG binding. Our findings expand the roles of Mcm10 during DNA replication and suggest a new model for Mcm10 function as an activator of the CMG complex throughout DNA replication. © 2017 Lõoke et al.; Published by Cold Spring Harbor Laboratory Press.

  8. Exploring manifold structure of face images via multiple graphs

    KAUST Repository

    Alghamdi, Masheal

    2013-01-01

    Geometric structure in the data provides important information for face image recognition and classification tasks. Graph regularized non-negative matrix factorization (GrNMF) performs well in this task. However, it is sensitive to the parameters selection. Wang et al. proposed multiple graph regularized non-negative matrix factorization (MultiGrNMF) to solve the parameter selection problem by testing it on medical images. In this paper, we introduce the MultiGrNMF algorithm in the context of still face Image classification, and conduct a comparative study of NMF, GrNMF, and MultiGrNMF using two well-known face databases. Experimental results show that MultiGrNMF outperforms NMF and GrNMF for most cases.

  9. Exploring manifold structure of face images via multiple graphs

    KAUST Repository

    Alghamdi, Masheal

    2013-12-24

    Geometric structure in the data provides important information for face image recognition and classification tasks. Graph regularized non-negative matrix factorization (GrNMF) performs well in this task. However, it is sensitive to the parameters selection. Wang et al. proposed multiple graph regularized non-negative matrix factorization (MultiGrNMF) to solve the parameter selection problem by testing it on medical images. In this paper, we introduce the MultiGrNMF algorithm in the context of still face Image classification, and conduct a comparative study of NMF, GrNMF, and MultiGrNMF using two well-known face databases. Experimental results show that MultiGrNMF outperforms NMF and GrNMF for most cases.

  10. A Brownian motor mechanism of translocation and strand separation by hepatitis C virus helicase.

    Science.gov (United States)

    Levin, Mikhail K; Gurjar, Madhura; Patel, Smita S

    2005-05-01

    Helicases translocate along their nucleic acid substrates using the energy of ATP hydrolysis and by changing conformations of their nucleic acid-binding sites. Our goal is to characterize the conformational changes of hepatitis C virus (HCV) helicase at different stages of ATPase cycle and to determine how they lead to translocation. We have reported that ATP binding reduces HCV helicase affinity for nucleic acid. Now we identify the stage of the ATPase cycle responsible for translocation and unwinding. We show that a rapid directional movement occurs upon helicase binding to DNA in the absence of ATP, resulting in opening of several base pairs. We propose that HCV helicase translocates as a Brownian motor with a simple two-stroke cycle. The directional movement step is fueled by single-stranded DNA binding energy while ATP binding allows for a brief period of random movement that prepares the helicase for the next cycle.

  11. GINS complex protein Sld5 recruits SIK1 to activate MCM helicase during DNA replication.

    Science.gov (United States)

    Joshi, Kiranmai; Shah, Varun Jayeshkumar; Maddika, Subbareddy

    2016-12-01

    In eukaryotes, proper loading and activation of MCM helicase at chromosomal origins plays a central role in DNA replication. Activation of MCM helicase requires its association with CDC45-GINS complex, but the mechanism of how this complex activates MCM helicase is poorly understood. Here we identified SIK1 (salt-inducible kinase 1), an AMPK related protein kinase, as a molecular link that connects GINS complex with MCM helicase activity. We demonstrated that Sld5 a component of GINS complex interacts with SIK1 and recruits it to the sites of DNA replication at the onset of S phase. Depletion of SIK1 leads to defective DNA replication. Further, we showed that SIK1 phosphorylates MCM2 at five conserved residues at its N-terminus, which is essential for the activation of MCM helicase. Collectively, our results suggest SIK1 as a novel integral component of CMG replicative helicase during eukaryotic DNA replication. Copyright © 2016 Elsevier Inc. All rights reserved.

  12. Inhibition of RNA Helicases of ssRNA+ Virus Belonging to Flaviviridae, Coronaviridae and Picornaviridae Families

    Directory of Open Access Journals (Sweden)

    Irene Briguglio

    2011-01-01

    Full Text Available Many viral pathogens encode the motor proteins named RNA helicases which display various functions in genome replication. General strategies to design specific and selective drugs targeting helicase for the treatment of viral infections could act via one or more of the following mechanisms: inhibition of the NTPase activity, by interferences with ATP binding and therefore by limiting the energy required for the unwinding and translocation, or by allosteric mechanism and therefore by stabilizing the conformation of the enzyme in low helicase activity state; inhibition of nucleic acids binding to the helicase; inhibition of coupling of ATP hydrolysis to unwinding; inhibition of unwinding by sterically blocking helicase translocation. Recently, by in vitro screening studies, it has been reported that several benzotriazole, imidazole, imidazodiazepine, phenothiazine, quinoline, anthracycline, triphenylmethane, tropolone, pyrrole, acridone, small peptide, and Bananin derivatives are endowed with helicase inhibition of pathogen viruses belonging to Flaviviridae, Coronaviridae, and Picornaviridae families.

  13. Mechanism of Archaeal MCM Helicase Recruitment to DNA Replication Origins

    Science.gov (United States)

    Samson, Rachel Y.; Abeyrathne, Priyanka D.; Bell, Stephen D.

    2015-01-01

    Summary Cellular DNA replication origins direct the recruitment of replicative helicases via the action of initiator proteins belonging to the AAA+ superfamily of ATPases. Archaea have a simplified subset of the eukaryotic DNA replication machinery proteins and possess initiators that appear ancestral to both eukaryotic Orc1 and Cdc6. We have reconstituted origin-dependent recruitment of the homohexameric archaeal MCM in vitro with purified recombinant proteins. Using this system, we reveal that archaeal Orc1-1 fulfills both Orc1 and Cdc6 functions by binding to a replication origin and directly recruiting MCM helicase. We identify the interaction interface between these proteins and reveal how ATP binding by Orc1-1 modulates recruitment of MCM. Additionally, we provide evidence that an open-ring form of the archaeal MCM homohexamer is loaded at origins. PMID:26725007

  14. Mycobacterium smegmatis SftH exemplifies a distinctive clade of superfamily II DNA-dependent ATPases with 3' to 5' translocase and helicase activities.

    Science.gov (United States)

    Yakovleva, Lyudmila; Shuman, Stewart

    2012-08-01

    Bacterial DNA helicases are nucleic acid-dependent NTPases that play important roles in DNA replication, recombination and repair. We are interested in the DNA helicases of Mycobacteria, a genus of the phylum Actinobacteria, which includes the human pathogen Mycobacterium tuberculosis and its avirulent relative Mycobacterium smegmatis. Here, we identify and characterize M. smegmatis SftH, a superfamily II helicase with a distinctive domain structure, comprising an N-terminal NTPase domain and a C-terminal DUF1998 domain (containing a putative tetracysteine metal-binding motif). We show that SftH is a monomeric DNA-dependent ATPase/dATPase that translocates 3' to 5' on single-stranded DNA and has 3' to 5' helicase activity. SftH homologs are found in bacteria representing 12 different phyla, being especially prevalent in Actinobacteria (including M. tuberculosis). SftH homologs are evident in more than 30 genera of Archaea. Among eukarya, SftH homologs are present in plants and fungi.

  15. Unique Helicase Determinants in the Essential Conjugative TraI Factor from Salmonella enterica Serovar Typhimurium Plasmid pCU1

    Energy Technology Data Exchange (ETDEWEB)

    McLaughlin, Krystle J.; Nash, Rebekah P.; Redinbo, Mathew R. (UNC)

    2014-06-16

    The widespread development of multidrug-resistant bacteria is a major health emergency. Conjugative DNA plasmids, which harbor a wide range of antibiotic resistance genes, also encode the protein factors necessary to orchestrate the propagation of plasmid DNA between bacterial cells through conjugative transfer. Successful conjugative DNA transfer depends on key catalytic components to nick one strand of the duplex DNA plasmid and separate the DNA strands while cell-to-cell transfer occurs. The TraI protein from the conjugative Salmonella plasmid pCU1 fulfills these key catalytic roles, as it contains both single-stranded DNA-nicking relaxase and ATP-dependent helicase domains within a single, 1,078-residue polypeptide. In this work, we unraveled the helicase determinants of Salmonella pCU1 TraI through DNA binding, ATPase, and DNA strand separation assays. TraI binds DNA substrates with high affinity in a manner influenced by nucleic acid length and the presence of a DNA hairpin structure adjacent to the nick site. TraI selectively hydrolyzes ATP, and mutations in conserved helicase motifs eliminate ATPase activity. Surprisingly, the absence of a relatively short (144-residue) domain at the extreme C terminus of the protein severely diminishes ATP-dependent strand separation. Collectively, these data define the helicase motifs of the conjugative factor TraI from Salmonella pCU1 and reveal a previously uncharacterized C-terminal functional domain that uncouples ATP hydrolysis from strand separation activity.

  16. The impacts of multiple stressors to model ecological structures

    International Nuclear Information System (INIS)

    Landis, W.G.; Kelly, S.A.; Markiewicz, A.J.; Matthews, R.A.; Matthews, G.B.

    1995-01-01

    The basis of the community conditioning hypothesis is that ecological structures are the result of their unique etiology. Systems that have been exposed to a variety of stressors should reflect this history. The authors how conducted a series of microcosm experiments that can compare the effects of multiple stressors upon community dynamics. The microcosm protocols are derived from the Standardized Aquatic Microcosm (SAM) and have Lemma and additional protozoan species. Two multiple stressor experiments have been conducted. In an extended length SAM (ELSAM), two of four treatments were dosed with the turbine fuel JP-8 one week into the experiment. Two treatments were later exposed to the heat stress, one that had received jet fuel and one that had not. Similarly, an ELSAM was conducted with the second stressor being the further addition of JP-8 replacing the heat shock. Biological, physical and chemical data were analyzed with multivariate techniques including nonmetric clustering and association analysis. Space-time worms and phase diagrams were also employed to ascertain the dynamic relationships of variables identified as important by the multivariate techniques. The experiments do not result in a simple additive linear response to the additional stressor. Examination of the relative population dynamics reveal alterations in trajectories that suggest treatment related effects. As in previous single stressor experiments, recovery does not occur even after extended experimental periods. The authors are now attempting to measure the resulting trajectories, changes in similarity vectors and overall dynamics. However, community conditioning does appear to be an important framework in understanding systems with a heterogeneous array of stressors

  17. Genome-wide identification of SF1 and SF2 helicases from archaea.

    Science.gov (United States)

    Chamieh, Hala; Ibrahim, Hiba; Kozah, Juliana

    2016-01-15

    Archaea microorganisms have long been used as model organisms for the study of protein molecular machines. Archaeal proteins are particularly appealing to study since archaea, even though prokaryotic, possess eukaryotic-like cellular processes. Super Family I (SF1) and Super Family II (SF2) helicase families have been studied in many model organisms, little is known about their presence and distribution in archaea. We performed an exhaustive search of homologs of SF1 and SF2 helicase proteins in 95 complete archaeal genomes. In the present study, we identified the complete sets of SF1 and SF2 helicases in archaea. Comparative analysis between archaea, human and the bacteria E. coli SF1 and SF2 helicases, resulted in the identification of seven helicase families conserved among representatives of the domains of life. This analysis suggests that these helicase families are highly conserved throughout evolution. We highlight the conserved motifs of each family and characteristic domains of the detected families. Distribution of SF1/SF2 families show that Ski2-like, Lhr, Sfth and Rad3-like helicases are ubiquitous among archaeal genomes while the other families are specific to certain archaeal groups. We also report the presence of a novel SF2 helicase specific to archaea domain named Archaea Specific Helicase (ASH). Phylogenetic analysis indicated that ASH has evolved in Euryarchaeota and is evolutionary related to the Ski2-like family with specific characteristic domains. Our study provides the first exhaustive analysis of SF1 and SF2 helicases from archaea. It expands the variety of SF1 and SF2 archaeal helicases known to exist to date and provides a starting point for new biochemical and genetic studies needed to validate their biological functions. Copyright © 2015 Elsevier B.V. All rights reserved.

  18. A role for the fission yeast Rqh1 helicase in chromosome segregation

    DEFF Research Database (Denmark)

    Win, Thein Z; Mankouri, Hocine W; Hickson, Ian D

    2005-01-01

    Schizosaccharomyces pombe Rqh1 protein is a member of the RecQ DNA helicase family. Members of this protein family are mutated in several human genome instability syndromes, including Bloom, Werner and Rothmund-Thomson syndromes. RecQ helicases participate in recombination repair of stalled...

  19. Multiple-source multiple-harmonic active vibration control of variable section cylindrical structures: A numerical study

    Science.gov (United States)

    Liu, Jinxin; Chen, Xuefeng; Gao, Jiawei; Zhang, Xingwu

    2016-12-01

    Air vehicles, space vehicles and underwater vehicles, the cabins of which can be viewed as variable section cylindrical structures, have multiple rotational vibration sources (e.g., engines, propellers, compressors and motors), making the spectrum of noise multiple-harmonic. The suppression of such noise has been a focus of interests in the field of active vibration control (AVC). In this paper, a multiple-source multiple-harmonic (MSMH) active vibration suppression algorithm with feed-forward structure is proposed based on reference amplitude rectification and conjugate gradient method (CGM). An AVC simulation scheme called finite element model in-loop simulation (FEMILS) is also proposed for rapid algorithm verification. Numerical studies of AVC are conducted on a variable section cylindrical structure based on the proposed MSMH algorithm and FEMILS scheme. It can be seen from the numerical studies that: (1) the proposed MSMH algorithm can individually suppress each component of the multiple-harmonic noise with an unified and improved convergence rate; (2) the FEMILS scheme is convenient and straightforward for multiple-source simulations with an acceptable loop time. Moreover, the simulations have similar procedure to real-life control and can be easily extended to physical model platform.

  20. Chl1 DNA helicase regulates Scc2 deposition specifically during DNA-replication in Saccharomyces cerevisiae.

    Directory of Open Access Journals (Sweden)

    Soumya Rudra

    Full Text Available The conserved family of cohesin proteins that mediate sister chromatid cohesion requires Scc2, Scc4 for chromatin-association and Eco1/Ctf7 for conversion to a tethering competent state. A popular model, based on the notion that cohesins form huge ring-like structures, is that Scc2, Scc4 function is essential only during G1 such that sister chromatid cohesion results simply from DNA replisome passage through pre-loaded cohesin rings. In such a scenario, cohesin deposition during G1 is temporally uncoupled from Eco1-dependent establishment reactions that occur during S-phase. Chl1 DNA helicase (homolog of human ChlR1/DDX11 and BACH1/BRIP1/FANCJ helicases implicated in Fanconi anemia, breast and ovarian cancer and Warsaw Breakage Syndrome plays a critical role in sister chromatid cohesion, however, the mechanism through which Chl1 promotes cohesion remains poorly understood. Here, we report that Chl1 promotes Scc2 loading unto DNA such that both Scc2 and cohesin enrichment to chromatin are defective in chl1 mutant cells. The results further show that both Chl1 expression and chromatin-recruitment are tightly regulated through the cell cycle, peaking during S-phase. Importantly, kinetic ChIP studies reveals that Chl1 is required for Scc2 chromatin-association specifically during S-phase, but not during G1. Despite normal chromatin enrichment of both Scc2 and cohesin during G1, chl1 mutant cells exhibit severe chromosome segregation and cohesion defects--revealing that G1-loaded cohesins is insufficient to promote cohesion. Based on these findings, we propose a new model wherein S-phase cohesin loading occurs during DNA replication and in concert with both cohesion establishment and chromatin assembly reactions--challenging the notion that DNA replication fork navigates through or around pre-loaded cohesin rings.

  1. Synthesis and SAR studies of 5-(pyridin-4-yl)-1,3,4-thiadiazol-2-amine derivatives as potent inhibitors of Bloom helicase

    DEFF Research Database (Denmark)

    Rosenthal, Andrew S; Dexheimer, Thomas S; Gileadi, Opher

    2013-01-01

    complementary strands of duplex DNA as well as atypical DNA structures such as Holliday junctions. Mutations of the BLM gene can result in Bloom syndrome, an autosomal recessive disorder associated with cancer predisposition. BLM-deficient cells exhibit increased sensitivity to DNA damaging agents indicating...... and related analogs, which possess potent BLM inhibition and exhibit selectivity over related helicases. Moreover, these compounds demonstrated cellular activity by inducing sister chromatid exchanges, a hallmark of Bloom syndrome....

  2. Relationships between avian richness and landscape structure at multiple scales using multiple landscapes

    Science.gov (United States)

    Michael S. Mitchell; Scott H. Rutzmoser; T. Bently Wigley; Craig Loehle; John A. Gerwin; Patrick D. Keyser; Richard A. Lancia; Roger W. Perry; Christopher L. Reynolds; Ronald E. Thill; Robert Weih; Don White; Petra Bohall Wood

    2006-01-01

    Little is known about factors that structure biodiversity on landscape scales, yet current land management protocols, such as forest certification programs, place an increasing emphasis on managing for sustainable biodiversity at landscape scales. We used a replicated landscape study to evaluate relationships between forest structure and avian diversity at both stand...

  3. Electronic structure of single- and multiple-shell carbon fullerenes

    International Nuclear Information System (INIS)

    Lin, Y.; Nori, F.

    1994-01-01

    We study the electronic states of giant single-shell and the recently discovered nested multiple-shell carbon fullerenes within the tight-binding approximation. We use two different approaches, one based on iterations and the other on symmetry, to obtain the π-state energy spectra of large fullerene cages: C 240 , C 540 , C 960 , C 1500 , C 2160 , and C 2940 . Our iteration technique reduces the size of the problem by more than one order of magnitude (factors of ∼12 and 20), while the symmetry-based approach reduces it by a factor of 10. We also find formulas for the highest occupied and lowest unoccupied molecular orbital energies of C 60n 2 fullerenes as a function of n, demonstrating a tendency towards a metallic regime for increasing n. For multiple-shell fullerenes, we analytically obtain the eigenvalues of the intershell interaction

  4. Structured plant metabolomics for the simultaneous exploration of multiple factors.

    Science.gov (United States)

    Vasilev, Nikolay; Boccard, Julien; Lang, Gerhard; Grömping, Ulrike; Fischer, Rainer; Goepfert, Simon; Rudaz, Serge; Schillberg, Stefan

    2016-11-17

    Multiple factors act simultaneously on plants to establish complex interaction networks involving nutrients, elicitors and metabolites. Metabolomics offers a better understanding of complex biological systems, but evaluating the simultaneous impact of different parameters on metabolic pathways that have many components is a challenging task. We therefore developed a novel approach that combines experimental design, untargeted metabolic profiling based on multiple chromatography systems and ionization modes, and multiblock data analysis, facilitating the systematic analysis of metabolic changes in plants caused by different factors acting at the same time. Using this method, target geraniol compounds produced in transgenic tobacco cell cultures were grouped into clusters based on their response to different factors. We hypothesized that our novel approach may provide more robust data for process optimization in plant cell cultures producing any target secondary metabolite, based on the simultaneous exploration of multiple factors rather than varying one factor each time. The suitability of our approach was verified by confirming several previously reported examples of elicitor-metabolite crosstalk. However, unravelling all factor-metabolite networks remains challenging because it requires the identification of all biochemically significant metabolites in the metabolomics dataset.

  5. ATPase activity measurement of DNA replicative helicase from Bacillus stearothermophilus by malachite green method.

    Science.gov (United States)

    Yang, Mu; Wang, Ganggang

    2016-09-15

    The DnaB helicase from Bacillus stearothermophilus (DnaBBst) was a model protein for studying the bacterial DNA replication. In this work, a non-radioactive method for measuring ATPase activity of DnaBBst helicase was described. The working parameters and conditions were optimized. Furthermore, this method was applied to investigate effects of DnaG primase, ssDNA and helicase loader protein (DnaI) on ATPase activity of DnaBBst. Our results showed this method was sensitive and efficient. Moreover, it is suitable for the investigation of functional interaction between DnaB and related factors. Copyright © 2016 Elsevier Inc. All rights reserved.

  6. Optimal simultaneous superpositioning of multiple structures with missing data.

    Science.gov (United States)

    Theobald, Douglas L; Steindel, Phillip A

    2012-08-01

    Superpositioning is an essential technique in structural biology that facilitates the comparison and analysis of conformational differences among topologically similar structures. Performing a superposition requires a one-to-one correspondence, or alignment, of the point sets in the different structures. However, in practice, some points are usually 'missing' from several structures, for example, when the alignment contains gaps. Current superposition methods deal with missing data simply by superpositioning a subset of points that are shared among all the structures. This practice is inefficient, as it ignores important data, and it fails to satisfy the common least-squares criterion. In the extreme, disregarding missing positions prohibits the calculation of a superposition altogether. Here, we present a general solution for determining an optimal superposition when some of the data are missing. We use the expectation-maximization algorithm, a classic statistical technique for dealing with incomplete data, to find both maximum-likelihood solutions and the optimal least-squares solution as a special case. The methods presented here are implemented in THESEUS 2.0, a program for superpositioning macromolecular structures. ANSI C source code and selected compiled binaries for various computing platforms are freely available under the GNU open source license from http://www.theseus3d.org. dtheobald@brandeis.edu Supplementary data are available at Bioinformatics online.

  7. TbPIF5 is a Trypanosoma brucei mitochondrial DNA helicase involved in processing of minicircle Okazaki fragments.

    Directory of Open Access Journals (Sweden)

    Beiyu Liu

    2009-09-01

    Full Text Available Trypanosoma brucei's mitochondrial genome, kinetoplast DNA (kDNA, is a giant network of catenated DNA rings. The network consists of a few thousand 1 kb minicircles and several dozen 23 kb maxicircles. Here we report that TbPIF5, one of T. brucei's six mitochondrial proteins related to Saccharomyces cerevisiae mitochondrial DNA helicase ScPIF1, is involved in minicircle lagging strand synthesis. Like its yeast homolog, TbPIF5 is a 5' to 3' DNA helicase. Together with other enzymes thought to be involved in Okazaki fragment processing, TbPIF5 localizes in vivo to the antipodal sites flanking the kDNA. Minicircles in wild type cells replicate unidirectionally as theta-structures and are unusual in that Okazaki fragments are not joined until after the progeny minicircles have segregated. We now report that overexpression of TbPIF5 causes premature removal of RNA primers and joining of Okazaki fragments on theta structures. Further elongation of the lagging strand is blocked, but the leading strand is completed and the minicircle progeny, one with a truncated H strand (ranging from 0.1 to 1 kb, are segregated. The minicircles with a truncated H strand electrophorese on an agarose gel as a smear. This replication defect is associated with kinetoplast shrinkage and eventual slowing of cell growth. We propose that TbPIF5 unwinds RNA primers after lagging strand synthesis, thus facilitating processing of Okazaki fragments.

  8. Mycobacterium smegmatis HelY Is an RNA-Activated ATPase/dATPase and 3'-to-5' Helicase That Unwinds 3'-Tailed RNA Duplexes and RNA:DNA Hybrids.

    Science.gov (United States)

    Uson, Maria Loressa; Ordonez, Heather; Shuman, Stewart

    2015-10-01

    Mycobacteria have a large and distinctive ensemble of DNA helicases that function in DNA replication, repair, and recombination. Little is known about the roster of RNA helicases in mycobacteria or their roles in RNA transactions. The 912-amino-acid Mycobacterium smegmatis HelY (MSMEG_3885) protein is a bacterial homolog of the Mtr4 and Ski2 helicases that regulate RNA 3' processing and turnover by the eukaryal exosome. Here we characterize HelY as an RNA-stimulated ATPase/dATPase and an ATP/dATP-dependent 3'-to-5' helicase. HelY requires a 3' single-strand RNA tail (a loading RNA strand) to displace the complementary strand of a tailed RNA:RNA or RNA:DNA duplex. The findings that HelY ATPase is unresponsive to a DNA polynucleotide cofactor and that HelY is unable to unwind a 3'-tailed duplex in which the loading strand is DNA distinguish HelY from other mycobacterial nucleoside triphosphatases/helicases characterized previously. The biochemical properties of HelY, which resemble those of Mtr4/Ski2, hint at a role for HelY in mycobacterial RNA catabolism. RNA helicases play crucial roles in transcription, RNA processing, and translation by virtue of their ability to alter RNA secondary structure or remodel RNA-protein interactions. In eukarya, the RNA helicases Mtr4 and Ski2 regulate RNA 3' resection by the exosome. Mycobacterium smegmatis HelY, a bacterial homolog of Mtr4/Ski2, is characterized here as a unidirectional helicase, powered by RNA-dependent ATP/dATP hydrolysis, that tracks 3' to 5' along a loading RNA strand to displace the complementary strand of a tailed RNA:RNA or RNA:DNA duplex. The biochemical properties of HelY suggest a role in bacterial RNA transactions. HelY homologs are present in pathogenic mycobacteria (e.g., M. tuberculosis and M. leprae) and are widely prevalent in Actinobacteria and Cyanobacteria but occur sporadically elsewhere in the bacterial domain. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  9. Fracture resistance enhancement of layered structures by multiple cracks

    DEFF Research Database (Denmark)

    Goutianos, Stergios; Sørensen, Bent F.

    2016-01-01

    A theoretical model is developed to test if the fracture resistance of a layered structure can be increased by introducing weak layers changing the cracking mechanism. An analytical model, based on the J integral, predicts a linear dependency between the number of cracks and the steady state...... fracture resistance. A finite element cohesive zone model, containing two cracking planes for simplicity, is used to check the theoretical model and its predictions. It is shown that for a wide range of cohesive law parameters, the numerical predictions agree well quantitatively with the theoretical model....... Thus, it is possible to enhance considerably the fracture resistance of a structure by adding weak layers....

  10. Multiple sclerosis, cannabis, and cognition: A structural MRI study

    Directory of Open Access Journals (Sweden)

    Kristoffer Romero

    2015-01-01

    Interpretation: These results suggest that cannabis use in MS results in more widespread cognitive deficits, which correlate with tissue volume in subcortical, medial temporal, and prefrontal regions. These are the first findings demonstrating an association between cannabis use, cognitive impairment and structural brain changes in MS patients.

  11. Energy prices, multiple structural breaks, and efficient market hypothesis

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Chien-Chiang; Lee, Jun-De [Department of Applied Economics, National Chung Hsing University, Taichung (China)

    2009-04-15

    This paper investigates the efficient market hypothesis using total energy price and four kinds of various disaggregated energy prices - coal, oil, gas, and electricity - for OECD countries over the period 1978-2006. We employ a highly flexible panel data stationarity test of Carrion-i-Silvestre et al. [Carrion-i-Silvestre JL, Del Barrio-Castro T, Lopez-Bazo E. Breaking the panels: an application to GDP per capita. J Econometrics 2005;8:159-75], which incorporates multiple shifts in level and slope, thereby controlling for cross-sectional dependence through bootstrap methods. Overwhelming evidence in favor of the broken stationarity hypothesis is found, implying that energy prices are not characterized by an efficient market. Thus, it shows the presence of profitable arbitrage opportunities among energy prices. The estimated breaks are meaningful and coincide with the most critical events which affected the energy prices. (author)

  12. Energy prices, multiple structural breaks, and efficient market hypothesis

    International Nuclear Information System (INIS)

    Lee, Chien-Chiang; Lee, Jun-De

    2009-01-01

    This paper investigates the efficient market hypothesis using total energy price and four kinds of various disaggregated energy prices - coal, oil, gas, and electricity - for OECD countries over the period 1978-2006. We employ a highly flexible panel data stationarity test of Carrion-i-Silvestre et al. [Carrion-i-Silvestre JL, Del Barrio-Castro T, Lopez-Bazo E. Breaking the panels: an application to GDP per capita. J Econometrics 2005;8:159-75], which incorporates multiple shifts in level and slope, thereby controlling for cross-sectional dependence through bootstrap methods. Overwhelming evidence in favor of the broken stationarity hypothesis is found, implying that energy prices are not characterized by an efficient market. Thus, it shows the presence of profitable arbitrage opportunities among energy prices. The estimated breaks are meaningful and coincide with the most critical events which affected the energy prices. (author)

  13. High-throughput screening assay of hepatitis C virus helicase inhibitors using fluorescence-quenching phenomenon

    International Nuclear Information System (INIS)

    Tani, Hidenori; Akimitsu, Nobuyoshi; Fujita, Osamu; Matsuda, Yasuyoshi; Miyata, Ryo; Tsuneda, Satoshi; Igarashi, Masayuki; Sekiguchi, Yuji; Noda, Naohiro

    2009-01-01

    We have developed a novel high-throughput screening assay of hepatitis C virus (HCV) nonstructural protein 3 (NS3) helicase inhibitors using the fluorescence-quenching phenomenon via photoinduced electron transfer between fluorescent dyes and guanine bases. We prepared double-stranded DNA (dsDNA) with a 5'-fluorescent-dye (BODIPY FL)-labeled strand hybridized with a complementary strand, the 3'-end of which has guanine bases. When dsDNA is unwound by helicase, the dye emits fluorescence owing to its release from the guanine bases. Our results demonstrate that this assay is suitable for quantitative assay of HCV NS3 helicase activity and useful for high-throughput screening for inhibitors. Furthermore, we applied this assay to the screening for NS3 helicase inhibitors from cell extracts of microorganisms, and found several cell extracts containing potential inhibitors.

  14. Hopping mixed hybrid excitations in multiple composite quantum wire structures

    International Nuclear Information System (INIS)

    Nguyen Ba An; Tran Thai Hoa

    1995-10-01

    A structure consisting of N pairs of inorganic semiconductor and organic quantum wires is considered theoretically. In such an isolated pair of wires, while the intrawire coupling forms Wannier-Mott exciton in an inorganic semiconductor quantum wire and Frenkel exciton in an organic one, the interwire coupling gives rise to hybrid excitons residing within the pair. When N pairs of wires are packed together 2N new mixed hybrid modes appear that are the true elementary excitations and can hop throughout the whole structure. Energies and wave functions of such hopping mixed hybrid excitations are derived analytically in detail accounting for the global interwire coupling and the different polarization configurations. (author). 19 refs

  15. Ebselen Inhibits Hepatitis C Virus NS3 Helicase Binding to Nucleic Acid and Prevents Viral Replication

    OpenAIRE

    Mukherjee, Sourav; Weiner, Warren S.; Schroeder, Chad E.; Simpson, Denise S.; Hanson, Alicia M.; Sweeney, Noreena L.; Marvin, Rachel K.; Ndjomou, Jean; Kolli, Rajesh; Isailovic, Dragan; Schoenen, Frank J.; Frick, David N.

    2014-01-01

    The hepatitis C virus (HCV) nonstructural protein 3 (NS3) is both a protease, which cleaves viral and host proteins, and a helicase that separates nucleic acid strands, using ATP hydrolysis to fuel the reaction. Many antiviral drugs, and compounds in clinical trials, target the NS3 protease, but few helicase inhibitors that function as antivirals have been reported. This study focuses on the analysis of the mechanism by which ebselen (2-phenyl-1,2-benzisoselenazol-3-one), a compound previousl...

  16. Cloning and expression of NS3 helicase fragment of hepatitis C virus and the study of its immunoreactivity in HCV infected patients

    Directory of Open Access Journals (Sweden)

    Mahrou Sadri

    2015-02-01

    Full Text Available Objective(s: Hepatitis C is a major cause of liver failure worldwide. Current therapies applied for this disease are not fully effective and produce side effects in most cases. Non-structural protein 3 helicase (NS3 of HCV is one of the key enzymes in viral replication and infection. Therefore, this region is a promising target to design new drugs and therapies against HCV infection. The aim of this study was cloning and expression of HCV NS3 helicase fragment in Escherichia coli BL21 (DE3 using pET102/D-TOPO expression vector and studying immunoreactivity of the expressed antigen in Iranian infected with hepatitis C. Materials and Methods: The viral RNA was extracted from the serum of HCV infected patient. The NS3 helicase region was amplified by RT-PCR. The PCR product was directionally cloned into the expression vector pET102/D-TOPO and transformed into the BL21 strain of E. coli (DE3. The transformed bacteria were then induced by adding 1mM isopropyl-β-D-thiogalactopyranoside (IPTG into the culture medium to enhance the protein expression. SDS-PAGE and western blotting were carried out to identify the protein under investigation, and finally purified recombinant fusion protein was used as the antigen for ELISA method. Results: Theinsertion of theDNA fragment of the NS3 regioninto the expression vectorwas further confirmed by PCR and sequencing. SDS-PAGE analysis showed the successful expression of the recombinant protein of interest. Furthermore, immunoreactivity of fusion NS3 helicase was confirmed by ELISA and western blotting. Conclusion: It seems that this recombinant protein could be a useful source of antigen for future studies on HCV diagnosis and therapy.

  17. RecQL5 promotes genome stabilization through two parallel mechanisms--interacting with RNA polymerase II and acting as a helicase.

    Science.gov (United States)

    Islam, M Nurul; Fox, David; Guo, Rong; Enomoto, Takemi; Wang, Weidong

    2010-05-01

    The RecQL5 helicase is essential for maintaining genome stability and reducing cancer risk. To elucidate its mechanism of action, we purified a RecQL5-associated complex and identified its major component as RNA polymerase II (Pol II). Bioinformatics and structural modeling-guided mutagenesis revealed two conserved regions in RecQL5 as KIX and SRI domains, already known in transcriptional regulators for Pol II. The RecQL5-KIX domain binds both initiation (Pol IIa) and elongation (Pol IIo) forms of the polymerase, whereas the RecQL5-SRI domain interacts only with the elongation form. Fully functional RecQL5 requires both helicase activity and associations with the initiation polymerase, because mutants lacking either activity are partially defective in the suppression of sister chromatid exchange and resistance to camptothecin-induced DNA damage, and mutants lacking both activities are completely defective. We propose that RecQL5 promotes genome stabilization through two parallel mechanisms: by participation in homologous recombination-dependent DNA repair as a RecQ helicase and by regulating the initiation of Pol II to reduce transcription-associated replication impairment and recombination.

  18. The RNA helicase Rm62 cooperates with SU(VAR3-9 to re-silence active transcription in Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Joern Boeke

    Full Text Available Gene expression is highly dynamic and many genes show a wide range in expression over several orders of magnitude. This regulation is often mediated by sequence specific transcription factors. In addition, the tight packaging of DNA into chromatin can provide an additional layer of control resulting in a dynamic range of gene expression covering several orders of magnitude. During transcriptional activation, chromatin barriers have to be eliminated to allow an efficient progression of the RNA polymerase. This repressive chromatin structure has to be re-established quickly after it has been activated in order to tightly regulate gene activity. We show that the DExD/H box containing RNA helicase Rm62 is targeted to a site of rapid induction of transcription where it is responsible for an increased degree of methylation at H3K9 at the heat shock locus after removal of the heat shock stimulus. The RNA helicase interacts with the well-characterized histone methyltransferase SU(VAR3-9 via its N-terminus, which provides a potential mechanism for the targeting of H3K9 methylation to highly regulated genes. The recruitment of SU(VAR3-9 through interaction with a RNA helicase to a site of active transcription might be a general mechanism that allows an efficient silencing of highly regulated genes thereby enabling a cell to fine tune its gene activity over a wide range.

  19. Multiple Approaches to Characterizing Pore Structure in Natural Rock

    Science.gov (United States)

    Hu, Q.; Dultz, S.; Hamamoto, S.; Ewing, R. P.

    2012-12-01

    Microscopic characteristics of porous media - pore shape, pore-size distribution, and pore connectivity - control fluid flow and chemical transport, and are important in hydrogeological studies of rock formations in the context of energy, environmental, and water resources management. This presentation discusses various approaches to investigating pore structure of rock, with a particular focus on the Barnett Shale in north Texas used for natural gas production. Approaches include imbibition, tracer diffusion, porosimetry (MIP, vapor adsorption/desorption isotherms, NMR cyroporometry), and imaging (μ-tomography, Wood's metal impregnation, FIB/SEM). Results show that the Barnett Shale pores are predominantly in the nm size range, with a measured median pore-throat diameter of 6.5 nm. But small pore size is not the major contributor to low gas recovery; rather, the low gas diffusivity appears to be caused by low pore connectivity. Chemical diffusion in sparsely-connected pore spaces is not well described by classical Fickian behavior; anomalous behavior is suggested by percolation theory, and confirmed by results of imbibition tests. Our evolving complementary approaches, with their several advantages and disadvantages, provide a rich toolbox for tackling the pore structure characteristics in the Barnett Shale and other natural rocks.

  20. Experimental investigation of multiple self-organized structures in plasma

    International Nuclear Information System (INIS)

    Ivan, L. M.; Gaman, C.; Aflori, M.; Mihai-Plugaru, M.; Dimitriu, D.G.; Lozneanu, E.; Sanduloviciu, M.

    2005-01-01

    Complex space charge configuration emerges by self-organization in front of an electrode immersed in plasma when its potential is increased at a certain critical value. Consisting from a nucleus protected from the surrounding plasma by an electrical double layer, the complexity reveals an internal structure and behaviour which remind us primitive organisms. Thus the complexity is not static but stationary open system in which continuous decay is constantly compensated by substance and energy from the surrounding plasma. Endowed with a special kind of memory the complexity can work as an intelligent multifunctional system and consequently it is also able to perform innovations after selective interaction with an environment in evolution. Additionally, the complexity is able to replicate by division. (authors)

  1. Introducing galactic structure finder: the multiple stellar kinematic structures of a simulated Milky Way mass galaxy

    Science.gov (United States)

    Obreja, Aura; Macciò, Andrea V.; Moster, Benjamin; Dutton, Aaron A.; Buck, Tobias; Wang, Gregory S. Stinson Liang

    2018-04-01

    We present the first results of applying Gaussian Mixture Models in the stellar kinematic space of normalized angular momentum and binding energy on NIHAO high resolution galaxies to separate the stars into multiple components. We exemplify this method using a simulated Milky Way analogue, whose stellar component hosts: thin and thick discs, classical and pseudo bulges, and a stellar halo. The properties of these stellar structures are in good agreement with observational expectations in terms of sizes, shapes and rotational support. Interestingly, the two kinematic discs show surface mass density profiles more centrally concentrated than exponentials, while the bulges and the stellar halo are purely exponential. We trace back in time the Lagrangian mass of each component separately to study their formation history. Between z ˜ 3 and the end of halo virialization, z ˜ 1.3, all components lose a fraction of their angular momentum. The classical bulge loses the most (˜95%) and the thin disc the least (˜60%). Both bulges formed their stars in-situ at high redshift, while the thin disc formed ˜98% in-situ, but with a constant SFR ˜ 1.5M⊙yr-1 over the last ˜ 11 Gyr. Accreted stars (6% of total stellar mass) are mainly incorporated to the thick disc or the stellar halo, which formed ex-situ 8% and 45% of their respective masses. Our analysis pipeline is freely available at https://github.com/aobr/gsf.

  2. DNA replication restart and cellular dynamics of Hef helicase/nuclease protein in Haloferax volcanii.

    Science.gov (United States)

    Lestini, Roxane; Delpech, Floriane; Myllykallio, Hannu

    2015-11-01

    Understanding how frequently spontaneous replication arrests occur and how archaea deal with these arrests are very interesting and challenging research topics. Here we will described how genetic and imaging studies have revealed the central role of the archaeal helicase/nuclease Hef belonging to the XPF/MUS81/FANCM family of endonucleases in repair of arrested replication forks. Special focus will be on description of a recently developed combination of genetic and imaging tools to study the dynamic localization of a functional Hef::GFP (Green Fluorescent Protein) fusion protein in the living cells of halophilic archaea Haloferax volcanii. As Archaea provide an excellent and unique model for understanding how DNA replication is regulated to allow replication of a circular DNA molecule either from single or multiple replication origins, we will also summarize recent studies that have revealed peculiar features regarding DNA replication, particularly in halophilic archaea. We strongly believe that fundamental knowledge of our on-going studies will shed light on the evolutionary history of the DNA replication machinery and will help to establish general rules concerning replication restart and the key role of recombination proteins not only in bacteria, yeast and higher eukaryotes but also in archaea. Copyright © 2015 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

  3. Tuneable complementary metamaterial structures based on graphene for single and multiple transparency windows.

    Science.gov (United States)

    Ding, Jun; Arigong, Bayaner; Ren, Han; Zhou, Mi; Shao, Jin; Lu, Meng; Chai, Yang; Lin, Yuankun; Zhang, Hualiang

    2014-08-22

    Novel graphene-based tunable plasmonic metamaterials featuring single and multiple transparency windows are numerically studied in this paper. The designed structures consist of a graphene layer perforated with quadrupole slot structures and dolmen-like slot structures printed on a substrate. Specifically, the graphene-based quadrupole slot structure can realize a single transparency window, which is achieved without breaking the structure symmetry. Further investigations have shown that the single transparency window in the proposed quadrupole slot structure is more likely originated from the quantum effect of Autler-Townes splitting. Then, by introducing a dipole slot to the quadrupole slot structure to form the dolmen-like slot structure, an additional transmission dip could occur in the transmission spectrum, thus, a multiple-transparency-window system can be achieved (for the first time for graphene-based devices). More importantly, the transparency windows for both the quadrupole slot and the dolmen-like slot structures can be dynamically controlled over a broad frequency range by varying the Fermi energy levels of the graphene layer (through electrostatic gating). The proposed slot metamaterial structures with tunable single and multiple transparency windows could find potential applications in many areas such as multiple-wavelength slow-light devices, active plasmonic switching, and optical sensing.

  4. Comparison of multiple crystal structures with NMR data for engrailed homeodomain

    Energy Technology Data Exchange (ETDEWEB)

    Religa, Tomasz L. [MRC Centre for Protein Engineering (United Kingdom)], E-mail: tlr25@mrc-lmb.cam.ac.uk

    2008-03-15

    Two methods are currently available to solve high resolution protein structures-X-ray crystallography and nuclear magnetic resonance (NMR). Both methods usually produce highly similar structures, but small differences between both solutions are always observed. Here the raw NMR data as well as the solved NMR structure were compared to the multiple crystal structures solved for the WT 60 residue three helix bundle engrailed homeodomain (EnHD) and single point mutants. There was excellent agreement between TALOS-predicted and crystal structure-observed dihedral angles and a good agreement for the {sup 3}J(H{sup N}H{sup {alpha}}) couplings for the multiple crystal structures. Around 1% of NOEs were violated for any crystal structure, but no NOE was inconsistent with all of the crystal structures. Violations usually occurred for surface residues or for residues for which multiple discreet conformations were observed between the crystal structures. Comparison of the disorder shown in the multiple crystal structures shows little correlation with dynamics under native conditions for this protein.

  5. Multiple Browsers Structure Tree Recruitment in Logged Temperate Forests.

    Directory of Open Access Journals (Sweden)

    Edward K Faison

    Full Text Available Historical extirpations have resulted in depauperate large herbivore assemblages in many northern forests. In eastern North America, most forests are inhabited by a single wild ungulate species, white-tailed deer (Odocoileus virginianus, and relationships between deer densities and impacts on forest regeneration are correspondingly well documented. Recent recolonizations by moose (Alces americanus in northeastern regions complicate established deer density thresholds and predictions of browsing impacts on forest dynamics because size and foraging differences between the two animals suggest a lack of functional redundancy. We asked to what extent low densities of deer + moose would structure forest communities differently from that of low densities of deer in recently logged patch cuts of Massachusetts, USA. In each site, a randomized block with three treatment levels of large herbivores-no-ungulates (full exclosure, deer (partial exclosure, and deer + moose (control was established. After 6-7 years, deer + moose reduced stem densities and basal area by 2-3-fold, Prunus pensylvanica and Quercus spp. recruitment by 3-6 fold, and species richness by 1.7 species (19%. In contrast, in the partial exclosures, deer had non-significant effects on stem density, basal area, and species composition, but significantly reduced species richness by 2.5 species on average (28%. Deer browsing in the partial exclosure was more selective than deer + moose browsing together, perhaps contributing to the decline in species richness in the former treatment and the lack of additional decline in the latter. Moose used the control plots at roughly the same frequency as deer (as determined by remote camera traps, suggesting that the much larger moose was the dominant browser species in terms of animal biomass in these cuts. A lack of functional redundancy with respect to foraging behavior between sympatric large herbivores may explain combined browsing effects that were

  6. Multiple browsers structure tree recruitment in logged temperate forests

    Science.gov (United States)

    Faison, Edward K.; DeStefano, Stephen; Foster, David R.; Rapp, Joshua M.; Compton, Justin A.

    2016-01-01

    Historical extirpations have resulted in depauperate large herbivore assemblages in many northern forests. In eastern North America, most forests are inhabited by a single wild ungulate species, white-tailed deer (Odocoileus virginianus), and relationships between deer densities and impacts on forest regeneration are correspondingly well documented. Recent recolonizations by moose (Alces americanus) in northeastern regions complicate established deer density thresholds and predictions of browsing impacts on forest dynamics because size and foraging differences between the two animals suggest a lack of functional redundancy. We asked to what extent low densities of deer + moose would structure forest communities differently from that of low densities of deer in recently logged patch cuts of Massachusetts, USA. In each site, a randomized block with three treatment levels of large herbivores–no-ungulates (full exclosure), deer (partial exclosure), and deer + moose (control) was established. After 6–7 years, deer + moose reduced stem densities and basal area by 2-3-fold, Prunus pensylvanica and Quercus spp. recruitment by 3–6 fold, and species richness by 1.7 species (19%). In contrast, in the partial exclosures, deer had non-significant effects on stem density, basal area, and species composition, but significantly reduced species richness by 2.5 species on average (28%). Deer browsing in the partial exclosure was more selective than deer + moose browsing together, perhaps contributing to the decline in species richness in the former treatment and the lack of additional decline in the latter. Moose used the control plots at roughly the same frequency as deer (as determined by remote camera traps), suggesting that the much larger moose was the dominant browser species in terms of animal biomass in these cuts. A lack of functional redundancy with respect to foraging behavior between sympatric large herbivores may explain combined browsing effects that were

  7. Physical and functional interactions of Caenorhabditis elegans WRN-1 helicase with RPA-1.

    Science.gov (United States)

    Hyun, Moonjung; Park, Sojin; Kim, Eunsun; Kim, Do-Hyung; Lee, Se-Jin; Koo, Hyeon-Sook; Seo, Yeon-Soo; Ahn, Byungchan

    2012-02-21

    The Caenorhabditis elegans Werner syndrome protein, WRN-1, a member of the RecQ helicase family, has a 3'-5' DNA helicase activity. Worms with defective wrn-1 exhibit premature aging phenotypes and an increased level of genome instability. In response to DNA damage, WRN-1 participates in the initial stages of checkpoint activation in concert with C. elegans replication protein A (RPA-1). WRN-1 helicase is stimulated by RPA-1 on long DNA duplex substrates. However, the mechanism by which RPA-1 stimulates DNA unwinding and the function of the WRN-1-RPA-1 interaction are not clearly understood. We have found that WRN-1 physically interacts with two RPA-1 subunits, CeRPA73 and CeRPA32; however, full-length WRN-1 helicase activity is stimulated by only the CeRPA73 subunit, while the WRN-1(162-1056) fragment that harbors the helicase activity requires both the CeRPA73 and CeRPA32 subunits for the stimulation. We also found that the CeRPA73(1-464) fragment can stimulate WRN-1 helicase activity and that residues 335-464 of CeRPA73 are important for physical interaction with WRN-1. Because CeRPA73 and the CeRPA73(1-464) fragment are able to bind single-stranded DNA (ssDNA), the stimulation of WRN-1 helicase by RPA-1 is most likely due to the ssDNA binding activity of CeRPA73 and the direct interaction of WRN-1 and CeRPA73.

  8. Evaluation of multiple protein docking structures using correctly predicted pairwise subunits

    Directory of Open Access Journals (Sweden)

    Esquivel-Rodríguez Juan

    2012-03-01

    Full Text Available Abstract Background Many functionally important proteins in a cell form complexes with multiple chains. Therefore, computational prediction of multiple protein complexes is an important task in bioinformatics. In the development of multiple protein docking methods, it is important to establish a metric for evaluating prediction results in a reasonable and practical fashion. However, since there are only few works done in developing methods for multiple protein docking, there is no study that investigates how accurate structural models of multiple protein complexes should be to allow scientists to gain biological insights. Methods We generated a series of predicted models (decoys of various accuracies by our multiple protein docking pipeline, Multi-LZerD, for three multi-chain complexes with 3, 4, and 6 chains. We analyzed the decoys in terms of the number of correctly predicted pair conformations in the decoys. Results and conclusion We found that pairs of chains with the correct mutual orientation exist even in the decoys with a large overall root mean square deviation (RMSD to the native. Therefore, in addition to a global structure similarity measure, such as the global RMSD, the quality of models for multiple chain complexes can be better evaluated by using the local measurement, the number of chain pairs with correct mutual orientation. We termed the fraction of correctly predicted pairs (RMSD at the interface of less than 4.0Å as fpair and propose to use it for evaluation of the accuracy of multiple protein docking.

  9. Cell characteristics of a multiple alloy nano-dots memory structure

    International Nuclear Information System (INIS)

    Bea, Ji Chel; Lee, Kang-Wook; Tanaka, Tetsu; Koyanagi, Mitsumasa; Song, Yun Heub; Lee, Gae-Hun

    2009-01-01

    A multiple alloy metal nano-dots memory using FN tunneling was investigated in order to confirm its structural possibility for future flash memory. In this work, a multiple FePt nano-dots device with a high work function (∼5.2 eV) and extremely high dot density (∼1.2 × 10 13 cm −2 ) was fabricated. Its structural effect for multiple layers was evaluated and compared to the one with a single layer in terms of the cell characteristics and reliability. We confirm that MOS capacitor structures with two to four multiple FePt nano-dot layers provide a larger threshold voltage window and better retention characteristics. Furthermore, it was also revealed that several process parameters for block oxide and inter-tunnel oxide between the nano-dot layers are very important to improve the efficiency of electron injection into multiple nano-dots. From these results, it is expected that a multiple FePt nano-dots memory using Fowler–Nordheim (FN) tunneling could be a candidate structure for future flash memory

  10. RNases and Helicases in Gram-Positive Bacteria.

    Science.gov (United States)

    Durand, Sylvain; Condon, Ciaran

    2018-04-01

    RNases are key enzymes involved in RNA maturation and degradation. Although they play a crucial role in all domains of life, bacteria, archaea, and eukaryotes have evolved with their own sets of RNases and proteins modulating their activities. In bacteria, these enzymes allow modulation of gene expression to adapt to rapidly changing environments. Today, >20 RNases have been identified in both Escherichia coli and Bacillus subtilis , the paradigms of the Gram-negative and Gram-positive bacteria, respectively. However, only a handful of these enzymes are common to these two organisms and some of them are essential to only one. Moreover, although sets of RNases can be very similar in closely related bacteria such as the Firmicutes Staphylococcus aureus and B. subtilis , the relative importance of individual enzymes in posttranscriptional regulation in these organisms varies. In this review, we detail the role of the main RNases involved in RNA maturation and degradation in Gram-positive bacteria, with an emphasis on the roles of RNase J1, RNase III, and RNase Y. We also discuss how other proteins such as helicases can modulate the RNA-degradation activities of these enzymes.

  11. Mycobacterium smegmatis RqlH defines a novel clade of bacterial RecQ-like DNA helicases with ATP-dependent 3'-5' translocase and duplex unwinding activities.

    Science.gov (United States)

    Ordonez, Heather; Unciuleac, Mihaela; Shuman, Stewart

    2012-05-01

    The Escherichia coli RecQ DNA helicase participates in a pathway of DNA repair that operates in parallel to the recombination pathway driven by the multisubunit helicase-nuclease machine RecBCD. The model mycobacterium Mycobacterium smegmatis executes homologous recombination in the absence of its helicase-nuclease machine AdnAB, though it lacks a homolog of E. coli RecQ. Here, we identify and characterize M. smegmatis RqlH, a RecQ-like helicase with a distinctive domain structure. The 691-amino acid RqlH polypeptide consists of a RecQ-like ATPase domain (amino acids 1-346) and tetracysteine zinc-binding domain (amino acids 435-499), separated by an RqlH-specific linker. RqlH lacks the C-terminal HRDC domain found in E. coli RecQ. Rather, the RqlH C-domain resembles bacterial ComF proteins and includes a phosphoribosyltransferase-like module. We show that RqlH is a DNA-dependent ATPase/dATPase that translocates 3'-5' on single-stranded DNA and has 3'-5' helicase activity. These functions inhere to RqlH-(1-505), a monomeric motor unit comprising the ATPase, linker and zinc-binding domains. RqlH homologs are distributed widely among bacterial taxa. The mycobacteria that encode RqlH lack a classical RecQ, though many other Actinobacteria have both RqlH and RecQ. Whereas E. coli K12 encodes RecQ but lacks a homolog of RqlH, other strains of E. coli have both RqlH and RecQ.

  12. Functional Dynamics of Hexameric Helicase Probed by Hydrogen Exchange and Simulation

    Science.gov (United States)

    Radou, Gaël; Dreyer, Frauke N.; Tuma, Roman; Paci, Emanuele

    2014-01-01

    The biological function of large macromolecular assemblies depends on their structure and their dynamics over a broad range of timescales; for this reason, it is a significant challenge to investigate these assemblies using conventional experimental techniques. One of the most promising experimental techniques is hydrogen-deuterium exchange detected by mass spectrometry. Here, we describe to our knowledge a new computational method for quantitative interpretation of deuterium exchange kinetics and apply it to a hexameric viral helicase P4 that unwinds and translocates RNA into a virus capsid at the expense of ATP hydrolysis. Room-temperature dynamics probed by a hundred nanoseconds of all-atom molecular dynamics simulations is sufficient to predict the exchange kinetics of most sequence fragments and provide a residue-level interpretation of the low-resolution experimental results. The strategy presented here is also a valuable tool to validate experimental data, e.g., assignments, and to probe mechanisms that cannot be observed by x-ray crystallography, or that occur over timescales longer than those that can be realistically simulated, such as the opening of the hexameric ring. PMID:25140434

  13. The C-terminal domain of the Bloom syndrome DNA helicase is essential for genomic stability

    Directory of Open Access Journals (Sweden)

    Noonan James P

    2001-07-01

    Full Text Available Abstract Background Bloom syndrome is a rare cancer-prone disorder in which the cells of affected persons have a high frequency of somatic mutation and genomic instability. Bloom syndrome cells have a distinctive high frequency of sister chromatid exchange and quadriradial formation. BLM, the protein altered in BS, is a member of the RecQ DNA helicase family, whose members share an average of 40% identity in the helicase domain and have divergent N-terminal and C-terminal flanking regions of variable lengths. The BLM DNA helicase has been shown to localize to the ND10 (nuclear domain 10 or PML (promyelocytic leukemia nuclear bodies, where it associates with TOPIIIα, and to the nucleolus. Results This report demonstrates that the N-terminal domain of BLM is responsible for localization of the protein to the nuclear bodies, while the C-terminal domain directs the protein to the nucleolus. Deletions of the N-terminal domain of BLM have little effect on sister chromatid exchange frequency and chromosome stability as compared to helicase and C-terminal mutations which can increase SCE frequency and chromosome abnormalities. Conclusion The helicase activity and the C-terminal domain of BLM are critical for maintaining genomic stability as measured by the sister chromatid exchange assay. The localization of BLM into the nucleolus by the C-terminal domain appears to be more important to genomic stability than localization in the nuclear bodies.

  14. Seismic response analysis of structural system subjected to multiple support excitation

    International Nuclear Information System (INIS)

    Wu, R.W.; Hussain, F.A.; Liu, L.K.

    1978-01-01

    In the seismic analysis of a multiply supported structural system subjected to nonuniform excitations at each support point, the single response spectrum, the time history, and the multiple response spectrum are the three commonly employed methods. In the present paper the three methods are developed, evaluated, and the limitations and advantages of each method assessed. A numerical example has been carried out for a typical piping system. Considerably smaller responses have been predicted by the time history method than that by the single response spectrum method. This is mainly due to the fact that the phase and amplitude relations between the support excitations are faithfully retained in the time history method. The multiple response spectrum prediction has been observed to compare favourably with the time history method prediction. Based on the present evaluation, the multiple response spectrum method is the most efficient method for seismic response analysis of structural systems subjected to multiple support excitation. (Auth.)

  15. Thermo-kinetic mechanisms for grain boundary structure multiplicity, thermal instability and defect interactions

    International Nuclear Information System (INIS)

    Burbery, N.J.; Das, R.; Ferguson, W.G.

    2016-01-01

    Grain boundaries (GBs) provide a source and/or a sink for crystal defects and store elastic energy due to the non-uniform atomic bonding structure of the GB core. GB structures are thermodynamically driven to transition to the lowest energy configuration possible; however to date there has been little evidence to explain why specific GB structures have a low energy state. Furthermore, there is little quantitative demonstration of the significance of physical and GB structure characteristics on the GB energy, thermal stability, and the effect of temporary local GB structure transformations on defect interactions. This paper evaluates the defect interactions and structure stability of multiple Σ5(310) GB structures in bi-crystals of pure aluminium, and systematically investigates the features at 0 K to characterise multiple metastable structures. Structure stability is evaluated by utilising unstable vacancy defects to initiate GB transformations, and using nudged elastic band simulations to quantify this with the activation energy. The emission of stable vacancy defects from the ‘stable’ and metastable grain boundaries is also evaluated in the same manner. A detailed analysis of dislocation nucleation at the atomistic scale demonstrates that local transformations of GB structure between stable and metastable intermediates can provide a mechanism to accommodate the generation of crystal defects. Kinetic (time-dependent) effects that compete with energetic driving forces for structural transformations of GBs are shown to cause a significant effect on the activation properties that may exceed the influence of GB potential energy. The results demonstrate that GB structural multiplicity can be associated with the generation and absorption of dislocations and vacancies. This paper demonstrates the suitability of atomistic simulations coupled with nudged elastic band simulations to evaluate fundamental thermodynamic properties of pure FCC metals. Overall, this paper

  16. Thermo-kinetic mechanisms for grain boundary structure multiplicity, thermal instability and defect interactions

    Energy Technology Data Exchange (ETDEWEB)

    Burbery, N.J. [Department of Mechanical Engineering, University of Auckland, Auckland 1010 (New Zealand); Das, R., E-mail: r.das@auckland.ac.nz [Department of Mechanical Engineering, University of Auckland, Auckland 1010 (New Zealand); Ferguson, W.G. [Department of Chemical and Materials Engineering, University of Auckland, Auckland 1010 (New Zealand)

    2016-08-15

    Grain boundaries (GBs) provide a source and/or a sink for crystal defects and store elastic energy due to the non-uniform atomic bonding structure of the GB core. GB structures are thermodynamically driven to transition to the lowest energy configuration possible; however to date there has been little evidence to explain why specific GB structures have a low energy state. Furthermore, there is little quantitative demonstration of the significance of physical and GB structure characteristics on the GB energy, thermal stability, and the effect of temporary local GB structure transformations on defect interactions. This paper evaluates the defect interactions and structure stability of multiple Σ5(310) GB structures in bi-crystals of pure aluminium, and systematically investigates the features at 0 K to characterise multiple metastable structures. Structure stability is evaluated by utilising unstable vacancy defects to initiate GB transformations, and using nudged elastic band simulations to quantify this with the activation energy. The emission of stable vacancy defects from the ‘stable’ and metastable grain boundaries is also evaluated in the same manner. A detailed analysis of dislocation nucleation at the atomistic scale demonstrates that local transformations of GB structure between stable and metastable intermediates can provide a mechanism to accommodate the generation of crystal defects. Kinetic (time-dependent) effects that compete with energetic driving forces for structural transformations of GBs are shown to cause a significant effect on the activation properties that may exceed the influence of GB potential energy. The results demonstrate that GB structural multiplicity can be associated with the generation and absorption of dislocations and vacancies. This paper demonstrates the suitability of atomistic simulations coupled with nudged elastic band simulations to evaluate fundamental thermodynamic properties of pure FCC metals. Overall, this paper

  17. Demonstration of helicase activity in the nonstructural protein, NSs, of the negative-sense RNA virus, groundnut bud necrosis virus.

    Science.gov (United States)

    Bhushan, Lokesh; Abraham, Ambily; Choudhury, Nirupam Roy; Rana, Vipin Singh; Mukherjee, Sunil Kumar; Savithri, Handanahal Subbarao

    2015-04-01

    The nonstructural protein NSs, encoded by the S RNA of groundnut bud necrosis virus (GBNV) (genus Tospovirus, family Bunyaviridae) has earlier been shown to possess nucleic-acid-stimulated NTPase and 5' α phosphatase activity. ATP hydrolysis is an essential function of a true helicase. Therefore, NSs was tested for DNA helicase activity. The results demonstrated that GBNV NSs possesses bidirectional DNA helicase activity. An alanine mutation in the Walker A motif (K189A rNSs) decreased DNA helicase activity substantially, whereas a mutation in the Walker B motif resulted in a marginal decrease in this activity. The parallel loss of the helicase and ATPase activity in the K189A mutant confirms that NSs acts as a non-canonical DNA helicase. Furthermore, both the wild-type and K189A NSs could function as RNA silencing suppressors, demonstrating that the suppressor activity of NSs is independent of its helicase or ATPase activity. This is the first report of a true helicase from a negative-sense RNA virus.

  18. Multivariate sparse group lasso for the multivariate multiple linear regression with an arbitrary group structure.

    Science.gov (United States)

    Li, Yanming; Nan, Bin; Zhu, Ji

    2015-06-01

    We propose a multivariate sparse group lasso variable selection and estimation method for data with high-dimensional predictors as well as high-dimensional response variables. The method is carried out through a penalized multivariate multiple linear regression model with an arbitrary group structure for the regression coefficient matrix. It suits many biology studies well in detecting associations between multiple traits and multiple predictors, with each trait and each predictor embedded in some biological functional groups such as genes, pathways or brain regions. The method is able to effectively remove unimportant groups as well as unimportant individual coefficients within important groups, particularly for large p small n problems, and is flexible in handling various complex group structures such as overlapping or nested or multilevel hierarchical structures. The method is evaluated through extensive simulations with comparisons to the conventional lasso and group lasso methods, and is applied to an eQTL association study. © 2015, The International Biometric Society.

  19. Identification of unique interactions between the flexible linker and the RecA-like domains of DEAD-box helicase Mss116

    International Nuclear Information System (INIS)

    Zhang, Yuan; Palla, Mirkó; Liao, Jung-Chi; Sun, Andrew

    2013-01-01

    DEAD-box RNA helicases are ATP-dependent proteins implicated in nearly all aspects of RNA metabolism. The yeast DEAD-box helicase Mss116 is unique in its functions of splicing group I and group II introns and activating mRNA translation, but the structural understanding of why it performs these unique functions remains unclear. Here we used sequence analysis and molecular dynamics simulation to identify residues in the flexible linker specific for yeast Mss116, potentially associated with its unique functions. We first identified residues that are 100% conserved in Mss116 of different species of the Saccharomycetaceae family. The amino acids of these conserved residues were then compared with the amino acids of the corresponding residue positions of other RNA helicases to identify residues that have distinct amino acids from other DEAD-box proteins. Four residues in the flexible linker, i.e. N334, E335, P336 and H339, are conserved and Mss116-specific. Molecular dynamics simulation was conducted for the wild-type Mss116 structure and mutant models to examine mutational effects of the linker on the conformational equilibrium. Relatively short MD simulation runs (within 20 ns) were enough for us to observe mutational effects, suggesting serious structural perturbations by these mutations. The mutation of E335 depletes the interactions between E335 and K95 in domain 1. The interactions between N334/P336 and N496/I497 of domain 2 are also abolished by mutation. Our results suggest that tight interactions between the Mss116-specific flexible linker and the two RecA-like domains may be mechanically required to crimp RNA for the unique RNA processes of yeast Mss116. (paper)

  20. Identification of unique interactions between the flexible linker and the RecA-like domains of DEAD-box helicase Mss116

    Science.gov (United States)

    Zhang, Yuan; Palla, Mirkó; Sun, Andrew; Liao, Jung-Chi

    2013-09-01

    DEAD-box RNA helicases are ATP-dependent proteins implicated in nearly all aspects of RNA metabolism. The yeast DEAD-box helicase Mss116 is unique in its functions of splicing group I and group II introns and activating mRNA translation, but the structural understanding of why it performs these unique functions remains unclear. Here we used sequence analysis and molecular dynamics simulation to identify residues in the flexible linker specific for yeast Mss116, potentially associated with its unique functions. We first identified residues that are 100% conserved in Mss116 of different species of the Saccharomycetaceae family. The amino acids of these conserved residues were then compared with the amino acids of the corresponding residue positions of other RNA helicases to identify residues that have distinct amino acids from other DEAD-box proteins. Four residues in the flexible linker, i.e. N334, E335, P336 and H339, are conserved and Mss116-specific. Molecular dynamics simulation was conducted for the wild-type Mss116 structure and mutant models to examine mutational effects of the linker on the conformational equilibrium. Relatively short MD simulation runs (within 20 ns) were enough for us to observe mutational effects, suggesting serious structural perturbations by these mutations. The mutation of E335 depletes the interactions between E335 and K95 in domain 1. The interactions between N334/P336 and N496/I497 of domain 2 are also abolished by mutation. Our results suggest that tight interactions between the Mss116-specific flexible linker and the two RecA-like domains may be mechanically required to crimp RNA for the unique RNA processes of yeast Mss116.

  1. Biophysical Characterization of G-Quadruplex Recognition in the PITX1 mRNA by the Specificity Domain of the Helicase RHAU.

    Directory of Open Access Journals (Sweden)

    Emmanuel O Ariyo

    Full Text Available Nucleic acids rich in guanine are able to fold into unique structures known as G-quadruplexes. G-quadruplexes consist of four tracts of guanylates arranged in parallel or antiparallel strands that are aligned in stacked G-quartet planes. The structure is further stabilized by Hoogsteen hydrogen bonds and monovalent cations centered between the planes. RHAU (RNA helicase associated with AU-rich element is a member of the ATP-dependent DExH/D family of RNA helicases and can bind and resolve G-quadruplexes. RHAU contains a core helicase domain with an N-terminal extension that enables recognition and full binding affinity to RNA and DNA G-quadruplexes. PITX1, a member of the bicoid class of homeobox proteins, is a transcriptional activator active during development of vertebrates, chiefly in the anterior pituitary gland and several other organs. We have previously demonstrated that RHAU regulates PITX1 levels through interaction with G-quadruplexes at the 3'-end of the PITX1 mRNA. To understand the structural basis of G-quadruplex recognition by RHAU, we characterize a purified minimal PITX1 G-quadruplex using a variety of biophysical techniques including electrophoretic mobility shift assays, UV-VIS spectroscopy, circular dichroism, dynamic light scattering, small angle X-ray scattering and nuclear magnetic resonance spectroscopy. Our biophysical analysis provides evidence that the RNA G-quadruplex, but not its DNA counterpart, can adopt a parallel orientation, and that only the RNA can interact with N-terminal domain of RHAU via the tetrad face of the G-quadruplex. This work extends our insight into how the N-terminal region of RHAU recognizes parallel G-quadruplexes.

  2. Structural invariance of multiple intelligences, based on the level of execution.

    Science.gov (United States)

    Almeida, Leandro S; Prieto, María Dolores; Ferreira, Arístides; Ferrando, Mercedes; Ferrandiz, Carmen; Bermejo, Rosario; Hernández, Daniel

    2011-11-01

    The independence of multiple intelligences (MI) of Gardner's theory has been debated since its conception. This article examines whether the one- factor structure of the MI theory tested in previous studies is invariant for low and high ability students. Two hundred ninety-four children (aged 5 to 7) participated in this study. A set of Gardner's Multiple Intelligence assessment tasks based on the Spectrum Project was used. To analyze the invariance of a general dimension of intelligence, the different models of behaviours were studied in samples of participants with different performance on the Spectrum Project tasks with Multi-Group Confirmatory Factor Analysis (MGCFA). Results suggest an absence of structural invariance in Gardner's tasks. Exploratory analyses suggest a three-factor structure for individuals with higher performance levels and a two-factor structure for individuals with lower performance levels.

  3. Optical design of multi-multiple expander structure of laser gas analysis and measurement device

    Science.gov (United States)

    Fu, Xiang; Wei, Biao

    2018-03-01

    The installation and debugging of optical circuit structure in the application of carbon monoxide distributed laser gas analysis and measurement, there are difficult key technical problems. Based on the three-component expansion theory, multi-multiple expander structure with expansion ratio of 4, 5, 6 and 7 is adopted in the absorption chamber to enhance the adaptability of the installation environment of the gas analysis and measurement device. According to the basic theory of aberration, the optimal design of multi-multiple beam expander structure is carried out. By using image quality evaluation method, the difference of image quality under different magnifications is analyzed. The results show that the optical quality of the optical system with the expanded beam structure is the best when the expansion ratio is 5-7.

  4. RNA helicase A is not required for RISC activity.

    Science.gov (United States)

    Liang, Xue-Hai; Crooke, Stanley T

    2013-10-01

    It has been shown that siRNAs can compete with each other or with endogenous miRNAs for RISC components. This competition may complicate the interpretations of phenotypes observed through siRNA-mediated knockdown of genes, especially those genes implicated in the RISC pathway. In this study, we re-examined the function of RNA helicase A (RHA), which has been previously proposed to function in RISC loading based on siRNA-mediated knockdown studies. Here we show that reduced RISC activity or loading of siRNAs was observed only in cells depleted of RHA using siRNA, but not using RNaseH-dependent antisense oligonucleotides (ASOs), suggesting that the impaired RISC function stems from the competition between pre-existing and newly transfected siRNAs, but not from reduction of the RHA protein. This view is further supported by the findings that cells depleted of a control protein, NCL1, using siRNA, but not ASO, exhibited similar defects on the loading and activity of a subsequently transfected siRNA. Transfection of RHA or NCL1 siRNAs, but not ASOs, reduced the levels of endogenous miRNAs, suggesting a competition mechanism. As a positive control, we showed that reduction of MOV10 by either siRNA or ASO decreased siRNA activity, confirming its role in RISC function. Together, our results indicate that RHA is not required for RISC activity or loading, and suggest that proper controls are required when using siRNAs to functionalize genes to avoid competition effects. © 2013. Published by Elsevier B.V. All rights reserved.

  5. Moral motivation based on multiple developmental structures: an exploration of cognitive and emotional dynamics.

    Science.gov (United States)

    Kaplan, Ulas; Tivnan, Terrence

    2014-01-01

    Intrapersonal variability and multiplicity in the complexity of moral motivation were examined from Dynamic Systems and Self-Determination Theory perspectives. L. Kohlberg's (1969) stages of moral development are reconceptualized as soft-assembled and dynamically transformable process structures of motivation that may operate simultaneously within person in different degrees. Moral motivation is conceptualized as the real-time process of self-organization of cognitive and emotional dynamics out of which moral judgment and action emerge. A detailed inquiry into intrapersonal variation in moral motivation is carried out based on the differential operation of multiple motivational structures. A total of 74 high school students and 97 college students participated in the study by completing a new questionnaire, involving 3 different hypothetical moral judgments. As hypothesized, findings revealed significant multiplicity in the within-person operation of developmental stage structures, and intrapersonal variability in the degrees to which stages were used. Developmental patterns were found in terms of different distributions of multiple stages between high school and college samples, as well as the association between age and overall motivation scores. Differential relations of specific emotions to moral motivation revealed and confirmed the value of differentiating multiple emotions. Implications of the present theoretical perspective and the findings for understanding the complexity of moral judgment and motivation are discussed.

  6. Cooperation of DNA-PKcs and WRN helicase in the maintenance of telomeric D-loops

    DEFF Research Database (Denmark)

    Kusumoto-Matsuo, Rika; Opresko, Patricia L; Ramsden, Dale

    2010-01-01

    Werner syndrome is an inherited human progeriod syndrome caused by mutations in the gene encoding the Werner Syndrome protein, WRN. It has both 3'-5' DNA helicase and exonuclease activities, and is suggested to have roles in many aspects of DNA metabolism, including DNA repair and telomere...... D-loop model substrate. In addition, the length of telomeric G-tails decreases in DNA-PKcs knockdown cells, and this phenotype is reversed by overexpression of WRN helicase. These results suggest that WRN and DNA-PKcs may cooperatively prevent G-tail shortening in vivo....

  7. Temperature Histories of Structural Steel Laser and Hybrid Laser-GMA Welds Calculated Using Multiple Constraints

    Science.gov (United States)

    2015-12-10

    Laboratory (Ret.), private communication. 33. S. Kou, Welding Metallurgy , 2nd Ed., John Wiley & Sons, Inc., 2003. DOI: 10.1002/0471434027. 34. J. K...Naval Research Laboratory Washington, DC 20375-5320 NRL/MR/6390--15-9665 Temperature Histories of Structural Steel Laser and Hybrid Laser-GMA Welds ...NUMBER OF PAGES 17. LIMITATION OF ABSTRACT Temperature Histories of Structural Steel Laser and Hybrid Laser-GMA Welds Calculated Using Multiple

  8. Automatic differentiation for design sensitivity analysis of structural systems using multiple processors

    Science.gov (United States)

    Nguyen, Duc T.; Storaasli, Olaf O.; Qin, Jiangning; Qamar, Ramzi

    1994-01-01

    An automatic differentiation tool (ADIFOR) is incorporated into a finite element based structural analysis program for shape and non-shape design sensitivity analysis of structural systems. The entire analysis and sensitivity procedures are parallelized and vectorized for high performance computation. Small scale examples to verify the accuracy of the proposed program and a medium scale example to demonstrate the parallel vector performance on multiple CRAY C90 processors are included.

  9. Should researchers use single indicators, best indicators, or multiple indicators in structural equation models?

    Directory of Open Access Journals (Sweden)

    Hayduk Leslie A

    2012-10-01

    Full Text Available Abstract Background Structural equation modeling developed as a statistical melding of path analysis and factor analysis that obscured a fundamental tension between a factor preference for multiple indicators and path modeling’s openness to fewer indicators. Discussion Multiple indicators hamper theory by unnecessarily restricting the number of modeled latents. Using the few best indicators – possibly even the single best indicator of each latent – encourages development of theoretically sophisticated models. Additional latent variables permit stronger statistical control of potential confounders, and encourage detailed investigation of mediating causal mechanisms. Summary We recommend the use of the few best indicators. One or two indicators are often sufficient, but three indicators may occasionally be helpful. More than three indicators are rarely warranted because additional redundant indicators provide less research benefit than single indicators of additional latent variables. Scales created from multiple indicators can introduce additional problems, and are prone to being less desirable than either single or multiple indicators.

  10. Children's representations of multiple family relationships: organizational structure and development in early childhood.

    Science.gov (United States)

    Schermerhorn, Alice C; Cummings, E Mark; Davies, Patrick T

    2008-02-01

    The authors examine mutual family influence processes at the level of children's representations of multiple family relationships, as well as the structure of those representations. From a community sample with 3 waves, each spaced 1 year apart, kindergarten-age children (105 boys and 127 girls) completed a story-stem completion task, tapping representations of multiple family relationships. Structural equation modeling with autoregressive controls indicated that representational processes involving different family relationships were interrelated over time, including links between children's representations of marital conflict and reactions to conflict, between representations of security about marital conflict and parent-child relationships, and between representations of security in father-child and mother-child relationships. Mixed support was found for notions of increasing stability in representations during this developmental period. Results are discussed in terms of notions of transactional family dynamics, including family-wide perspectives on mutual influence processes attributable to multiple family relationships.

  11. Consequences the extensive use of multiple-choice questions might have on student's reasoning structure

    OpenAIRE

    Raduta, C. M.

    2013-01-01

    Learning physics is a context dependent process. I consider a broader interdisciplinary problem of where differences in understanding and reasoning arise. I suggest the long run effects a multiple choice based learning system as well as society cultural habits and rules might have on student reasoning structure.

  12. Electrical and optical properties of multiple quantum well structures and their applications to infrared detectors

    International Nuclear Information System (INIS)

    Helgesen, P.

    1992-04-01

    In this work the author investigate the subband nature of multiple quantum well structures by photoconductance spectroscopy, optical absorption measurements and tunneling experiments. Both interband and intraband transitions have been studied. The work is aimed at making an infrared detector using wide band gap semiconductors. 14 refs

  13. Evidence for multiple polytypes of semiconducting boron carbide (C2B10) from electronic structure

    International Nuclear Information System (INIS)

    Lunca-Popa, Petru; Brand, J I; Balaz, Snjezana; Rosa, Luis G; Boag, N M; Bai Mengjun; Robertson, B W; Dowben, P A

    2005-01-01

    Boron carbides fabricated via plasma enhanced chemical vapour deposition from different isomeric source compounds with the same C 2 B 10 H 12 closo-icosahedral structure result in materials with very different direct (optical) band gaps. This provides compelling evidence for the existence of multiple polytypes of C 2 B 10 boron carbide and is consistent with electron diffraction results

  14. Testing Mediation Using Multiple Regression and Structural Equation Modeling Analyses in Secondary Data

    Science.gov (United States)

    Li, Spencer D.

    2011-01-01

    Mediation analysis in child and adolescent development research is possible using large secondary data sets. This article provides an overview of two statistical methods commonly used to test mediated effects in secondary analysis: multiple regression and structural equation modeling (SEM). Two empirical studies are presented to illustrate the…

  15. Fault diagnosis of sensor networked structures with multiple faults using a virtual beam based approach

    Science.gov (United States)

    Wang, H.; Jing, X. J.

    2017-07-01

    This paper presents a virtual beam based approach suitable for conducting diagnosis of multiple faults in complex structures with limited prior knowledge of the faults involved. The "virtual beam", a recently-proposed concept for fault detection in complex structures, is applied, which consists of a chain of sensors representing a vibration energy transmission path embedded in the complex structure. Statistical tests and adaptive threshold are particularly adopted for fault detection due to limited prior knowledge of normal operational conditions and fault conditions. To isolate the multiple faults within a specific structure or substructure of a more complex one, a 'biased running' strategy is developed and embedded within the bacterial-based optimization method to construct effective virtual beams and thus to improve the accuracy of localization. The proposed method is easy and efficient to implement for multiple fault localization with limited prior knowledge of normal conditions and faults. With extensive experimental results, it is validated that the proposed method can localize both single fault and multiple faults more effectively than the classical trust index subtract on negative add on positive (TI-SNAP) method.

  16. Assessment of Dengue virus helicase and methyltransferase as targets for fragment-based drug discovery.

    Science.gov (United States)

    Coutard, Bruno; Decroly, Etienne; Li, Changqing; Sharff, Andrew; Lescar, Julien; Bricogne, Gérard; Barral, Karine

    2014-06-01

    Seasonal and pandemic flaviviruses continue to be leading global health concerns. With the view to help drug discovery against Dengue virus (DENV), a fragment-based experimental approach was applied to identify small molecule ligands targeting two main components of the flavivirus replication complex: the NS3 helicase (Hel) and the NS5 mRNA methyltransferase (MTase) domains. A library of 500 drug-like fragments was first screened by thermal-shift assay (TSA) leading to the identification of 36 and 32 fragment hits binding Hel and MTase from DENV, respectively. In a second stage, we set up a fragment-based X-ray crystallographic screening (FBS-X) in order to provide both validated fragment hits and structural binding information. No fragment hit was confirmed for DENV Hel. In contrast, a total of seven fragments were identified as DENV MTase binders and structures of MTase-fragment hit complexes were solved at resolution at least 2.0Å or better. All fragment hits identified contain either a five- or six-membered aromatic ring or both, and three novel binding sites were located on the MTase. To further characterize the fragment hits identified by TSA and FBS-X, we performed enzymatic assays to assess their inhibition effect on the N7- and 2'-O-MTase enzymatic activities: five of these fragment hits inhibit at least one of the two activities with IC50 ranging from 180μM to 9mM. This work validates the FBS-X strategy for identifying new anti-flaviviral hits targeting MTase, while Hel might not be an amenable target for fragment-based drug discovery (FBDD). This approach proved to be a fast and efficient screening method for FBDD target validation and discovery of starting hits for the development of higher affinity molecules that bind to novel allosteric sites. Copyright © 2014 Elsevier B.V. All rights reserved.

  17. Mcm3 replicative helicase mutation impairs neuroblast proliferation and memory in Drosophila.

    Science.gov (United States)

    Blumröder, R; Glunz, A; Dunkelberger, B S; Serway, C N; Berger, C; Mentzel, B; de Belle, J S; Raabe, T

    2016-09-01

    In the developing Drosophila brain, a small number of neural progenitor cells (neuroblasts) generate in a co-ordinated manner a high variety of neuronal cells by integration of temporal, spatial and cell-intrinsic information. In this study, we performed the molecular and phenotypic characterization of a structural brain mutant called small mushroom bodies (smu), which was isolated in a screen for mutants with altered brain structure. Focusing on the mushroom body neuroblast lineages we show that failure of neuroblasts to generate the normal number of mushroom body neurons (Kenyon cells) is the major cause of the smu phenotype. In particular, the premature loss of mushroom body neuroblasts caused a pronounced effect on the number of late-born Kenyon cells. Neuroblasts showed no obvious defects in processes controlling asymmetric cell division, but generated less ganglion mother cells. Cloning of smu uncovered a single amino acid substitution in an evolutionarily conserved protein interaction domain of the Minichromosome maintenance 3 (Mcm3) protein. Mcm3 is part of the multimeric Cdc45/Mcm/GINS (CMG) complex, which functions as a helicase during DNA replication. We propose that at least in the case of mushroom body neuroblasts, timely replication is not only required for continuous proliferation but also for their survival. The absence of Kenyon cells in smu reduced learning and early phases of conditioned olfactory memory. Corresponding to the absence of late-born Kenyon cells projecting to α'/β' and α/β lobes, smu is profoundly defective in later phases of persistent memory. © 2016 John Wiley & Sons Ltd and International Behavioural and Neural Genetics Society.

  18. High-Resolution Printing of 3D Structures Using an Electrohydrodynamic Inkjet with Multiple Functional Inks.

    Science.gov (United States)

    An, Byeong Wan; Kim, Kukjoo; Lee, Heejoo; Kim, So-Yun; Shim, Yulhui; Lee, Dae-Young; Song, Jun Yeob; Park, Jang-Ung

    2015-08-05

    Electrohydrodynamic-inkjet-printed high-resolution complex 3D structures with multiple functional inks are demonstrated. Printed 3D structures can have a variety of fine patterns, such as vertical or helix-shaped pillars and straight or rounded walls, with high aspect ratios (greater than ≈50) and narrow diameters (≈0.7 μm). Furthermore, the formation of freestanding, bridge-like Ag wire structures on plastic substrates suggests substantial potentials as high-precision, flexible 3D interconnects. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Fabrication of InN/InGaN multiple quantum well structures by RF-MBE

    Energy Technology Data Exchange (ETDEWEB)

    Kurouchi, M.; Muto, D.; Takado, S.; Araki, T.; Nanishi, Y. [Department of Photonics, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga 525-8577 (Japan); Na, H.; Naoi, H. [Center for Promotion of The 21st Century COE Program, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga 525-8577 (Japan); Miyajima, T. [Optoelectronics Laboratory, Materials Laboratories, Sony Corporation, 4-14-1 Asahi, Atsugi, Kanagawa 243-0014 (Japan)

    2006-06-15

    InN/InGaN multiple quantum well structures have been fabricated on InN templates grown on (0 0 0 1) sapphire substrates by radio-frequency plasma-assisted molecular beam epitaxy. The structures were confirmed by X-ray diffraction, and satellite peaks up to the 3rd order were observed. From InN/InGaN multiple quantum well structures with different well widths, photoluminescence (PL) emission from the well layers was observed at 77 K, and the PL peak energy slightly blueshifted with decreasing the well width. This dependence can be explained by combined effects of quantum size effect, quantum confined Stark effect, and band filling effect. (copyright 2006 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  20. Helicase and Polymerase Move Together Close to the Fork Junction and Copy DNA in One-Nucleotide Steps

    Directory of Open Access Journals (Sweden)

    Manjula Pandey

    2014-03-01

    Full Text Available By simultaneously measuring DNA synthesis and dNTP hydrolysis, we show that T7 DNA polymerase and T7 gp4 helicase move in sync during leading-strand synthesis, taking one-nucleotide steps and hydrolyzing one dNTP per base-pair unwound/copied. The cooperative catalysis enables the helicase and polymerase to move at a uniformly fast rate without guanine:cytosine (GC dependency or idling with futile NTP hydrolysis. We show that the helicase and polymerase are located close to the replication fork junction. This architecture enables the polymerase to use its strand-displacement synthesis to increase the unwinding rate, whereas the helicase aids this process by translocating along single-stranded DNA and trapping the unwound bases. Thus, in contrast to the helicase-only unwinding model, our results suggest a model in which the helicase and polymerase are moving in one-nucleotide steps, DNA synthesis drives fork unwinding, and a role of the helicase is to trap the unwound bases and prevent DNA reannealing.

  1. RNA helicase HEL-1 promotes longevity by specifically activating DAF-16/FOXO transcription factor signaling in Caenorhabditis elegans

    Science.gov (United States)

    Seo, Mihwa; Seo, Keunhee; Hwang, Wooseon; Koo, Hee Jung; Hahm, Jeong-Hoon; Yang, Jae-Seong; Han, Seong Kyu; Hwang, Daehee; Kim, Sanguk; Jang, Sung Key; Lee, Yoontae; Nam, Hong Gil; Lee, Seung-Jae V.

    2015-01-01

    The homeostatic maintenance of the genomic DNA is crucial for regulating aging processes. However, the role of RNA homeostasis in aging processes remains unknown. RNA helicases are a large family of enzymes that regulate the biogenesis and homeostasis of RNA. However, the functional significance of RNA helicases in aging has not been explored. Here, we report that a large fraction of RNA helicases regulate the lifespan of Caenorhabditis elegans. In particular, we show that a DEAD-box RNA helicase, helicase 1 (HEL-1), promotes longevity by specifically activating the DAF-16/forkhead box O (FOXO) transcription factor signaling pathway. We find that HEL-1 is required for the longevity conferred by reduced insulin/insulin-like growth factor 1 (IGF-1) signaling (IIS) and is sufficient for extending lifespan. We further show that the expression of HEL-1 in the intestine and neurons contributes to longevity. HEL-1 enhances the induction of a large fraction of DAF-16 target genes. Thus, the RNA helicase HEL-1 appears to promote longevity in response to decreased IIS as a transcription coregulator of DAF-16. Because HEL-1 and IIS are evolutionarily well conserved, a similar mechanism for longevity regulation via an RNA helicase-dependent regulation of FOXO signaling may operate in mammals, including humans. PMID:26195740

  2. The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences

    DEFF Research Database (Denmark)

    Seemann, Ernst Stefan; Menzel, Karl Peter; Backofen, Rolf

    2011-01-01

    gene. We present web servers to analyze multiple RNA sequences for common RNA structure and for RNA interaction sites. The web servers are based on the recent PET (Probabilistic Evolutionary and Thermodynamic) models PETfold and PETcofold, but add user friendly features ranging from a graphical layer...... to interactive usage of the predictors. Additionally, the web servers provide direct access to annotated RNA alignments, such as the Rfam 10.0 database and multiple alignments of 16 vertebrate genomes with human. The web servers are freely available at: http://rth.dk/resources/petfold/...

  3. Broadband Structural Dynamics: Understanding the Impulse-Response of Structures Across Multiple Length and Time Scales

    Science.gov (United States)

    2010-08-18

    Spectral domain response calculated • Time domain response obtained through inverse transform Approach 4: WASABI Wavelet Analysis of Structural Anomalies...differences at unity scale! Time Function Transform Apply Spectral Domain Transfer Function Time Function Inverse Transform Transform Transform  mtP

  4. A Small Molecule Inhibitor of the BLM Helicase Modulates Chromosome Stability in Human Cells

    DEFF Research Database (Denmark)

    Nguyen, Giang Huong; Dexheimer, Thomas S; Rosenthal, Andrew S

    2013-01-01

    The Bloom's syndrome protein, BLM, is a member of the conserved RecQ helicase family. Although cell lines lacking BLM exist, these exhibit progressive genomic instability that makes distinguishing primary from secondary effects of BLM loss problematic. In order to be able to acutely disable BLM f...

  5. BLM helicase measures DNA unwound before switching strands and hRPA promotes unwinding reinitiation

    Czech Academy of Sciences Publication Activity Database

    Yodh, J.G.; Stevens, B.C.; Kanagaraj, R.; Janščák, Pavel; Ha, T.

    2009-01-01

    Roč. 28, č. 4 (2009), s. 405-416 ISSN 0261-4189 Institutional research plan: CEZ:AV0Z50520514 Keywords : Bloom syndrome * FRET * helicase * hRPA * single molecule Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 8.993, year: 2009

  6. BLM helicase suppresses recombination at G-quadruplex motifs in transcribed genes

    NARCIS (Netherlands)

    van Wietmarschen, Niek; Merzouk, Sarra; Halsema, Nancy; Spierings, Diana C J; Guryev, Victor; Lansdorp, Peter M

    2018-01-01

    Bloom syndrome is a cancer predisposition disorder caused by mutations in the BLM helicase gene. Cells from persons with Bloom syndrome exhibit striking genomic instability characterized by excessive sister chromatid exchange events (SCEs). We applied single-cell DNA template strand sequencing

  7. Human RecQL4 helicase plays critical roles in prostate carcinogenesis

    DEFF Research Database (Denmark)

    Su, Yanrong; Meador, Jarah A; Calaf, Gloria M

    2010-01-01

    Prostate cancer is the second leading cause of cancer-associated deaths among men in the western countries. Here, we report that human RecQL4 helicase, which is implicated in the pathogenesis of a subset of cancer-prone Rothmund-Thomson syndrome, is highly elevated in metastatic prostate cancer c...

  8. The Helicase Activity of Hyperthermophilic Archaeal MCM is Enhanced at High Temperatures by Lysine Methylation.

    Science.gov (United States)

    Xia, Yisui; Niu, Yanling; Cui, Jiamin; Fu, Yang; Chen, Xiaojiang S; Lou, Huiqiang; Cao, Qinhong

    2015-01-01

    Lysine methylation and methyltransferases are widespread in the third domain of life, archaea. Nevertheless, the effects of methylation on archaeal proteins wait to be defined. Here, we report that recombinant sisMCM, an archaeal homolog of Mcm2-7 eukaryotic replicative helicase, is methylated by aKMT4 in vitro. Mono-methylation of these lysine residues occurs coincidently in the endogenous sisMCM protein purified from the hyperthermophilic Sulfolobus islandicus cells as indicated by mass spectra. The helicase activity of mini-chromosome maintenance (MCM) is stimulated by methylation, particularly at temperatures over 70°C. The methylated MCM shows optimal DNA unwinding activity after heat-treatment between 76 and 82°C, which correlates well with the typical growth temperatures of hyperthermophilic Sulfolobus. After methylation, the half life of MCM helicase is dramatically extended at 80°C. The methylated sites are located on the accessible protein surface, which might modulate the intra- and inter- molecular interactions through changing the hydrophobicity and surface charge. Furthermore, the methylation-mimic mutants of MCM show heat resistance helicase activity comparable to the methylated MCM. These data provide the biochemical evidence that posttranslational modifications such as methylation may enhance kinetic stability of proteins under the elevated growth temperatures of hyperthermophilic archaea.

  9. MRE11 complex links RECQ5 helicase to sites of DNA damage

    Czech Academy of Sciences Publication Activity Database

    Zheng, L.; Kanagaraj, R.; Mihaljevic, B.; Schwendener, S.; Sartori, A.A.; Gerrits, B.; Shevelev, Igor; Janščák, Pavel

    2009-01-01

    Roč. 37, č. 8 (2009), s. 2645-2657 ISSN 0305-1048 R&D Projects: GA ČR GA204/09/0565 Institutional research plan: CEZ:AV0Z50520514 Keywords : homologous recombination, * RECQ5 helicase * MRE11 * DNA repair Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 7.479, year: 2009

  10. TFIIH with inactive XPD helicase functions in transcription initiation but is defective in DNA repair

    NARCIS (Netherlands)

    G.S. Winkler (Sebastiaan); U. Fiedler; W. Vermeulen (Wim); F. Coin (Frédéric); R.D. Wood (Richard); H.T.M. Timmers (Marc); G. Weeda (Geert); J.H.J. Hoeijmakers (Jan); S.J. Araú jo; J-M. Egly (Jean-Marc)

    2000-01-01

    textabstractTFIIH is a multisubunit protein complex involved in RNA polymerase II transcription and nucleotide excision repair, which removes a wide variety of DNA lesions including UV-induced photoproducts. Mutations in the DNA-dependent ATPase/helicase subunits of TFIIH, XPB and

  11. FBH1 Helicase Disrupts RAD51 Filaments in Vitro and Modulates Homologous Recombination in Mammalian Cells

    Czech Academy of Sciences Publication Activity Database

    Šimandlová, Jitka; Zagelbaum, J.; Payne, M.J.; Chu, W.K.; Shevelev, Igor; Hanada, K.; Chatterjee, S.; Reid, D.A.; Liu, Y.; Janščák, Pavel; Rothenberg, E.; Hickson, I.D.

    2013-01-01

    Roč. 288, č. 47 (2013), s. 34168-34180 ISSN 0021-9258 R&D Projects: GA ČR GAP305/10/0281 Institutional support: RVO:68378050 Keywords : DNA damage * DNA helicase * DNA recombination * DNA repair * DNA replication Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.600, year: 2013

  12. Interaction between the helicases genetically linked to Fanconi anemia group J and Bloom's syndrome

    DEFF Research Database (Denmark)

    Suhasini, Avvaru N; Rawtani, Nina A; Wu, Yuliang

    2011-01-01

    Bloom's syndrome (BS) and Fanconi anemia (FA) are autosomal recessive disorders characterized by cancer and chromosomal instability. BS and FA group J arise from mutations in the BLM and FANCJ genes, respectively, which encode DNA helicases. In this work, FANCJ and BLM were found to interact...

  13. MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing

    DEFF Research Database (Denmark)

    Lindgreen, Stinus; Gardner, Paul P; Krogh, Anders

    2007-01-01

    function that considers sequence conservation, covariation and basepairing probabilities. The results show that the method is very competitive to similar programs available today, both in terms of accuracy and computational efficiency. AVAILABILITY: Source code available from http://mastr.binf.ku.dk/......MOTIVATION: As more non-coding RNAs are discovered, the importance of methods for RNA analysis increases. Since the structure of ncRNA is intimately tied to the function of the molecule, programs for RNA structure prediction are necessary tools in this growing field of research. Furthermore......, it is known that RNA structure is often evolutionarily more conserved than sequence. However, few existing methods are capable of simultaneously considering multiple sequence alignment and structure prediction. RESULT: We present a novel solution to the problem of simultaneous structure prediction...

  14. Protein structure modeling for CASP10 by multiple layers of global optimization.

    Science.gov (United States)

    Joo, Keehyoung; Lee, Juyong; Sim, Sangjin; Lee, Sun Young; Lee, Kiho; Heo, Seungryong; Lee, In-Ho; Lee, Sung Jong; Lee, Jooyoung

    2014-02-01

    In the template-based modeling (TBM) category of CASP10 experiment, we introduced a new protocol called protein modeling system (PMS) to generate accurate protein structures in terms of side-chains as well as backbone trace. In the new protocol, a global optimization algorithm, called conformational space annealing (CSA), is applied to the three layers of TBM procedure: multiple sequence-structure alignment, 3D chain building, and side-chain re-modeling. For 3D chain building, we developed a new energy function which includes new distance restraint terms of Lorentzian type (derived from multiple templates), and new energy terms that combine (physical) energy terms such as dynamic fragment assembly (DFA) energy, DFIRE statistical potential energy, hydrogen bonding term, etc. These physical energy terms are expected to guide the structure modeling especially for loop regions where no template structures are available. In addition, we developed a new quality assessment method based on random forest machine learning algorithm to screen templates, multiple alignments, and final models. For TBM targets of CASP10, we find that, due to the combination of three stages of CSA global optimizations and quality assessment, the modeling accuracy of PMS improves at each additional stage of the protocol. It is especially noteworthy that the side-chains of the final PMS models are far more accurate than the models in the intermediate steps. Copyright © 2013 Wiley Periodicals, Inc.

  15. Base Isolation for Seismic Retrofitting of a Multiple Building Structure: Design, Construction, and Assessment

    Directory of Open Access Journals (Sweden)

    Massimiliano Ferraioli

    2017-01-01

    Full Text Available The paper deals with the seismic retrofit of a multiple building structure belonging to the Hospital Centre of Avellino (Italy. At first, the paper presents the preliminary investigations, the in situ measurements and laboratory tests, and the seismic assessment of the existing fixed-base structures. Having studied different strategies, base isolation proved to be the more appropriate, also for the possibility offered by the geometry of the building to easily create an isolation interface at the ground level. The paper presents the design project, the construction process, and the details of the isolation intervention. Some specific issues of base isolation for seismic retrofitting of multiple building structures were lightened. Finally, the seismic assessment of the base-isolated building was carried out. The seismic response was evaluated through nonlinear time-history analysis, using the well-known Bouc-Wen model as the constitutive law of the isolation bearings. For reliable dynamic analyses, a suite of natural accelerograms compatible with acceleration spectra of Italian Code was first selected and then applied along both horizontal directions. The results were finally used to address some of the critical issues of the seismic response of the base-isolated multiple building structure: accidental torsional effects and potential poundings during strong earthquakes.

  16. Enzyme catalysis captured using multiple structures from one crystal at varying temperatures

    Directory of Open Access Journals (Sweden)

    Sam Horrell

    2018-05-01

    Full Text Available High-resolution crystal structures of enzymes in relevant redox states have transformed our understanding of enzyme catalysis. Recent developments have demonstrated that X-rays can be used, via the generation of solvated electrons, to drive reactions in crystals at cryogenic temperatures (100 K to generate `structural movies' of enzyme reactions. However, a serious limitation at these temperatures is that protein conformational motion can be significantly supressed. Here, the recently developed MSOX (multiple serial structures from one crystal approach has been applied to nitrite-bound copper nitrite reductase at room temperature and at 190 K, close to the glass transition. During both series of multiple structures, nitrite was initially observed in a `top-hat' geometry, which was rapidly transformed to a `side-on' configuration before conversion to side-on NO, followed by dissociation of NO and substitution by water to reform the resting state. Density functional theory calculations indicate that the top-hat orientation corresponds to the oxidized type 2 copper site, while the side-on orientation is consistent with the reduced state. It is demonstrated that substrate-to-product conversion within the crystal occurs at a lower radiation dose at 190 K, allowing more of the enzyme catalytic cycle to be captured at high resolution than in the previous 100 K experiment. At room temperature the reaction was very rapid, but it remained possible to generate and characterize several structural states. These experiments open up the possibility of obtaining MSOX structural movies at multiple temperatures (MSOX-VT, providing an unparallelled level of structural information during catalysis for redox enzymes.

  17. Archaeal orthologs of Cdc45 and GINS form a stable complex that stimulates the helicase activity of MCM.

    Science.gov (United States)

    Xu, Yuli; Gristwood, Tamzin; Hodgson, Ben; Trinidad, Jonathan C; Albers, Sonja-Verena; Bell, Stephen D

    2016-11-22

    The regulated recruitment of Cdc45 and GINS is key to activating the eukaryotic MCM(2-7) replicative helicase. We demonstrate that the homohexameric archaeal MCM helicase associates with orthologs of GINS and Cdc45 in vivo and in vitro. Association of these factors with MCM robustly stimulates the MCM helicase activity. In contrast to the situation in eukaryotes, archaeal Cdc45 and GINS form an extremely stable complex before binding MCM. Further, the archaeal GINS•Cdc45 complex contains two copies of Cdc45. Our analyses give insight into the function and evolution of the conserved core of the archaeal/eukaryotic replisome.

  18. The roles of the Saccharomyces cerevisiae RecQ helicase SGS1 in meiotic genome surveillance.

    Directory of Open Access Journals (Sweden)

    Amit Dipak Amin

    2010-11-01

    Full Text Available The Saccharomyces cerevisiae RecQ helicase Sgs1 is essential for mitotic and meiotic genome stability. The stage at which Sgs1 acts during meiosis is subject to debate. Cytological experiments showed that a deletion of SGS1 leads to an increase in synapsis initiation complexes and axial associations leading to the proposal that it has an early role in unwinding surplus strand invasion events. Physical studies of recombination intermediates implicate it in the dissolution of double Holliday junctions between sister chromatids.In this work, we observed an increase in meiotic recombination between diverged sequences (homeologous recombination and an increase in unequal sister chromatid events when SGS1 is deleted. The first of these observations is most consistent with an early role of Sgs1 in unwinding inappropriate strand invasion events while the second is consistent with unwinding or dissolution of recombination intermediates in an Mlh1- and Top3-dependent manner. We also provide data that suggest that Sgs1 is involved in the rejection of 'second strand capture' when sequence divergence is present. Finally, we have identified a novel class of tetrads where non-sister spores (pairs of spores where each contains a centromere marker from a different parent are inviable. We propose a model for this unusual pattern of viability based on the inability of sgs1 mutants to untangle intertwined chromosomes. Our data suggest that this role of Sgs1 is not dependent on its interaction with Top3. We propose that in the absence of SGS1 chromosomes may sometimes remain entangled at the end of pre-meiotic replication. This, combined with reciprocal crossing over, could lead to physical destruction of the recombined and entangled chromosomes. We hypothesise that Sgs1, acting in concert with the topoisomerase Top2, resolves these structures.This work provides evidence that Sgs1 interacts with various partner proteins to maintain genome stability throughout

  19. Multiple linear combination (MLC) regression tests for common variants adapted to linkage disequilibrium structure.

    Science.gov (United States)

    Yoo, Yun Joo; Sun, Lei; Poirier, Julia G; Paterson, Andrew D; Bull, Shelley B

    2017-02-01

    By jointly analyzing multiple variants within a gene, instead of one at a time, gene-based multiple regression can improve power, robustness, and interpretation in genetic association analysis. We investigate multiple linear combination (MLC) test statistics for analysis of common variants under realistic trait models with linkage disequilibrium (LD) based on HapMap Asian haplotypes. MLC is a directional test that exploits LD structure in a gene to construct clusters of closely correlated variants recoded such that the majority of pairwise correlations are positive. It combines variant effects within the same cluster linearly, and aggregates cluster-specific effects in a quadratic sum of squares and cross-products, producing a test statistic with reduced degrees of freedom (df) equal to the number of clusters. By simulation studies of 1000 genes from across the genome, we demonstrate that MLC is a well-powered and robust choice among existing methods across a broad range of gene structures. Compared to minimum P-value, variance-component, and principal-component methods, the mean power of MLC is never much lower than that of other methods, and can be higher, particularly with multiple causal variants. Moreover, the variation in gene-specific MLC test size and power across 1000 genes is less than that of other methods, suggesting it is a complementary approach for discovery in genome-wide analysis. The cluster construction of the MLC test statistics helps reveal within-gene LD structure, allowing interpretation of clustered variants as haplotypic effects, while multiple regression helps to distinguish direct and indirect associations. © 2016 The Authors Genetic Epidemiology Published by Wiley Periodicals, Inc.

  20. Enzymatic activities and DNA substrate specificity of Mycobacterium tuberculosis DNA helicase XPB.

    Science.gov (United States)

    Balasingham, Seetha V; Zegeye, Ephrem Debebe; Homberset, Håvard; Rossi, Marie L; Laerdahl, Jon K; Bohr, Vilhelm A; Tønjum, Tone

    2012-01-01

    XPB, also known as ERCC3 and RAD25, is a 3' → 5' DNA repair helicase belonging to the superfamily 2 of helicases. XPB is an essential core subunit of the eukaryotic basal transcription factor complex TFIIH. It has two well-established functions: in the context of damaged DNA, XPB facilitates nucleotide excision repair by unwinding double stranded DNA (dsDNA) surrounding a DNA lesion; while in the context of actively transcribing genes, XPB facilitates initiation of RNA polymerase II transcription at gene promoters. Human and other eukaryotic XPB homologs are relatively well characterized compared to conserved homologs found in mycobacteria and archaea. However, more insight into the function of bacterial helicases is central to understanding the mechanism of DNA metabolism and pathogenesis in general. Here, we characterized Mycobacterium tuberculosis XPB (Mtb XPB), a 3'→5' DNA helicase with DNA-dependent ATPase activity. Mtb XPB efficiently catalyzed DNA unwinding in the presence of significant excess of enzyme. The unwinding activity was fueled by ATP or dATP in the presence of Mg(2+)/Mn(2+). Consistent with the 3'→5' polarity of this bacterial XPB helicase, the enzyme required a DNA substrate with a 3' overhang of 15 nucleotides or more. Although Mtb XPB efficiently unwound DNA model substrates with a 3' DNA tail, it was not active on substrates containing a 3' RNA tail. We also found that Mtb XPB efficiently catalyzed ATP-independent annealing of complementary DNA strands. These observations significantly enhance our understanding of the biological roles of Mtb XPB.

  1. Enzymatic activities and DNA substrate specificity of Mycobacterium tuberculosis DNA helicase XPB.

    Directory of Open Access Journals (Sweden)

    Seetha V Balasingham

    Full Text Available XPB, also known as ERCC3 and RAD25, is a 3' → 5' DNA repair helicase belonging to the superfamily 2 of helicases. XPB is an essential core subunit of the eukaryotic basal transcription factor complex TFIIH. It has two well-established functions: in the context of damaged DNA, XPB facilitates nucleotide excision repair by unwinding double stranded DNA (dsDNA surrounding a DNA lesion; while in the context of actively transcribing genes, XPB facilitates initiation of RNA polymerase II transcription at gene promoters. Human and other eukaryotic XPB homologs are relatively well characterized compared to conserved homologs found in mycobacteria and archaea. However, more insight into the function of bacterial helicases is central to understanding the mechanism of DNA metabolism and pathogenesis in general. Here, we characterized Mycobacterium tuberculosis XPB (Mtb XPB, a 3'→5' DNA helicase with DNA-dependent ATPase activity. Mtb XPB efficiently catalyzed DNA unwinding in the presence of significant excess of enzyme. The unwinding activity was fueled by ATP or dATP in the presence of Mg(2+/Mn(2+. Consistent with the 3'→5' polarity of this bacterial XPB helicase, the enzyme required a DNA substrate with a 3' overhang of 15 nucleotides or more. Although Mtb XPB efficiently unwound DNA model substrates with a 3' DNA tail, it was not active on substrates containing a 3' RNA tail. We also found that Mtb XPB efficiently catalyzed ATP-independent annealing of complementary DNA strands. These observations significantly enhance our understanding of the biological roles of Mtb XPB.

  2. A scheme of hidden-structure attribute-based encryption with multiple authorities

    Science.gov (United States)

    Ling, J.; Weng, A. X.

    2018-05-01

    In the most of the CP-ABE schemes with hidden access structure, both all the user attributes and the key generation are managed by only one authority. The key generation efficiency will decrease as the number of user increases, and the data will encounter security issues as the only authority is attacked. We proposed a scheme of hidden-structure attribute-based encryption with multiple authorities, which introduces multiple semi-trusted attribute authorities, avoiding the threat even though one or more authorities are attacked. We also realized user revocation by managing a revocation list. Based on DBDH assumption, we proved that our scheme is of IND-CMA security. The analysis shows that our scheme improves the key generation efficiency.

  3. Multiple trapping on a comb structure as a model of electron transport in disordered nanostructured semiconductors

    International Nuclear Information System (INIS)

    Sibatov, R. T.; Morozova, E. V.

    2015-01-01

    A model of dispersive transport in disordered nanostructured semiconductors has been proposed taking into account the percolation structure of a sample and joint action of several mechanisms. Topological and energy disorders have been simultaneously taken into account within the multiple trapping model on a comb structure modeling the percolation character of trajectories. The joint action of several mechanisms has been described within random walks with a mixture of waiting time distributions. Integral transport equations with fractional derivatives have been obtained for an arbitrary density of localized states. The kinetics of the transient current has been calculated within the proposed new model in order to analyze time-of-flight experiments for nanostructured semiconductors

  4. Simultaneous Structural Variation Discovery in Multiple Paired-End Sequenced Genomes

    Science.gov (United States)

    Hormozdiari, Fereydoun; Hajirasouliha, Iman; McPherson, Andrew; Eichler, Evan E.; Sahinalp, S. Cenk

    Next generation sequencing technologies have been decreasing the costs and increasing the world-wide capacity for sequence production at an unprecedented rate, making the initiation of large scale projects aiming to sequence almost 2000 genomes [1]. Structural variation detection promises to be one of the key diagnostic tools for cancer and other diseases with genomic origin. In this paper, we study the problem of detecting structural variation events in two or more sequenced genomes through high throughput sequencing . We propose to move from the current model of (1) detecting genomic variations in single next generation sequenced (NGS) donor genomes independently, and (2) checking whether two or more donor genomes indeed agree or disagree on the variations (in this paper we name this framework Independent Structural Variation Discovery and Merging - ISV&M), to a new model in which we detect structural variation events among multiple genomes simultaneously.

  5. Cyclic saturation dislocation structures of multiple-slip-oriented copper single crystals

    International Nuclear Information System (INIS)

    Li, X.W.; Chinese Academy of Sciences, Shenyang; Umakoshi, Y.; Li, S.X.; Wang, Z.G.

    2001-01-01

    The dislocation structures of [011] and [ anti 111] multiple-slip-oriented Cu single crystals cyclically saturated at constant plastic strain amplitudes were investigated through transmission electron microscopy. The results obtained on [001] multiple-slip-oriented Cu single crystals were also included for summarization. Unlike the case for single-slip-oriented Cu single crystals, the crystallographic orientation has a strong effect on the saturation dislocation structure in these three multiple-slip-oriented crystals. For the [011] crystal, different dislocation patterns such as veins, PSB walls, labyrinths and PSB ladders were observed. The formation of PSB ladders is believed to be a major reason for the existence of a plateau region in the cyclic stress-strain (CSS) curve for the [011] crystal. The cyclic saturation dislocation structure of a [ anti 111] crystal cycled at a low applied strain amplitude γ pl of 2.0 x 10 -4 was found to consist of irregular cells, which would develop into a more regular arrangement (e. g. PSB ladder-like) and the scale of which tends to decrease with increasing γ pl . Finally, three kinds of representative micro-deformation mode were summarized and termed as labyrinth-mode (or [001]-mode), cell-mode (or [ anti 111]-mode) and PSB ladder-mode (or [011]-mode). (orig.)

  6. Comprehensive Protein Interactome Analysis of a Key RNA Helicase: Detection of Novel Stress Granule Proteins

    Directory of Open Access Journals (Sweden)

    Rebecca Bish

    2015-07-01

    Full Text Available DDX6 (p54/RCK is a human RNA helicase with central roles in mRNA decay and translation repression. To help our understanding of how DDX6 performs these multiple functions, we conducted the first unbiased, large-scale study to map the DDX6-centric protein-protein interactome using immunoprecipitation and mass spectrometry. Using DDX6 as bait, we identify a high-confidence and high-quality set of protein interaction partners which are enriched for functions in RNA metabolism and ribosomal proteins. The screen is highly specific, maximizing the number of true positives, as demonstrated by the validation of 81% (47/58 of the RNA-independent interactors through known functions and interactions. Importantly, we minimize the number of indirect interaction partners through use of a nuclease-based digestion to eliminate RNA. We describe eleven new interactors, including proteins involved in splicing which is an as-yet unknown role for DDX6. We validated and characterized in more detail the interaction of DDX6 with Nuclear fragile X mental retardation-interacting protein 2 (NUFIP2 and with two previously uncharacterized proteins, FAM195A and FAM195B (here referred to as granulin-1 and granulin-2, or GRAN1 and GRAN2. We show that NUFIP2, GRAN1, and GRAN2 are not P-body components, but re-localize to stress granules upon exposure to stress, suggesting a function in translation repression in the cellular stress response. Using a complementary analysis that resolved DDX6’s multiple complex memberships, we further validated these interaction partners and the presence of splicing factors. As DDX6 also interacts with the E3 SUMO ligase TIF1β, we tested for and observed a significant enrichment of sumoylation amongst DDX6’s interaction partners. Our results represent the most comprehensive screen for direct interaction partners of a key regulator of RNA life cycle and localization, highlighting new stress granule components and possible DDX6 functions

  7. Dancing multiplicity states supported by a carboxylated group in dicopper structures bonded to O2

    KAUST Repository

    Poater, Albert

    2013-01-29

    The present study pretends to assign the correct multiplicity state to dinuclear copper complexes when interacting with free molecular oxygen. Recently, the formation of a bridge butterfly μ-η2: η2-peroxo dicopper core structure stabilized by the direct interaction of the counterion, a carboxylate group that allows the double bridge linking both metal-centre atoms, was characterized by crystallography. This system was assigned as a diradical singlet with Ms = 0. However, after new calculations it has turned out to be triplet (Ms = 1) despite the stabilization for this latter multiplicity state is not high. Here, the factors that contribute to make this structure display a multiplicity different with respect to the previously expected diradical singlet are described. In the present theoretical study, the roles of the αSp ligand constraints and the counterion are unravelled. On the other hand, the relative stability between the butterfly μ-η2: η2-peroxo structure and the isomeric bis(μ-oxo) species is also on discussion. Despite the relative stabilities of all these either structural or electronic isomeric species are supposed to depend on the computational method, which is a difficulty to reach a definite conclusion about the nature of the active species, all DFT methods using either pure or not pure DFT functionals here reach the same conclusion, favoring the triplet as the ground state for the butterfly μ-η2: η2-peroxo dicopper core structure, and the bis(μ-oxo) species when removing the benzoate counterion. © Springer-Verlag Berlin Heidelberg 2013.

  8. A developmentally plastic adult mouse kidney cell line spontaneously generates multiple adult kidney structures

    International Nuclear Information System (INIS)

    Webb, Carol F.; Ratliff, Michelle L.; Powell, Rebecca; Wirsig-Wiechmann, Celeste R.; Lakiza, Olga; Obara, Tomoko

    2015-01-01

    Despite exciting new possibilities for regenerative therapy posed by the ability to induce pluripotent stem cells, recapitulation of three-dimensional kidneys for repair or replacement has not been possible. ARID3a-deficient mouse tissues generated multipotent, developmentally plastic cells. Therefore, we assessed the adult mouse ARID3a−/− kidney cell line, KKPS5, which expresses renal progenitor surface markers as an alternative cell source for modeling kidney development. Remarkably, these cells spontaneously developed into multicellular nephron-like structures in vitro, and engrafted into immunocompromised medaka mesonephros, where they formed mouse nephron structures. These data implicate KKPS5 cells as a new model system for studying kidney development. - Highlights: • An ARID3a-deficient mouse kidney cell line expresses multiple progenitor markers. • This cell line spontaneously forms multiple nephron-like structures in vitro. • This cell line formed mouse kidney structures in immunocompromised medaka fish kidneys. • Our data identify a novel model system for studying kidney development

  9. A developmentally plastic adult mouse kidney cell line spontaneously generates multiple adult kidney structures

    Energy Technology Data Exchange (ETDEWEB)

    Webb, Carol F., E-mail: carol-webb@omrf.org [Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK (United States); Immunobiology and Cancer Research, Oklahoma Medical Research Foundation, Oklahoma City, OK (United States); Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK (United States); Ratliff, Michelle L., E-mail: michelle-ratliff@omrf.org [Immunobiology and Cancer Research, Oklahoma Medical Research Foundation, Oklahoma City, OK (United States); Powell, Rebecca, E-mail: rebeccapowell@gmail.com [Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK (United States); Wirsig-Wiechmann, Celeste R., E-mail: celeste-wirsig@ouhsc.edu [Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK (United States); Lakiza, Olga, E-mail: olga-lakiza@ouhsc.edu [Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK (United States); Obara, Tomoko, E-mail: tomoko-obara@ouhsc.edu [Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK (United States)

    2015-08-07

    Despite exciting new possibilities for regenerative therapy posed by the ability to induce pluripotent stem cells, recapitulation of three-dimensional kidneys for repair or replacement has not been possible. ARID3a-deficient mouse tissues generated multipotent, developmentally plastic cells. Therefore, we assessed the adult mouse ARID3a−/− kidney cell line, KKPS5, which expresses renal progenitor surface markers as an alternative cell source for modeling kidney development. Remarkably, these cells spontaneously developed into multicellular nephron-like structures in vitro, and engrafted into immunocompromised medaka mesonephros, where they formed mouse nephron structures. These data implicate KKPS5 cells as a new model system for studying kidney development. - Highlights: • An ARID3a-deficient mouse kidney cell line expresses multiple progenitor markers. • This cell line spontaneously forms multiple nephron-like structures in vitro. • This cell line formed mouse kidney structures in immunocompromised medaka fish kidneys. • Our data identify a novel model system for studying kidney development.

  10. Multiple Memory Structure Bit Reversal Algorithm Based on Recursive Patterns of Bit Reversal Permutation

    Directory of Open Access Journals (Sweden)

    K. K. L. B. Adikaram

    2014-01-01

    Full Text Available With the increasing demand for online/inline data processing efficient Fourier analysis becomes more and more relevant. Due to the fact that the bit reversal process requires considerable processing time of the Fast Fourier Transform (FFT algorithm, it is vital to optimize the bit reversal algorithm (BRA. This paper is to introduce an efficient BRA with multiple memory structures. In 2009, Elster showed the relation between the first and the second halves of the bit reversal permutation (BRP and stated that it may cause serious impact on cache performance of the computer, if implemented. We found exceptions, especially when the said index mapping was implemented with multiple one-dimensional memory structures instead of multidimensional or one-dimensional memory structure. Also we found a new index mapping, even after the recursive splitting of BRP into equal sized slots. The four-array and the four-vector versions of BRA with new index mapping reported 34% and 16% improvement in performance in relation to similar versions of Linear BRA of Elster which uses single one-dimensional memory structure.

  11. Genetic diversity and population structure of Lantana camara in India indicates multiple introductions and gene flow.

    Science.gov (United States)

    Ray, A; Quader, S

    2014-05-01

    Lantana camara is a highly invasive plant, which has spread over 60 countries and island groups of Asia, Africa and Australia. In India, it was introduced in the early nineteenth century, since when it has expanded and gradually established itself in almost every available ecosystem. We investigated the genetic diversity and population structure of this plant in India in order to understand its introduction, subsequent range expansion and gene flow. A total of 179 individuals were sequenced at three chloroplast loci and 218 individuals were genotyped for six nuclear microsatellites. Both chloroplasts (nine haplotypes) and microsatellites (83 alleles) showed high genetic diversity. Besides, each type of marker confirmed the presence of private polymorphism. We uncovered low to medium population structure in both markers, and found a faint signal of isolation by distance with microsatellites. Bayesian clustering analyses revealed multiple divergent genetic clusters. Taken together, these findings (i.e. high genetic diversity with private alleles and multiple genetic clusters) suggest that Lantana was introduced multiple times and gradually underwent spatial expansion with recurrent gene flow. © 2013 German Botanical Society and The Royal Botanical Society of the Netherlands.

  12. Structured diagnostic imaging in patients with multiple trauma; Strukturierte radiologische Diagnostik beim Polytrauma

    Energy Technology Data Exchange (ETDEWEB)

    Linsenmaier, U.; Rieger, J.; Rock, C.; Pfeifer, K.J.; Reiser, M. [Institut fuer Klinische Radiologie, Klinikum der Universitaet Muenchen, Innenstadt (Germany); Kanz, K.G. [Chirurgische Klinik, Klinikum der Universitaet Muenchen, Innenstadt (Germany)

    2002-07-01

    Purpose. Development of a concept for structured diagnostic imaging in patients with multiple trauma.Material and methods. Evaluation of data from a prospective trial with over 2400 documented patients with multiple trauma. All diagnostic and therapeutic steps, primary and secondary death and the 90 days lethality were documented.Structured diagnostic imaging of multiple injured patients requires the integration of an experienced radiologist in an interdisciplinary trauma team consisting of anesthesia, radiology and trauma surgery. Radiology itself deserves standardized concepts for equipment, personnel and logistics to perform diagnostic imaging for a 24-h-coverage with constant quality.Results. This paper describes criteria for initiation of a shock room or emergency room treatment, strategies for documentation and interdisciplinary algorithms for the early clinical care coordinating diagnostic imaging and therapeutic procedures following standardized guidelines. Diagnostic imaging consists of basic diagnosis, radiological ABC-rule, radiological follow-up and structured organ diagnosis using CT. Radiological trauma scoring allows improved quality control of diagnosis and therapy of multiple injured patients.Conclusion. Structured diagnostic imaging of multiple injured patients leads to a standardization of diagnosis and therapy and ensures constant process quality. (orig.) [German] Fragestellung. Entwicklung eines strukturierten Konzeptes zur radiologischen Diagnostik polytraumatisierter Patienten.Methodik. Die Datenevaluation erfolgte auf Basis einer prospektiven interdisziplinaere Polytraumastudie mit ueber 2400 Patienten. Alle diagnostischen und therapeutischen Schritte werden jeweils unter Angabe von Zeitpunkt und auftretenden Komplikationen erfasst, ein primaeres oder sekundaeres Versterben und die 90-Tage-Letalitaet werden dokumentiert.Die strukturierte radiologische Diagnostik von Mehrfachverletzen verlangt die Integration eines erfahrenen Radiologen in

  13. Functional and structural balances of homologous sensorimotor regions in multiple sclerosis fatigue

    DEFF Research Database (Denmark)

    Cogliati Dezza, I; Zito, G; Tomasevic, L

    2015-01-01

    regions-known to be crucial for sensorimotor networks effectiveness-decrease with MS fatigue increase. Functional connectivity measures at rest and during a simple motor task (weak handgrip of either the right or left hand) were derived from primary sensorimotor areas electroencephalographic recordings......Fatigue in multiple sclerosis (MS) is a highly disabling symptom. Among the central mechanisms behind it, an involvement of sensorimotor networks is clearly evident from structural and functional studies. We aimed at assessing whether functional/structural balances of homologous sensorimotor...... in 27 mildly disabled MS patients. Structural MRI-derived inter-hemispheric asymmetries included the cortical thickness of Rolandic regions and the volume of thalami. Fatigue symptoms increased together with the functional inter-hemispheric imbalance of sensorimotor homologous areas activities at rest...

  14. Structural Design of Systems with Safe Behavior under Single and Multiple Faults

    DEFF Research Database (Denmark)

    Blanke, Mogens; Staroswiecki, Marcel

    2006-01-01

    Handling of multiple simultaneous faults is a complex issue in fault-tolerant control. The design task is particularly made difficult by to the numerous different cases that need be analyzed. Aiming at safe fault-handling, this paper shows how structural analysis can be applied to find...... to structural analysis to disclose which faults could be isolated from a structural point of view using active fault isolation. Results from application on a marine control system illustrate the concepts....... the analytical redundancy relations for all relevant combinations of faults, and can cope with the complexity and size of a real system. Being essential for fault-tolerant control schemes that shall handle particular cases of faults/failures, fault isolation is addressed. The paper introduces an extension...

  15. Multiple quasi-monoenergetic electron beams from laser-wakefield acceleration with spatially structured laser pulse

    Energy Technology Data Exchange (ETDEWEB)

    Ma, Y.; Li, M. H.; Li, Y. F.; Wang, J. G.; Tao, M. Z.; Han, Y. J.; Zhao, J. R.; Huang, K.; Yan, W. C.; Ma, J. L.; Li, Y. T. [Beijing National Laboratory of Condensed Matter Physics, Institute of Physics, CAS, Beijing 100080 (China); Chen, L. M., E-mail: lmchen@iphy.ac.cn [Beijing National Laboratory of Condensed Matter Physics, Institute of Physics, CAS, Beijing 100080 (China); Department of Physics and Astronomy and IFSA Collaborative Innovation Center, Shanghai Jiao Tong University, Shanghai 200240 (China); Li, D. Z. [Institute of High Energy Physics, CAS, Beijing 100049 (China); Chen, Z. Y. [Institute of Fluid Physics, China Academy of Engineering Physics, Mianyang, Sichuan 621999 (China); Sheng, Z. M. [Department of Physics and Astronomy and IFSA Collaborative Innovation Center, Shanghai Jiao Tong University, Shanghai 200240 (China); Department of Physics, Scottish Universities Physics Alliance, University of Strathclyde, Glasgow G4 0NG (United Kingdom); Zhang, J. [Department of Physics and Astronomy and IFSA Collaborative Innovation Center, Shanghai Jiao Tong University, Shanghai 200240 (China)

    2015-08-15

    By adjusting the focus geometry of a spatially structured laser pulse, single, double, and treble quasi-monoenergetic electron beams were generated, respectively, in laser-wakefield acceleration. Single electron beam was produced as focusing the laser pulse to a single spot. While focusing the laser pulse to two spots that are approximately equal in energy and size and intense enough to form their own filaments, two electron beams were produced. Moreover, with a proper distance between those two focal spots, three electron beams emerged with a certain probability owing to the superposition of the diffractions of those two spots. The energy spectra of the multiple electron beams are quasi-monoenergetic, which are different from that of the large energy spread beams produced due to the longitudinal multiple-injection in the single bubble.

  16. Multiple continuous coverage of the earth based on multi-satellite systems with linear structure

    Science.gov (United States)

    Saulskiy, V. K.

    2009-04-01

    A new and wider definition is given to multi-satellite systems with linear structure (SLS), and efficiency of their application to multiple continuous coverage of the Earth is substantiated. Owing to this widening, SLS have incorporated already well-recognized “polar systems” by L. Rider and W.S. Adams, “kinematically regular systems” by G.V. Mozhaev, and “delta-systems” by J.G. Walker, as well as “near-polar systems” by Yu.P. Ulybyshev, and some other satellite constellations unknown before. A universal method of SLS optimization is presented, valid for any values of coverage multiplicity and the number of satellites in a system. The method uses the criterion of minimum radius of a circle seen from a satellite on the surface of the globe. Among the best SLS found in this way there are both systems representing the well-known classes mentioned above and new orbit constellations of satellites.

  17. Skin and scales of teleost fish: Simple structure but high performance and multiple functions

    Science.gov (United States)

    Vernerey, Franck J.; Barthelat, Francois

    2014-08-01

    Natural and man-made structural materials perform similar functions such as structural support or protection. Therefore they rely on the same types of properties: strength, robustness, lightweight. Nature can therefore provide a significant source of inspiration for new and alternative engineering designs. We report here some results regarding a very common, yet largely unknown, type of biological material: fish skin. Within a thin, flexible and lightweight layer, fish skins display a variety of strain stiffening and stabilizing mechanisms which promote multiple functions such as protection, robustness and swimming efficiency. We particularly discuss four important features pertaining to scaled skins: (a) a strongly elastic tensile behavior that is independent from the presence of rigid scales, (b) a compressive response that prevents buckling and wrinkling instabilities, which are usually predominant for thin membranes, (c) a bending response that displays nonlinear stiffening mechanisms arising from geometric constraints between neighboring scales and (d) a robust structure that preserves the above characteristics upon the loss or damage of structural elements. These important properties make fish skin an attractive model for the development of very thin and flexible armors and protective layers, especially when combined with the high penetration resistance of individual scales. Scaled structures inspired by fish skin could find applications in ultra-light and flexible armor systems, flexible electronics or the design of smart and adaptive morphing structures for aerospace vehicles.

  18. NS3 from Hepatitis C Virus Strain JFH-1 Is an Unusually Robust Helicase That Is Primed To Bind and Unwind Viral RNA

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Ting; Ren, Xiaoming; Adams, Rebecca L.; Pyle, Anna Marie; Ou, J. -H. James

    2017-10-25

    Hepatitis C viruses (HCV) encode a helicase enzyme that is essential for viral replication and assembly (nonstructural protein 3 [NS3]). This helicase has become the focus of extensive basic research on the general helicase mechanism, and it is also of interest as a novel drug target. Despite the importance of this protein, mechanistic work on NS3 has been conducted almost exclusively on variants from HCV genotype 1. Our understanding of NS3 from the highly active HCV strains that are used to study HCV genetics and mechanism in cell culture (such as JFH-1) is lacking. We therefore set out to determine whether NS3 from the replicatively efficient genotype 2a strain JFH-1 displays novel functional or structural properties. Using biochemical assays for RNA binding and duplex unwinding, we show that JFH-1 NS3 binds RNA much more rapidly than the previously studied NS3 variants from genotype 1b. Unlike NS3 variants from other genotypes, JFH-1 NS3 binds RNA with high affinity in a functionally active form that is capable of immediately unwinding RNA duplexes without undergoing rate-limiting conformational changes that precede activation. Unlike other superfamily 2 (SF2) helicases, JFH-1 NS3 does not require long 3' overhangs, and it unwinds duplexes that are flanked by only a few nucleotides, as in the folded HCV genome. To understand the physical basis for this, we solved the crystal structure of JFH-1 NS3, revealing a novel conformation that contains an open, positively charged RNA binding cleft that is primed for productive interaction with RNA targets, potentially explaining robust replication by HCV JFH-1.

    IMPORTANCEGenotypes of HCV are as divergent as different types of flavivirus, and yet mechanistic features of HCV variants are presumed to be held in common. One of the most well-studied components of the HCV replication complex is a helicase known as nonstructural protein 3 (NS3). We set out to determine whether this important

  19. Multiple imputation to account for measurement error in marginal structural models

    Science.gov (United States)

    Edwards, Jessie K.; Cole, Stephen R.; Westreich, Daniel; Crane, Heidi; Eron, Joseph J.; Mathews, W. Christopher; Moore, Richard; Boswell, Stephen L.; Lesko, Catherine R.; Mugavero, Michael J.

    2015-01-01

    Background Marginal structural models are an important tool for observational studies. These models typically assume that variables are measured without error. We describe a method to account for differential and non-differential measurement error in a marginal structural model. Methods We illustrate the method estimating the joint effects of antiretroviral therapy initiation and current smoking on all-cause mortality in a United States cohort of 12,290 patients with HIV followed for up to 5 years between 1998 and 2011. Smoking status was likely measured with error, but a subset of 3686 patients who reported smoking status on separate questionnaires composed an internal validation subgroup. We compared a standard joint marginal structural model fit using inverse probability weights to a model that also accounted for misclassification of smoking status using multiple imputation. Results In the standard analysis, current smoking was not associated with increased risk of mortality. After accounting for misclassification, current smoking without therapy was associated with increased mortality [hazard ratio (HR): 1.2 (95% CI: 0.6, 2.3)]. The HR for current smoking and therapy (0.4 (95% CI: 0.2, 0.7)) was similar to the HR for no smoking and therapy (0.4; 95% CI: 0.2, 0.6). Conclusions Multiple imputation can be used to account for measurement error in concert with methods for causal inference to strengthen results from observational studies. PMID:26214338

  20. Multiple Imputation to Account for Measurement Error in Marginal Structural Models.

    Science.gov (United States)

    Edwards, Jessie K; Cole, Stephen R; Westreich, Daniel; Crane, Heidi; Eron, Joseph J; Mathews, W Christopher; Moore, Richard; Boswell, Stephen L; Lesko, Catherine R; Mugavero, Michael J

    2015-09-01

    Marginal structural models are an important tool for observational studies. These models typically assume that variables are measured without error. We describe a method to account for differential and nondifferential measurement error in a marginal structural model. We illustrate the method estimating the joint effects of antiretroviral therapy initiation and current smoking on all-cause mortality in a United States cohort of 12,290 patients with HIV followed for up to 5 years between 1998 and 2011. Smoking status was likely measured with error, but a subset of 3,686 patients who reported smoking status on separate questionnaires composed an internal validation subgroup. We compared a standard joint marginal structural model fit using inverse probability weights to a model that also accounted for misclassification of smoking status using multiple imputation. In the standard analysis, current smoking was not associated with increased risk of mortality. After accounting for misclassification, current smoking without therapy was associated with increased mortality (hazard ratio [HR]: 1.2 [95% confidence interval [CI] = 0.6, 2.3]). The HR for current smoking and therapy [0.4 (95% CI = 0.2, 0.7)] was similar to the HR for no smoking and therapy (0.4; 95% CI = 0.2, 0.6). Multiple imputation can be used to account for measurement error in concert with methods for causal inference to strengthen results from observational studies.

  1. Structural controls on the megathrust segmentation of the Middle America Trench from multiple geophysical observations

    Science.gov (United States)

    Naif, S.; Bassett, D.

    2016-12-01

    Subduction zone megathrusts display complex seismogenic behaviors that vary at intra- and inter-margin scales. Many different physical properties have been proposed to be primarily responsible for this behavior, such as the composition of subducted sediments, the hydration state of the incoming oceanic plate, and the pore-fluid pressure at the plate interface. Here, we focus on the northern Middle America Trench and show that subducting plate structures control megathrust segmentation. We analyze multiple types of seafloor geophysical observations and compare them to the distinct behavioral and spatial characteristics of the 1992 Nicaragua (Mw7.6), 2012 El Salvador (Mw7.3), 2012 Guatemala (Mw7.4), and 2012 Costa Rica (Mw7.6) events. The residual topography, residual gravity, and magnetic anomaly structure of the incoming oceanic plate and forearc seafloor are correlated. The forearc is composed of multiple unique segments that are bounded by subducting fracture zones. These boundaries correlate with foreshock and aftershock seismicity and also coincide with the hypocenter of all four earthquakes. The relationship between observed structures, earthquake slip inversions, and radiated energy of the four large events will be discussed.

  2. Structural phylogeny by profile extraction and multiple superimposition using electrostatic congruence as a discriminator

    Energy Technology Data Exchange (ETDEWEB)

    Chakraborty, Sandeep [Tata Inst. of Fundamental Research, Bombay (India); Rao, Basuthkar J. [Tata Inst. of Fundamental Research, Bombay (India); Baker, Nathan A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Asgeirsson, Bjarni [Univ. of Iceland, Reykjavik (Iceland)

    2013-04-01

    Phylogenetic analysis of proteins using multiple sequence alignment (MSA) assumes an underlying evolutionary relationship in these proteins which occasionally remains undetected due to considerable sequence divergence. Structural alignment programs have been developed to unravel such fuzzy relationships. However, none of these structure based methods have used electrostatic properties to discriminate between spatially equivalent residues. We present a methodology for MSA of a set of related proteins with known structures using electrostatic properties as an additional discriminator (STEEP). STEEP first extracts a profile, then generates a multiple structural superimposition providing a consolidated spatial framework for comparing residues and finally emits the MSA. Residues that are aligned differently by including or excluding electrostatic properties can be targeted by directed evolution experiments to transform the enzymatic properties of one protein into another. We have compared STEEP results to those obtained from a MSA program (ClustalW) and a structural alignment method (MUSTANG) for chymotrypsin serine proteases. Subsequently, we used PhyML to generate phylogenetic trees for the serine and metallo-β-lactamase superfamilies from the STEEP generated MSA, and corroborated the accepted relationships in these superfamilies. We have observed that STEEP acts as a functional classifier when electrostatic congruence is used as a discriminator, and thus identifies potential targets for directed evolution experiments. In summary, STEEP is unique among phylogenetic methods for its ability to use electrostatic congruence to specify mutations that might be the source of the functional divergence in a protein family. Based on our results, we also hypothesize that the active site and its close vicinity contains enough information to infer the correct phylogeny for related proteins.

  3. Voting-based consensus clustering for combining multiple clusterings of chemical structures

    Directory of Open Access Journals (Sweden)

    Saeed Faisal

    2012-12-01

    Full Text Available Abstract Background Although many consensus clustering methods have been successfully used for combining multiple classifiers in many areas such as machine learning, applied statistics, pattern recognition and bioinformatics, few consensus clustering methods have been applied for combining multiple clusterings of chemical structures. It is known that any individual clustering method will not always give the best results for all types of applications. So, in this paper, three voting and graph-based consensus clusterings were used for combining multiple clusterings of chemical structures to enhance the ability of separating biologically active molecules from inactive ones in each cluster. Results The cumulative voting-based aggregation algorithm (CVAA, cluster-based similarity partitioning algorithm (CSPA and hyper-graph partitioning algorithm (HGPA were examined. The F-measure and Quality Partition Index method (QPI were used to evaluate the clusterings and the results were compared to the Ward’s clustering method. The MDL Drug Data Report (MDDR dataset was used for experiments and was represented by two 2D fingerprints, ALOGP and ECFP_4. The performance of voting-based consensus clustering method outperformed the Ward’s method using F-measure and QPI method for both ALOGP and ECFP_4 fingerprints, while the graph-based consensus clustering methods outperformed the Ward’s method only for ALOGP using QPI. The Jaccard and Euclidean distance measures were the methods of choice to generate the ensembles, which give the highest values for both criteria. Conclusions The results of the experiments show that consensus clustering methods can improve the effectiveness of chemical structures clusterings. The cumulative voting-based aggregation algorithm (CVAA was the method of choice among consensus clustering methods.

  4. Secure Degrees of Freedom Regions of Multiple Access and Interference Channels: The Polytope Structure

    OpenAIRE

    Xie, Jianwei; Ulukus, Sennur

    2014-01-01

    The sum secure degrees of freedom (s.d.o.f.) of two fundamental multi-user network structures, the K-user Gaussian multiple access (MAC) wiretap channel and the K-user interference channel (IC) with secrecy constraints, have been determined recently as K(K-1)/(K(K-1)+1) [1,2] and K(K-1)/(2K-1) [3,4], respectively. In this paper, we determine the entire s.d.o.f. regions of these two channel models. The converse for the MAC follows from a middle step in the converse of [1,2]. The converse for t...

  5. SiteBinder: an improved approach for comparing multiple protein structural motifs.

    Science.gov (United States)

    Sehnal, David; Vařeková, Radka Svobodová; Huber, Heinrich J; Geidl, Stanislav; Ionescu, Crina-Maria; Wimmerová, Michaela; Koča, Jaroslav

    2012-02-27

    There is a paramount need to develop new techniques and tools that will extract as much information as possible from the ever growing repository of protein 3D structures. We report here on the development of a software tool for the multiple superimposition of large sets of protein structural motifs. Our superimposition methodology performs a systematic search for the atom pairing that provides the best fit. During this search, the RMSD values for all chemically relevant pairings are calculated by quaternion algebra. The number of evaluated pairings is markedly decreased by using PDB annotations for atoms. This approach guarantees that the best fit will be found and can be applied even when sequence similarity is low or does not exist at all. We have implemented this methodology in the Web application SiteBinder, which is able to process up to thousands of protein structural motifs in a very short time, and which provides an intuitive and user-friendly interface. Our benchmarking analysis has shown the robustness, efficiency, and versatility of our methodology and its implementation by the successful superimposition of 1000 experimentally determined structures for each of 32 eukaryotic linear motifs. We also demonstrate the applicability of SiteBinder using three case studies. We first compared the structures of 61 PA-IIL sugar binding sites containing nine different sugars, and we found that the sugar binding sites of PA-IIL and its mutants have a conserved structure despite their binding different sugars. We then superimposed over 300 zinc finger central motifs and revealed that the molecular structure in the vicinity of the Zn atom is highly conserved. Finally, we superimposed 12 BH3 domains from pro-apoptotic proteins. Our findings come to support the hypothesis that there is a structural basis for the functional segregation of BH3-only proteins into activators and enablers.

  6. Barrier potential design criteria in multiple-quantum-well-based solar-cell structures

    Science.gov (United States)

    Mohaidat, Jihad M.; Shum, Kai; Wang, W. B.; Alfano, R. R.

    1994-01-01

    The barrier potential design criteria in multiple-quantum-well (MQW)-based solar-cell structures is reported for the purpose of achieving maximum efficiency. The time-dependent short-circuit current density at the collector side of various MQW solar-cell structures under resonant condition was numerically calculated using the time-dependent Schroedinger equation. The energy efficiency of solar cells based on the InAs/Ga(y)In(1-y)As and GaAs/Al(x)Ga(1-x)As MQW structues were compared when carriers are excited at a particular solar-energy band. Using InAs/Ga(y)In(1-y)As MQW structures it is found that a maximum energy efficiency can be achieved if the structure is designed with barrier potential of about 450 meV. The efficiency is found to decline linearly as the barrier potential increases for GaAs/Al(x)Ga(1-x)As MQW-structure-based solar cells.

  7. Light Absorption Enhancement of Silicon-Based Photovoltaic Devices with Multiple Bandgap Structures of Porous Silicon

    Directory of Open Access Journals (Sweden)

    Kuen-Hsien Wu

    2015-09-01

    Full Text Available Porous-silicon (PS multi-layered structures with three stacked PS layers of different porosity were prepared on silicon (Si substrates by successively tuning the electrochemical-etching parameters in an anodization process. The three PS layers have different optical bandgap energy and construct a triple-layered PS (TLPS structure with multiple bandgap energy. Photovoltaic devices were fabricated by depositing aluminum electrodes of Schottky contacts on the surfaces of the developed TLPS structures. The TLPS-based devices exhibit broadband photoresponses within the spectrum of the solar irradiation and get high photocurrent for the incident light of a tungsten lamp. The improved spectral responses of devices are owing to the multi-bandgap structures of TLPS, which are designed with a layered configuration analog to a tandem cell for absorbing a wider energy range of the incidental sun light. The large photocurrent is mainly ascribed to an enhanced light-absorption ability as a result of applying nanoporous-Si thin films as the surface layers to absorb the short-wavelength light and to improve the Schottky contacts of devices. Experimental results reveal that the multi-bandgap PS structures produced from electrochemical-etching of Si wafers are potentially promising for development of highly efficient Si-based solar cells.

  8. Multiple tuned mass damper based vibration mitigation of offshore wind turbine considering soil-structure interaction

    Science.gov (United States)

    Hussan, Mosaruf; Sharmin, Faria; Kim, Dookie

    2017-08-01

    The dynamics of jacket supported offshore wind turbine (OWT) in earthquake environment is one of the progressing focuses in the renewable energy field. Soil-structure interaction (SSI) is a fundamental principle to analyze stability and safety of the structure. This study focuses on the performance of the multiple tuned mass damper (MTMD) in minimizing the dynamic responses of the structures objected to seismic loads combined with static wind and wave loads. Response surface methodology (RSM) has been applied to design the MTMD parameters. The analyses have been performed under two different boundary conditions: fixed base (without SSI) and flexible base (with SSI). Two vibration modes of the structure have been suppressed by multi-mode vibration control principle in both cases. The effectiveness of the MTMD in reducing the dynamic response of the structure is presented. The dynamic SSI plays an important role in the seismic behavior of the jacket supported OWT, especially resting on the soft soil deposit. Finally, it shows that excluding the SSI effect could be the reason of overestimating the MTMD performance.

  9. hSSB1 associates with and promotes stability of the BLM helicase

    OpenAIRE

    O'BYRNE, KEN

    2017-01-01

    Background Maintenance of genome stability is critical in human cells. Mutations in or loss of genome stability pathways can lead to a number of pathologies including cancer. hSSB1 is a critical DNA repair protein functioning in the repair and signalling of stalled DNA replication forks, double strand DNA breaks and oxidised DNA lesions. The BLM helicase is central to the repair of both collapsed DNA replication forks and double strand DNA breaks by homologous recombination. Results In this s...

  10. The human RecQ helicases BLM and RECQL4 cooperate to preserve genome stability

    Czech Academy of Sciences Publication Activity Database

    Singh, D.K.; Popuri, V.; Kulikowicz, T.; Shevelev, Igor; Ghosh, A.K.; Ramamoorthy, M.; Rossi, M.L.; Janščák, Pavel; Croteau, D.L.; Bohr, V.A.

    2012-01-01

    Roč. 40, č. 14 (2012), s. 6632-6648 ISSN 0305-1048 R&D Projects: GA ČR GAP305/10/0281 Grant - others:NIH(US) Z01-AG000726-17 Institutional research plan: CEZ:AV0Z50520514 Institutional support: RVO:68378050 Keywords : RecQ helicase * genome stability * BLM * RECQL4 Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 8.278, year: 2012

  11. The eIF4AIII RNA helicase is a critical determinant of human cytomegalovirus replication

    International Nuclear Information System (INIS)

    Ziehr, Ben; Lenarcic, Erik; Cecil, Chad; Moorman, Nathaniel J.

    2016-01-01

    Human cytomegalovirus (HCMV) was recently shown to encode a large number of spliced mRNAs. While the nuclear export of unspliced viral transcripts has been extensively studied, the role of host mRNA export factors in HCMV mRNA trafficking remains poorly defined. We found that the eIF4AIII RNA helicase, a component of the exon junction complex, was necessary for efficient virus replication. Depletion of eIF4AIII limited viral DNA accumulation, export of viral mRNAs from the nucleus, and the production of progeny virus. However eIF4AIII was dispensable for the association of viral transcripts with ribosomes. We found that pateamine A, a natural compound that inhibits both eIF4AI/II and eIF4AIII, has potent antiviral activity and inhibits HCMV replication throughout the virus lytic cycle. Our results demonstrate that eIF4AIII is required for efficient HCMV replication, and suggest that eIF4A family helicases may be a new class of targets for the development of host-directed antiviral therapeutics. - Highlights: • The host eIF4AIII RNA helicase is required for efficient HCMV replication. • Depleting eIF4AIII inhibited the nuclear export of HCMV mRNAs. • HCMV mRNAs did not require eIF4AIII to associate with polyribosomes. • The eIF4A family helicases may be new targets for host-directed antiviral drugs.

  12. Evolution of the DEAD box helicase family in chicken: chickens have no DHX9 ortholog.

    Science.gov (United States)

    Sato, Haruko; Oshiumi, Hiroyuki; Takaki, Hiromi; Hikono, Hirokazu; Seya, Tsukasa

    2015-10-01

    Viral RNA represents a pattern molecule that can be recognized by RNA sensors in innate immunity. Humans and mice possess cytoplasmic DNA/RNA sensors for detecting viral replication. There are a number of DEAD (Asp-Glu-Ala-Asp; DExD/H) box-type helicases in mammals, among which retinoic acid-inducible gene 1 (RIG-I) and melanoma differentiation-associated protein 5 (MDA50) are indispensable for RNA sensing; however, they are functionally supported by a number of sensors that directly bind viral RNA or replicative RNA intermediates to convey signals to RIG-I and MDA5. Some DEAD box helicase members recognize DNA irrespective of the origin. These sensors transmit IFN-inducing signals through adaptors, including mitochondrial antiviral signaling. Viral double-stranded RNAs are reportedly sensed by the helicases DDX1, DDX21, DHX36, DHX9, DDX3, DDX41, LGP2 and DDX60, in addition to RIG-I and MDA5, and induce type I IFNs, thereby blocking viral replication. Humans and mice have all nucleic acid sensors listed here. In the RNA sensing system in chicken, it was found in the present study that most DEAD box helicases are conserved; however, DHX9 is genetically deficient in addition to reported RIG-I. Based on the current genome databases, similar DHX9 deficiency was observed in ducks and several other bird species. Because chicken, but not duck, was found to be deficient in RIG-I, the RNA-sensing system of chicken lacks RIG-I and DHX9 and is thus more fragile than that of duck or mammal. DHX9 may generally compensate for the function of RIG-I and deficiency of DHX9 possibly participates in exacerbations of viral infection such as influenza in chickens. © 2015 The Societies and Wiley Publishing Asia Pty Ltd.

  13. Physical interaction of RECQ5 helicase with RAD51 facilitates its anti-recombinase activity

    Czech Academy of Sciences Publication Activity Database

    Schwendener, S.; Raynard, S.; Paliwal, S.; Cheng, A.; Kanagaraj, R.; Shevelev, Igor; Stark, J.M.; Sung, P.; Janscak, P.

    2010-01-01

    Roč. 285, č. 21 (2010), s. 15739-15745 ISSN 0021-9258 Grant - others:NIH(US) R01CA120954; NIH(US) ES015632; SNSF(CH) 3100A0-116008 Institutional research plan: CEZ:AV0Z50520514 Keywords : DNA helicase * double-strand breaks * homologous recombination Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.328, year: 2010

  14. DEAD-box RNA helicase is dispensable for mitochondrial translation in Trypanosoma brucei

    Czech Academy of Sciences Publication Activity Database

    Richterová, Lenka; Vávrová, Zuzana; Lukeš, Julius

    2011-01-01

    Roč. 127, č. 1 (2011), 300-303 ISSN 0014-4894 R&D Projects: GA ČR GA204/09/1667; GA MŠk LC07032; GA MŠk 2B06129 Institutional research plan: CEZ:AV0Z60220518 Keywords : Trypanosoma * Mitochondrial translation * RNA helicase * Cytochrome c oxidase * Mitochondrion Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.122, year: 2011

  15. The eIF4AIII RNA helicase is a critical determinant of human cytomegalovirus replication

    Energy Technology Data Exchange (ETDEWEB)

    Ziehr, Ben; Lenarcic, Erik; Cecil, Chad; Moorman, Nathaniel J., E-mail: nmoorman@med.unc.edu

    2016-02-15

    Human cytomegalovirus (HCMV) was recently shown to encode a large number of spliced mRNAs. While the nuclear export of unspliced viral transcripts has been extensively studied, the role of host mRNA export factors in HCMV mRNA trafficking remains poorly defined. We found that the eIF4AIII RNA helicase, a component of the exon junction complex, was necessary for efficient virus replication. Depletion of eIF4AIII limited viral DNA accumulation, export of viral mRNAs from the nucleus, and the production of progeny virus. However eIF4AIII was dispensable for the association of viral transcripts with ribosomes. We found that pateamine A, a natural compound that inhibits both eIF4AI/II and eIF4AIII, has potent antiviral activity and inhibits HCMV replication throughout the virus lytic cycle. Our results demonstrate that eIF4AIII is required for efficient HCMV replication, and suggest that eIF4A family helicases may be a new class of targets for the development of host-directed antiviral therapeutics. - Highlights: • The host eIF4AIII RNA helicase is required for efficient HCMV replication. • Depleting eIF4AIII inhibited the nuclear export of HCMV mRNAs. • HCMV mRNAs did not require eIF4AIII to associate with polyribosomes. • The eIF4A family helicases may be new targets for host-directed antiviral drugs.

  16. Distinct functions of human RecQ helicases during DNA replication

    Czech Academy of Sciences Publication Activity Database

    Urban, Václav; Dobrovolná, Jana; Janščák, Pavel

    2017-01-01

    Roč. 225, červen (2017), s. 20-26 ISSN 0301-4622 R&D Projects: GA ČR(CZ) GA14-05743S; GA MŠk LH14037 Institutional support: RVO:68378050 Keywords : DNA replication * Replication stress * RecQ helicases * Genomic instability * Cancer Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Biochemistry and molecular biology Impact factor: 2.402, year: 2016

  17. Relocalization of nuclear DNA helicase II during the growth period of bovine oocytes

    Czech Academy of Sciences Publication Activity Database

    Baran, V.; Kovářová, Hana; Klíma, Jiří; Hozák, Pavel; Motlík, Jan

    2006-01-01

    Roč. 125, 1-2 (2006), s. 155-164 ISSN 0948-6143 R&D Projects: GA ČR GA523/03/0857 Grant - others:Slovenská Akademie věd(SK) VEGA 2/3065/23 Institutional research plan: CEZ:AV0Z50450515; CEZ:AV0Z50390512 Keywords : DNA helicase II * fibroblasts * oocytes Subject RIV: EB - Genetics ; Molecular Biology Impact factor : 3.220, year: 2006

  18. Senataxin, the ortholog of a yeast RNA helicase, is mutant in ataxia-ocular apraxia 2.

    Science.gov (United States)

    Moreira, Maria-Céu; Klur, Sandra; Watanabe, Mitsunori; Németh, Andrea H; Le Ber, Isabelle; Moniz, José-Carlos; Tranchant, Christine; Aubourg, Patrick; Tazir, Meriem; Schöls, Lüdger; Pandolfo, Massimo; Schulz, Jörg B; Pouget, Jean; Calvas, Patrick; Shizuka-Ikeda, Masami; Shoji, Mikio; Tanaka, Makoto; Izatt, Louise; Shaw, Christopher E; M'Zahem, Abderrahim; Dunne, Eimear; Bomont, Pascale; Benhassine, Traki; Bouslam, Naïma; Stevanin, Giovanni; Brice, Alexis; Guimarães, João; Mendonça, Pedro; Barbot, Clara; Coutinho, Paula; Sequeiros, Jorge; Dürr, Alexandra; Warter, Jean-Marie; Koenig, Michel

    2004-03-01

    Ataxia-ocular apraxia 2 (AOA2) was recently identified as a new autosomal recessive ataxia. We have now identified causative mutations in 15 families, which allows us to clinically define this entity by onset between 10 and 22 years, cerebellar atrophy, axonal sensorimotor neuropathy, oculomotor apraxia and elevated alpha-fetoprotein (AFP). Ten of the fifteen mutations cause premature termination of a large DEAxQ-box helicase, the human ortholog of yeast Sen1p, involved in RNA maturation and termination.

  19. Role of the hydrophilic channels of simian virus 40 T-antigen helicase in DNA replication.

    Science.gov (United States)

    Wang, Weiping; Manna, David; Simmons, Daniel T

    2007-05-01

    The simian virus 40 (SV40) hexameric helicase consists of a central channel and six hydrophilic channels located between adjacent large tier domains within each hexamer. To study the function of the hydrophilic channels in SV40 DNA replication, a series of single-point substitutions were introduced at sites not directly involved in protein-protein contacts. The mutants were characterized biochemically in various ways. All mutants oligomerized normally in the absence of DNA. Interestingly, 8 of the 10 mutants failed to unwind an origin-containing DNA fragment and nine of them were totally unable to support SV40 DNA replication in vitro. The mutants fell into four classes based on their biochemical properties. Class A mutants bound DNA normally and had normal ATPase and helicase activities but failed to unwind origin DNA and support SV40 DNA replication. Class B mutants were compromised in single-stranded DNA and origin DNA binding at low protein concentrations. They were defective in helicase activity and unwinding of the origin and in supporting DNA replication. Class C and D mutants possessed higher-than-normal single-stranded DNA binding activity at low protein concentrations. The class C mutants failed to separate origin DNA and support DNA replication. The class D mutants unwound origin DNA normally but were compromised in their ability to support DNA replication. Taken together, these results suggest that the hydrophilic channels have an active role in the unwinding of SV40 DNA from the origin and the placement of the resulting single strands within the helicase.

  20. RTEL1: an essential helicase for telomere maintenance and the regulation of homologous recombination

    OpenAIRE

    Uringa, Evert-Jan; Youds, Jillian L.; Lisaingo, Kathleen; Lansdorp, Peter M.; Boulton, Simon J.

    2010-01-01

    Telomere maintenance and DNA repair are crucial processes that protect the genome against instability. RTEL1, an essential iron–sulfur cluster-containing helicase, is a dominant factor that controls telomere length in mice and is required for telomere integrity. In addition, RTEL1 promotes synthesis-dependent strand annealing to direct DNA double-strand breaks into non-crossover outcomes during mitotic repair and in meiosis. Here, we review the role of RTEL1 in telomere maintenance and homolo...

  1. Analysis of Multiple Structural Changes in Financial Contagion Based on the Largest Lyapunov Exponents

    Directory of Open Access Journals (Sweden)

    Rui Wang

    2014-01-01

    Full Text Available A modified multiple structural changes model is built to test structural breaks of the financial system based on calculating the largest Lyapunov exponents of the financial time series. Afterwards, the Lorenz system is used as a simulation example to inspect the new model. As the Lorenz system has strong nonlinearity, the verification results show that the new model has good capability in both finding the breakpoint and revealing the changes in nonlinear characteristics of the time series. The empirical study based on the model used daily data from the S&P 500 stock index during the global financial crisis from 2005 to 2012. The results provide four breakpoints of the period, which divide the contagion into four stages: stationary, local outbreak, global outbreak, and recovery period. An additional significant result is the obvious chaos characteristic difference in the largest Lyapunov exponents and the standard deviation at various stages, particularly at the local outbreak stage.

  2. Joint source based analysis of multiple brain structures in studying major depressive disorder

    Science.gov (United States)

    Ramezani, Mahdi; Rasoulian, Abtin; Hollenstein, Tom; Harkness, Kate; Johnsrude, Ingrid; Abolmaesumi, Purang

    2014-03-01

    We propose a joint Source-Based Analysis (jSBA) framework to identify brain structural variations in patients with Major Depressive Disorder (MDD). In this framework, features representing position, orientation and size (i.e. pose), shape, and local tissue composition are extracted. Subsequently, simultaneous analysis of these features within a joint analysis method is performed to generate the basis sources that show signi cant di erences between subjects with MDD and those in healthy control. Moreover, in a cross-validation leave- one-out experiment, we use a Fisher Linear Discriminant (FLD) classi er to identify individuals within the MDD group. Results show that we can classify the MDD subjects with an accuracy of 76% solely based on the information gathered from the joint analysis of pose, shape, and tissue composition in multiple brain structures.

  3. Generalized linear longitudinal mixed models with linear covariance structure and multiplicative random effects

    DEFF Research Database (Denmark)

    Holst, René; Jørgensen, Bent

    2015-01-01

    The paper proposes a versatile class of multiplicative generalized linear longitudinal mixed models (GLLMM) with additive dispersion components, based on explicit modelling of the covariance structure. The class incorporates a longitudinal structure into the random effects models and retains...... a marginal as well as a conditional interpretation. The estimation procedure is based on a computationally efficient quasi-score method for the regression parameters combined with a REML-like bias-corrected Pearson estimating function for the dispersion and correlation parameters. This avoids...... the multidimensional integral of the conventional GLMM likelihood and allows an extension of the robust empirical sandwich estimator for use with both association and regression parameters. The method is applied to a set of otholit data, used for age determination of fish....

  4. Isolation and Characterization of Pepper Genes Interacting with the CMV-P1 Helicase Domain.

    Directory of Open Access Journals (Sweden)

    Yoomi Choi

    Full Text Available Cucumber mosaic virus (CMV is a destructive pathogen affecting Capsicum annuum (pepper production. The pepper Cmr1 gene confers resistance to most CMV strains, but is overcome by CMV-P1 in a process dependent on the CMV-P1 RNA1 helicase domain (P1 helicase. Here, to identify host factors involved in CMV-P1 infection in pepper, a yeast two-hybrid library derived from a C. annuum 'Bukang' cDNA library was screened, producing a total of 76 potential clones interacting with the P1 helicase. Beta-galactosidase filter lift assay, PCR screening, and sequencing analysis narrowed the candidates to 10 genes putatively involved in virus infection. The candidate host genes were silenced in Nicotiana benthamiana plants that were then inoculated with CMV-P1 tagged with the green fluorescent protein (GFP. Plants silenced for seven of the genes showed development comparable to N. benthamiana wild type, whereas plants silenced for the other three genes showed developmental defects including stunting and severe distortion. Silencing formate dehydrogenase and calreticulin-3 precursor led to reduced virus accumulation. Formate dehydrogenase-silenced plants showed local infection in inoculated leaves, but not in upper (systemic leaves. In the calreticulin-3 precursor-silenced plants, infection was not observed in either the inoculated or the upper leaves. Our results demonstrate that formate dehydrogenase and calreticulin-3 precursor are required for CMV-P1 infection.

  5. A new role for FBP21 as regulator of Brr2 helicase activity.

    Science.gov (United States)

    Henning, Lisa M; Santos, Karine F; Sticht, Jana; Jehle, Stefanie; Lee, Chung-Tien; Wittwer, Malte; Urlaub, Henning; Stelzl, Ulrich; Wahl, Markus C; Freund, Christian

    2017-07-27

    Splicing of eukaryotic pre-mRNA is carried out by the spliceosome, which assembles stepwise on each splicing substrate. This requires the concerted action of snRNPs and non-snRNP accessory proteins, the functions of which are often not well understood. Of special interest are B complex factors that enter the spliceosome prior to catalytic activation and may alter splicing kinetics and splice site selection. One of these proteins is FBP21, for which we identified several spliceosomal binding partners in a yeast-two-hybrid screen, among them the RNA helicase Brr2. Biochemical and biophysical analyses revealed that an intrinsically disordered region of FBP21 binds to an extended surface of the C-terminal Sec63 unit of Brr2. Additional contacts in the C-terminal helicase cassette are required for allosteric inhibition of Brr2 helicase activity. Furthermore, the direct interaction between FBP21 and the U4/U6 di-snRNA was found to reduce the pool of unwound U4/U6 di-snRNA. Our results suggest FBP21 as a novel key player in the regulation of Brr2. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. Determination of the populations and structures of multiple conformers in an ensemble from NMR data: Multiple-copy refinement of nucleic acid structures using floating weights

    International Nuclear Information System (INIS)

    Goerler, Adrian; Ulyanov, Nikolai B.; James, Thomas L.

    2000-01-01

    A new algorithm is presented for determination of structural conformers and their populations based on NMR data. Restrained Metropolis Monte Carlo simulations or restrained energy minimizations are performed for several copies of a molecule simultaneously. The calculations are restrained with dipolar relaxation rates derived from measured NOE intensities via complete relaxation matrix analysis. The novel feature of the algorithm is that the weights of individual conformers are determined in every refinement step, by the quadratic programming algorithm, in such a way that the restraint energy is minimized. Its design ensures that the calculated populations of the individual conformers are based only on experimental restraints. Presence of internally inconsistent restraints is the driving force for determination of distinct multiple conformers. The method is applied to various simulated test systems. Conformational calculations on nucleic acids are carried out using generalized helical parameters with the program DNAminiCarlo. From different mixtures of A- and B-DNA, minor fractions as low as 10% could be determined with restrained energy minimization. For B-DNA with three local conformers (C2'-endo, O4'-exo, C3'-endo), the minor O4'-exo conformer could not be reliably determined using NOE data typically measured for DNA. The other two conformers, C2'-endo and C3'-endo, could be reproduced by Metropolis Monte Carlo simulated annealing. The behavior of the algorithm in various situations is analyzed, and a number of refinement protocols are discussed. Prior to application of this algorithm to each experimental system, it is suggested that the presence of internal inconsistencies in experimental data be ascertained. In addition, because the performance of the algorithm depends on the type of conformers involved and experimental data available, it is advisable to carry out test calculations with simulated data modeling each experimental system studied

  7. SoftSearch: integration of multiple sequence features to identify breakpoints of structural variations.

    Directory of Open Access Journals (Sweden)

    Steven N Hart

    Full Text Available BACKGROUND: Structural variation (SV represents a significant, yet poorly understood contribution to an individual's genetic makeup. Advanced next-generation sequencing technologies are widely used to discover such variations, but there is no single detection tool that is considered a community standard. In an attempt to fulfil this need, we developed an algorithm, SoftSearch, for discovering structural variant breakpoints in Illumina paired-end next-generation sequencing data. SoftSearch combines multiple strategies for detecting SV including split-read, discordant read-pair, and unmated pairs. Co-localized split-reads and discordant read pairs are used to refine the breakpoints. RESULTS: We developed and validated SoftSearch using real and synthetic datasets. SoftSearch's key features are 1 not requiring secondary (or exhaustive primary alignment, 2 portability into established sequencing workflows, and 3 is applicable to any DNA-sequencing experiment (e.g. whole genome, exome, custom capture, etc.. SoftSearch identifies breakpoints from a small number of soft-clipped bases from split reads and a few discordant read-pairs which on their own would not be sufficient to make an SV call. CONCLUSIONS: We show that SoftSearch can identify more true SVs by combining multiple sequence features. SoftSearch was able to call clinically relevant SVs in the BRCA2 gene not reported by other tools while offering significantly improved overall performance.

  8. Differential Diagnosis Tool for Parkinsonian Syndrome Using Multiple Structural Brain Measures

    Directory of Open Access Journals (Sweden)

    Miho Ota

    2013-01-01

    Full Text Available Clinical differentiation of parkinsonian syndromes such as the Parkinson variant of multiple system atrophy (MSA-P and cerebellar subtype (MSA-C from Parkinson's disease is difficult in the early stage of the disease. To identify the correlative pattern of brain changes for differentiating parkinsonian syndromes, we applied discriminant analysis techniques by magnetic resonance imaging (MRI. T1-weighted volume data and diffusion tensor images were obtained by MRI in eighteen patients with MSA-C, 12 patients with MSA-P, 21 patients with Parkinson’s disease, and 21 healthy controls. They were evaluated using voxel-based morphometry and tract-based spatial statistics, respectively. Discriminant functions derived by step wise methods resulted in correct classification rates of 0.89. When differentiating these diseases with the use of three independent variables together, the correct classification rate was the same as that obtained with step wise methods. These findings support the view that each parkinsonian syndrome has structural deviations in multiple brain areas and that a combination of structural brain measures can help to distinguish parkinsonian syndromes.

  9. Multiple-scale structures: from Faraday waves to soft-matter quasicrystals

    Directory of Open Access Journals (Sweden)

    Samuel Savitz

    2018-05-01

    Full Text Available For many years, quasicrystals were observed only as solid-state metallic alloys, yet current research is now actively exploring their formation in a variety of soft materials, including systems of macromolecules, nanoparticles and colloids. Much effort is being invested in understanding the thermodynamic properties of these soft-matter quasicrystals in order to predict and possibly control the structures that form, and hopefully to shed light on the broader yet unresolved general questions of quasicrystal formation and stability. Moreover, the ability to control the self-assembly of soft quasicrystals may contribute to the development of novel photonics or other applications based on self-assembled metamaterials. Here a path is followed, leading to quantitative stability predictions, that starts with a model developed two decades ago to treat the formation of multiple-scale quasiperiodic Faraday waves (standing wave patterns in vibrating fluid surfaces and which was later mapped onto systems of soft particles, interacting via multiple-scale pair potentials. The article reviews, and substantially expands, the quantitative predictions of these models, while correcting a few discrepancies in earlier calculations, and presents new analytical methods for treating the models. In so doing, a number of new stable quasicrystalline structures are found with octagonal, octadecagonal and higher-order symmetries, some of which may, it is hoped, be observed in future experiments.

  10. Multiple-scale structures: from Faraday waves to soft-matter quasicrystals.

    Science.gov (United States)

    Savitz, Samuel; Babadi, Mehrtash; Lifshitz, Ron

    2018-05-01

    For many years, quasicrystals were observed only as solid-state metallic alloys, yet current research is now actively exploring their formation in a variety of soft materials, including systems of macromolecules, nanoparticles and colloids. Much effort is being invested in understanding the thermodynamic properties of these soft-matter quasicrystals in order to predict and possibly control the structures that form, and hopefully to shed light on the broader yet unresolved general questions of quasicrystal formation and stability. Moreover, the ability to control the self-assembly of soft quasicrystals may contribute to the development of novel photonics or other applications based on self-assembled metamaterials. Here a path is followed, leading to quantitative stability predictions, that starts with a model developed two decades ago to treat the formation of multiple-scale quasiperiodic Faraday waves (standing wave patterns in vibrating fluid surfaces) and which was later mapped onto systems of soft particles, interacting via multiple-scale pair potentials. The article reviews, and substantially expands, the quantitative predictions of these models, while correcting a few discrepancies in earlier calculations, and presents new analytical methods for treating the models. In so doing, a number of new stable quasicrystalline structures are found with octagonal, octadecagonal and higher-order symmetries, some of which may, it is hoped, be observed in future experiments.

  11. Base Isolation for Seismic Retrofitting of a Multiple Building Structure: Evaluation of Equivalent Linearization Method

    Directory of Open Access Journals (Sweden)

    Massimiliano Ferraioli

    2016-01-01

    Full Text Available Although the most commonly used isolation systems exhibit nonlinear inelastic behaviour, the equivalent linear elastic analysis is commonly used in the design and assessment of seismic-isolated structures. The paper investigates if the linear elastic model is suitable for the analysis of a seismically isolated multiple building structure. To this aim, its computed responses were compared with those calculated by nonlinear dynamic analysis. A common base isolation plane connects the isolation bearings supporting the adjacent structures. In this situation, the conventional equivalent linear elastic analysis may have some problems of accuracy because this method is calibrated on single base-isolated structures. Moreover, the torsional characteristics of the combined system are significantly different from those of separate isolated buildings. A number of numerical simulations and parametric studies under earthquake excitations were performed. The accuracy of the dynamic response obtained by the equivalent linear elastic model was calculated by the magnitude of the error with respect to the corresponding response considering the nonlinear behaviour of the isolation system. The maximum displacements at the isolation level, the maximum interstorey drifts, and the peak absolute acceleration were selected as the most important response measures. The influence of mass eccentricity, torsion, and high-modes effects was finally investigated.

  12. Multiplicative congruential generators, their lattice structure, its relation to lattice-sublattice transformations and applications in crystallography

    Science.gov (United States)

    Hornfeck, W.; Harbrecht, B.

    2009-11-01

    An analysis of certain types of multiplicative congruential generators - otherwise known for their application to the sequential generation of pseudo-random numbers - reveals their relation to lattice-sublattice transformations and the coordinate description of crystal structures.

  13. TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences

    Directory of Open Access Journals (Sweden)

    Sharma Gaurav

    2011-04-01

    Full Text Available Abstract Background The prediction of secondary structure, i.e. the set of canonical base pairs between nucleotides, is a first step in developing an understanding of the function of an RNA sequence. The most accurate computational methods predict conserved structures for a set of homologous RNA sequences. These methods usually suffer from high computational complexity. In this paper, TurboFold, a novel and efficient method for secondary structure prediction for multiple RNA sequences, is presented. Results TurboFold takes, as input, a set of homologous RNA sequences and outputs estimates of the base pairing probabilities for each sequence. The base pairing probabilities for a sequence are estimated by combining intrinsic information, derived from the sequence itself via the nearest neighbor thermodynamic model, with extrinsic information, derived from the other sequences in the input set. For a given sequence, the extrinsic information is computed by using pairwise-sequence-alignment-based probabilities for co-incidence with each of the other sequences, along with estimated base pairing probabilities, from the previous iteration, for the other sequences. The extrinsic information is introduced as free energy modifications for base pairing in a partition function computation based on the nearest neighbor thermodynamic model. This process yields updated estimates of base pairing probability. The updated base pairing probabilities in turn are used to recompute extrinsic information, resulting in the overall iterative estimation procedure that defines TurboFold. TurboFold is benchmarked on a number of ncRNA datasets and compared against alternative secondary structure prediction methods. The iterative procedure in TurboFold is shown to improve estimates of base pairing probability with each iteration, though only small gains are obtained beyond three iterations. Secondary structures composed of base pairs with estimated probabilities higher than a

  14. Structural abnormalities and altered regional brain activity in multiple sclerosis with simple spinal cord involvement.

    Science.gov (United States)

    Yin, Ping; Liu, Yi; Xiong, Hua; Han, Yongliang; Sah, Shambhu Kumar; Zeng, Chun; Wang, Jingjie; Li, Yongmei

    2018-02-01

    To assess the changes of the structural and functional abnormalities in multiple sclerosis with simple spinal cord involvement (MS-SSCI) by using resting-state functional MRI (RS-fMRI), voxel based morphology (VBM) and diffusion tensor tractography. The amplitude of low-frequency fluctuation (ALFF) of 22 patients with MS-SSCI and 22 healthy controls (HCs) matched for age, gender and education were compared by using RS-fMRI. We also compared the volume, fractional anisotropy (FA) and apparent diffusion coefficient of the brain regions in baseline brain activity by using VBM and diffusion tensor imaging. The relationships between the expanded disability states scale (EDSS) scores, changed parameters of structure and function were further explored. (1) Compared with HCs, the ALFF of the bilateral hippocampus and right middle temporal gyrus in MS-SSCI decreased significantly. However, patients exhibited increased ALFF in the left middle frontal gyrus, left posterior cingulate gyrus and right middle occipital gyrus ( two-sample t-test, after AlphaSim correction, p 40). The volume of right middle frontal gyrus reduced significantly (p right hippocampus, the FA of left hippocampus and right middle temporal gyrus were significantly different. (2) A significant correlation between EDSS scores and ALFF was noted only in the left posterior cingulate gyrus. Our results detected structural and functional abnormalities in MS-SSCI and functional parameters were associated with clinical abnormalities. Multimodal imaging plays an important role in detecting structural and functional abnormalities in MS-SSCI. Advances in knowledge: This is the first time to apply RS-fMRI, VBM and diffusion tensor tractography to study the structural and functional abnormalities in MS-SSCI, and to explore its correlation with EDSS score.

  15. Structural networks involved in attention and executive functions in multiple sclerosis

    Directory of Open Access Journals (Sweden)

    Sara Llufriu

    2017-01-01

    Full Text Available Attention and executive deficits are disabling symptoms in multiple sclerosis (MS that have been related to disconnection mechanisms. We aimed to investigate changes in structural connectivity in MS and their association with attention and executive performance applying an improved framework that combines high order probabilistic tractography and anatomical exclusion criteria postprocessing. We compared graph theory metrics of structural networks and fractional anisotropy (FA of white matter (WM connections or edges between 72 MS subjects and 38 healthy volunteers (HV and assessed their correlation with cognition. Patients displayed decreased network transitivity, global efficiency and increased path length compared with HV (p < 0.05, corrected. Also, nodal strength was decreased in 26 of 84 gray matter regions. The distribution of nodes with stronger connections or hubs of the network was similar among groups except for the right pallidum and left insula, which became hubs in patients. MS subjects presented reduced edge FA widespread in the network, while FA was increased in 24 connections (p < 0.05, corrected. Decreased integrity of frontoparietal networks, deep gray nuclei and insula correlated with worse attention and executive performance (r between 0.38 and 0.55, p < 0.05, corrected. Contrarily, higher strength in the right transverse temporal cortex and increased FA of several connections (mainly from cingulate, frontal and occipital cortices were associated with worse functioning (r between −0.40 and −0.47, p < 0.05 corrected. In conclusion, structural brain connectivity is disturbed in MS due to widespread impairment of WM connections and gray matter structures. The increased edge connectivity suggests the presence of reorganization mechanisms at the structural level. Importantly, attention and executive performance relates to frontoparietal networks, deep gray nuclei and insula. These results support the relevance of

  16. Band structures in a two-dimensional phononic crystal with rotational multiple scatterers

    Science.gov (United States)

    Song, Ailing; Wang, Xiaopeng; Chen, Tianning; Wan, Lele

    2017-03-01

    In this paper, the acoustic wave propagation in a two-dimensional phononic crystal composed of rotational multiple scatterers is investigated. The dispersion relationships, the transmission spectra and the acoustic modes are calculated by using finite element method. In contrast to the system composed of square tubes, there exist a low-frequency resonant bandgap and two wide Bragg bandgaps in the proposed structure, and the transmission spectra coincide with band structures. Specially, the first bandgap is based on locally resonant mechanism, and the simulation results agree well with the results of electrical circuit analogy. Additionally, increasing the rotation angle can remarkably influence the band structures due to the transfer of sound pressure between the internal and external cavities in low-order modes, and the redistribution of sound pressure in high-order modes. Wider bandgaps are obtained in arrays composed of finite unit cells with different rotation angles. The analysis results provide a good reference for tuning and obtaining wide bandgaps, and hence exploring the potential applications of the proposed phononic crystal in low-frequency noise insulation.

  17. Validation and calibration of structural models that combine information from multiple sources.

    Science.gov (United States)

    Dahabreh, Issa J; Wong, John B; Trikalinos, Thomas A

    2017-02-01

    Mathematical models that attempt to capture structural relationships between their components and combine information from multiple sources are increasingly used in medicine. Areas covered: We provide an overview of methods for model validation and calibration and survey studies comparing alternative approaches. Expert commentary: Model validation entails a confrontation of models with data, background knowledge, and other models, and can inform judgments about model credibility. Calibration involves selecting parameter values to improve the agreement of model outputs with data. When the goal of modeling is quantitative inference on the effects of interventions or forecasting, calibration can be viewed as estimation. This view clarifies issues related to parameter identifiability and facilitates formal model validation and the examination of consistency among different sources of information. In contrast, when the goal of modeling is the generation of qualitative insights about the modeled phenomenon, calibration is a rather informal process for selecting inputs that result in model behavior that roughly reproduces select aspects of the modeled phenomenon and cannot be equated to an estimation procedure. Current empirical research on validation and calibration methods consists primarily of methodological appraisals or case-studies of alternative techniques and cannot address the numerous complex and multifaceted methodological decisions that modelers must make. Further research is needed on different approaches for developing and validating complex models that combine evidence from multiple sources.

  18. Bridging Three Orders of Magnitude: Multiple Scattered Waves Sense Fractal Microscopic Structures via Dispersion

    Science.gov (United States)

    Lambert, Simon A.; Näsholm, Sven Peter; Nordsletten, David; Michler, Christian; Juge, Lauriane; Serfaty, Jean-Michel; Bilston, Lynne; Guzina, Bojan; Holm, Sverre; Sinkus, Ralph

    2015-08-01

    Wave scattering provides profound insight into the structure of matter. Typically, the ability to sense microstructure is determined by the ratio of scatterer size to probing wavelength. Here, we address the question of whether macroscopic waves can report back the presence and distribution of microscopic scatterers despite several orders of magnitude difference in scale between wavelength and scatterer size. In our analysis, monosized hard scatterers 5 μ m in radius are immersed in lossless gelatin phantoms to investigate the effect of multiple reflections on the propagation of shear waves with millimeter wavelength. Steady-state monochromatic waves are imaged in situ via magnetic resonance imaging, enabling quantification of the phase velocity at a voxel size big enough to contain thousands of individual scatterers, but small enough to resolve the wavelength. We show in theory, experiments, and simulations that the resulting coherent superposition of multiple reflections gives rise to power-law dispersion at the macroscopic scale if the scatterer distribution exhibits apparent fractality over an effective length scale that is comparable to the probing wavelength. Since apparent fractality is naturally present in any random medium, microstructure can thereby leave its fingerprint on the macroscopically quantifiable power-law exponent. Our results are generic to wave phenomena and carry great potential for sensing microstructure that exhibits intrinsic fractality, such as, for instance, vasculature.

  19. The structure of service quality perceptions for multiple-encounter services.

    Science.gov (United States)

    Andaleeb, Syed Saad; Kara, Ali

    2013-01-01

    The objective of this study was to examine a complex service environment-hospitals-to suggest how service quality could be reframed and measured for multiple-encounter service situations more effectively. In this cross-sectional study, a sample of 371 patients completed the survey instrument. Service quality measures were guided by the literature but allowed to flow from the respondents at the preliminary stage. Confirmatory factor analysis, along with structural equation modeling, was used to test the hypothesized relationships among key actors' performance metrics (KAPMs). Patient satisfaction is significantly influenced by perceived service quality based on KAPMs. For multiple-encounter services, service quality dimensions and measures ought to be tied to KAPMs. Primary actors-ie, doctors-need knowledge and skills about patient psychology, negotiation, handling difficult patients, and, importantly, "putting the customer first." Sensitivity training on such matters should be provided. The secondary actors are the nurses who have more frequent contact with the patients. Nurses need to be perceived as "patient advocates." Effective advocacy begins with prompt and caring services to build trust. The tertiary actors in their support role also ought to be integrated into becoming vital part of the service provided.

  20. Characterisation of ultrasonic structural noise in multiple scattering media using phased arrays

    International Nuclear Information System (INIS)

    Bedetti, T; Dorval, V; Jenson, F; Derode, A

    2013-01-01

    The ultrasonic inspection of multiple scattering media gives rise to structural noise which makes it difficult to detect potential damage or crack inside the component. In order to predict the performances of ultrasonic inspection over such complex media, scattering models can be used. Such models rely on specific key parameters describing the multiple scattering process, which can be determined by specific measurements and post-processing techniques. Such experiments were carried out on stainless steel plates using linear phased-arrays. They consist in recording the response matrix constituted by impulse responses between all the elements of the array. By conducting post-processing on this matrix, we measure the elastic mean free path l e and the correlation distance d c of the recorded noise. Additionally, the dynamic behaviour of the coherent backscattering effect was studied in order to measure the diffusion constant D. Plane-wave beamforming has been applied to the response matrix to improve the angular resolution and the signal-to-noise ratio of the backscattered intensity. Details of postprocessing techniques will be shown

  1. Reliability-based assessment of deteriorating ship structures operating in multiple sea loading climates

    Energy Technology Data Exchange (ETDEWEB)

    Moan, Torgeir [Centre for Ships and Ocean Structures, Norwegian University of Science and Technology, Marine Technology Centre, Tyholt, N 7491 Trondheim (Norway)], E-mail: tormo@marin.ntnu.no; Ayala-Uraga, Efren [Department of Marine Technology, Norwegian University of Science and Technology, Marine Technology Centre, Tyholt, N 7491 Trondheim (Norway)

    2008-03-15

    A reliability-based model for assessment of deteriorating ships subjected to multiple environmental conditions is established. Deterioration due to combined crack growth and corrosion in structural components of a ship hull is accounted for based on a fracture mechanics formulation. The model enables to take into account the corrosion-induced increased crack growth rate in two ways: (1) the increased stress range produced by the plate thinning (wastage) effect and (2) corrosion fatigue itself. Sensitivity studies are carried out to evaluate the effect of inspection updating on a production ship subjected to two different climate conditions. The hazard rate concept is adopted as a measure of reliability and emphasized throughout the different case studies.

  2. Effect of multiple Higgs fields on the phase structure of the SU(2)-Higgs model

    International Nuclear Information System (INIS)

    Wurtz, Mark; Steele, T. G.; Lewis, Randy

    2009-01-01

    The SU(2)-Higgs model, with a single Higgs field in the fundamental representation and a quartic self-interaction, has a Higgs region and a confinement region which are analytically connected in the parameter space of the theory; these regions thus represent a single phase. The effect of multiple Higgs fields on this phase structure is examined via Monte Carlo lattice simulations. For the case of N≥2 identical Higgs fields, there is no remaining analytic connection between the Higgs and confinement regions, at least when Lagrangian terms that directly couple different Higgs flavors are omitted. An explanation of this result in terms of enhancement from overlapping phase transitions is explored for N=2 by introducing an asymmetry in the hopping parameters of the Higgs fields. It is found that an enhancement of the phase transitions can still occur for a moderate (10%) asymmetry in the resulting hopping parameters.

  3. Probing nuclear shell structure beyond the N=40 subshell using multiple Coulomb excitation and transfer experiments

    Energy Technology Data Exchange (ETDEWEB)

    Hellgartner, Stefanie Christine

    2015-11-13

    In this work, the N=40 subshell closure is investigated with two complementary methods using a radioactive {sup 72}Zn ISOLDE beam: One- and two-neutron transfer reactions and multiple Coulomb excitation. In the one-neutron transfer reaction, two new levels of {sup 73}Zn were discovered. The two-neutron transfer channel allowed to study the differential cross section of the ground state and the 2{sup +}{sub 1} state of {sup 74}Zn. In the Coulomb excitation experiment, the measured B(E2) values and quadrupole moments of {sup 72}Zn showed that the yrast states 0{sup +}{sub 1}, 2{sup +}{sub 1} and 4{sup +}{sub 1} are moderately collective. Contrary, the 0{sup +}{sub 2} state has a different structure, since it features a stronger closed N=40 configuration compared to the ground state.

  4. Long-term structural retinal changes in patients with optic neuritis related to multiple sclerosis

    DEFF Research Database (Denmark)

    Andersen, Maria Rene; Roar, Malte; Sejbaek, Tobias

    2017-01-01

    fiber layer (RNFL) thickness (56 vs 67 μm, P=0.01). In an age- and sex-adjusted logistic regression model, lower inferior and temporal RNFL were associated with a higher risk of ON (odds ratio [OR] 1.56 [95% confidence interval {CI} 1.01-2.41] and OR 1.74 [95% CI 1.10-2.77] per 10 μm decrement in RNFL......PURPOSE: To evaluate the long-term structural and functional outcome in patients with multiple sclerosis (MS) with and without a history of optic neuritis (ON). METHODS: This was a cross-sectional study of 82 patients diagnosed with MS between 2000 and 2006 from a tertiary hospital center...

  5. Structural analysis of CdS thin films obtained by multiple dips of oscillating chemical bath

    Energy Technology Data Exchange (ETDEWEB)

    Gutierrez Lazos, C.D. [Seccion de Electronica del Estado Solido, Centro de Investigacion y de Estudios Avanzados, Av. Instituto Politecnico Nacional 2508, Col. San Pedro Zacatenco, 07360 Mexico, D.F. (Mexico); Rosendo, E., E-mail: erosendo@siu.buap.m [Centro de Investigacion en Dispositivos Semiconductores, Universidad Autonoma de Puebla, 14 Sur y San Claudio, Col. San Manuel, C.P. 72570, Puebla (Mexico); Ortega, M. [Seccion de Electronica del Estado Solido, Centro de Investigacion y de Estudios Avanzados, Av. Instituto Politecnico Nacional 2508, Col. San Pedro Zacatenco, 07360 Mexico, D.F. (Mexico); Oliva, A.I. [Departamento de Fisica Aplicada, Centro de Investigacion y de Estudios Avanzados, Unidad Merida, A.P. 73 Cordemex, 97310 Merida, Yucatan (Mexico); Tapia, O.; Diaz, T.; Juarez, H.; Garcia, G. [Centro de Investigacion en Dispositivos Semiconductores, Universidad Autonoma de Puebla, 14 Sur y San Claudio, Col. San Manuel, C.P. 72570, Puebla (Mexico); Rubin, M. [Facultad de Ciencias de la Computacion, 14 Sur y San Claudio, Col. San Manuel, C.P. 72570, Puebla (Mexico)

    2009-11-25

    Highly oriented CdS thin films with thicknesses greater than 1 mum were deposited by multiple dips, using oscillating chemical bath deposition (OCBD) at the bath temperature of 75 deg. C, and deposition time ranging from 15 to 75 min for a single dip. Samples with different thickness were prepared by repeating the deposition process for two and three times. The films deposited by a single dip have the alpha-greenockite structure showing the (0 0 2) as preferred orientation, as indicated by the X-ray diffraction measurements. This notable characteristic is preserved in the samples obtained from two or three dips. The crystallite size for the samples deposited by a single dip depends on the deposition time, because it varied from 23 to 37 nm as the deposition time increased. Nevertheless for samples deposited by two and three dips, the grain size shows no noticeable change, being about 22 nm.

  6. Moisture migration, microstructure damage and protein structure changes in porcine longissimus muscle as influenced by multiple freeze-thaw cycles.

    Science.gov (United States)

    Zhang, Mingcheng; Li, Fangfei; Diao, Xinping; Kong, Baohua; Xia, Xiufang

    2017-11-01

    This study investigated the effects of multiple freeze-thaw (F-T) cycles on water mobility, microstructure damage and protein structure changes in porcine longissimus muscle. The transverse relaxation time T 2 increased significantly when muscles were subjected to multiple F-T cycles (Pcycles caused sarcomere shortening, Z line fractures, and I band weakening and also led to microstructural destruction of muscle tissue. The decreased free amino group content and increased dityrosine in myofibrillar protein (MP) revealed that multiple F-T cycles caused protein cross-linking and oxidation. In addition, the results of size exclusion chromatography, circular dichroism spectra, UV absorption spectra, and intrinsic fluorescence spectroscopy indirectly proved that multiple F-T cycles could cause protein aggregation and degradation, α-helix structure disruption, hydrophobic domain exposure, and conformational changes of MP. Overall, repeated F-T cycles changed the protein structure and water distribution within meat. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Near Real Time Structural Health Monitoring with Multiple Sensors in a Cloud Environment

    Science.gov (United States)

    Bock, Y.; Todd, M.; Kuester, F.; Goldberg, D.; Lo, E.; Maher, R.

    2017-12-01

    A repeated near real time 3-D digital surrogate representation of critical engineered structures can be used to provide actionable data on subtle time-varying displacements in support of disaster resiliency. We describe a damage monitoring system of optimally-integrated complementary sensors, including Global Navigation Satellite Systems (GNSS), Micro-Electro-Mechanical Systems (MEMS) accelerometers coupled with the GNSS (seismogeodesy), light multi-rotor Unmanned Aerial Vehicles (UAVs) equipped with high-resolution digital cameras and GNSS/IMU, and ground-based Light Detection and Ranging (LIDAR). The seismogeodetic system provides point measurements of static and dynamic displacements and seismic velocities of the structure. The GNSS ties the UAV and LIDAR imagery to an absolute reference frame with respect to survey stations in the vicinity of the structure to isolate the building response to ground motions. The GNSS/IMU can also estimate the trajectory of the UAV with respect to the absolute reference frame. With these constraints, multiple UAVs and LIDAR images can provide 4-D displacements of thousands of points on the structure. The UAV systematically circumnavigates the target structure, collecting high-resolution image data, while the ground LIDAR scans the structure from different perspectives to create a detailed baseline 3-D reference model. UAV- and LIDAR-based imaging can subsequently be repeated after extreme events, or after long time intervals, to assess before and after conditions. The unique challenge is that disaster environments are often highly dynamic, resulting in rapidly evolving, spatio-temporal data assets with the need for near real time access to the available data and the tools to translate these data into decisions. The seismogeodetic analysis has already been demonstrated in the NASA AIST Managed Cloud Environment (AMCE) designed to manage large NASA Earth Observation data projects on Amazon Web Services (AWS). The Cloud provides

  8. 3D fluid-structure modelling and vibration analysis for fault diagnosis of Francis turbine using multiple ANN and multiple ANFIS

    Science.gov (United States)

    Saeed, R. A.; Galybin, A. N.; Popov, V.

    2013-01-01

    This paper discusses condition monitoring and fault diagnosis in Francis turbine based on integration of numerical modelling with several different artificial intelligence (AI) techniques. In this study, a numerical approach for fluid-structure (turbine runner) analysis is presented. The results of numerical analysis provide frequency response functions (FRFs) data sets along x-, y- and z-directions under different operating load and different position and size of faults in the structure. To extract features and reduce the dimensionality of the obtained FRF data, the principal component analysis (PCA) has been applied. Subsequently, the extracted features are formulated and fed into multiple artificial neural networks (ANN) and multiple adaptive neuro-fuzzy inference systems (ANFIS) in order to identify the size and position of the damage in the runner and estimate the turbine operating conditions. The results demonstrated the effectiveness of this approach and provide satisfactory accuracy even when the input data are corrupted with certain level of noise.

  9. Optimal design of structures with multiple design variables per group and multiple loading conditions on the personal computer

    Science.gov (United States)

    Nguyen, D. T.; Rogers, J. L., Jr.

    1986-01-01

    A finite element based programming system for minimum weight design of a truss-type structure subjected to displacement, stress, and lower and upper bounds on design variables is presented. The programming system consists of a number of independent processors, each performing a specific task. These processors, however, are interfaced through a well-organized data base, thus making the tasks of modifying, updating, or expanding the programming system much easier in a friendly environment provided by many inexpensive personal computers. The proposed software can be viewed as an important step in achieving a 'dummy' finite element for optimization. The programming system has been implemented on both large and small computers (such as VAX, CYBER, IBM-PC, and APPLE) although the focus is on the latter. Examples are presented to demonstrate the capabilities of the code. The present programming system can be used stand-alone or as part of the multilevel decomposition procedure to obtain optimum design for very large scale structural systems. Furthermore, other related research areas such as developing optimization algorithms (or in the larger level: a structural synthesis program) for future trends in using parallel computers may also benefit from this study.

  10. Analysis, Design, and Construction of a Base-Isolated Multiple Building Structure

    Directory of Open Access Journals (Sweden)

    Stefano Sorace

    2014-01-01

    Full Text Available The analysis and design of a multiple residential building, seismically protected by a base isolation system incorporating double friction pendulum sliders as protective devices, are presented in the paper. The building, situated in the suburban area of Florence, is composed of four independent reinforced concrete framed structures, mutually separated by three thermal expansion joints. The plan is L-shaped, with dimensions of about 75 m in the longitudinal direction and about 30 m along the longest side of the transversal direction. These characteristics identify the structure as the largest example of a base-isolated “artificial ground” ever built in Italy. The base isolation solution guarantees lower costs, a much greater performance, and a finer architectural look, as compared to a conventional fixed-base antiseismic design. The characteristics of the building and the isolators, the mechanical properties and the experimental characterization campaign and preliminary sizing carried out on the latter, and the nonlinear time-history design and performance assessment analyses developed on the base isolated building are reported in this paper, along with details about the installation of the isolators and the plants and highlights of the construction works.

  11. Long-term structural retinal changes in patients with optic neuritis related to multiple sclerosis

    Directory of Open Access Journals (Sweden)

    Andersen MR

    2017-08-01

    Full Text Available Maria Rene Andersen,1 Malte Roar,2,3 Tobias Sejbaek,2,3 Zsolt Illes,2,3 Jakob Grauslund1,3 1Department of Ophthalmology, Odense University Hospital, Odense, Denmark; 2Department of Neurology, Odense University Hospital, Odense, Denmark; 3Department of Clinical Research, University of Southern Denmark, Odense, Denmark Purpose: To evaluate the long-term structural and functional outcome in patients with multiple sclerosis (MS with and without a history of optic neuritis (ON.Methods: This was a cross-sectional study of 82 patients diagnosed with MS between 2000 and 2006 from a tertiary hospital center in Denmark. Patients gave a self-reported history of ON, and functional (visual acuity and color vision and structural (spectra domain optical coherence tomography markers of vision were tested.Results: Median age and MS duration at the time of the clinical examination were 49.9 years (range 30.7–72.6 years and 13 years (range 9–15 years, respectively. ON was not associated with impairment of visual acuity or color vision. Twenty-three patients had a history of ON in at least one eye. Compared to non-affected patients, these had a lower inferior (109 vs 113 µm, P=0.04 and temporal retinal nerve fiber layer (RNFL thickness (56 vs 67 µm, P=0.01. In an age- and sex-adjusted logistic regression model, lower inferior and temporal RNFL were associated with a higher risk of ON (odds ratio [OR] 1.56 [95% confidence interval {CI} 1.01–2.41] and OR 1.74 [95% CI 1.10–2.77] per 10 µm decrement in RNFL thickness, respectively. Twenty patients had a history of ON in one eye. Compared to the non-affected eye, this eye had a lower RNFL (109 vs 115 µm, P=0.04 and a higher central retinal thickness/mean RNFL ratio (2.7 vs 2.4, P=0.04.Conclusion: Although patients with long-term MS and a previous history of ON did not have any functional loss of vision, structural neurodegeneration could be demonstrated in the affected eye. Keywords: optic neuritis

  12. Conserved helicase domain of human RecQ4 is required for strand annealing-independent DNA unwinding

    DEFF Research Database (Denmark)

    Rossi, Marie L; Ghosh, Avik K; Kulikowicz, Tomasz

    2010-01-01

    Humans have five members of the well conserved RecQ helicase family: RecQ1, Bloom syndrome protein (BLM), Werner syndrome protein (WRN), RecQ4, and RecQ5, which are all known for their roles in maintaining genome stability. BLM, WRN, and RecQ4 are associated with premature aging and cancer...... provide the first evidence that human RecQ4's unwinding is independent of strand annealing, and that it does not require the presence of excess ssDNA. Moreover, we demonstrate that a point mutation of the conserved lysine in the Walker A motif abolished helicase activity, implying that not the N...... activities and protein partners of RecQ4 are conserved with those of the other RecQ helicases....

  13. Association between MRI structural features and cognitive measures in pediatric multiple sclerosis

    Science.gov (United States)

    Amoroso, N.; Bellotti, R.; Fanizzi, A.; Lombardi, A.; Monaco, A.; Liguori, M.; Margari, L.; Simone, M.; Viterbo, R. G.; Tangaro, S.

    2017-09-01

    Multiple sclerosis (MS) is an inflammatory and demyelinating disease associated with neurodegenerative processes that lead to brain structural changes. The disease affects mostly young adults, but 3-5% of cases has a pediatric onset (POMS). Magnetic Resonance Imaging (MRI) is generally used for diagnosis and follow-up in MS patients, however the most common MRI measures (e.g. new or enlarging T2-weighted lesions, T1-weighted gadolinium- enhancing lesions) have often failed as surrogate markers of MS disability and progression. MS is clinically heterogenous with symptoms that can include both physical changes (such as visual loss or walking difficulties) and cognitive impairment. 30-50% of POMS experience prominent cognitive dysfunction. In order to investigate the association between cognitive measures and brain morphometry, in this work we present a fully automated pipeline for processing and analyzing MRI brain scans. Relevant anatomical structures are segmented with FreeSurfer; besides, statistical features are computed. Thus, we describe the data referred to 12 patients with early POMS (mean age at MRI: 15.5 +/- 2.7 years) with a set of 181 structural features. The major cognitive abilities measured are verbal and visuo-spatial learning, expressive language and complex attention. Data was collected at the Department of Basic Sciences, Neurosciences and Sense Organs, University of Bari, and exploring different abilities like the verbal and visuo-spatial learning, expressive language and complex attention. Different regression models and parameter configurations are explored to assess the robustness of the results, in particular Generalized Linear Models, Bayes Regression, Random Forests, Support Vector Regression and Artificial Neural Networks are discussed.

  14. Multiple amino acid sequence alignment nitrogenase component 1: insights into phylogenetics and structure-function relationships.

    Directory of Open Access Journals (Sweden)

    James B Howard

    Full Text Available Amino acid residues critical for a protein's structure-function are retained by natural selection and these residues are identified by the level of variance in co-aligned homologous protein sequences. The relevant residues in the nitrogen fixation Component 1 α- and β-subunits were identified by the alignment of 95 protein sequences. Proteins were included from species encompassing multiple microbial phyla and diverse ecological niches as well as the nitrogen fixation genotypes, anf, nif, and vnf, which encode proteins associated with cofactors differing at one metal site. After adjusting for differences in sequence length, insertions, and deletions, the remaining >85% of the sequence co-aligned the subunits from the three genotypes. Six Groups, designated Anf, Vnf , and Nif I-IV, were assigned based upon genetic origin, sequence adjustments, and conserved residues. Both subunits subdivided into the same groups. Invariant and single variant residues were identified and were defined as "core" for nitrogenase function. Three species in Group Nif-III, Candidatus Desulforudis audaxviator, Desulfotomaculum kuznetsovii, and Thermodesulfatator indicus, were found to have a seleno-cysteine that replaces one cysteinyl ligand of the 8Fe:7S, P-cluster. Subsets of invariant residues, limited to individual groups, were identified; these unique residues help identify the gene of origin (anf, nif, or vnf yet should not be considered diagnostic of the metal content of associated cofactors. Fourteen of the 19 residues that compose the cofactor pocket are invariant or single variant; the other five residues are highly variable but do not correlate with the putative metal content of the cofactor. The variable residues are clustered on one side of the cofactor, away from other functional centers in the three dimensional structure. Many of the invariant and single variant residues were not previously recognized as potentially critical and their identification

  15. Long-term structural retinal changes in patients with optic neuritis related to multiple sclerosis

    Science.gov (United States)

    Andersen, Maria Rene; Roar, Malte; Sejbaek, Tobias; Illes, Zsolt; Grauslund, Jakob

    2017-01-01

    Purpose To evaluate the long-term structural and functional outcome in patients with multiple sclerosis (MS) with and without a history of optic neuritis (ON). Methods This was a cross-sectional study of 82 patients diagnosed with MS between 2000 and 2006 from a tertiary hospital center in Denmark. Patients gave a self-reported history of ON, and functional (visual acuity and color vision) and structural (spectra domain optical coherence tomography) markers of vision were tested. Results Median age and MS duration at the time of the clinical examination were 49.9 years (range 30.7–72.6 years) and 13 years (range 9–15 years), respectively. ON was not associated with impairment of visual acuity or color vision. Twenty-three patients had a history of ON in at least one eye. Compared to non-affected patients, these had a lower inferior (109 vs 113 μm, P=0.04) and temporal retinal nerve fiber layer (RNFL) thickness (56 vs 67 μm, P=0.01). In an age- and sex-adjusted logistic regression model, lower inferior and temporal RNFL were associated with a higher risk of ON (odds ratio [OR] 1.56 [95% confidence interval {CI} 1.01–2.41] and OR 1.74 [95% CI 1.10–2.77] per 10 μm decrement in RNFL thickness, respectively). Twenty patients had a history of ON in one eye. Compared to the non-affected eye, this eye had a lower RNFL (109 vs 115 μm, P=0.04) and a higher central retinal thickness/mean RNFL ratio (2.7 vs 2.4, P=0.04). Conclusion Although patients with long-term MS and a previous history of ON did not have any functional loss of vision, structural neurodegeneration could be demonstrated in the affected eye. PMID:28860702

  16. Long-term structural retinal changes in patients with optic neuritis related to multiple sclerosis.

    Science.gov (United States)

    Andersen, Maria Rene; Roar, Malte; Sejbaek, Tobias; Illes, Zsolt; Grauslund, Jakob

    2017-01-01

    To evaluate the long-term structural and functional outcome in patients with multiple sclerosis (MS) with and without a history of optic neuritis (ON). This was a cross-sectional study of 82 patients diagnosed with MS between 2000 and 2006 from a tertiary hospital center in Denmark. Patients gave a self-reported history of ON, and functional (visual acuity and color vision) and structural (spectra domain optical coherence tomography) markers of vision were tested. Median age and MS duration at the time of the clinical examination were 49.9 years (range 30.7-72.6 years) and 13 years (range 9-15 years), respectively. ON was not associated with impairment of visual acuity or color vision. Twenty-three patients had a history of ON in at least one eye. Compared to non-affected patients, these had a lower inferior (109 vs 113 μm, P =0.04) and temporal retinal nerve fiber layer (RNFL) thickness (56 vs 67 μm, P =0.01). In an age- and sex-adjusted logistic regression model, lower inferior and temporal RNFL were associated with a higher risk of ON (odds ratio [OR] 1.56 [95% confidence interval {CI} 1.01-2.41] and OR 1.74 [95% CI 1.10-2.77] per 10 μm decrement in RNFL thickness, respectively). Twenty patients had a history of ON in one eye. Compared to the non-affected eye, this eye had a lower RNFL (109 vs 115 μm, P =0.04) and a higher central retinal thickness/mean RNFL ratio (2.7 vs 2.4, P =0.04). Although patients with long-term MS and a previous history of ON did not have any functional loss of vision, structural neurodegeneration could be demonstrated in the affected eye.

  17. Quantitative analysis of structural variations in corpus callosum in adults with multiple system atrophy (MSA)

    Science.gov (United States)

    Bhattacharya, Debanjali; Sinha, Neelam; Saini, Jitender

    2017-03-01

    Multiple system atrophy (MSA) is a rare, non-curable, progressive neurodegenerative disorder that affects nervous system and movement, poses a considerable diagnostic challenge to medical researchers. Corpus callosum (CC) being the largest white matter structure in brain, enabling inter-hemispheric communication, quantification of callosal atrophy may provide vital information at the earliest possible stages. The main objective is to identify the differences in CC structure for this disease, based on quantitative analysis on the pattern of callosal atrophy. We report results of quantification of structural changes in regional anatomical thickness, area and length of CC between patient-groups with MSA with respect to healthy controls. The method utilizes isolating and parcellating the mid-sagittal CC into 100 segments along the length - measuring the width of each segment. It also measures areas within geometrically defined five callosal compartments of the well-known Witelson, and Hofer-Frahma schemes. For quantification, statistical tests are performed on these different callosal measurements. From the statistical analysis, it is concluded that compared to healthy controls, width is reduced drastically throughout CC for MSA group and as well as changes in area and length are also significant for MSA. The study is further extended to check if any significant difference in thickness is found between the two variations of MSA, Parkinsonian MSA and Cerebellar MSA group, using the same methodology. However area and length of this two sub-MSA group, no substantial difference is obtained. The study is performed on twenty subjects for each control and MSA group, who had T1-weighted MRI.

  18. Evaluating the effect of multiple sclerosis lesions on automatic brain structure segmentation

    Directory of Open Access Journals (Sweden)

    Sandra González-Villà

    2017-01-01

    Full Text Available In recent years, many automatic brain structure segmentation methods have been proposed. However, these methods are commonly tested with non-lesioned brains and the effect of lesions on their performance has not been evaluated. Here, we analyze the effect of multiple sclerosis (MS lesions on three well-known automatic brain structure segmentation methods, namely, FreeSurfer, FIRST and multi-atlas fused by majority voting, which use learning-based, deformable and atlas-based strategies, respectively. To perform a quantitative analysis, 100 synthetic images of MS patients with a total of 2174 lesions are simulated on two public databases with available brain structure ground truth information (IBSR18 and MICCAI’12. The Dice similarity coefficient (DSC differences and the volume differences between the healthy and the simulated images are calculated for the subcortical structures and the brainstem. We observe that the three strategies are affected when lesions are present. However, the effects of the lesions do not follow the same pattern; the lesions either make the segmentation method underperform or surprisingly augment the segmentation accuracy. The obtained results show that FreeSurfer is the method most affected by the presence of lesions, with DSC differences (generated − healthy ranging from −0.11 ± 0.54 to 9.65 ± 9.87, whereas FIRST tends to be the most robust method when lesions are present (−2.40 ± 5.54 to 0.44 ± 0.94. Lesion location is not important for global strategies such as FreeSurfer or majority voting, where structure segmentation is affected wherever the lesions exist. On the other hand, FIRST is more affected when the lesions are overlaid or close to the structure of analysis. The most affected structure by the presence of lesions is the nucleus accumbens (from −1.12 ± 2.53 to 1.32 ± 4.00 for the left hemisphere and from −2.40 ± 5.54 to 9.65 ± 9.87 for the right hemisphere, whereas the

  19. In vivo mapping of the functional regions of the DEAD-box helicase Vasa

    Directory of Open Access Journals (Sweden)

    Mehrnoush Dehghani

    2015-03-01

    Full Text Available The maternally expressed Drosophila melanogaster DEAD-box helicase Vasa (Vas is necessary for many cellular and developmental processes, including specification of primordial germ cells (pole cells, posterior patterning of the embryo, piRNA-mediated repression of transposon-encoded mRNAs, translational activation of gurken (grk mRNA, and completion of oogenesis itself. Vas protein accumulates in the perinuclear nuage in nurse cells soon after their specification, and then at stage 10 Vas translocates to the posterior pole plasm of the oocyte. We produced a series of transgenic constructs encoding eGFP-Vas proteins carrying mutations affecting different regions of the protein, and analyzed in vivo which Vas functions each could support. We identified novel domains in the N- and C-terminal regions of the protein that are essential for localization, transposon repression, posterior patterning, and pole cell specification. One such functional region, the most C-terminal seven amino acids, is specific to Vas orthologues and is thus critical to distinguishing Vas from other closely related DEAD-box helicases. Surprisingly, we also found that many eGFP-Vas proteins carrying mutations that would be expected to abrogate DEAD-box helicase function localized to the nuage and posterior pole, and retained the capacity to support oogenesis, although they did not function in embryonic patterning, pole cell specification, grk activation, or transposon repression. We conclude from these experiments that Vas, a multifunctional protein, uses different domains and different molecular associations to carry out its various cellular and developmental roles.

  20. Functional interaction between Smad, CREB binding protein, and p68 RNA helicase

    International Nuclear Information System (INIS)

    Warner, Dennis R.; Bhattacherjee, Vasker; Yin, Xiaolong; Singh, Saurabh; Mukhopadhyay, Partha; Pisano, M. Michele; Greene, Robert M.

    2004-01-01

    The transforming growth factors β control a diversity of biological processes including cellular proliferation, differentiation, apoptosis, and extracellular matrix production, and are critical effectors of embryonic patterning and development, including that of the orofacial region. TGFβ superfamily members signal through specific cell surface receptors that phosphorylate the cytoplasmic Smad proteins, resulting in their translocation to the nucleus and interaction with promoters of TGFβ-responsive genes. Subsequent alterations in transcription are cell type-specific and dependent on recruitment to the Smad/transcription factor complex of coactivators, such as CBP and p300, or corepressors, such as c-ski and SnoN. Since the affinity of Smads for DNA is generally low, additional accessory proteins that facilitate Smad/DNA binding are required, and are often cell- and tissue-specific. In order to identify novel Smad 3 binding proteins in developing orofacial tissue, a yeast two hybrid assay was employed in which the MH2 domain of Smad 3 was used to screen an expression library derived from mouse embryonic orofacial tissue. The RNA helicase, p68, was identified as a unique Smad binding protein, and the specificity of the interaction was confirmed through various in vitro and in vivo assays. Co-expression of Smad 3 and a CBP-Gal4 DNA binding domain fusion protein in a Gal4-luciferase reporter assay resulted in increased TGFβ-stimulated reporter gene transcription. Moreover, co-expression of p68 RNA helicase along with Smad 3 and CBP-Gal4 resulted in synergistic activation of Gal4-luciferase reporter expression. Collectively, these data indicate that the RNA helicase, p68, can directly interact with Smad 3 resulting in formation of a transcriptionally active ternary complex containing Smad 3, p68, and CBP. This offers a means of enhancing TGFβ-mediated cellular responses in developing orofacial tissue

  1. Probabilistic risk assessment framework for structural systems under multiple hazards using Bayesian statistics

    International Nuclear Information System (INIS)

    Kwag, Shinyoung; Gupta, Abhinav

    2017-01-01

    Highlights: • This study presents the development of Bayesian framework for probabilistic risk assessment (PRA) of structural systems under multiple hazards. • The concepts of Bayesian network and Bayesian inference are combined by mapping the traditionally used fault trees into a Bayesian network. • The proposed mapping allows for consideration of dependencies as well as correlations between events. • Incorporation of Bayesian inference permits a novel way for exploration of a scenario that is likely to result in a system level “vulnerability.” - Abstract: Conventional probabilistic risk assessment (PRA) methodologies (USNRC, 1983; IAEA, 1992; EPRI, 1994; Ellingwood, 2001) conduct risk assessment for different external hazards by considering each hazard separately and independent of each other. The risk metric for a specific hazard is evaluated by a convolution of the fragility and the hazard curves. The fragility curve for basic event is obtained by using empirical, experimental, and/or numerical simulation data for a particular hazard. Treating each hazard as an independently can be inappropriate in some cases as certain hazards are statistically correlated or dependent. Examples of such correlated events include but are not limited to flooding induced fire, seismically induced internal or external flooding, or even seismically induced fire. In the current practice, system level risk and consequence sequences are typically calculated using logic trees to express the causative relationship between events. In this paper, we present the results from a study on multi-hazard risk assessment that is conducted using a Bayesian network (BN) with Bayesian inference. The framework can consider statistical dependencies among risks from multiple hazards, allows updating by considering the newly available data/information at any level, and provide a novel way to explore alternative failure scenarios that may exist due to vulnerabilities.

  2. Probabilistic risk assessment framework for structural systems under multiple hazards using Bayesian statistics

    Energy Technology Data Exchange (ETDEWEB)

    Kwag, Shinyoung [North Carolina State University, Raleigh, NC 27695 (United States); Korea Atomic Energy Research Institute, Daejeon 305-353 (Korea, Republic of); Gupta, Abhinav, E-mail: agupta1@ncsu.edu [North Carolina State University, Raleigh, NC 27695 (United States)

    2017-04-15

    Highlights: • This study presents the development of Bayesian framework for probabilistic risk assessment (PRA) of structural systems under multiple hazards. • The concepts of Bayesian network and Bayesian inference are combined by mapping the traditionally used fault trees into a Bayesian network. • The proposed mapping allows for consideration of dependencies as well as correlations between events. • Incorporation of Bayesian inference permits a novel way for exploration of a scenario that is likely to result in a system level “vulnerability.” - Abstract: Conventional probabilistic risk assessment (PRA) methodologies (USNRC, 1983; IAEA, 1992; EPRI, 1994; Ellingwood, 2001) conduct risk assessment for different external hazards by considering each hazard separately and independent of each other. The risk metric for a specific hazard is evaluated by a convolution of the fragility and the hazard curves. The fragility curve for basic event is obtained by using empirical, experimental, and/or numerical simulation data for a particular hazard. Treating each hazard as an independently can be inappropriate in some cases as certain hazards are statistically correlated or dependent. Examples of such correlated events include but are not limited to flooding induced fire, seismically induced internal or external flooding, or even seismically induced fire. In the current practice, system level risk and consequence sequences are typically calculated using logic trees to express the causative relationship between events. In this paper, we present the results from a study on multi-hazard risk assessment that is conducted using a Bayesian network (BN) with Bayesian inference. The framework can consider statistical dependencies among risks from multiple hazards, allows updating by considering the newly available data/information at any level, and provide a novel way to explore alternative failure scenarios that may exist due to vulnerabilities.

  3. Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework

    Directory of Open Access Journals (Sweden)

    Toh Hiroyuki

    2008-04-01

    Full Text Available Abstract Background Structural alignment of RNAs is becoming important, since the discovery of functional non-coding RNAs (ncRNAs. Recent studies, mainly based on various approximations of the Sankoff algorithm, have resulted in considerable improvement in the accuracy of pairwise structural alignment. In contrast, for the cases with more than two sequences, the practical merit of structural alignment remains unclear as compared to traditional sequence-based methods, although the importance of multiple structural alignment is widely recognized. Results We took a different approach from a straightforward extension of the Sankoff algorithm to the multiple alignments from the viewpoints of accuracy and time complexity. As a new option of the MAFFT alignment program, we developed a multiple RNA alignment framework, X-INS-i, which builds a multiple alignment with an iterative method incorporating structural information through two components: (1 pairwise structural alignments by an external pairwise alignment method such as SCARNA or LaRA and (2 a new objective function, Four-way Consistency, derived from the base-pairing probability of every sub-aligned group at every multiple alignment stage. Conclusion The BRAliBASE benchmark showed that X-INS-i outperforms other methods currently available in the sum-of-pairs score (SPS criterion. As a basis for predicting common secondary structure, the accuracy of the present method is comparable to or rather higher than those of the current leading methods such as RNA Sampler. The X-INS-i framework can be used for building a multiple RNA alignment from any combination of algorithms for pairwise RNA alignment and base-pairing probability. The source code is available at the webpage found in the Availability and requirements section.

  4. Dissection of the functional domains of an archaeal holliday junction helicase

    DEFF Research Database (Denmark)

    Hong, Ye; Chu, Mingzhu; Li, Yansheng

    2012-01-01

    Helicases and nucleases form complexes that play very important roles in DNA repair pathways some of which interact with each other at Holliday junctions. In this study, we present in vitro and in vivo analysis of Hjm and its interaction with Hjc in Sulfolobus. In vitro studies employed Hjm from...... conformation change of the enzyme. Furthermore, StoHjm is able to prevent the formation of Hjc/HJ high complex, suggesting a regulation mechanism of Hjm to the activity of Hjc. We show that Hjm is essential for cell viability using recently developed genetic system and mutant propagation assay, suggesting...

  5. Yeast as a model system to study RecQ helicase function

    DEFF Research Database (Denmark)

    Ashton, Thomas M; Hickson, Ian David

    2010-01-01

    Mutations in the highly conserved RecQ helicase, BLM, cause the rare cancer predisposition disorder, Bloom's syndrome. The orthologues of BLM in Saccharomyces cerevisiae and Schizosaccharomyces pombe are SGS1 and rqh1(+), respectively. Studies in these yeast species have revealed a plethora...... of roles for the Sgs1 and Rqh1 proteins in repair of double strand breaks, restart of stalled replication forks, processing of aberrant intermediates that arise during meiotic recombination, and maintenance of telomeres. In this review, we focus on the known roles of Sgs1 and Rqh1 and how studies in yeast...

  6. New roles of the human Suv3 helicase in genome maintenance

    DEFF Research Database (Denmark)

    Venø, Susanne Trillingsgaard

    During her PhD studies, Susanne Trillingsgaard Venø carried out research into the role of the human Suv3 protein in stabilising the human genome – DNA. Suv3 is a helicase that separates the two strands of the DNA’s double helix. Throughout our lives, the DNA in our cells is constantly exposed...... maintenance. Based on these new research results, the Suv3 protein could be a valuable model for genome stability as an important factor in our understanding of why we get old....

  7. RTEL1: an essential helicase for telomere maintenance and the regulation of homologous recombination.

    Science.gov (United States)

    Uringa, Evert-Jan; Youds, Jillian L; Lisaingo, Kathleen; Lansdorp, Peter M; Boulton, Simon J

    2011-03-01

    Telomere maintenance and DNA repair are crucial processes that protect the genome against instability. RTEL1, an essential iron-sulfur cluster-containing helicase, is a dominant factor that controls telomere length in mice and is required for telomere integrity. In addition, RTEL1 promotes synthesis-dependent strand annealing to direct DNA double-strand breaks into non-crossover outcomes during mitotic repair and in meiosis. Here, we review the role of RTEL1 in telomere maintenance and homologous recombination and discuss models linking RTEL1's enzymatic activity to its function in telomere maintenance and DNA repair.

  8. The helicase and ATPase activities of RECQL4 are compromised by mutations reported in three human patients

    DEFF Research Database (Denmark)

    Jensen, Martin Borch; Dunn, Christopher A; Keijzers, Guido

    2012-01-01

    RECQL4 is one of five members of the human RecQ helicase family, and is implicated in three syndromes displaying accelerating aging, developmental abnormalities and a predisposition to cancer. In this study, we purified three variants of RECQL4 carrying previously reported patient mutations....... These three mutant proteins were analyzed for the known biochemical activities of RECQL4: DNA binding, unwinding of duplex DNA, ATP hydrolysis and annealing of simplex DNA. Further, the mutant proteins were evaluated for stability and recruitment to sites of laser-induced DNA damage. One mutant was helicase...

  9. Interface and photoluminescence characteristics of graphene-(GaN/InGaN){sub n} multiple quantum wells hybrid structure

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Liancheng, E-mail: wanglc@semi.ac.cn, E-mail: lzq@semi.ac.cn, E-mail: zh.zhang@hebut.edu.cn [Engineering Product Development Pillar (EPD), Singapore University of Technology & Design (SUTD), 8 Somapah Road, Singapore 487372 (Singapore); Semiconductor Lighting Technology Research and Development Center, Institute of Semiconductors, Chinese Academy of Sciences, Beijing 100083 (China); Mind Star (Beijing) Technology Co., Ltd., Zhongguancun South Street, Haidian District, No. 45 Hing Fat Building 1001, Beijing 100872 (China); Liu, Zhiqiang, E-mail: wanglc@semi.ac.cn, E-mail: lzq@semi.ac.cn, E-mail: zh.zhang@hebut.edu.cn; Tian, Ying Dong; Yi, Xiaoyan; Wang, Junxi; Li, Jinmin; Wang, Guohong [Semiconductor Lighting Technology Research and Development Center, Institute of Semiconductors, Chinese Academy of Sciences, Beijing 100083 (China); Zhang, Zi-Hui, E-mail: wanglc@semi.ac.cn, E-mail: lzq@semi.ac.cn, E-mail: zh.zhang@hebut.edu.cn [Key Laboratory of Electronic Materials and Devices of Tianjin, School of Electronics and Information Engineering, Hebei University of Technology, Tianjin 300401 (China)

    2016-04-14

    The effects of graphene on the optical properties of active system, e.g., the InGaN/GaN multiple quantum wells, are thoroughly investigated and clarified. Here, we have investigated the mechanisms accounting for the photoluminescence reduction for the graphene covered GaN/InGaN multiple quantum wells hybrid structure. Compared to the bare multiple quantum wells, the photoluminescence intensity of graphene covered multiple quantum wells showed a 39% decrease after excluding the graphene absorption losses. The responsible mechanisms have been identified with the following factors: (1) the graphene two dimensional hole gas intensifies the polarization field in multiple quantum wells, thus steepening the quantum well band profile and causing hole-electron pairs to further separate; (2) a lower affinity of graphene compared to air leading to a weaker capability to confine the excited hot electrons in multiple quantum wells; and (3) exciton transfer through non-radiative energy transfer process. These factors are theoretically analysed based on advanced physical models of semiconductor devices calculations and experimentally verified by varying structural parameters, such as the indium fraction in multiple quantum wells and the thickness of the last GaN quantum barrier spacer layer.

  10. Galaxy structure from multiple tracers - III. Radial variations in M87's IMF

    Science.gov (United States)

    Oldham, Lindsay; Auger, Matthew

    2018-03-01

    We present the first constraints on stellar mass-to-light ratio gradients in an early-type galaxy (ETG) using multiple dynamical tracer populations to model the dark and luminous mass structure simultaneously. We combine the kinematics of the central starlight, two globular cluster populations and satellite galaxies in a Jeans analysis to obtain new constraints on M87's mass structure, employing a flexible mass model which allows for radial gradients in the stellar-mass-to-light ratio. We find that, in the context of our model, a radially declining stellar-mass-to-light ratio is strongly favoured. Modelling the stellar-mass-to-light ratio as following a power law, ϒ⋆ ˜ R-μ, we infer a power-law slope μ = -0.54 ± 0.05; equally, parametrizing the stellar-mass-to-light ratio via a central mismatch parameter relative to a Salpeter initial mass function (IMF), α, and scale radius RM, we find α > 1.48 at 95% confidence and RM = 0.35 ± 0.04 kpc. We use stellar population modelling of high-resolution 11-band HST photometry to show that such a steep gradient cannot be achieved by variations in only the metallicity, age, dust extinction and star formation history if the stellar IMF remains spatially constant. On the other hand, the stellar-mass-to-light ratio gradient that we find is consistent with an IMF whose inner slope changes such that it is Salpeter-like in the central ˜0.5 kpc and becomes Chabrier-like within the stellar effective radius. This adds to recent evidence that the non-universality of the IMF in ETGs may be confined to their core regions, and points towards a picture in which the stars in these central regions may have formed in fundamentally different physical conditions.

  11. Structural MRI correlates of cognitive impairment in patients with multiple sclerosis: A Multicenter Study.

    Science.gov (United States)

    Preziosa, Paolo; Rocca, Maria A; Pagani, Elisabetta; Stromillo, Maria Laura; Enzinger, Christian; Gallo, Antonio; Hulst, Hanneke E; Atzori, Matteo; Pareto, Deborah; Riccitelli, Gianna C; Copetti, Massimiliano; De Stefano, Nicola; Fazekas, Franz; Bisecco, Alvino; Barkhof, Frederik; Yousry, Tarek A; Arévalo, Maria J; Filippi, Massimo

    2016-04-01

    In a multicenter setting, we applied voxel-based methods to different structural MR imaging modalities to define the relative contributions of focal lesions, normal-appearing white matter (NAWM), and gray matter (GM) damage and their regional distribution to cognitive deficits as well as impairment of specific cognitive domains in multiple sclerosis (MS) patients. Approval of the institutional review boards was obtained, together with written informed consent from all participants. Standardized neuropsychological assessment and conventional, diffusion tensor and volumetric brain MRI sequences were collected from 61 relapsing-remitting MS patients and 61 healthy controls (HC) from seven centers. Patients with ≥2 abnormal tests were considered cognitively impaired (CI). The distribution of focal lesions, GM and WM atrophy, and microstructural WM damage were assessed using voxel-wise approaches. A random forest analysis identified the best imaging predictors of global cognitive impairment and deficits of specific cognitive domains. Twenty-three (38%) MS patients were CI. Compared with cognitively preserved (CP), CI MS patients had GM atrophy of the left thalamus, right hippocampus and parietal regions. They also showed atrophy of several WM tracts, mainly located in posterior brain regions and widespread WM diffusivity abnormalities. WM diffusivity abnormalities in cognitive-relevant WM tracts followed by atrophy of cognitive-relevant GM regions explained global cognitive impairment. Variable patterns of NAWM and GM damage were associated with deficits in selected cognitive domains. Structural, multiparametric, voxel-wise MRI approaches are feasible in a multicenter setting. The combination of different imaging modalities is needed to assess and monitor cognitive impairment in MS. © 2016 Wiley Periodicals, Inc.

  12. Structure Determination of Cisplatin-Amino Acid Analogues by Infrared Multiple Photon Dissociation Action Spectroscopy

    Science.gov (United States)

    He, Chenchen; Bao, Xun; Zhu, Yanlong; Strobehn, Stephen; Kimutai, Bett; Nei, Y.-W.; Chow, C. S.; Rodgers, M. T.; Gao, Juehan; Oomens, J.

    2015-06-01

    To gain a better understanding of the binding mechanism and assist in the optimization of relevant drug and chemical probe design, both experimental and theoretical studies were performed on a series of amino acid-linked cisplatin derivatives, including glycine-, lysine-, and ornithine-linked cisplatin, Gplatin, Kplatin, and Oplatin, respectively. Cisplatin, the first FDA-approved platinum-based anticancer drug, has been widely used in cancer chemotherapy. Its pharmacological mechanism has been identified as its ability to coordinate to genomic DNA, and guanine is its major target. In previous reports, cisplatin was successfully utilized as a chemical probe to detect solvent accessible sites in ribosomal RNA (rRNA). Among the amino-acid-linked cisplatin derivatives, Oplatin exhibits preference for adenine over guanine. The mechanism behind its different selectivity compared to cisplatin may relate to its potential of forming a hydrogen bond between the carboxylate group in Pt (II) complex and the 6-amino moiety of adenosine stabilizes A-Oplatin products. Tandem mass spectrometry analysis also indicates that different coordination sites of Oplatin on adenosine affect glycosidic bond stability. Infrared multiple photon dissociation (IRMPD) action spectroscopy experiments were performed on all three amino acid-linked cisplatin to characterize their structures. An extensive theoretical study has been performed on Gplatin to guide the selection of the most effective theory and basis set based on its geometric information. The results for Gplatin provide the foundation for characterization of the more complex amino acid-linked cisplatin derivatives, Oplatin and Kplatin. Structural and energetic information elucidated for these compounds, particularly Oplatin reveal the reason for its alternative selectivity compared to cisplatin.

  13. Genetic structuring of northern myotis (Myotis septentrionalis) at multiple spatial scales

    Science.gov (United States)

    Johnson, Joshua B.; Roberts, James H.; King, Timothy L.; Edwards, John W.; Ford, W. Mark; Ray, David A.

    2014-01-01

    Although groups of bats may be genetically distinguishable at large spatial scales, the effects of forest disturbances, particularly permanent land use conversions on fine-scale population structure and gene flow of summer aggregations of philopatric bat species are less clear. We genotyped and analyzed variation at 10 nuclear DNA microsatellite markers in 182 individuals of the forest-dwelling northern myotis (Myotis septentrionalis) at multiple spatial scales, from within first-order watersheds scaling up to larger regional areas in West Virginia and New York. Our results indicate that groups of northern myotis were genetically indistinguishable at any spatial scale we considered, and the collective population maintained high genetic diversity. It is likely that the ability to migrate, exploit small forest patches, and use networks of mating sites located throughout the Appalachian Mountains, Interior Highlands, and elsewhere in the hibernation range have allowed northern myotis to maintain high genetic diversity and gene flow regardless of forest disturbances at local and regional spatial scales. A consequence of maintaining high gene flow might be the potential to minimize genetic founder effects following population declines caused currently by the enzootic White-nose Syndrome.

  14. Multiple quantum collapse of the inflaton field and its implications on the birth of cosmic structure

    Energy Technology Data Exchange (ETDEWEB)

    Leon, Gabriel [Instituto de Ciencias Nucleares, Universidad Nacional Autonoma de Mexico, Mexico DF 04510 (Mexico); De Unanue, Adolfo [C3 Centro de Ciencias de la Complejidad, Universidad Nacional Autonoma de Mexico, Torre de IngenierIa, Circuito Exterior S/N Ciudad Universitaria, Mexico DF 04510 (Mexico); Sudarsky, Daniel, E-mail: gabriel.leon@nucleares.unam.mx, E-mail: adolfo@nucleares.unam.mx, E-mail: sudarsky@nucleares.unam.mx [Instituto de AstronomIa y Fisica del Espacio (UBA-CONICET), Casilla de Correos 67, Sucursal 28, 1428 Buenos Aires (Argentina)

    2011-08-07

    The standard inflationary account for the origin of cosmic structure is, without a doubt, extremely successful. However, it is not fully satisfactory as has been argued in Perez et al (2006 Class. Quantum Grav. 23 2317). The central point is that, in the standard accounts, the inhomogeneity and anisotropy of our universe seem to emerge, unexplained, from an exactly homogeneous and isotropic initial state through processes that do not break those symmetries. The proposal made there to address this shortcoming calls for a dynamical and self-induced quantum collapse of the original homogeneous and isotropic state of the inflaton. In this paper, we consider the possibility of a multiplicity of collapses in each one of the modes of the quantum field. As we will see, the results are sensitive to a more detailed characterization of the collapse than those studied in the previous works, and in this regard two simple options will be studied. We find important constraints on the model, most remarkably on the number of possible collapses for each mode.

  15. Multiple Skills Underlie Arithmetic Performance: A Large-Scale Structural Equation Modeling Analysis

    Directory of Open Access Journals (Sweden)

    Sarit Ashkenazi

    2017-12-01

    Full Text Available Current theoretical approaches point to the importance of several cognitive skills not specific to mathematics for the etiology of mathematics disorders (MD. In the current study, we examined the role of many of these skills, specifically: rapid automatized naming, attention, reading, and visual perception, on mathematics performance among a large group of college students (N = 1,322 with a wide range of arithmetic proficiency. Using factor analysis, we discovered that our data clustered to four latent variables 1 mathematics, 2 perception speed, 3 attention and 4 reading. In subsequent structural equation modeling, we found that the latent variable perception speed had a strong and meaningful effect on mathematics performance. Moreover, sustained attention, independent from the effect of the latent variable perception speed, had a meaningful, direct effect on arithmetic fact retrieval and procedural knowledge. The latent variable reading had a modest effect on mathematics performance. Specifically, reading comprehension, independent from the effect of the latent variable reading, had a meaningful direct effect on mathematics, and particularly on number line knowledge. Attention, tested by the attention network test, had no effect on mathematics, reading or perception speed. These results indicate that multiple factors can affect mathematics performance supporting a heterogeneous approach to mathematics. These results have meaningful implications for the diagnosis and intervention of pure and comorbid learning disorders.

  16. Functional and Structural Brain Plasticity Enhanced by Motor and Cognitive Rehabilitation in Multiple Sclerosis

    Directory of Open Access Journals (Sweden)

    Luca Prosperini

    2015-01-01

    Full Text Available Rehabilitation is recognized to be important in ameliorating motor and cognitive functions, reducing disease burden, and improving quality of life in patients with multiple sclerosis (MS. In this systematic review, we summarize the existing evidences that motor and cognitive rehabilitation may enhance functional and structural brain plasticity in patients with MS, as assessed by means of the most advanced neuroimaging techniques, including diffusion tensor imaging and task-related and resting-state functional magnetic resonance imaging (MRI. In most cases, the rehabilitation program was based on computer-assisted/video game exercises performed in either an outpatient or home setting. Despite their heterogeneity, all the included studies describe changes in white matter microarchitecture, in task-related activation, and/or in functional connectivity following both task-oriented and selective training. When explored, relevant correlation between improved function and MRI-detected brain changes was often found, supporting the hypothesis that training-induced brain plasticity is specifically linked to the trained domain. Small sample sizes, lack of randomization and/or an active control group, as well as missed relationship between MRI-detected changes and clinical performance, are the major drawbacks of the selected studies. Knowledge gaps in this field of research are also discussed to provide a framework for future investigations.

  17. The DNA repair endonuclease XPG interacts directly and functionally with the WRN helicase defective in Werner syndrome

    Energy Technology Data Exchange (ETDEWEB)

    Trego, Kelly S.; Chernikova, Sophia B.; Davalos, Albert R.; Perry, J. Jefferson P.; Finger, L. David; Ng, Cliff; Tsai, Miaw-Sheue; Yannone, Steven M.; Tainer, John A.; Campisi, Judith; Cooper, Priscilla K.

    2011-04-20

    XPG is a structure-specific endonuclease required for nucleotide excision repair (NER). XPG incision defects result in the cancer-prone syndrome xeroderma pigmentosum, whereas truncating mutations of XPG cause the severe postnatal progeroid developmental disorder Cockayne syndrome. We show that XPG interacts directly with WRN protein, which is defective in the premature aging disorder Werner syndrome, and that the two proteins undergo similar sub-nuclear redistribution in S-phase and co-localize in nuclear foci. The co-localization was observed in mid- to late-S-phase, when WRN moves from nucleoli to nuclear foci that have been shown to contain protein markers of both stalled replication forks and telomeric proteins. We mapped the interaction between XPG and WRN to the C-terminal domains of each and show that interaction with the C-terminal domain of XPG strongly stimulates WRN helicase activity. WRN also possesses a competing DNA single-strand annealing activity that, combined with unwinding, has been shown to coordinate regression of model replication forks to form Holliday junction/chicken foot intermediate structures. We tested whether XPG stimulated WRN annealing activity and found that XPG itself has intrinsic strand annealing activity that requires the unstructured R- and C-terminal domains, but not the conserved catalytic core or endonuclease activity. Annealing by XPG is cooperative, rather than additive, with WRN annealing. Taken together, our results suggest a novel function for XPG in S-phase that is at least in part carried out coordinately with WRN, and which may contribute to the severity of the phenotypes that occur upon loss of XPG.

  18. Iterative solution of multiple radiation and scattering problems in structural acoustics using the BL-QMR algorithm

    Energy Technology Data Exchange (ETDEWEB)

    Malhotra, M. [Stanford Univ., CA (United States)

    1996-12-31

    Finite-element discretizations of time-harmonic acoustic wave problems in exterior domains result in large sparse systems of linear equations with complex symmetric coefficient matrices. In many situations, these matrix problems need to be solved repeatedly for different right-hand sides, but with the same coefficient matrix. For instance, multiple right-hand sides arise in radiation problems due to multiple load cases, and also in scattering problems when multiple angles of incidence of an incoming plane wave need to be considered. In this talk, we discuss the iterative solution of multiple linear systems arising in radiation and scattering problems in structural acoustics by means of a complex symmetric variant of the BL-QMR method. First, we summarize the governing partial differential equations for time-harmonic structural acoustics, the finite-element discretization of these equations, and the resulting complex symmetric matrix problem. Next, we sketch the special version of BL-QMR method that exploits complex symmetry, and we describe the preconditioners we have used in conjunction with BL-QMR. Finally, we report some typical results of our extensive numerical tests to illustrate the typical convergence behavior of BL-QMR method for multiple radiation and scattering problems in structural acoustics, to identify appropriate preconditioners for these problems, and to demonstrate the importance of deflation in block Krylov-subspace methods. Our numerical results show that the multiple systems arising in structural acoustics can be solved very efficiently with the preconditioned BL-QMR method. In fact, for multiple systems with up to 40 and more different right-hand sides we get consistent and significant speed-ups over solving the systems individually.

  19. Structural and optical characteristics of InN/GaN multiple quantum wells grown by metalorganic chemical vapor deposition

    International Nuclear Information System (INIS)

    Kim, Je Won; Lee, Kyu Han; Hong, Sangsu

    2007-01-01

    The structural and electrical properties of InN/GaN multiple quantum wells, which were grown by metalorganic chemical vapor deposition, were characterized by transmission electron microscopy (TEM) and electroluminescence measurements. From the TEM micrographs, it was shown that the well layer was grown like a quantum dot. The well layer is expected to be the nano-size structures in the InN multiple quantum well layers. The multi-photon confocal laser scanning microscopy was used to investigate the optical properties of the light emitting diode (LED) structures with InN active layers. It was found that the two-photon excitation was possible in InN system. The pit density was measured by using the far-field optical technique. In the varied current conditions, the blue LED with the InN multiple quantum well structures did not have the wavelength shift. With this result, we can expect that the white LEDs with the InN multiple quantum well structures do not show the color temperature changes with the variations of applied currents

  20. The nuclear import of RNA helicase A is mediated by importin-α3

    International Nuclear Information System (INIS)

    Aratani, Satoko; Oishi, Takayuki; Fujita, Hidetoshi; Nakazawa, Minako; Fujii, Ryouji; Imamoto, Naoko; Yoneda, Yoshihiro; Fukamizu, Akiyoshi; Nakajima, Toshihiro

    2006-01-01

    RNA helicase A (RHA), an ATPase/helicase, regulates the gene expression at various steps including transcriptional activation and RNA processing. RHA is known to shuttle between the nucleus and cytoplasm. We identified the nuclear localization signal (NLS) of RHA and analyzed the nuclear import mechanisms. The NLS of RHA (RHA-NLS) consisting of 19 amino acid residues is highly conserved through species and does not have the consensus classical NLS. In vitro nuclear import assays revealed that the nuclear import of RHA was Ran-dependent and mediated with the classical importin-α/β-dependent pathway. The binding assay indicated that the basic residues in RHA-NLS were used for interaction with importin-α. Furthermore, the nuclear import of RHA-NLS was supported by importin-α1 and preferentially importin-α3. Our results indicate that the nuclear import of RHA is mediated by the importin-α3/importin-β-dependent pathway and suggest that the specificity for importin may regulate the functions of cargo proteins

  1. The adnAB Locus, Encoding a Putative Helicase-Nuclease Activity, Is Essential in Streptomyces

    Science.gov (United States)

    Zhang, Lingli; Nguyen, Hoang Chuong; Chipot, Ludovic; Piotrowski, Emilie; Bertrand, Claire

    2014-01-01

    Homologous recombination is a crucial mechanism that repairs a wide range of DNA lesions, including the most deleterious ones, double-strand breaks (DSBs). This multistep process is initiated by the resection of the broken DNA ends by a multisubunit helicase-nuclease complex exemplified by Escherichia coli RecBCD, Bacillus subtilis AddAB, and newly discovered Mycobacterium tuberculosis AdnAB. Here we show that in Streptomyces, neither recBCD nor addAB homologues could be detected. The only putative helicase-nuclease-encoding genes identified were homologous to M. tuberculosis adnAB genes. These genes are conserved as a single copy in all sequenced genomes of Streptomyces. The disruption of adnAB in Streptomyces ambofaciens and Streptomyces coelicolor could not be achieved unless an ectopic copy was provided, indicating that adnAB is essential for growth. Both adnA and adnB genes were shown to be inducible in response to DNA damage (mitomycin C) and to be independently transcribed. Introduction of S. ambofaciens adnAB genes in an E. coli recB mutant restored viability and resistance to UV light, suggesting that Streptomyces AdnAB could be a functional homologue of RecBCD and be involved in DNA damage resistance. PMID:24837284

  2. Real-time electrochemical monitoring of isothermal helicase-dependent amplification of nucleic acids.

    Science.gov (United States)

    Kivlehan, Francine; Mavré, François; Talini, Luc; Limoges, Benoît; Marchal, Damien

    2011-09-21

    We described an electrochemical method to monitor in real-time the isothermal helicase-dependent amplification of nucleic acids. The principle of detection is simple and well-adapted to the development of portable, easy-to-use and inexpensive nucleic acids detection technologies. It consists of monitoring a decrease in the electrochemical current response of a reporter DNA intercalating redox probe during the isothermal DNA amplification. The method offers the possibility to quantitatively analyze target nucleic acids in less than one hour at a single constant temperature, and to perform at the end of the isothermal amplification a DNA melt curve analysis for differentiating between specific and non-specific amplifications. To illustrate the potentialities of this approach for the development of a simple, robust and low-cost instrument with high throughput capability, the method was validated with an electrochemical system capable of monitoring up to 48 real-time isothermal HDA reactions simultaneously in a disposable microplate consisting of 48-electrochemical microwells. Results obtained with this approach are comparable to that obtained with a well-established but more sophisticated and expensive fluorescence-based method. This makes for a promising alternative detection method not only for real-time isothermal helicase-dependent amplification of nucleic acid, but also for other isothermal DNA amplification strategies.

  3. Germline mutations of regulator of telomere elongation helicase 1, RTEL1, in Dyskeratosis congenita.

    Science.gov (United States)

    Ballew, Bari J; Yeager, Meredith; Jacobs, Kevin; Giri, Neelam; Boland, Joseph; Burdett, Laurie; Alter, Blanche P; Savage, Sharon A

    2013-04-01

    Dyskeratosis congenita (DC) is an inherited bone marrow failure and cancer predisposition syndrome caused by aberrant telomere biology. The classic triad of dysplastic nails, abnormal skin pigmentation, and oral leukoplakia is diagnostic of DC, but substantial clinical heterogeneity exists; the clinically severe variant Hoyeraal Hreidarsson syndrome (HH) also includes cerebellar hypoplasia, severe immunodeficiency, enteropathy, and intrauterine growth retardation. Germline mutations in telomere biology genes account for approximately one-half of known DC families. Using exome sequencing, we identified mutations in RTEL1, a helicase with critical telomeric functions, in two families with HH. In the first family, two siblings with HH and very short telomeres inherited a premature stop codon from their mother who has short telomeres. The proband from the second family has HH and inherited a premature stop codon in RTEL1 from his father and a missense mutation from his mother, who also has short telomeres. In addition, inheritance of only the missense mutation led to very short telomeres in the proband's brother. Targeted sequencing identified a different RTEL1 missense mutation in one additional DC proband who has bone marrow failure and short telomeres. Both missense mutations affect the helicase domain of RTEL1, and three in silico prediction algorithms suggest that they are likely deleterious. The nonsense mutations both cause truncation of the RTEL1 protein, resulting in loss of the PIP box; this may abrogate an important protein-protein interaction. These findings implicate a new telomere biology gene, RTEL1, in the etiology of DC.

  4. Direction-of-arrival estimation for co-located multiple-input multiple-output radar using structural sparsity Bayesian learning

    International Nuclear Information System (INIS)

    Wen Fang-Qing; Zhang Gong; Ben De

    2015-01-01

    This paper addresses the direction of arrival (DOA) estimation problem for the co-located multiple-input multiple-output (MIMO) radar with random arrays. The spatially distributed sparsity of the targets in the background makes compressive sensing (CS) desirable for DOA estimation. A spatial CS framework is presented, which links the DOA estimation problem to support recovery from a known over-complete dictionary. A modified statistical model is developed to accurately represent the intra-block correlation of the received signal. A structural sparsity Bayesian learning algorithm is proposed for the sparse recovery problem. The proposed algorithm, which exploits intra-signal correlation, is capable being applied to limited data support and low signal-to-noise ratio (SNR) scene. Furthermore, the proposed algorithm has less computation load compared to the classical Bayesian algorithm. Simulation results show that the proposed algorithm has a more accurate DOA estimation than the traditional multiple signal classification (MUSIC) algorithm and other CS recovery algorithms. (paper)

  5. Direction-of-arrival estimation for co-located multiple-input multiple-output radar using structural sparsity Bayesian learning

    Science.gov (United States)

    Wen, Fang-Qing; Zhang, Gong; Ben, De

    2015-11-01

    This paper addresses the direction of arrival (DOA) estimation problem for the co-located multiple-input multiple-output (MIMO) radar with random arrays. The spatially distributed sparsity of the targets in the background makes compressive sensing (CS) desirable for DOA estimation. A spatial CS framework is presented, which links the DOA estimation problem to support recovery from a known over-complete dictionary. A modified statistical model is developed to accurately represent the intra-block correlation of the received signal. A structural sparsity Bayesian learning algorithm is proposed for the sparse recovery problem. The proposed algorithm, which exploits intra-signal correlation, is capable being applied to limited data support and low signal-to-noise ratio (SNR) scene. Furthermore, the proposed algorithm has less computation load compared to the classical Bayesian algorithm. Simulation results show that the proposed algorithm has a more accurate DOA estimation than the traditional multiple signal classification (MUSIC) algorithm and other CS recovery algorithms. Project supported by the National Natural Science Foundation of China (Grant Nos. 61071163, 61271327, and 61471191), the Funding for Outstanding Doctoral Dissertation in Nanjing University of Aeronautics and Astronautics, China (Grant No. BCXJ14-08), the Funding of Innovation Program for Graduate Education of Jiangsu Province, China (Grant No. KYLX 0277), the Fundamental Research Funds for the Central Universities, China (Grant No. 3082015NP2015504), and the Priority Academic Program Development of Jiangsu Higher Education Institutions (PADA), China.

  6. Human SUV3 helicase regulates growth rate of the HeLa cells and can localize in the nucleoli.

    Science.gov (United States)

    Szewczyk, Maciej; Fedoryszak-Kuśka, Natalia; Tkaczuk, Katarzyna; Dobrucki, Jurek; Waligórska, Agnieszka; Stępień, Piotr P

    2017-01-01

    The human SUV3 helicase (SUV3, hSUV3, SUPV3L1) is a DNA/RNA unwinding enzyme belonging to the class of DexH-box helicases. It localizes predominantly in the mitochondria, where it forms an RNA-degrading complex called mitochondrial degradosome with exonuclease PNP (polynucleotide phosphorylase). Association of this complex with the polyA polymerase can modulate mitochondrial polyA tails. Silencing of the SUV3 gene was shown to inhibit the cell cycle and to induce apoptosis in human cell lines. However, since small amounts of the SUV3 helicase were found in the cell nuclei, it was not clear whether the observed phenotypes of SUV3 depletion were of mitochondrial or nuclear origin. In order to answer this question we have designed gene constructs able to inhibit the SUV3 activity exclusively in the cell nuclei. The results indicate that the observed growth rate impairment upon SUV3 depletion is due to its nuclear function(s). Unexpectedly, overexpression of the nuclear-targeted wild-type copies of the SUV3 gene resulted in a higher growth rate. In addition, we demonstrate that the SUV3 helicase can be found in the HeLa cell nucleoli, but it is not detectable in the DNA-repair foci. Our results indicate that the nucleolar-associated human SUV3 protein is an important factor in regulation of the cell cycle.

  7. Regulation of gene expression by the BLM helicase correlates with the presence of G-quadruplex DNA motifs

    DEFF Research Database (Denmark)

    Nguyen, Giang Huong; Tang, Weiliang; Robles, Ana I

    2014-01-01

    Bloom syndrome is a rare autosomal recessive disorder characterized by genetic instability and cancer predisposition, and caused by mutations in the gene encoding the Bloom syndrome, RecQ helicase-like (BLM) protein. To determine whether altered gene expression might be responsible for pathologic...

  8. Molecular architecture of the recombinant human MCM2-7 helicase in complex with nucleotides and DNA

    DEFF Research Database (Denmark)

    Boskovic, Jasminka; Bragado-Nilsson, Elisabeth; Saligram Prabhakar, Bhargav

    2016-01-01

    DNA replication is a key biological process that involves different protein complexes whose assembly is rigorously regulated in a successive order. One of these complexes is a replicative hexameric helicase, the MCM complex, which is essential for the initiation and elongation phases of replicati...

  9. Single molecule measurements of DNA helicase activity with magnetic tweezers and t-test based step-finding analysis

    Science.gov (United States)

    Seol, Yeonee; Strub, Marie-Paule; Neuman, Keir C.

    2016-01-01

    Magnetic tweezers is a versatile and easy to implement single-molecule technique that has become increasingly prevalent in the study of nucleic acid based molecular motors. Here, we provide a description of the magnetic tweezers instrument and guidelines for measuring and analyzing DNA helicase activity. Along with experimental methods, we describe a robust method of single-molecule trajectory analysis based on the Student’s t-test that accommodates continuous transitions in addition to the discrete transitions assumed in most widely employed analysis routines. To illustrate the single-molecule unwinding assay and the analysis routine, we provide DNA unwinding measurements of Escherichia coli RecQ helicase under a variety of conditions (Na+, ATP, temperature, and DNA substrate geometry). These examples reveal that DNA unwinding measurements under various conditions can aid in elucidating the unwinding mechanism of DNA helicase but also emphasize that environmental effects on DNA helicase activity must be considered in relation to in vivo activity and mechanism. PMID:27131595

  10. Ufd1-Npl4 Recruit Cdc48 for Disassembly of Ubiquitylated CMG Helicase at the End of Chromosome Replication

    Directory of Open Access Journals (Sweden)

    Marija Maric

    2017-03-01

    Full Text Available Disassembly of the Cdc45-MCM-GINS (CMG DNA helicase is the key regulated step during DNA replication termination in eukaryotes, involving ubiquitylation of the Mcm7 helicase subunit, leading to a disassembly process that requires the Cdc48 “segregase”. Here, we employ a screen to identify partners of budding yeast Cdc48 that are important for disassembly of ubiquitylated CMG helicase at the end of chromosome replication. We demonstrate that the ubiquitin-binding Ufd1-Npl4 complex recruits Cdc48 to ubiquitylated CMG. Ubiquitylation of CMG in yeast cell extracts is dependent upon lysine 29 of Mcm7, which is the only detectable site of ubiquitylation both in vitro and in vivo (though in vivo other sites can be modified when K29 is mutated. Mutation of K29 abrogates in vitro recruitment of Ufd1-Npl4-Cdc48 to the CMG helicase, supporting a model whereby Ufd1-Npl4 recruits Cdc48 to ubiquitylated CMG at the end of chromosome replication, thereby driving the disassembly reaction.

  11. Acute inactivation of the replicative helicase in human cells triggers MCM8-9-dependent DNA synthesis

    DEFF Research Database (Denmark)

    Natsume, Toyoaki; Nishimura, Kohei; Minocherhomji, Sheroy

    2017-01-01

    stemming from replisome dissociation during DNA replication perturbation, we used a degron-based system for inducible proteolysis of a subunit of the replicative helicase. We show that MCM2-depleted cells activate a DNA damage response pathway and generate replication-associated DNA double-strand breaks...

  12. RNA helicase DDX3 is a regulatory subunit of casein kinase 1 in Wnt-beta-catenin signaling

    NARCIS (Netherlands)

    Cruciat, C.M.; Dolde, C.; de Groot, R.E.; Ohkawara, B.; Reinhard, C.; Korswagen, H.C.; Niehrs, C.

    2013-01-01

    Casein kinase 1 (CK1) members play key roles in numerous biological processes. They are considered "rogue" kinases, because their enzymatic activity appears unregulated. Contrary to this notion, we have identified the DEAD-box RNA helicase DDX3 as a regulator of the Wnt-beta-catenin network, where

  13. Disrupted Module Efficiency of Structural and Functional Brain Connectomes in Clinically Isolated Syndrome and Multiple Sclerosis

    Directory of Open Access Journals (Sweden)

    Yaou Liu

    2018-04-01

    Full Text Available Recent studies have demonstrated disrupted topological organization of brain connectome in multiple sclerosis (MS. However, whether the communication efficiency between different functional systems is affected in the early stage of MS remained largely unknown. In this study, we constructed the structural connectivity (SC and functional connectivity (FC networks in 41 patients with clinically isolated syndrome (CIS, 32 MS patients and 35 healthy controls (HC based on diffusion and resting-state functional MRI. To quantify the communication efficiency within and between different functional systems, we proposed two measures called intra- and inter-module efficiency. Based on the module parcellation of functional backbone network, the intra- and inter-module efficiency of SC and FC networks was calculated for each participant. For the SC network, CIS showed decreased inter-module efficiency between the sensory-motor network (SMN, the visual network (VN, the default-mode network (DMN and the fronto-parietal network (FPN compared with HC, while MS showed more widespread decreased module efficiency both within and between modules relative to HC and CIS. For the FC network, no differences were found between CIS and HC, and a decreased inter-module efficiency between SMN and FPN and between VN and FPN was identified in MS, compared with HC and CIS. Moreover, both intra- and inter-module efficiency of SC network were correlated with the disability and cognitive scores in MS. Therefore, our results demonstrated early SC changes between modules in CIS, and more widespread SC alterations and inter-module FC changes were observed in MS, which were further associated with cognitive impairment and physical disability.

  14. Interfacial sharpness and intermixing in a Ge-SiGe multiple quantum well structure

    Science.gov (United States)

    Bashir, A.; Gallacher, K.; Millar, R. W.; Paul, D. J.; Ballabio, A.; Frigerio, J.; Isella, G.; Kriegner, D.; Ortolani, M.; Barthel, J.; MacLaren, I.

    2018-01-01

    A Ge-SiGe multiple quantum well structure created by low energy plasma enhanced chemical vapour deposition, with nominal well thickness of 5.4 nm separated by 3.6 nm SiGe spacers, is analysed quantitatively using scanning transmission electron microscopy. Both high angle annular dark field imaging and electron energy loss spectroscopy show that the interfaces are not completely sharp, suggesting that there is some intermixing of Si and Ge at each interface. Two methods are compared for the quantification of the spectroscopy datasets: a self-consistent approach that calculates binary substitutional trends without requiring experimental or computational k-factors from elsewhere and a standards-based cross sectional calculation. Whilst the cross section approach is shown to be ultimately more reliable, the self-consistent approach provides surprisingly good results. It is found that the Ge quantum wells are actually about 95% Ge and that the spacers, whilst apparently peaking at about 35% Si, contain significant interdiffused Ge at each side. This result is shown to be not just an artefact of electron beam spreading in the sample, but mostly arising from a real chemical interdiffusion resulting from the growth. Similar results are found by use of X-ray diffraction from a similar area of the sample. Putting the results together suggests a real interdiffusion with a standard deviation of about 0.87 nm, or put another way—a true width defined from 10%-90% of the compositional gradient of about 2.9 nm. This suggests an intrinsic limit on how sharp such interfaces can be grown by this method and, whilst 95% Ge quantum wells (QWs) still behave well enough to have good properties, any attempt to grow thinner QWs would require modifications to the growth procedure to reduce this interdiffusion, in order to maintain a composition of ≥95% Ge.

  15. Thermoelectric material including a multiple transition metal-doped type I clathrate crystal structure

    Science.gov (United States)

    Yang, Jihui [Lakeshore, CA; Shi, Xun [Troy, MI; Bai, Shengqiang [Shanghai, CN; Zhang, Wenqing [Shanghai, CN; Chen, Lidong [Shanghai, CN; Yang, Jiong [Shanghai, CN

    2012-01-17

    A thermoelectric material includes a multiple transition metal-doped type I clathrate crystal structure having the formula A.sub.8TM.sub.y.sub.1.sup.1TM.sub.y.sub.2.sup.2 . . . TM.sub.y.sub.n.sup.nM.sub.zX.sub.46-y.sub.1.sub.-y.sub.2.sub.- . . . -y.sub.n.sub.-z. In the formula, A is selected from the group consisting of barium, strontium, and europium; X is selected from the group consisting of silicon, germanium, and tin; M is selected from the group consisting of aluminum, gallium, and indium; TM.sup.1, TM.sup.2, and TM.sup.n are independently selected from the group consisting of 3d, 4d, and 5d transition metals; and y.sub.1, y.sub.2, y.sub.n and Z are actual compositions of TM.sup.1, TM.sup.2, TM.sup.n, and M, respectively. The actual compositions are based upon nominal compositions derived from the following equation: z=8q.sub.A-|.DELTA.q.sub.1|y.sub.1-|.DELTA.q.sub.2|y.sub.2- . . . -|.DELTA.q.sub.n|y.sub.n, wherein q.sub.A is a charge state of A, and wherein .DELTA.q.sub.1, .DELTA.q.sub.2, .DELTA.q.sub.n are, respectively, the nominal charge state of the first, second, and n-th TM.

  16. Managing forest and marginal agricultural land for multiple tradeoffs : compromising on economic, carbon and structural biodiversity objectives

    NARCIS (Netherlands)

    Krcmar, E.; Kooten, van G.C.; Vertinsky, I.

    2005-01-01

    In this paper, we use compromise programming to solve a multiple-objective land use and forest management planning model. Long- and short- (`fast¿) term carbon uptake, maintenance of structural diversity, and economic (net returns to forestry and agriculture) objectives are simultaneously achieved

  17. MULTIPLE OBJECTS

    Directory of Open Access Journals (Sweden)

    A. A. Bosov

    2015-04-01

    Full Text Available Purpose. The development of complicated techniques of production and management processes, information systems, computer science, applied objects of systems theory and others requires improvement of mathematical methods, new approaches for researches of application systems. And the variety and diversity of subject systems makes necessary the development of a model that generalizes the classical sets and their development – sets of sets. Multiple objects unlike sets are constructed by multiple structures and represented by the structure and content. The aim of the work is the analysis of multiple structures, generating multiple objects, the further development of operations on these objects in application systems. Methodology. To achieve the objectives of the researches, the structure of multiple objects represents as constructive trio, consisting of media, signatures and axiomatic. Multiple object is determined by the structure and content, as well as represented by hybrid superposition, composed of sets, multi-sets, ordered sets (lists and heterogeneous sets (sequences, corteges. Findings. In this paper we study the properties and characteristics of the components of hybrid multiple objects of complex systems, proposed assessments of their complexity, shown the rules of internal and external operations on objects of implementation. We introduce the relation of arbitrary order over multiple objects, we define the description of functions and display on objects of multiple structures. Originality.In this paper we consider the development of multiple structures, generating multiple objects.Practical value. The transition from the abstract to the subject of multiple structures requires the transformation of the system and multiple objects. Transformation involves three successive stages: specification (binding to the domain, interpretation (multiple sites and particularization (goals. The proposed describe systems approach based on hybrid sets

  18. A protocol for the refinement of NMR structures using simultaneously pseudocontact shift restraints from multiple lanthanide ions

    Energy Technology Data Exchange (ETDEWEB)

    Sala, Davide; Giachetti, Andrea; Luchinat, Claudio, E-mail: luchinat@cerm.unifi.it; Rosato, Antonio, E-mail: rosato@cerm.unifi.it [University of Florence, Magnetic Resonance Center (CERM) (Italy)

    2016-11-15

    The binding of paramagnetic metal ions to proteins produces a number of different effects on the NMR spectra of the system. In particular, when the magnetic susceptibility of the metal ion is anisotropic, pseudocontact shifts (PCSs) arise and can be easily measured. They constitute very useful restraints for the solution structure determination of metal-binding proteins. In this context, there has been great interest in the use of lanthanide(III) ions to induce PCSs in diamagnetic proteins, e.g. through the replacement native calcium(II) ions. By preparing multiple samples in each of which a different ion of the lanthanide series is introduced, it is possible to obtain multiple independent PCS datasets that can be used synergistically to generate protein structure ensembles (typically called bundles). For typical NMR-based determination of protein structure, it is necessary to perform an energetic refinement of such initial bundles to obtain final structures whose geometric quality is suitable for deposition in the PDB. This can be conveniently done by using restrained molecular dynamics simulations (rMD) in explicit solvent. However, there are no available protocols for rMD using multiple PCS datasets as part of the restraints. In this work, we extended the PCS module of the AMBER MD package to handle multiple datasets and tuned a previously developed protocol for NMR structure refinement to achieve consistent convergence with PCS restraints. Test calculations with real experimental data show that this new implementation delivers the expected improvement of protein geometry, resulting in final structures that are of suitable quality for deposition. Furthermore, we observe that also initial structures generated only with traditional restraints can be successfully refined using traditional and PCS restraints simultaneously.

  19. The RTR Complex Partner RMI2 and the DNA Helicase RTEL1 Are Both Independently Involved in Preserving the Stability of 45S rDNA Repeats in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Sarah Röhrig

    2016-10-01

    Full Text Available The stability of repetitive sequences in complex eukaryotic genomes is safeguarded by factors suppressing homologues recombination. Prominent in this is the role of the RTR complex. In plants, it consists of the RecQ helicase RECQ4A, the topoisomerase TOP3α and RMI1. Like mammals, but not yeast, plants harbor an additional complex partner, RMI2. Here, we demonstrate that, in Arabidopsis thaliana, RMI2 is involved in the repair of aberrant replication intermediates in root meristems as well as in intrastrand crosslink repair. In both instances, RMI2 is involved independently of the DNA helicase RTEL1. Surprisingly, simultaneous loss of RMI2 and RTEL1 leads to loss of male fertility. As both the RTR complex and RTEL1 are involved in suppression of homologous recombination (HR, we tested the efficiency of HR in the double mutant rmi2-2 rtel1-1 and found a synergistic enhancement (80-fold. Searching for natural target sequences we found that RTEL1 is required for stabilizing 45S rDNA repeats. In the double mutant with rmi2-2 the number of 45S rDNA repeats is further decreased sustaining independent roles of both factors in this process. Thus, loss of suppression of HR does not only lead to a destabilization of rDNA repeats but might be especially deleterious for tissues undergoing multiple cell divisions such as the male germline.

  20. The RTR Complex Partner RMI2 and the DNA Helicase RTEL1 Are Both Independently Involved in Preserving the Stability of 45S rDNA Repeats in Arabidopsis thaliana.

    Science.gov (United States)

    Röhrig, Sarah; Schröpfer, Susan; Knoll, Alexander; Puchta, Holger

    2016-10-01

    The stability of repetitive sequences in complex eukaryotic genomes is safeguarded by factors suppressing homologues recombination. Prominent in this is the role of the RTR complex. In plants, it consists of the RecQ helicase RECQ4A, the topoisomerase TOP3α and RMI1. Like mammals, but not yeast, plants harbor an additional complex partner, RMI2. Here, we demonstrate that, in Arabidopsis thaliana, RMI2 is involved in the repair of aberrant replication intermediates in root meristems as well as in intrastrand crosslink repair. In both instances, RMI2 is involved independently of the DNA helicase RTEL1. Surprisingly, simultaneous loss of RMI2 and RTEL1 leads to loss of male fertility. As both the RTR complex and RTEL1 are involved in suppression of homologous recombination (HR), we tested the efficiency of HR in the double mutant rmi2-2 rtel1-1 and found a synergistic enhancement (80-fold). Searching for natural target sequences we found that RTEL1 is required for stabilizing 45S rDNA repeats. In the double mutant with rmi2-2 the number of 45S rDNA repeats is further decreased sustaining independent roles of both factors in this process. Thus, loss of suppression of HR does not only lead to a destabilization of rDNA repeats but might be especially deleterious for tissues undergoing multiple cell divisions such as the male germline.

  1. Preliminary Investigation of Impact on Multiple-Sheet Structures and an Evaluation of the Meteoroid Hazard to Space Vehicles

    Science.gov (United States)

    Nysmith, C. Robert; Summers, James L.

    1961-01-01

    Small pyrex glass spheres, representative of stoney meteoroids, were fired into 2024-T3 aluminum alclad multiple-sheet structures at velocities to 11,000 feet per second to evaluate the effectiveness of multisheet hull construction as a means of increasing the resistance of a spacecraft to meteoroid penetrations. The results of these tests indicate that increasing the number of sheets in a structure while keeping the total sheet thickness constant and increasing the spacing between sheets both tend to increase the penetration resistance of a structure of constant weight per unit area. In addition, filling the space between the sheets with a light filler material was found to substantially increase structure penetration resistance with a small increase in weight. An evaluation of the meteoroid hazard to space vehicles is presented in the form of an illustrative-example for two specific lunar mission vehicles, a single-sheet, monocoque hull vehicle and a glass-wool filled, double-sheet hull vehicle. The evaluation is presented in terms of the "best" and the "worst" conditions that might be expected as determined from astronomical and satellite measurements, high-speed impact data, and hypothesized meteoroid structures and compositions. It was observed that the vehicle flight time without penetration can be increased significantly by use of multiple-sheet rather than single-sheet hull construction with no increase in hull weight. Nevertheless, it is evident that a meteoroid hazard exists, even for the vehicle with the selected multiple-sheet hull.

  2. Mosaic Structure of a Multiple-Drug-Resistant, Conjugative Plasmid from Campylobacter jejuni

    National Research Council Canada - National Science Library

    Nirdnoy, Warawadee; Mason, Carl J; Guerry, Patricia

    2005-01-01

    ..., where it apparently integrated into the chromosome and expressed high-level resistance to multiple aminoglycoside antibiotics. This work provides new information about both the nature of drug resistance in C...

  3. Substrate-assisted mechanism of RNP disruption by the spliceosomal Brr2 RNA helicase

    Science.gov (United States)

    Theuser, Matthias; Höbartner, Claudia; Wahl, Markus C.; Santos, Karine F.

    2016-01-01

    The Brr2 RNA helicase disrupts the U4/U6 di-small nuclear RNA–protein complex (di-snRNP) during spliceosome activation via ATP-driven translocation on the U4 snRNA strand. However, it is unclear how bound proteins influence U4/U6 unwinding, which regions of the U4/U6 duplex the helicase actively unwinds, and whether U4/U6 components are released as individual molecules or as subcomplexes. Here, we set up a recombinant Brr2-mediated U4/U6 di-snRNP disruption system, showing that sequential addition of the U4/U6 proteins small nuclear ribonucleoprotein-associated protein 1 (Snu13), pre-mRNA processing factor 31 (Prp31), and Prp3 to U4/U6 di-snRNA leads to a stepwise decrease of Brr2-mediated U4/U6 unwinding, but that unwinding is largely restored by a Brr2 cofactor, the C-terminal Jab1/MPN domain of the Prp8 protein. Brr2-mediated U4/U6 unwinding was strongly inhibited by mutations in U4/U6 di-snRNAs that diminish the ability of U6 snRNA to adopt an alternative conformation but leave the number and kind of U4/U6 base pairs unchanged. Irrespective of the presence of the cofactor, the helicase segregated a Prp3-Prp31-Snu13-U4/U6 RNP into an intact Prp31-Snu13-U4 snRNA particle, free Prp3, and free U6 snRNA. Together, these observations suggest that Brr2 translocates only a limited distance on the U4 snRNA strand and does not actively release RNA-bound proteins. Unwinding is then completed by the partially displaced U6 snRNA adopting an alternative conformation, which leads to dismantling of the Prp3-binding site on U4/U6 di-snRNA but leaves the Prp31- and Snu13-binding sites on U4 snRNA unaffected. In this fashion, Brr2 can activate the spliceosome by stripping U6 snRNA of all precatalytic binding partners, while minimizing logistic requirements for U4/U6 di-snRNP reassembly after splicing. PMID:27354531

  4. Further evidence for jet structure in large transverse momentum reactions from rapidity correlations and associated multiplicities

    International Nuclear Information System (INIS)

    Ranft, J.; Ranft, G.

    1976-10-01

    Using the hard collision model and a simple parametrisation for jet fragmentation expressions for same side and opposite side two-particle correlations and multiplicities associated with large transverse momentum trigger particles are derived. Recent data on rapidity correlations and associated multiplicities can be well understood in such a model. This result is interpreted as further evidence for the presence of jets in large transverse momentum reactions. (author)

  5. FBH1 helicase disrupts RAD51 filaments in vitro and modulates homologous recombination in mammalian cells

    DEFF Research Database (Denmark)

    Simandlova, Jitka; Zagelbaum, Jennifer; Payne, Miranda J

    2013-01-01

    Efficient repair of DNA double strand breaks and interstrand cross-links requires the homologous recombination (HR) pathway, a potentially error-free process that utilizes a homologous sequence as a repair template. A key player in HR is RAD51, the eukaryotic ortholog of bacterial RecA protein. RAD......51 can polymerize on DNA to form a nucleoprotein filament that facilitates both the search for the homologous DNA sequences and the subsequent DNA strand invasion required to initiate HR. Because of its pivotal role in HR, RAD51 is subject to numerous positive and negative regulatory influences...... filaments on DNA through its ssDNA translocase function. Consistent with this, a mutant mouse embryonic stem cell line with a deletion in the FBH1 helicase domain fails to limit RAD51 chromatin association and shows hyper-recombination. Our data are consistent with FBH1 restraining RAD51 DNA binding under...

  6. RTEL1 is a replisome-associated helicase that promotes telomere and genome-wide replication.

    Science.gov (United States)

    Vannier, Jean-Baptiste; Sandhu, Sumit; Petalcorin, Mark I R; Wu, Xiaoli; Nabi, Zinnatun; Ding, Hao; Boulton, Simon J

    2013-10-11

    Regulator of telomere length 1 (RTEL1) is an essential DNA helicase that disassembles telomere loops (T loops) and suppresses telomere fragility to maintain the integrity of chromosome ends. We established that RTEL1 also associates with the replisome through binding to proliferating cell nuclear antigen (PCNA). Mouse cells disrupted for the RTEL1-PCNA interaction (PIP mutant) exhibited accelerated senescence, replication fork instability, reduced replication fork extension rates, and increased origin usage. Although T-loop disassembly at telomeres was unaffected in the mutant cells, telomere replication was compromised, leading to fragile sites at telomeres. RTEL1-PIP mutant mice were viable, but loss of the RTEL1-PCNA interaction accelerated the onset of tumorigenesis in p53-deficient mice. We propose that RTEL1 plays a critical role in both telomere and genome-wide replication, which is crucial for genetic stability and tumor avoidance.

  7. Association between regulator of telomere elongation helicase1 (RTEL1) gene and HAPE risk

    Science.gov (United States)

    Rong, Hao; He, Xue; Zhu, Linhao; Zhu, Xikai; Kang, Longli; Wang, Li; He, Yongjun; Yuan, Dongya; Jin, Tianbo

    2017-01-01

    Abstract High altitude pulmonary edema (HAPE) is a paradigm of pulmonary edema. Mutations in regulator of telomere elongation helicase1 (RTEL1) represent an important contributor to risk for pulmonary fibrosis. However, little information is found about the association between RTEL1 and HAPE risk. The present study was undertaken to tentatively explore the potential relation between single-nucleotide polymorphisms (SNPs) in RTEL1 and HAPE risk in Chinese Han population. A total of 265 HAPE patients and 303 healthy controls were included in our case-control study. Four SNPs in RTEL1 were selected and genotyped using the Sequenom MassARRAY method. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated by unconditional logistic regression with adjustment for gender and age. All P values were Bonferroni corrected, and statistical significance was set at P RTEL1 and a decreased risk HAPE in the Chinese population. The results need further confirmation. PMID:28953687

  8. Hold your horSSEs: controlling structure-selective endonucleases MUS81 and Yen1/GEN1.

    Science.gov (United States)

    Blanco, Miguel G; Matos, Joao

    2015-01-01

    Repair of DNA lesions through homologous recombination promotes the establishment of stable chromosomal interactions. Multiple helicases, topoisomerases and structure-selective endonucleases (SSEs) act upon recombining joint molecules (JMs) to disengage chromosomal connections and safeguard chromosome segregation. Recent studies on two conserved SSEs - MUS81 and Yen1/GEN1- uncovered multiple layers of regulation that operate to carefully tailor JM-processing according to specific cellular needs. Temporal restriction of SSE function imposes a hierarchy in pathway usage that ensures efficient JM-processing while minimizing reciprocal exchanges between the recombining DNAs. Whereas a conserved strategy of fine-tuning SSE functions exists in different model systems, the precise molecular mechanisms to implement it appear to be significantly different. Here, we summarize the current knowledge on the cellular switches that are in place to control MUS81 and Yen1/GEN1 functions.

  9. Retinitis Pigmentosa Mutations in Bad Response to Refrigeration 2 (Brr2) Impair ATPase and Helicase Activity.

    Science.gov (United States)

    Ledoux, Sarah; Guthrie, Christine

    2016-06-03

    Brr2 is an RNA-dependent ATPase required to unwind the U4/U6 snRNA duplex during spliceosome assembly. Mutations within the ratchet helix of the Brr2 RNA binding channel result in a form of degenerative human blindness known as retinitis pigmentosa (RP). The biochemical consequences of these mutations on Brr2's RNA binding, helicase, and ATPase activity have not yet been characterized. Therefore, we identified the largest construct of Brr2 that is soluble in vitro, which truncates the first 247 amino acids of the N terminus (Δ247-Brr2), to characterize the effects of the RP mutations on Brr2 activity. The Δ247-Brr2 RP mutants exhibit a gradient of severity of weakened RNA binding, reduced helicase activity, and reduced ATPase activity compared with wild type Δ247-Brr2. The globular C-terminal Jab1/Mpn1-like domain of Prp8 increases the ability of Δ247-Brr2 to bind the U4/U6 snRNA duplex at high pH and increases Δ247-Brr2's RNA-dependent ATPase activity and the extent of RNA unwinding. However, this domain of Prp8 does not differentially affect the Δ247-Brr2 RP mutants compared with the wild type Δ247-Brr2. When stimulated by Prp8, wild type Δ247-Brr2 is able to unwind long stable duplexes in vitro, and even the RP mutants capable of binding RNA with tight affinity are incapable of fully unwinding short duplex RNAs. Our data suggest that the RP mutations within the ratchet helix impair Brr2 translocation through RNA helices. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  10. Structure, function, and phylogeny of the mating locus in the Rhizopus oryzae complex.

    Directory of Open Access Journals (Sweden)

    Andrii P Gryganskyi

    2010-12-01

    Full Text Available The Rhizopus oryzae species complex is a group of zygomycete fungi that are common, cosmopolitan saprotrophs. Some strains are used beneficially for production of Asian fermented foods but they can also act as opportunistic human pathogens. Although R. oryzae reportedly has a heterothallic (+/- mating system, most strains have not been observed to undergo sexual reproduction and the genetic structure of its mating locus has not been characterized. Here we report on the mating behavior and genetic structure of the mating locus for 54 isolates of the R. oryzae complex. All 54 strains have a mating locus similar in overall organization to Phycomyces blakesleeanus and Mucor circinelloides (Mucoromycotina, Zygomycota. In all of these fungi, the minus (- allele features the SexM high mobility group (HMG gene flanked by an RNA helicase gene and a TP transporter gene (TPT. Within the R. oryzae complex, the plus (+ mating allele includes an inserted region that codes for a BTB/POZ domain gene and the SexP HMG gene. Phylogenetic analyses of multiple genes, including the mating loci (HMG, TPT, RNA helicase, ITS1-5.8S-ITS2 rDNA, RPB2, and LDH genes, identified two distinct groups of strains. These correspond to previously described sibling species R. oryzae sensu stricto and R. delemar. Within each species, discordant gene phylogenies among multiple loci suggest an outcrossing population structure. The hypothesis of random-mating is also supported by a 50:50 ratio of plus and minus mating types in both cryptic species. When crossed with tester strains of the opposite mating type, most isolates of R. delemar failed to produce zygospores, while isolates of R. oryzae produced sterile zygospores. In spite of the reluctance of most strains to mate in vitro, the conserved sex locus structure and evidence for outcrossing suggest that a normal sexual cycle occurs in both species.

  11. Human regulator of telomere elongation helicase 1 (RTEL1) is required for the nuclear and cytoplasmic trafficking of pre-U2 RNA

    OpenAIRE

    Schertzer , Michael; Jouravleva , Karina; Perderiset , Mylène; Dingli , Florent; Loew , Damarys; Le Guen , Tangui; Bardoni , Barbara; De Villartay , Jean-Pierre; Revy , Patrick; Londono-Vallejo , Arturo

    2015-01-01

    International audience; Hoyeraal-Hreidarsson syndrome (HHS) is a severe form of Dyskeratosis congenita characterized by developmental defects, bone marrow failure and im-munodeficiency and has been associated with telom-ere dysfunction. Recently, mutations in Regulator of Telomere ELongation helicase 1 (RTEL1), a helicase first identified in Mus musculus as being responsible for the maintenance of long telomeres, have been identified in several HHS patients. Here we show that RTEL1 is require...

  12. Inference regarding multiple structural changes in linear models with endogenous regressors

    NARCIS (Netherlands)

    Boldea, O.; Hall, A.R.; Han, S.

    2012-01-01

    This paper considers the linear model with endogenous regressors and multiple changes in the parameters at unknown times. It is shown that minimization of a Generalized Method of Moments criterion yields inconsistent estimators of the break fractions, but minimization of the Two Stage Least Squares

  13. Student Strategies Suggesting Emergence of Mental Structures Supporting Logical and Abstract Thinking: Multiplicative Reasoning

    Science.gov (United States)

    Carrier, Jim

    2014-01-01

    For many students, developing mathematical reasoning can prove to be challenging. Such difficulty may be explained by a deficit in the core understanding of many arithmetical concepts taught in early school years. Multiplicative reasoning is one such concept that produces an essential foundation upon which higher-level mathematical thinking skills…

  14. Structure Determination of Anionic Metal Clusters via Infrared Resonance Enhanced Multiple Photon Electron Detachment Spectroscopy

    NARCIS (Netherlands)

    Haertelt, M.; Lapoutre, V. J. F.; Bakker, J. M.; Redlich, B.; Harding, D. J.; Fielicke, A.; Meijer, G.

    2011-01-01

    We report vibrational spectra of anionic metal clusters, measured via electron detachment following resonant absorption of multiple infrared photons. To facilitate the sequential absorption of the required large number of photons, the cluster beam interacts with the infrared radiation inside the

  15. Disruption of Structural and Functional Networks in Long-Standing Multiple Sclerosis

    NARCIS (Netherlands)

    Tewarie, P.; Steenwijk, M.D.; Tijms, B.M.; Daams, M.; Balk, L.J.; Stam, C.J.; Uitdehaag, B.M.J.; Polman, C.H.; Geurts, J.J.G.; Barkhof, F.; Pouwels, P.J.W.; Vrenken, H.; Hillebrand, A.

    2014-01-01

    Both gray matter atrophy and disruption of functional networks are important predictors for physical disability and cognitive impairment in multiple sclerosis (MS), yet their relationship is poorly understood. Graph theory provides a modality invariant framework to analyze patterns of gray matter

  16. Influence of Number Size, Problem Structure and Response Mode on Children's Solutions of Multiplication Word Problems.

    Science.gov (United States)

    De Corte, E.; And Others

    One important finding from recent research on multiplication word problems is that children's performances are strongly affected by the nature of the multiplier (whether it is an integer, decimal larger than 1 or a decimal smaller than 1). On the other hand, the size of the multiplicand has little or no effect on problem difficulty. The aim of the…

  17. Optically controlled reflection modulator using GaAs-AlGaAs n-i-p-i/multiple-quantum-well structures

    Science.gov (United States)

    Law, K.-K.; Simes, R. J.; Coldren, L. A.; Gossard, A. C.; Maserjian, J.

    1989-01-01

    An optically controlled reflection modulator has been demonstrated that consists of a combination of a GaAs-AlGaAs n-i-p-i doping structure with a multiple-quantum-well structures on top of a distributed Bragg reflector, all grown by MBE. A modulation of approximately 60 percent is obtained on the test structure, corresponding to a differential change of absorption coefficient in the quantum wells of approximately 7500/cm. Changes in reflectance can be observed with a control beam power as low as 1.5 microW. This device structure has the potential of being developed as an optically addressed spatial light modulator for optical information processing.

  18. Identification and Biochemical Characterization of Halisulfate 3 and Suvanine as Novel Inhibitors of Hepatitis C Virus NS3 Helicase from a Marine Sponge

    Directory of Open Access Journals (Sweden)

    Atsushi Furuta

    2014-01-01

    Full Text Available Hepatitis C virus (HCV is an important etiological agent that is responsible for the development of chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. HCV nonstructural protein 3 (NS3 helicase is a possible target for novel drug development due to its essential role in viral replication. In this study, we identified halisulfate 3 (hal3 and suvanine as novel NS3 helicase inhibitors, with IC50 values of 4 and 3 µM, respectively, from a marine sponge by screening extracts of marine organisms. Both hal3 and suvanine inhibited the ATPase, RNA binding, and serine protease activities of NS3 helicase with IC50 values of 8, 8, and 14 µM, and 7, 3, and 34 µM, respectively. However, the dengue virus (DENV NS3 helicase, which shares a catalytic core (consisting mainly of ATPase and RNA binding sites with HCV NS3 helicase, was not inhibited by hal3 and suvanine, even at concentrations of 100 µM. Therefore, we conclude that hal3 and suvanine specifically inhibit HCV NS3 helicase via an interaction with an allosteric site in NS3 rather than binding to the catalytic core. This led to the inhibition of all NS3 activities, presumably by inducing conformational changes.

  19. Parameter analysis on the temperature and thermal stress of the cylindrical structure with multiple holes

    International Nuclear Information System (INIS)

    Kang, Y. H.; Lee, Y. S.; Choi, Y. J.

    2001-01-01

    During fuel irradiation tests in the in-core of HANARO, all components of the capsule with multiple holes act as heat sources due to high gamma and fission heat. In the design stage, a series of design parameter study were performed to confirm the thermal integrity of the capsule with multiple holes. The main parameter reviewed in this study are as follows: the position of the specimen, the thickness of the support tube and gap size. From the analysis performed by using of the FEM code ANSYS. it is confirmed that gap size effect on the capsule is one of the most important parameter of the capsule integrity. And the final thermal stress and displacement of the support tube with a increase of gap size are also under the allowable limits of ASME code

  20. Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions

    DEFF Research Database (Denmark)

    Seemann, Ernst Stefan; Richter, Andreas S.; Gorodkin, Jan

    2010-01-01

    of that used for individual multiple alignments. Results: We derived a rather extensive algorithm. One of the advantages of our approach (in contrast to other RNARNA interaction prediction methods) is the application of covariance detection and prediction of pseudoknots between intra- and inter-molecular base...... pairs. As a proof of concept, we show an example and discuss the strengths and weaknesses of the approach....

  1. Associations between proprioceptive neural pathway structural connectivity and balance in people with multiple sclerosis

    OpenAIRE

    Brett W Fling; Brett W Fling; Geetanjali eGera-Dutta; Heather eSchlueter; Michelle H Cameron; Michelle H Cameron; Fay B Horak; Fay B Horak

    2014-01-01

    Mobility and balance impairments are a hallmark of multiple sclerosis (MS), affecting nearly half of patients at presentation and resulting in decreased activity and participation, falls, injuries, and reduced quality of life. A growing body of work suggests that balance impairments in people with mild MS are primarily the result of deficits in proprioception, the ability to determine body position in space in the absence of vision. A better understanding of the pathophysiology of balance dis...

  2. Associations between Proprioceptive Neural Pathway Structural Connectivity and Balance in People with Multiple Sclerosis

    OpenAIRE

    Fling, Brett W.; Dutta, Geetanjali Gera; Schlueter, Heather; Cameron, Michelle H.; Horak, Fay B.

    2014-01-01

    Mobility and balance impairments are a hallmark of multiple sclerosis (MS), affecting nearly half of patients at presentation and resulting in decreased activity and participation, falls, injuries, and reduced quality of life. A growing body of work suggests that balance impairments in people with mild MS are primarily the result of deficits in proprioception, the ability to determine body position in space in the absence of vision. A better understanding of the pathophysiology of balance dis...

  3. The DEAD-Box RNA Helicase DDX3 Interacts with m6A RNA Demethylase ALKBH5

    Directory of Open Access Journals (Sweden)

    Abdullah Shah

    2017-01-01

    Full Text Available DDX3 is a member of the family of DEAD-box RNA helicases. DDX3 is a multifaceted helicase and plays essential roles in key biological processes such as cell cycle, stress response, apoptosis, and RNA metabolism. In this study, we found that DDX3 interacted with ALKBH5, an m6A RNA demethylase. The ATP domain of DDX3 and DSBH domain of ALKBH5 were indispensable to their interaction with each other. Furthermore, DDX3 could modulate the demethylation of mRNAs. We also showed that DDX3 regulated the methylation status of microRNAs and there was an interaction between DDX3 and AGO2. The dynamics of m6A RNA modification is still a field demanding further investigation, and here, we add a link by showing that RNA demethylation can be regulated by proteins such as DDX3.

  4. SAD-3, a Putative Helicase Required for Meiotic Silencing by Unpaired DNA, Interacts with Other Components of the Silencing Machinery

    Science.gov (United States)

    Hammond, Thomas M.; Xiao, Hua; Boone, Erin C.; Perdue, Tony D.; Pukkila, Patricia J.; Shiu, Patrick K. T.

    2011-01-01

    In Neurospora crassa, genes lacking a pairing partner during meiosis are suppressed by a process known as meiotic silencing by unpaired DNA (MSUD). To identify novel MSUD components, we have developed a high-throughput reverse-genetic screen for use with the N. crassa knockout library. Here we describe the screening method and the characterization of a gene (sad-3) subsequently discovered. SAD-3 is a putative helicase required for MSUD and sexual spore production. It exists in a complex with other known MSUD proteins in the perinuclear region, a center for meiotic silencing activity. Orthologs of SAD-3 include Schizosaccharomyces pombe Hrr1, a helicase required for RNAi-induced heterochromatin formation. Both SAD-3 and Hrr1 interact with an RNA-directed RNA polymerase and an Argonaute, suggesting that certain aspects of silencing complex formation may be conserved between the two fungal species. PMID:22384347

  5. AN ORIGIN OF MULTIPLE RING STRUCTURE AND HIDDEN PLANETS IN HL TAU: A UNIFIED PICTURE BY SECULAR GRAVITATIONAL INSTABILITY

    International Nuclear Information System (INIS)

    Takahashi, Sanemichi Z.; Inutsuka, Shu-ichiro

    2016-01-01

    Recent ALMA observation has revealed multiple ring structures formed in a protoplanetary disk around HL Tau. Prior to the ALMA observation of HL Tau, theoretical analysis of secular gravitational instability (GI) described a possible formation of multiple ring structures with separations of 13 au around a radius of 100 au in protoplanetary disks under certain conditions. In this article, we reanalyze the viability of secular GI by adopting the physical values inferred from the observations. We derive the radial distributions of the most unstable wavelength and the growth timescale of secular GI and verify that secular GI can form the ring structures observed in HL Tau. When a turbulent viscosity coefficient α remains small in the inner region of the disk, secular GI grows in the whole disk. Thus, the formation of planetary mass objects should occur first in the inner region as a result of gravitational fragmentation after the nonlinear growth of secular GI. In this case, the resulting objects are expected to create gaps at r  ∼ 10 au and ∼30 au. As a result, all ring structures in HL Tau can be created by secular GI. If this scenario is realized in HL Tau, the outer region corresponds to the earlier growth phase of the most unstable mode of secular GI, and the inner region corresponds to the outcome of the nonlinear growth of secular GI. Therefore, this interpretation suggests that we are possibly witnessing both the beginning and the end of planet formation in HL Tau.

  6. Structural health monitoring and damage assessment using measured FRFs from multiple sensors. Part I. The indicator of correlation criteria

    Energy Technology Data Exchange (ETDEWEB)

    Zang, C.; Friswell, M.I. [Dept. of Aerospace Engineering, Univ. of Bristol, Bristol (United Kingdom); Imregun, M. [Dept. of Mechanical Engineering, Imperial Coll., London (United Kingdom)

    2003-07-01

    This paper presents two criteria for correlating measured frequency responses from multiple sensors and proposes to use them as indicators for structural damage detection. The first criterion is a global shape correlation (GSC) function that is sensitive to mode shape differences but not to relative scales. The second criterion, a global amplitude correlation (GAC) function, is based on actual response amplitudes. Both correlation criteria are a function of frequency and uniquely map a set of complex responses to a real scalar between zero and unity. The averaged integrations of GSC and GAC functions along the frequency points over the measurement range, also called damage indicators, are used to describe the correlation between two sets of vibration data. When a structure state remains unchanged, both correlation criteria are as close to unity simultaneously. Otherwise, the correlation with the reference data will be decreased with changes of structure states. Using GSC and GAC functions has the advantage of being able to deal with incomplete measurements. Also, all available response data are used and hence there is no critical selection of frequency points for damage detection. The above correlation criteria were applied to a bookshelf structure and various cases such as undamaged states, damage locations (single and multiple), damage levels, as well as environmental variability are discussed. As expected, it was found that indicators of correlation criteria were able to identify all various cases correctly. (orig.)

  7. AN ORIGIN OF MULTIPLE RING STRUCTURE AND HIDDEN PLANETS IN HL TAU: A UNIFIED PICTURE BY SECULAR GRAVITATIONAL INSTABILITY

    Energy Technology Data Exchange (ETDEWEB)

    Takahashi, Sanemichi Z. [Astronomical Institute, Tohoku University, 6-3 Aoba, Aramaki-aza, Aoba-ku, Sendai, Miyagi (Japan); Inutsuka, Shu-ichiro, E-mail: sanemichi@astr.tohoku.ac.jp, E-mail: inutsuka@nagoya-u.jp [Department of Physics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602 (Japan)

    2016-12-01

    Recent ALMA observation has revealed multiple ring structures formed in a protoplanetary disk around HL Tau. Prior to the ALMA observation of HL Tau, theoretical analysis of secular gravitational instability (GI) described a possible formation of multiple ring structures with separations of 13 au around a radius of 100 au in protoplanetary disks under certain conditions. In this article, we reanalyze the viability of secular GI by adopting the physical values inferred from the observations. We derive the radial distributions of the most unstable wavelength and the growth timescale of secular GI and verify that secular GI can form the ring structures observed in HL Tau. When a turbulent viscosity coefficient α remains small in the inner region of the disk, secular GI grows in the whole disk. Thus, the formation of planetary mass objects should occur first in the inner region as a result of gravitational fragmentation after the nonlinear growth of secular GI. In this case, the resulting objects are expected to create gaps at r  ∼ 10 au and ∼30 au. As a result, all ring structures in HL Tau can be created by secular GI. If this scenario is realized in HL Tau, the outer region corresponds to the earlier growth phase of the most unstable mode of secular GI, and the inner region corresponds to the outcome of the nonlinear growth of secular GI. Therefore, this interpretation suggests that we are possibly witnessing both the beginning and the end of planet formation in HL Tau.

  8. Essential and distinct roles of the F-box and helicase domains of Fbh1 in DNA damage repair

    Directory of Open Access Journals (Sweden)

    Shinagawa Hideo

    2008-03-01

    Full Text Available Abstract Background DNA double-strand breaks (DSBs are induced by exogenous insults such as ionizing radiation and chemical exposure, and they can also arise as a consequence of stalled or collapsed DNA replication forks. Failure to repair DSBs can lead to genomic instability or cell death and cancer in higher eukaryotes. The Schizosaccharomyces pombe fbh1 gene encodes an F-box DNA helicase previously described to play a role in the Rhp51 (an orthologue of S. cerevisiae RAD51-dependent recombinational repair of DSBs. Fbh1 fused to GFP localizes to discrete nuclear foci following DNA damage. Results To determine the functional roles of the highly conserved F-box and helicase domains, we have characterized fbh1 mutants carrying specific mutations in these domains. We show that the F-box mutation fbh1-fb disturbs the nuclear localization of Fbh1, conferring an fbh1 null-like phenotype. Moreover, nuclear foci do not form in fbh1-fb cells with DNA damage even if Fbh1-fb is targeted to the nucleus by fusion to a nuclear localization signal sequence. In contrast, the helicase mutation fbh1-hl causes the accumulation of Fbh1 foci irrespective of the presence of DNA damage and confers damage sensitivity greater than that conferred by the null allele. Additional mutation of the F-box alleviates the hypermorphic phenotype of the fbh1-hl mutant. Conclusion These results suggest that the F-box and DNA helicase domains play indispensable but distinct roles in Fbh1 function. Assembly of the SCFFbh1 complex is required for both the nuclear localization and DNA damage-induced focus formation of Fbh1 and is therefore prerequisite for the Fbh1 recombination function.

  9. DEAD-Box RNA Helicases are among the Constituents of the Tobacco Pollen mRNA Storing Bodies

    Czech Academy of Sciences Publication Activity Database

    Hafidh, Said; Potěšil, D.; Zdráhal, Z.; Honys, David

    2013-01-01

    Roč. 1, č. 3 (2013) ISSN 2329-9029 R&D Projects: GA ČR GPP501/11/P321; GA ČR(CZ) GAP501/11/1462; GA MŠk(CZ) ED1.1.00/02.0068; GA MŠk(CZ) LD13049 Institutional support: RVO:61389030 Keywords : Translation * mRNA storage * RNA helicase Subject RIV: EB - Genetics ; Molecular Biology

  10. Seismic Analysis of Intake Towers Considering Multiple-Support Excitation and Soil-Structure Interaction Effects

    National Research Council Canada - National Science Library

    Vidot, Aidcer

    2004-01-01

    .... The other effect examined is the soil-structure interaction. First, a direct approach based on a finite element model of the tower, bridge, and dam with the earthquake motion applied at the bedrock is used...

  11. Multiple Fano-Like MIM Plasmonic Structure Based on Triangular Resonator for Refractive Index Sensing

    OpenAIRE

    Jankovic, Nikolina; Cselyuszka, Norbert

    2018-01-01

    In this paper, we present a Fano metal-insulator-metal (MIM) structure based on an isosceles triangular cavity resonator for refractive index sensing applications. Due to the specific feeding scheme and asymmetry introduced in the triangular cavity, the resonator exhibits four sharp Fano-like resonances. The behavior of the structure is analyzed in detail and its sensing capabilities demonstrated through the responses for various refractive indices. The results show that the sensor has very g...

  12. Active joint mechanism driven by multiple actuators made of flexible bags: a proposal of dual structural actuator.

    Science.gov (United States)

    Kimura, Hitoshi; Matsuzaki, Takuya; Kataoka, Mokutaro; Inou, Norio

    2013-01-01

    An actuator is required to change its speed and force depending on the situation. Using multiple actuators for one driving axis is one of the possible solutions; however, there is an associated problem of output power matching. This study proposes a new active joint mechanism using multiple actuators. Because the actuator is made of a flexible bag, it does not interfere with other actuators when it is depressurized. The proposed joint achieved coordinated motion of multiple actuators. This report also discusses a new actuator which has dual cylindrical structure. The cylinders are composed of flexible bags with different diameters. The joint torque is estimated based on the following factors: empirical formula for the flexible actuator torque, geometric relationship between the joint and the actuator, and the principle of virtual work. The prototype joint mechanism achieves coordinated motion of multiple actuators for one axis. With this motion, small inner actuator contributes high speed motion, whereas large outer actuator generates high torque. The performance of the prototype joint is examined by speed and torque measurements. The joint showed about 30% efficiency at 2.0 Nm load torque under 0.15 MPa air input.

  13. Exploring the potential of a structural alphabet-based tool for mining multiple target conformations and target flexibility insight.

    Science.gov (United States)

    Regad, Leslie; Chéron, Jean-Baptiste; Triki, Dhoha; Senac, Caroline; Flatters, Delphine; Camproux, Anne-Claude

    2017-01-01

    Protein flexibility is often implied in binding with different partners and is essential for protein function. The growing number of macromolecular structures in the Protein Data Bank entries and their redundancy has become a major source of structural knowledge of the protein universe. The analysis of structural variability through available redundant structures of a target, called multiple target conformations (MTC), obtained using experimental or modeling methods and under different biological conditions or different sources is one way to explore protein flexibility. This analysis is essential to improve the understanding of various mechanisms associated with protein target function and flexibility. In this study, we explored structural variability of three biological targets by analyzing different MTC sets associated with these targets. To facilitate the study of these MTC sets, we have developed an efficient tool, SA-conf, dedicated to capturing and linking the amino acid and local structure variability and analyzing the target structural variability space. The advantage of SA-conf is that it could be applied to divers sets composed of MTCs available in the PDB obtained using NMR and crystallography or homology models. This tool could also be applied to analyze MTC sets obtained by dynamics approaches. Our results showed that SA-conf tool is effective to quantify the structural variability of a MTC set and to localize the structural variable positions and regions of the target. By selecting adapted MTC subsets and comparing their variability detected by SA-conf, we highlighted different sources of target flexibility such as induced by binding partner, by mutation and intrinsic flexibility. Our results support the interest to mine available structures associated with a target using to offer valuable insight into target flexibility and interaction mechanisms. The SA-conf executable script, with a set of pre-compiled binaries are available at http://www.mti.univ-paris-diderot.fr/recherche/plateformes/logiciels.

  14. Exploring the potential of a structural alphabet-based tool for mining multiple target conformations and target flexibility insight.

    Directory of Open Access Journals (Sweden)

    Leslie Regad

    Full Text Available Protein flexibility is often implied in binding with different partners and is essential for protein function. The growing number of macromolecular structures in the Protein Data Bank entries and their redundancy has become a major source of structural knowledge of the protein universe. The analysis of structural variability through available redundant structures of a target, called multiple target conformations (MTC, obtained using experimental or modeling methods and under different biological conditions or different sources is one way to explore protein flexibility. This analysis is essential to improve the understanding of various mechanisms associated with protein target function and flexibility. In this study, we explored structural variability of three biological targets by analyzing different MTC sets associated with these targets. To facilitate the study of these MTC sets, we have developed an efficient tool, SA-conf, dedicated to capturing and linking the amino acid and local structure variability and analyzing the target structural variability space. The advantage of SA-conf is that it could be applied to divers sets composed of MTCs available in the PDB obtained using NMR and crystallography or homology models. This tool could also be applied to analyze MTC sets obtained by dynamics approaches. Our results showed that SA-conf tool is effective to quantify the structural variability of a MTC set and to localize the structural variable positions and regions of the target. By selecting adapted MTC subsets and comparing their variability detected by SA-conf, we highlighted different sources of target flexibility such as induced by binding partner, by mutation and intrinsic flexibility. Our results support the interest to mine available structures associated with a target using to offer valuable insight into target flexibility and interaction mechanisms. The SA-conf executable script, with a set of pre-compiled binaries are available at

  15. Examining the Dynamic Structure of Daily Internalizing and Externalizing Behavior at Multiple Levels of Analysis

    Directory of Open Access Journals (Sweden)

    Aidan G.C. Wright

    2015-12-01

    Full Text Available Psychiatric diagnostic covariation suggests that the underlying structure of psychopathology is not one of circumscribed disorders. Quantitative modeling of individual differences in diagnostic patterns has uncovered several broad domains of mental disorder liability, of which the Internalizing and Externalizing spectra have garnered the greatest support. These dimensions have generally been estimated from lifetime or past-year comorbidity patters, which are distal from the covariation of symptoms and maladaptive behavior that ebb and flow in daily life. In this study, structural models are applied to daily diary data (Median = 94 days of maladaptive behaviors collected from a sample (N = 101 of individuals diagnosed with personality disorders. Using multilevel and unified structural equation modeling, between-person, within-person, and person-specific structures were estimated from 16 behaviors that are encompassed by the Internalizing and Externalizing spectra. At the between-person level (i.e., individual differences in average endorsement across days we found support for a two-factor Internalizing-Externalizing model, which exhibits significant associations with corresponding diagnostic spectra. At the within-person level (i.e., dynamic covariation among daily behavior pooled across individuals we found support for a more differentiated, four-factor, Negative Affect-Detachment-Hostility-Impulsivity structure. Finally, we demonstrate that the person-specific structures of associations between these four domains are highly idiosyncratic.

  16. Examining the Dynamic Structure of Daily Internalizing and Externalizing Behavior at Multiple Levels of Analysis

    Science.gov (United States)

    Wright, Aidan G. C.; Beltz, Adriene M.; Gates, Kathleen M.; Molenaar, Peter C. M.; Simms, Leonard J.

    2015-01-01

    Psychiatric diagnostic covariation suggests that the underlying structure of psychopathology is not one of circumscribed disorders. Quantitative modeling of individual differences in diagnostic patterns has uncovered several broad domains of mental disorder liability, of which the Internalizing and Externalizing spectra have garnered the greatest support. These dimensions have generally been estimated from lifetime or past-year comorbidity patters, which are distal from the covariation of symptoms and maladaptive behavior that ebb and flow in daily life. In this study, structural models are applied to daily diary data (Median = 94 days) of maladaptive behaviors collected from a sample (N = 101) of individuals diagnosed with personality disorders (PDs). Using multilevel and unified structural equation modeling, between-person, within-person, and person-specific structures were estimated from 16 behaviors that are encompassed by the Internalizing and Externalizing spectra. At the between-person level (i.e., individual differences in average endorsement across days) we found support for a two-factor Internalizing–Externalizing model, which exhibits significant associations with corresponding diagnostic spectra. At the within-person level (i.e., dynamic covariation among daily behavior pooled across individuals) we found support for a more differentiated, four-factor, Negative Affect-Detachment-Hostility-Disinhibition structure. Finally, we demonstrate that the person-specific structures of associations between these four domains are highly idiosyncratic. PMID:26732546

  17. 2 D electron transport in selectively doped Ga As/Inx Ga1-x As multiple quantum well structures

    International Nuclear Information System (INIS)

    Kulbachinskii, V.A.; Kytin, V.G.; Babushkina, T.S.; Malkina, I.G.

    1996-01-01

    Photoluminescence, temperature dependence of conductivity (0.4 x Ga 1-x As multiple quantum well (MQW) structures were investigated. The dependence of electron mobility on the width of the quantum wells and temperature were measured. It was shown that in narrow MQW structures the value of mobility is restricted by interface roughness scattering. In wider MQW structures neither interface roughness scattering nor change impurity scattering can describe the values and temperature dependence of mobility. Negative magnetoresistance was observed. From detailed comparison between theory of weak localization and experiment the relaxation time of the wave function phase τ ψ and temperature dependence of τ ψ were evaluated. Quantum Hall effect was investigated in all samples at T=0.4-4.2 K in magnetic fields up to 40 T. (author). 9 refs., 5 figs., 1 tab

  18. Zebrafish P54 RNA helicases are cytoplasmic granule residents that are required for development and stress resilience

    Directory of Open Access Journals (Sweden)

    Cecilia Zampedri

    2016-10-01

    Full Text Available Stress granules are cytoplasmic foci that directly respond to the protein synthesis status of the cell. Various environmental insults, such as oxidative stress or extreme heat, block protein synthesis; consequently, mRNA will stall in translation, and stress granules will immediately form and become enriched with mRNAs. P54 DEAD box RNA helicases are components of RNA granules such as P-bodies and stress granules. We studied the expression, in cytoplasmic foci, of both zebrafish P54 RNA helicases (P54a and P54b during development and found that they are expressed in cytoplasmic granules under both normal conditions and stress conditions. In zebrafish embryos exposed to heat shock, some proportion of P54a and P54b helicases move to larger granules that exhibit the properties of genuine stress granules. Knockdown of P54a and/or P54b in zebrafish embryos produces developmental abnormalities restricted to the posterior trunk; further, these embryos do not form stress granules, and their survival upon exposure to heat-shock conditions is compromised. Our observations fit the model that cells lacking stress granules have no resilience or ability to recover once the stress has ended, indicating that stress granules play an essential role in the way organisms adapt to a changing environment.

  19. Inference regarding multiple structural changes in linear models with endogenous regressors☆

    Science.gov (United States)

    Hall, Alastair R.; Han, Sanggohn; Boldea, Otilia

    2012-01-01

    This paper considers the linear model with endogenous regressors and multiple changes in the parameters at unknown times. It is shown that minimization of a Generalized Method of Moments criterion yields inconsistent estimators of the break fractions, but minimization of the Two Stage Least Squares (2SLS) criterion yields consistent estimators of these parameters. We develop a methodology for estimation and inference of the parameters of the model based on 2SLS. The analysis covers the cases where the reduced form is either stable or unstable. The methodology is illustrated via an application to the New Keynesian Phillips Curve for the US. PMID:23805021

  20. Nanoelectrospray high capacity ion trap multiple stage mass spectrometry for the structural analysis of human brain gangliosides

    International Nuclear Information System (INIS)

    Vukelic, Zeljka; Ratiu, Cornelia; Grozescu, Ioan; Zamfir, Alina Diana

    2006-01-01

    Full text: A novel protocol based on electrospray ionization (ESI) multiple stage high capacity ion trap (HCT) mass spectrometry (MS) was developed for glycosphingolipidomic surveys. The method was optimized for detailed structural elucidation of human brain gangliosides and particularly applied to human hippocampus-associated structures. The multiple stage MS experiments allowed for a complete structural characterization of GM1 ganglioside species, which was achieved by elucidation of the oligosaccharide sequence, identification of the GM1 a structural isomer from the data upon sialic acid localization along the sugar backbone and determination of the d18:1/18:0 of fatty acid/sphingoid base composition of the ceramide moiety. The methodology developed here is of general practical applicability for glycolipids and represents a step forward in the implementation of the advanced and most modern MS methods in glycomics. Gangliosides are glycosphingolipids, which consist of a mono- to polysialylated oligosaccharide chain of variable length attached to a ceramide portion of different composition with respect to the type of sphingoid base and fatty acid residues. Among all body systems, the central nervous system (CNS) possesses the highest content of gangliosides and they are playing a particularly important biological role at this level. Specific changes in the ganglioside expression and type of the expressed structures were observed to occur during brain development, maturation, and aging, and due to diseases or neurodegeneration processes. Gangliosides represent, therefore, an important class of biomarkers, carriers of information upon various CNS processes and events. Though in the human brain, their expression was observed to have a regional and tissue development induced specificity, the differences in ganglioside structure, composition and quantity were not systematically investigated or rigorously determined so far. (authors)

  1. Towards methodical modelling: Differences between the structure and output dynamics of multiple conceptual models

    Science.gov (United States)

    Knoben, Wouter; Woods, Ross; Freer, Jim

    2016-04-01

    Conceptual hydrologic models consist of a certain arrangement of spatial and temporal dynamics consisting of stores, fluxes and transformation functions, depending on the modeller's choices and intended use. They have the advantages of being computationally efficient, being relatively easy model structures to reconfigure and having relatively low input data demands. This makes them well-suited for large-scale and large-sample hydrology, where appropriately representing the dominant hydrologic functions of a catchment is a main concern. Given these requirements, the number of parameters in the model cannot be too high, to avoid equifinality and identifiability issues. This limits the number and level of complexity of dominant hydrologic processes the model can represent. Specific purposes and places thus require a specific model and this has led to an abundance of conceptual hydrologic models. No structured overview of these models exists and there is no clear method to select appropriate model structures for different catchments. This study is a first step towards creating an overview of the elements that make up conceptual models, which may later assist a modeller in finding an appropriate model structure for a given catchment. To this end, this study brings together over 30 past and present conceptual models. The reviewed model structures are simply different configurations of three basic model elements (stores, fluxes and transformation functions), depending on the hydrologic processes the models are intended to represent. Differences also exist in the inner workings of the stores, fluxes and transformations, i.e. the mathematical formulations that describe each model element's intended behaviour. We investigate the hypothesis that different model structures can produce similar behavioural simulations. This can clarify the overview of model elements by grouping elements which are similar, which can improve model structure selection.

  2. Do multiple fires interact to affect vegetation structure in temperate eucalypt forests?

    Science.gov (United States)

    Haslem, Angie; Leonard, Steve W J; Bruce, Matthew J; Christie, Fiona; Holland, Greg J; Kelly, Luke T; MacHunter, Josephine; Bennett, Andrew F; Clarke, Michael F; York, Alan

    2016-12-01

    Fire plays an important role in structuring vegetation in fire-prone regions worldwide. Progress has been made towards documenting the effects of individual fire events and fire regimes on vegetation structure; less is known of how different fire history attributes (e.g., time since fire, fire frequency) interact to affect vegetation. Using the temperate eucalypt foothill forests of southeastern Australia as a case study system, we examine two hypotheses about such interactions: (1) post-fire vegetation succession (e.g., time-since-fire effects) is influenced by other fire regime attributes and (2) the severity of the most recent fire overrides the effect of preceding fires on vegetation structure. Empirical data on vegetation structure were collected from 540 sites distributed across central and eastern Victoria, Australia. Linear mixed models were used to examine these hypotheses and determine the relative influence of fire and environmental attributes on vegetation structure. Fire history measures, particularly time since fire, affected several vegetation attributes including ground and canopy strata; others such as low and sub-canopy vegetation were more strongly influenced by environmental characteristics like rainfall. There was little support for the hypothesis that post-fire succession is influenced by fire history attributes other than time since fire; only canopy regeneration was influenced by another variable (fire type, representing severity). Our capacity to detect an overriding effect of the severity of the most recent fire was limited by a consistently weak effect of preceding fires on vegetation structure. Overall, results suggest the primary way that fire affects vegetation structure in foothill forests is via attributes of the most recent fire, both its severity and time since its occurrence; other attributes of fire regimes (e.g., fire interval, frequency) have less influence. The strong effect of environmental drivers, such as rainfall and

  3. Sensitivity of Microstructural Factors Influencing the Impact Toughness of Hypoeutectoid Steels with Ferrite-Pearlite Structure using Multiple Regression Analysis

    International Nuclear Information System (INIS)

    Lee, Seung-Yong; Lee, Sang-In; Hwang, Byoung-chul

    2016-01-01

    In this study, the effect of microstructural factors on the impact toughness of hypoeutectoid steels with ferrite-pearlite structure was quantitatively investigated using multiple regression analysis. Microstructural analysis results showed that the pearlite fraction increased with increasing austenitizing temperature and decreasing transformation temperature which substantially decreased the pearlite interlamellar spacing and cementite thickness depending on carbon content. The impact toughness of hypoeutectoid steels usually increased as interlamellar spacing or cementite thickness decreased, although the impact toughness was largely associated with pearlite fraction. Based on these results, multiple regression analysis was performed to understand the individual effect of pearlite fraction, interlamellar spacing, and cementite thickness on the impact toughness. The regression analysis results revealed that pearlite fraction significantly affected impact toughness at room temperature, while cementite thickness did at low temperature.

  4. Semiorders, Intervals Orders and Pseudo Orders Preference Structures in Multiple Criteria Decision Aid Methods

    Directory of Open Access Journals (Sweden)

    Fernández Barberis, Gabriela

    2013-06-01

    Full Text Available During the last decades, an important number of Multicriteria Decision Aid Methods (MCDA has been proposed to help the decision maker to select the best compromise alternative. Meanwhile, the PROMETHEE (Preference Ranking Organization Method for Enrichment Evaluations family of outranking method and their applications has attracted much attention from academics and practitioners. In this paper, an extension of these methods is presented, consisting of analyze its functioning under New Preference Structures (NPS. The preference structures taken into account are, namely: semiorders, intervals orders and pseudo orders. These structures outstandingly improve the modelization as they give more flexibility, amplitude and certainty at the preferences formulation, since they tend to abandon the Complete Transitive Comparability Axiom of Preferences in order to substitute it by the Partial Comparability Axiom of Preferences. It must be remarked the introduction of Incomparability relations to the analysis and the consideration of preference structures that accept the Indifference intransitivity. The NPS incorporation is carried out in three phases that the PROMETHEE Methodology takes in: preference structure enrichment, dominance relation enrichment and outranking relation exploitation for decision aid, in order to finally arrive at solving the alternatives ranking problem through the PROMETHEE I or the PROMETHEE II utilization, according to whether a partial ranking or a complete one, is respectively required under the NPS

  5. Structure of the EGF receptor transactivation circuit integrates multiple signals with cell context

    Energy Technology Data Exchange (ETDEWEB)

    Joslin, Elizabeth J.; Shankaran, Harish; Opresko, Lee K.; Bollinger, Nikki; Lauffenburger, Douglas A.; Wiley, H. S.

    2010-05-10

    Transactivation of the epidermal growth factor receptor (EGFR) has been proposed to be a mechanism by which a variety of cellular inputs can be integrated into a single signaling pathway, but the regulatory topology of this important system is unclear. To understand the transactivation circuit, we first created a “non-binding” reporter for ligand shedding. We then quantitatively defined how signals from multiple agonists were integrated both upstream and downstream of the EGFR into the extracellular signal regulated kinase (ERK) cascade in human mammary epithelial cells. We found that transactivation is mediated by a recursive autocrine circuit where ligand shedding drives EGFR-stimulated ERK that in turn drives further ligand shedding. The time from shedding to ERK activation is fast (<5 min) whereas the recursive feedback is slow (>15 min). Simulations showed that this delay in positive feedback greatly enhanced system stability and robustness. Our results indicate that the transactivation circuit is constructed so that the magnitude of ERK signaling is governed by the sum of multiple direct inputs, while recursive, autocrine ligand shedding controls signal duration.

  6. A novel multiple super junction power device structure with low specific on-resistance

    International Nuclear Information System (INIS)

    Zhu Hui; Li Haiou; Li Qi; Huang Yuanhao; Xu Xiaoning; Zhao Hailiang

    2014-01-01

    A novel multiple super junction (MSJ) LDMOS power device is proposed to decrease R on due to lateral and vertical interactions between the N-pillar and P-pillar. In the studied device: multiple layers of SJ are introduced oppositely under surface SJ; when compared with 2D-depleting of the conventional super junction (CSJ), a 3D-depleted effect is formed in the MSJ thanks to vertical electric field modulation; and, current distribution is improved by deep drain, which increases the drift doping concentration and results in a lower on-resistance. The high electric field around the drain region by substrate-assisted depleted effect is reduced due to the charge balance result from the electric field shielding effect of the bottom SJ, which causes the uniform electric field in the drift region and the high breakdown voltage. The numerical simulation results indicate that the specific on-resistance of the MSJ device is reduced by 42% compared with that of CSJ device, while maintaining a high breakdown voltage; the cell pitch of the device is 12 μm. (semiconductor devices)

  7. Structural health monitoring and damage assessment using measured FRFs from multiple sensors. Part II. Decision making with RBF networks

    Energy Technology Data Exchange (ETDEWEB)

    Zang, C.; Friswell, M.I. [Dept. of Aerospace Engineering, Univ. of Bristol, Bristol (United Kingdom); Imregun, M. [Dept. of Mechanical Engineering, Imperial Coll., London (United Kingdom)

    2003-07-01

    This paper is the second of two papers concerned with structural health monitoring and damage assessment using measured FRFs from multiple sensors, and discusses the decision making technique with radial basis function (RBF) neural networks. In PART 1 of the paper, the correlation criteria showed their capability to indicate various changes to the structure's state. PART 2, presented here, develops the methodology of decision theory to identify precisely all of the structure states. Although, the statistical approach can be used for classification, interpreting the information is difficult. Neural network techniques have been proven to possess many advantages for classification due to their learning ability and good generalization. In this paper, the radial basis function neural network is applied for function approximation and recognition. The key idea is to partition the input space (the indicators of the correlation criteria) into a number of subspaces that are in the form of hyper spheres. Then, the widely used k-mean clustering algorithm was selected as a logical approach to detecting the structure states. A bookshelf structure with measured frequency responses from 24 accelerometers was used to demonstrate the effectiveness of the method. The results show the successful classification of all structure states, for instance, the undamaged and damage states, damage locations and damage levels, and the environmental variability. (orig.)

  8. All together now: concurrent learning of multiple structures in an artificial language.

    Science.gov (United States)

    Romberg, Alexa R; Saffran, Jenny R

    2013-01-01

    Natural languages contain many layers of sequential structure, from the distribution of phonemes within words to the distribution of phrases within utterances. However, most research modeling language acquisition using artificial languages has focused on only one type of distributional structure at a time. In two experiments, we investigated adult learning of an artificial language that contains dependencies between both adjacent and non-adjacent words. We found that learners rapidly acquired both types of regularities and that the strength of the adjacent statistics influenced learning of both adjacent and non-adjacent dependencies. Additionally, though accuracy was similar for both types of structure, participants' knowledge of the deterministic non-adjacent dependencies was more explicit than their knowledge of the probabilistic adjacent dependencies. The results are discussed in the context of current theories of statistical learning and language acquisition. © 2013 Cognitive Science Society, Inc.

  9. Multiple roles of biosurfactants in structural biofilm development by Pseudomonas aeruginosa

    DEFF Research Database (Denmark)

    Pamp, Sünje Johanna; Tolker-Nielsen, Tim

    2007-01-01

    Recent studies have indicated that biosurfactants produced by Pseudomonas aeruginosa play a role both in maintaining channels between multicellular structures in biofilms and in dispersal of cells from biofilms. Through the use of flow cell technology and enhanced confocal laser scanning microscopy......, we have obtained results which suggest that the biosurfactants produced by P. aeruginosa play additional roles in structural biofilm development. We present genetic evidence that during biofilm development by P. aeruginosa, biosurfactants promote microcolony formation in the initial phase...... and facilitate migration-dependent structural development in the later phase. P. aeruginosa rhl4 mutants, deficient in synthesis of biosurfactants, were not capable of forming microcolonies in the initial phase of biofilm formation. Experiments involving two-color-coded mixed-strain biofilms showed that P...

  10. Amyloid structure exhibits polymorphism on multiple length scales in human brain tissue

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Jiliang; Costantino, Isabel; Venugopalan, Nagarajan; Fischetti, Robert F.; Hyman, Bradley; Frosch, Matthew; Gomez-Isla, Teresa; Makowski, Lee

    2016-09-15

    Although aggregation of Aβ amyloid fibrils into plaques in the brain is a hallmark of Alzheimer's Disease (AD), the correlation between amyloid burden and severity of symptoms is weak. One possible reason is that amyloid fibrils are structurally polymorphic and different polymorphs may contribute differentially to disease. However, the occurrence and distribution of amyloid polymorphisms in human brain is poorly documented. Here we seek to fill this knowledge gap by using X-ray microdiffraction of histological sections of human tissue to map the abundance, orientation and structural heterogeneities of amyloid within individual plaques; among proximal plaques and in subjects with distinct clinical histories. A 5 µ x-ray beam was used to generate diffraction data with each pattern arising from a scattering volume of only ~ 450 µ3 , making possible collection of dozens to hundreds of diffraction patterns from a single amyloid plaque. X-ray scattering from these samples exhibited all the properties expected for scattering from amyloid. Amyloid distribution was mapped using the intensity of its signature 4.7 Å reflection which also provided information on the orientation of amyloid fibrils across plaques. Margins of plaques exhibited a greater degree of orientation than cores and orientation around blood vessels frequently appeared tangential. Variation in the structure of Aβ fibrils is reflected in the shape of the 4.7 Å peak which usually appears as a doublet. Variations in this peak correspond to differences between the structure of amyloid within cores of plaques and at their periphery. Examination of tissue from a mismatch case - an individual with high plaque burden but no overt signs of dementia at time of death - revealed a diversity of structure and spatial distribution of amyloid that is distinct from typical AD cases. We demonstrate the existence of structural polymorphisms among amyloid within and among plaques of a single individual and suggest

  11. Relationships between the structure of wheat gluten and ACE inhibitory activity of hydrolysate: stepwise multiple linear regression analysis.

    Science.gov (United States)

    Zhang, Yanyan; Ma, Haile; Wang, Bei; Qu, Wenjuan; Wali, Asif; Zhou, Cunshan

    2016-08-01

    Ultrasound pretreatment of wheat gluten (WG) before enzymolysis can improve the angiotensin converting enzyme (ACE) inhibitory activity of the hydrolysates by alerting the structure of substrate proteins. Establishment of a relationship between the structure of WG and ACE inhibitory activity of the hydrolysates to judge the end point of the ultrasonic pretreatment is vital. The results of stepwise multiple linear regression (MLR) showed that the contents of free sulfhydryl, α-helix, disulfide bond, surface hydrophobicity and random coil were significantly correlated to ACE Inhibitory activity of the hydrolysate, with the standard partial regression coefficients were 3.729, -0.676, -0.252, 0.022 and 0.156, respectively. The R(2) of this model was 0.970. External validation showed that the stepwise MLR model could well predict the ACE inhibitory activity of hydrolysate based on the content of free sulfhydryl, α-helix, disulfide bond, surface hydrophobicity and random coil of WG before hydrolysis. A stepwise multiple linear regression model describing the quantitative relationships between the structure of WG and the ACE Inhibitory activity of the hydrolysates was established. This model can be used to predict the endpoint of the ultrasonic pretreatment. © 2015 Society of Chemical Industry. © 2015 Society of Chemical Industry.

  12. A functional and structural basis for TCR cross-resctivity in multiple sclerosis

    DEFF Research Database (Denmark)

    Lang, Heather L.E.; Jacobsen, Helle; Ikemizu, S.

    2002-01-01

    influence susceptibility to MS. We demonstrate that a T cell receptor (TCR) from an MS patient recognized both a DRB1*1501-restricted myelin basic protein (MBP) and DRB5*0101-restricted Epstein-Barr virus (EBV) peptide. Crystal structure determination of the DRB5*0101-EBV peptide complex revealed a marked......-associated diseases....

  13. Plant pathogens structure arthropod communities across multiple spatial and temporal scales

    NARCIS (Netherlands)

    Tack, A.J.M.; Dicke, M.

    2013-01-01

    Plant pathogens and herbivores frequently co-occur on the same host plants. Despite this, little is known about the impact of their interactions on the structure of plant-based ecological communities. Here, we synthesize evidence that indicates that plant pathogens may profoundly impact arthropod

  14. Characteristics of multiple auroral inverted-V structures and the problem of magnetospheric plasma stratification

    International Nuclear Information System (INIS)

    Antonova, E.E.; Stepanova, M.V.; Teltzov, M.V.; Tverskoy, B.A.

    1993-01-01

    The concept of hot stratification of magnetospheric plasma is presented. The stratification mechanism is based on the assumption that in the center of plasma sheet the pressure is approximately isotropic and under steady state conditions the gradient and curvature drift currents play the principal role. The number of formed structures is determined by the parameter of stratification. 7 figs., 2 tabs

  15. Dancing multiplicity states supported by a carboxylated group in dicopper structures bonded to O2

    KAUST Repository

    Poater, Albert; Cavallo, Luigi

    2013-01-01

    (μ-oxo) species is also on discussion. Despite the relative stabilities of all these either structural or electronic isomeric species are supposed to depend on the computational method, which is a difficulty to reach a definite conclusion about the nature

  16. Structural characterization of tartrate dehydrogenase: a versatile enzyme catalyzing multiple reactions

    International Nuclear Information System (INIS)

    Malik, Radhika; Viola, Ronald E.

    2010-01-01

    The first structure of an NAD-dependent tartrate dehydrogenase (TDH) has been solved to 2 (angstrom) resolution by single anomalous diffraction (SAD) phasing as a complex with the intermediate analog oxalate, Mg 2+ and NADH. This TDH structure from Pseudomonas putida has a similar overall fold and domain organization to other structurally characterized members of the hydroxy-acid dehydrogenase family. However, there are considerable differences between TDH and these functionally related enzymes in the regions connecting the core secondary structure and in the relative positioning of important loops and helices. The active site in these complexes is highly ordered, allowing the identification of the substrate-binding and cofactor-binding groups and the ligands to the metal ions. Residues from the adjacent subunit are involved in both the substrate and divalent metal ion binding sites, establishing a dimer as the functional unit and providing structural support for an alternating-site reaction mechanism. The divalent metal ion plays a prominent role in substrate binding and orientation, together with several active-site arginines. Functional groups from both subunits form the cofactor-binding site and the ammonium ion aids in the orientation of the nicotinamide ring of the cofactor. A lysyl amino group (Lys192) is the base responsible for the water-mediated proton abstraction from the C2 hydroxyl group of the substrate that begins the catalytic reaction, followed by hydride transfer to NAD. A tyrosyl hydroxyl group (Tyr141) functions as a general acid to protonate the enolate intermediate. Each substrate undergoes the initial hydride transfer, but differences in substrate orientation are proposed to account for the different reactions catalyzed by TDH.

  17. A conserved helicase processivity factor is needed for conjugation and replication of an integrative and conjugative element.

    Directory of Open Access Journals (Sweden)

    Jacob Thomas

    Full Text Available Integrative and conjugative elements (ICEs are agents of horizontal gene transfer and have major roles in evolution and acquisition of new traits, including antibiotic resistances. ICEs are found integrated in a host chromosome and can excise and transfer to recipient bacteria via conjugation. Conjugation involves nicking of the ICE origin of transfer (oriT by the ICE-encoded relaxase and transfer of the nicked single strand of ICE DNA. For ICEBs1 of Bacillus subtilis, nicking of oriT by the ICEBs1 relaxase NicK also initiates rolling circle replication. This autonomous replication of ICEBs1 is critical for stability of the excised element in growing cells. We found a conserved and previously uncharacterized ICE gene that is required for conjugation and replication of ICEBs1. Our results indicate that this gene, helP (formerly ydcP, encodes a helicase processivity factor that enables the host-encoded helicase PcrA to unwind the double-stranded ICEBs1 DNA. HelP was required for both conjugation and replication of ICEBs1, and HelP and NicK were the only ICEBs1 proteins needed for replication from ICEBs1 oriT. Using chromatin immunoprecipitation, we measured association of HelP, NicK, PcrA, and the host-encoded single-strand DNA binding protein Ssb with ICEBs1. We found that NicK was required for association of HelP and PcrA with ICEBs1 DNA. HelP was required for association of PcrA and Ssb with ICEBs1 regions distal, but not proximal, to oriT, indicating that PcrA needs HelP to progress beyond nicked oriT and unwind ICEBs1. In vitro, HelP directly stimulated the helicase activity of the PcrA homologue UvrD. Our findings demonstrate that HelP is a helicase processivity factor needed for efficient unwinding of ICEBs1 for conjugation and replication. Homologues of HelP and PcrA-type helicases are encoded on many known and putative ICEs. We propose that these factors are essential for ICE conjugation, replication, and genetic stability.

  18. Structural reconstruction of the catalytic center of LiPDF through multiple scattering calculation with MXAN

    Science.gov (United States)

    Guo, Xiaoyun; Chu, Wangsheng; Ma, Sixuan; Gong, Weimin; Benfatto, Maurizio; Hu, Tiandou; Xie, Yaning; Wu, ZiYu

    2006-11-01

    Peptide deformylase (PDF, EC 3.5.1.27) is essential for the normal growth of eubacterium but not for mammalians. Recently, PDF has been studied as a target for new antibiotics. In this paper, X-ray absorption spectroscopy was employed to determine the local structure around the zinc ion of PDF from Leptospira Interrogans in dry powder, because it is very difficult to obtain the crystallized sample of LiPDF. We performed X-ray absorption near edge structure (XANES) calculation and reconstructed successfully the local geometry of the active center, and the results from calculations show that a water molecule (Wat1) has moved towards the zinc ion and lies in the distance range to coordinate with the zinc ion weakly. In addition, the sensitivity of theoretical spectra to the different ligand bodies was evaluated in terms of goodness-of-fit.

  19. Structural reconstruction of the catalytic center of LiPDF through multiple scattering calculation with MXAN

    Energy Technology Data Exchange (ETDEWEB)

    Guo Xiaoyun [Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, CAS, 100049 Beijing (China); School of Life Science, Key Laboratory of Structural Biology, University of Science and Technology of China, 230026 Hefei, Anhui (China); Chu Wangsheng [Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, CAS, 100049 Beijing (China); Department of Physics, University of Science and Technology of China, 230026 Hefei, Anhui (China); Ma Sixuan [Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, CAS, 100049 Beijing (China); Gong Weimin [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing (China); Benfatto, Maurizio [Instituto Nazionale di Fisica Nucleare, Laboratori Nazionali di Frascati, P.O. Box 13, 00044 Frascati (Italy); Hu Tiandou [Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, CAS, 100049 Beijing (China); Xie Yaning [Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, CAS, 100049 Beijing (China); Wu Ziyu [Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, CAS, 100049 Beijing (China) and Instituto Nazionale di Fisica Nucleare, Laboratori Nazionali di Frascati, P.O. Box 13, 00044 Frascati (Italy)]. E-mail: wuzy@mail.ihep.ac.cn

    2006-11-15

    Peptide deformylase (PDF, EC 3.5.1.27) is essential for the normal growth of eubacterium but not for mammalians. Recently, PDF has been studied as a target for new antibiotics. In this paper, X-ray absorption spectroscopy was employed to determine the local structure around the zinc ion of PDF from Leptospira Interrogans in dry powder, because it is very difficult to obtain the crystallized sample of LiPDF. We performed X-ray absorption near edge structure (XANES) calculation and reconstructed successfully the local geometry of the active center, and the results from calculations show that a water molecule (Wat1) has moved towards the zinc ion and lies in the distance range to coordinate with the zinc ion weakly. In addition, the sensitivity of theoretical spectra to the different ligand bodies was evaluated in terms of goodness-of-fit.

  20. A multiple-scales model of the shock-cell structure of imperfectly expanded supersonic jets

    Science.gov (United States)

    Tam, C. K. W.; Jackson, J. A.; Seiner, J. M.

    1985-01-01

    The present investigation is concerned with the development of an analytical model of the quasi-periodic shock-cell structure of an imperfectly expanded supersonic jet. The investigation represents a part of a program to develop a mathematical theory of broadband shock-associated noise of supersonic jets. Tam and Tanna (1982) have suggested that this type of noise is generated by the weak interaction between the quasi-periodic shock cells and the downstream-propagating large turbulence structures in the mixing layer of the jet. In the model developed in this paper, the effect of turbulence in the mixing layer of the jet is simulated by the addition of turbulent eddy-viscosity terms to the momentum equation. Attention is given to the mean-flow profile and the numerical solution, and a comparison of the numerical results with experimental data.

  1. Structural reconstruction of the catalytic center of LiPDF through multiple scattering calculation with MXAN

    International Nuclear Information System (INIS)

    Guo Xiaoyun; Chu Wangsheng; Ma Sixuan; Gong Weimin; Benfatto, Maurizio; Hu Tiandou; Xie Yaning; Wu Ziyu

    2006-01-01

    Peptide deformylase (PDF, EC 3.5.1.27) is essential for the normal growth of eubacterium but not for mammalians. Recently, PDF has been studied as a target for new antibiotics. In this paper, X-ray absorption spectroscopy was employed to determine the local structure around the zinc ion of PDF from Leptospira Interrogans in dry powder, because it is very difficult to obtain the crystallized sample of LiPDF. We performed X-ray absorption near edge structure (XANES) calculation and reconstructed successfully the local geometry of the active center, and the results from calculations show that a water molecule (Wat1) has moved towards the zinc ion and lies in the distance range to coordinate with the zinc ion weakly. In addition, the sensitivity of theoretical spectra to the different ligand bodies was evaluated in terms of goodness-of-fit

  2. Multiple Fano-Like MIM Plasmonic Structure Based on Triangular Resonator for Refractive Index Sensing.

    Science.gov (United States)

    Jankovic, Nikolina; Cselyuszka, Norbert

    2018-01-19

    In this paper, we present a Fano metal-insulator-metal (MIM) structure based on an isosceles triangular cavity resonator for refractive index sensing applications. Due to the specific feeding scheme and asymmetry introduced in the triangular cavity, the resonator exhibits four sharp Fano-like resonances. The behavior of the structure is analyzed in detail and its sensing capabilities demonstrated through the responses for various refractive indices. The results show that the sensor has very good sensitivity and maximal figure of merit (FOM) value of 3.2 × 10⁵. In comparison to other similar sensors, the proposed one has comparable sensitivity and significantly higher FOM, which clearly demonstrates its high sensing potential.

  3. Flow structure of conical distributed multiple gas jets injected into a water chamber

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Jiajun; Yu, Yonggang [Nanjing University of Science and Technology, Nanjing (China)

    2017-04-15

    Based on an underwater gun firing project, a mock bullet with several holes on the head was designed and experimented to observe the combustion gas injected into a cylindrical water chamber through this mock bullet. The combustion gas jets contain one vertical central jet and 4 to 8 slant lateral jets. A high speed camera system was used to record the expansion of gas jets in the experimental study. In numerical simulations, the Euler two-fluid model and volume of fluid method were adopted to describe the gas-liquid flow. The results show the backflow zone in lateral jet is the main factor influencing the gas-liquid turbulent mixing in downstream. On cross sections, the gas volume fraction increased with time but the growth rate decreased. With a change of nozzle structure, the gas fraction was more affected than the shock structure.

  4. Humic acids: Structural properties and multiple functionalities for novel technological developments.

    Science.gov (United States)

    de Melo, Bruna Alice Gomes; Motta, Fernanda Lopes; Santana, Maria Helena Andrade

    2016-05-01

    Humic acids (HAs) are macromolecules that comprise humic substances (HS), which are organic matter distributed in terrestrial soil, natural water, and sediment. HAs differ from the other HS fractions (fulvic acid and humins) in that they are soluble in alkaline media, partially soluble in water, and insoluble in acidic media. Due to their amphiphilic character, HAs form micelle-like structures in neutral to acidic conditions, which are useful in agriculture, pollution remediation, medicine and pharmaceuticals. HAs have undefined compositions that vary according to the origin, process of obtainment, and functional groups present in their structures, such as quinones, phenols, and carboxylic acids. Quinones are responsible for the formation of reactive oxygen species (ROS) in HAs, which are useful for wound healing and have fungicidal/bactericidal properties. Phenols and carboxylic acids deprotonate in neutral and alkaline media and are responsible for various other functions, such as the antioxidant and anti-inflammatory properties of HAs. In particular, the presence of phenolic groups in HAs provides antioxidant properties due to their free radical scavenging capacity. This paper describes the main multifunctionalities of HAs associated with their structures and properties, focusing on human health applications, and we note perspectives that may lead to novel technological developments. To the best of our knowledge, this is the first review to address this topic from this approach. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. Multiple independent structural dynamic events in the evolution of snake mitochondrial genomes.

    Science.gov (United States)

    Qian, Lifu; Wang, Hui; Yan, Jie; Pan, Tao; Jiang, Shanqun; Rao, Dingqi; Zhang, Baowei

    2018-05-10

    Mitochondrial DNA sequences have long been used in phylogenetic studies. However, little attention has been paid to the changes in gene arrangement patterns in the snake's mitogenome. Here, we analyzed the complete mitogenome sequences and structures of 65 snake species from 14 families and examined their structural patterns, organization and evolution. Our purpose was to further investigate the evolutionary implications and possible rearrangement mechanisms of the mitogenome within snakes. In total, eleven types of mitochondrial gene arrangement patterns were detected (Type I, II, III, III-A, III-B, III-B1, III-C, III-D, III-E, III-F, III-G), with mitochondrial genome rearrangements being a major trend in snakes, especially in Alethinophidia. In snake mitogenomes, the rearrangements mainly involved three processes, gene loss, translocation and duplication. Within Scolecophidia, the O L was lost several times in Typhlopidae and Leptotyphlopidae, but persisted as a plesiomorphy in the Alethinophidia. Duplication of the control region and translocation of the tRNA Leu gene are two visible features in Alethinophidian mitochondrial genomes. Independently and stochastically, the duplication of pseudo-Pro (P*) emerged in seven different lineages of unequal size in three families, indicating that the presence of P* was a polytopic event in the mitogenome. The WANCY tRNA gene cluster and the control regions and their adjacent segments were hotspots for mitogenome rearrangement. Maintenance of duplicate control regions may be the source for snake mitogenome structural diversity.

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

    DEFF Research Database (Denmark)

    Han, Yang; Shen, Pan; Zhao, Xin

    2017-01-01

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

  7. Multiple chromosomal rearrangements structured the ancestral vertebrate Hox-bearing protochromosomes.

    Directory of Open Access Journals (Sweden)

    Vincent J Lynch

    2009-01-01

    Full Text Available While the proposal that large-scale genome expansions occurred early in vertebrate evolution is widely accepted, the exact mechanisms of the expansion--such as a single or multiple rounds of whole genome duplication, bloc chromosome duplications, large-scale individual gene duplications, or some combination of these--is unclear. Gene families with a single invertebrate member but four vertebrate members, such as the Hox clusters, provided early support for Ohno's hypothesis that two rounds of genome duplication (the 2R-model occurred in the stem lineage of extant vertebrates. However, despite extensive study, the duplication history of the Hox clusters has remained unclear, calling into question its usefulness in resolving the role of large-scale gene or genome duplications in early vertebrates. Here, we present a phylogenetic analysis of the vertebrate Hox clusters and several linked genes (the Hox "paralogon" and show that different phylogenies are obtained for Dlx and Col genes than for Hox and ErbB genes. We show that these results are robust to errors in phylogenetic inference and suggest that these competing phylogenies can be resolved if two chromosomal crossover events occurred in the ancestral vertebrate. These results resolve conflicting data on the order of Hox gene duplications and the role of genome duplication in vertebrate evolution and suggest that a period of genome reorganization occurred after genome duplications in early vertebrates.

  8. Monolithic mode locked DBR laser with multiple-bandgap MQW structure realized by selective area growth

    Energy Technology Data Exchange (ETDEWEB)

    Schilling, M.; Bouayad-Amine, J.; Feeser, T.; Haisch, H.; Kuehn, E.; Lach, E.; Satzke, K.; Weber, J.; Zielinski, E. [Alcatel Telecom, Stuttgart (Germany). Research Div.

    1996-12-31

    The realization of novel monolithically integrated multiple-segment pulse laser sources in InGaAsP MQW technology is reported. The MQW layers for all functional sections of these devices, the modulator, the active (gain) and the passive waveguide, as well as the Bragg section were grown in a single selective area growth (SAG) step by LP-MOVPE on SiO{sub 2} patterned 2 inch InP substrates. Due to a properly selected pattern geometry 3 different bandgap regions with smooth interfaces are thereby formed along the laser cavity. The more than 4 mm long DBR lasers which exhibit a threshold current as low as 30 mA were mode locked by an intra-cavity electroabsorption modulator applying a sinusoidal voltage at around 10 GHz. In this way an optical pulse train with pulse widths < 13 ps (measured with a streak camera) and high extinction ratio was generated. A time-bandwidth product of 0.5 close to the Fourier limit is obtained. This device is very attractive for signal generation in 40 Gb/s OTDM transmission systems at 1.55 {micro}m wavelength.

  9. Multiple Scales of Control on the Structure and Spatial Distribution of Woody Vegetation in African Savanna Watersheds.

    Directory of Open Access Journals (Sweden)

    Nicholas R Vaughn

    Full Text Available Factors controlling savanna woody vegetation structure vary at multiple spatial and temporal scales, and as a consequence, unraveling their combined effects has proven to be a classic challenge in savanna ecology. We used airborne LiDAR (light detection and ranging to map three-dimensional woody vegetation structure throughout four savanna watersheds, each contrasting in geologic substrate and climate, in Kruger National Park, South Africa. By comparison of the four watersheds, we found that geologic substrate had a stronger effect than climate in determining watershed-scale differences in vegetation structural properties, including cover, height and crown density. Generalized Linear Models were used to assess the spatial distribution of woody vegetation structural properties, including cover, height and crown density, in relation to mapped hydrologic, topographic and fire history traits. For each substrate and climate combination, models incorporating topography, hydrology and fire history explained up to 30% of the remaining variation in woody canopy structure, but inclusion of a spatial autocovariate term further improved model performance. Both crown density and the cover of shorter woody canopies were determined more by unknown factors likely to be changing on smaller spatial scales, such as soil texture, herbivore abundance or fire behavior, than by our mapped regional-scale changes in topography and hydrology. We also detected patterns in spatial covariance at distances up to 50-450 m, depending on watershed and structural metric. Our results suggest that large-scale environmental factors play a smaller role than is often attributed to them in determining woody vegetation structure in southern African savannas. This highlights the need for more spatially-explicit, wide-area analyses using high resolution remote sensing techniques.

  10. The roles of WRN and BLM RecQ helicases in the Alternative Lengthening of Telomeres.

    Science.gov (United States)

    Mendez-Bermudez, Aaron; Hidalgo-Bravo, Alberto; Cotton, Victoria E; Gravani, Athanasia; Jeyapalan, Jennie N; Royle, Nicola J

    2012-11-01

    Approximately 10% of all cancers, but a higher proportion of sarcomas, use the recombination-based alternative lengthening of telomeres (ALT) to maintain telomeres. Two RecQ helicase genes, BLM and WRN, play important roles in homologous recombination repair and they have been implicated in telomeric recombination activity, but their precise roles in ALT are unclear. Using analysis of sequence variation present in human telomeres, we found that a WRN- ALT+ cell line lacks the class of complex telomere mutations attributed to inter-telomeric recombination in other ALT+ cell lines. This suggests that WRN facilitates inter-telomeric recombination when there are sequence differences between the donor and recipient molecules or that sister-telomere interactions are suppressed in the presence of WRN and this promotes inter-telomeric recombination. Depleting BLM in the WRN- ALT+ cell line increased the mutation frequency at telomeres and at the MS32 minisatellite, which is a marker of ALT. The absence of complex telomere mutations persisted in BLM-depleted clones, and there was a clear increase in sequence homogenization across the telomere and MS32 repeat arrays. These data indicate that BLM suppresses unequal sister chromatid interactions that result in excessive homogenization at MS32 and at telomeres in ALT+ cells.

  11. A rapid Salmonella detection method involving thermophilic helicase-dependent amplification and a lateral flow assay.

    Science.gov (United States)

    Du, Xin-Jun; Zhou, Tian-Jiao; Li, Ping; Wang, Shuo

    2017-08-01

    Salmonella is a major foodborne pathogen that is widespread in the environment and can cause serious human and animal disease. Since conventional culture methods to detect Salmonella are time-consuming and laborious, rapid and accurate techniques to detect this pathogen are critically important for food safety and diagnosing foodborne illness. In this study, we developed a rapid, simple and portable Salmonella detection strategy that combines thermophilic helicase-dependent amplification (tHDA) with a lateral flow assay to provide a detection result based on visual signals within 90 min. Performance analyses indicated that the method had detection limits for DNA and pure cultured bacteria of 73.4-80.7 fg and 35-40 CFU, respectively. Specificity analyses showed no cross reactions with Escherichia coli, Staphylococcus aureus, Listeria monocytogenes, Enterobacter aerogenes, Shigella and Campylobacter jejuni. The results for detection in real food samples showed that 1.3-1.9 CFU/g or 1.3-1.9 CFU/mL of Salmonella in contaminated chicken products and infant nutritional cereal could be detected after 2 h of enrichment. The same amount of Salmonella in contaminated milk could be detected after 4 h of enrichment. This tHDA-strip can be used for the rapid detection of Salmonella in food samples and is particularly suitable for use in areas with limited equipment. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Antiviral drug resistance and helicase-primase inhibitors of herpes simplex virus.

    Science.gov (United States)

    Field, Hugh J; Biswas, Subhajit

    2011-02-01

    A new class of chemical inhibitors has been discovered that interferes with the process of herpesvirus DNA replication. To date, the majority of useful herpesvirus antivirals are nucleoside analogues that block herpesvirus DNA replication by targeting the DNA polymerase. The new helicase-primase inhibitors (HPI) target a different enzyme complex that is also essential for herpesvirus DNA replication. This review will place the HPI in the context of previous work on the nucleoside analogues. Several promising highly potent HPI will be described with a particular focus on the identification of drug-resistance mutations. Several HPI have good pharmacological profiles and are now at the outset of phase II clinical trials. Provided there are no safety issues to stop their progress, this new class of compound will be a major advance in the herpesvirus antiviral field. Furthermore, HPI are likely to have a major impact on the therapy and prevention of herpes simplex virus and varicella zoster in both immunocompetent and immunocompromised patients alone or in combination with current nucleoside analogues. The possibility of acquired drug-resistance to HPI will then become an issue of great practical importance. Copyright © 2010 Elsevier Ltd. All rights reserved.

  13. Mutation and Methylation Analysis of the Chromodomain-Helicase-DNA Binding 5 Gene in Ovarian Cancer

    Directory of Open Access Journals (Sweden)

    Kylie L. Gorringe

    2008-11-01

    Full Text Available Chromodomain, helicase, DNA binding 5 (CHD5 is a member of a subclass of the chromatin remodeling Swi/Snf proteins and has recently been proposed as a tumor suppressor in a diverse range of human cancers. We analyzed all 41 coding exons of CHD5 for somatic mutations in 123 primary ovarian cancers as well as 60 primary breast cancers using high-resolution melt analysis. We also examined methylation of the CHD5 promoter in 48 ovarian cancer samples by methylation-specific single-stranded conformation polymorphism and bisulfite sequencing. In contrast to previous studies, no mutations were identified in the breast cancers, but somatic heterozygous missense mutations were identified in 3 of 123 ovarian cancers. We identified promoter methylation in 3 of 45 samples with normal CHD5 and in 2 of 3 samples with CHD5 mutation, suggesting these tumors may have biallelic inactivation of CHD5. Hemizygous copy number loss at CHD5 occurred in 6 of 85 samples as assessed by single nucleotide polymorphism array. Tumors with CHD5 mutation or methylation were more likely to have mutation of KRAS or BRAF (P = .04. The aggregate frequency of CHD5 haploinsufficiency or inactivation is 16.2% in ovarian cancer. Thus, CHD5 may play a role as a tumor suppressor gene in ovarian cancer; however, it is likely that there is another target of the frequent copy number neutral loss of heterozygosity observed at 1p36.

  14. Helicase Dependent Isothermal Amplification of DNA and RNA using Self-Avoiding Molecular Recognition Systems

    Science.gov (United States)

    Yang, Zunyi; McLendon, Chris; Hutter, Daniel; Bradley, Kevin M.; Hoshika, Shuichi; Frye, Carole; Benner, Steven A.

    2015-01-01

    Assays that target DNA or RNA (xNA) are highly sensitive, as small amounts of xNA can be amplified by PCR. Unfortunately, PCR is inconvenient in low resource environments, requiring equipment and power that may not be available in these environments. However, isothermal procedures that avoid thermal cycling are often confounded by primer dimers, off-target priming, and other artifacts. Here, we show how a “self avoiding molecular recognition system” (SAMRS) eliminates these artifacts to give clean amplicons in a helicase-dependent isothermal amplification (SAMRS-HDA). We also show that incorporating SAMRS into the 3′-ends of primers facilitates the design and screening of primers for HDA assays. Finally, we show that SAMRS-HDA can be twofold multiplexed, something difficult to achieve with HDA using standard primers. This shows that SAMRS-HDA is a more versatile approach than standard HDA with a broader applicability for xNA-targeted diagnostics and research. PMID:25953623

  15. AAA-ATPase FIDGETIN-LIKE 1 and Helicase FANCM Antagonize Meiotic Crossovers by Distinct Mechanisms.

    Directory of Open Access Journals (Sweden)

    Chloe Girard

    2015-07-01

    Full Text Available Meiotic crossovers (COs generate genetic diversity and are critical for the correct completion of meiosis in most species. Their occurrence is tightly constrained but the mechanisms underlying this limitation remain poorly understood. Here we identified the conserved AAA-ATPase FIDGETIN-LIKE-1 (FIGL1 as a negative regulator of meiotic CO formation. We show that Arabidopsis FIGL1 limits CO formation genome-wide, that FIGL1 controls dynamics of the two conserved recombinases DMC1 and RAD51 and that FIGL1 hinders the interaction between homologous chromosomes, suggesting that FIGL1 counteracts DMC1/RAD51-mediated inter-homologue strand invasion to limit CO formation. Further, depleting both FIGL1 and the previously identified anti-CO helicase FANCM synergistically increases crossover frequency. Additionally, we showed that the effect of mutating FANCM on recombination is much lower in F1 hybrids contrasting from the phenotype of inbred lines, while figl1 mutation equally increases crossovers in both contexts. This shows that the modes of action of FIGL1 and FANCM are differently affected by genomic contexts. We propose that FIGL1 and FANCM represent two successive barriers to CO formation, one limiting strand invasion, the other disassembling D-loops to promote SDSA, which when both lifted, leads to a large increase of crossovers, without impairing meiotic progression.

  16. The DEAD box helicase RDE-12 promotes amplification of RNAi in cytoplasmic foci in C. elegans.

    Science.gov (United States)

    Yang, Huan; Vallandingham, Jim; Shiu, Philip; Li, Hua; Hunter, Craig P; Mak, Ho Yi

    2014-04-14

    RNAi is a potent mechanism for downregulating gene expression. Conserved RNAi pathway components are found in animals, plants, fungi, and other eukaryotes. In C. elegans, the RNAi response is greatly amplified by the synthesis of abundant secondary small interfering RNAs (siRNAs). Exogenous double-stranded RNA is processed by Dicer and RDE-1/Argonaute into primary siRNA that guides target mRNA recognition. The RDE-10/RDE-11 complex and the RNA-dependent RNA polymerase RRF-1 then engage the target mRNA for secondary siRNA synthesis. However, the molecular link between primary siRNA production and secondary siRNA synthesis remains largely unknown. Furthermore, it is unclear whether the subcellular sites for target mRNA recognition and degradation coincide with sites where siRNA synthesis and amplification occur. In the C. elegans germline, cytoplasmic P granules at the nuclear pores and perinuclear Mutator foci contribute to target mRNA surveillance and siRNA amplification, respectively. We report that RDE-12, a conserved phenylalanine-glycine (FG) domain-containing DEAD box helicase, localizes in P granules and cytoplasmic foci that are enriched in RSD-6 but are excluded from the Mutator foci. Our results suggest that RDE-12 promotes secondary siRNA synthesis by orchestrating the recruitment of RDE-10 and RRF-1 to primary siRNA-targeted mRNA in distinct cytoplasmic compartments. Copyright © 2014 Elsevier Ltd. All rights reserved.

  17. Phosphopeptide binding by Sld3 links Dbf4-dependent kinase to MCM replicative helicase activation.

    Science.gov (United States)

    Deegan, Tom D; Yeeles, Joseph Tp; Diffley, John Fx

    2016-05-02

    The initiation of eukaryotic DNA replication requires the assembly of active CMG (Cdc45-MCM-GINS) helicases at replication origins by a set of conserved and essential firing factors. This process is controlled during the cell cycle by cyclin-dependent kinase (CDK) and Dbf4-dependent kinase (DDK), and in response to DNA damage by the checkpoint kinase Rad53/Chk1. Here we show that Sld3, previously shown to be an essential CDK and Rad53 substrate, is recruited to the inactive MCM double hexamer in a DDK-dependent manner. Sld3 binds specifically to DDK-phosphorylated peptides from two MCM subunits (Mcm4, 6) and then recruits Cdc45. MCM mutants that cannot bind Sld3 or Sld3 mutants that cannot bind phospho-MCM or Cdc45 do not support replication. Moreover, phosphomimicking mutants in Mcm4 and Mcm6 bind Sld3 without DDK and facilitate DDK-independent replication. Thus, Sld3 is an essential "reader" of DDK phosphorylation, integrating signals from three distinct protein kinase pathways to coordinate DNA replication during S phase. © 2016 The Authors. Published under the terms of the CC BY 4.0 license.

  18. Helicase-primase inhibitor amenamevir for herpesvirus infection: Towards practical application for treating herpes zoster.

    Science.gov (United States)

    Shiraki, K

    2017-11-01

    Valacyclovir and famciclovir enabled successful systemic therapy for treating herpes simplex virus (HSV) and varicella zoster virus (VZV) infection by their phosphorylation with viral thymidine kinase. Helicase-primase inhibitors (HPIs) inhibit the progression of the replication fork, an initial step in DNA synthesis to separate the double strand into two single strands. The HPIs amenamevir and pritelivir have a novel mechanism of action, once-daily administration with nonrenal excretory characteristics, and clinical efficacy for genital herpes. Amenamevir exhibits anti-VZV and anti-HSV activity while pritelivir only has anti-HSV activity. A clinical trial of amenamevir for herpes zoster has been completed, and amenamevir has been licensed and successfully used in 20,000 patients with herpes zoster so far in Japan. We have characterized the features of the antiviral action of amenamevir and, unlike acyclovir, the drug's antiviral activity is not influenced by the viral replication cycle. Amenamevir is opening a new era of antiherpes therapy. Copyright 2017 Clarivate Analytics.

  19. Inherited mutations in the helicase RTEL1 cause telomere dysfunction and Hoyeraal-Hreidarsson syndrome.

    Science.gov (United States)

    Deng, Zhong; Glousker, Galina; Molczan, Aliah; Fox, Alan J; Lamm, Noa; Dheekollu, Jayaraju; Weizman, Orr-El; Schertzer, Michael; Wang, Zhuo; Vladimirova, Olga; Schug, Jonathan; Aker, Memet; Londoño-Vallejo, Arturo; Kaestner, Klaus H; Lieberman, Paul M; Tzfati, Yehuda

    2013-09-03

    Telomeres repress the DNA damage response at the natural chromosome ends to prevent cell-cycle arrest and maintain genome stability. Telomeres are elongated by telomerase in a tightly regulated manner to ensure a sufficient number of cell divisions throughout life, yet prevent unlimited cell division and cancer development. Hoyeraal-Hreidarsson syndrome (HHS) is characterized by accelerated telomere shortening and a broad range of pathologies, including bone marrow failure, immunodeficiency, and developmental defects. HHS-causing mutations have previously been found in telomerase and the shelterin component telomeric repeat binding factor 1 (TRF1)-interacting nuclear factor 2 (TIN2). We identified by whole-genome exome sequencing compound heterozygous mutations in four siblings affected with HHS, in the gene encoding the regulator of telomere elongation helicase 1 (RTEL1). Rtel1 was identified in mouse by its genetic association with telomere length. However, its mechanism of action and whether it regulates telomere length in human remained unknown. Lymphoblastoid cell lines obtained from a patient and from the healthy parents carrying heterozygous RTEL1 mutations displayed telomere shortening, fragility and fusion, and growth defects in culture. Ectopic expression of WT RTEL1 suppressed the telomere shortening and growth defect, confirming the causal role of the RTEL1 mutations in HHS and demonstrating the essential function of human RTEL1 in telomere protection and elongation. Finally, we show that human RTEL1 interacts with the shelterin protein TRF1, providing a potential recruitment mechanism of RTEL1 to telomeres.

  20. Inherited mutations in the helicase RTEL1 cause telomere dysfunction and Hoyeraal–Hreidarsson syndrome

    Science.gov (United States)

    Deng, Zhong; Glousker, Galina; Molczan, Aliah; Fox, Alan J.; Lamm, Noa; Dheekollu, Jayaraju; Weizman, Orr-El; Schertzer, Michael; Wang, Zhuo; Vladimirova, Olga; Schug, Jonathan; Aker, Memet; Londoño-Vallejo, Arturo; Kaestner, Klaus H.; Lieberman, Paul M.; Tzfati, Yehuda

    2013-01-01

    Telomeres repress the DNA damage response at the natural chromosome ends to prevent cell-cycle arrest and maintain genome stability. Telomeres are elongated by telomerase in a tightly regulated manner to ensure a sufficient number of cell divisions throughout life, yet prevent unlimited cell division and cancer development. Hoyeraal–Hreidarsson syndrome (HHS) is characterized by accelerated telomere shortening and a broad range of pathologies, including bone marrow failure, immunodeficiency, and developmental defects. HHS-causing mutations have previously been found in telomerase and the shelterin component telomeric repeat binding factor 1 (TRF1)-interacting nuclear factor 2 (TIN2). We identified by whole-genome exome sequencing compound heterozygous mutations in four siblings affected with HHS, in the gene encoding the regulator of telomere elongation helicase 1 (RTEL1). Rtel1 was identified in mouse by its genetic association with telomere length. However, its mechanism of action and whether it regulates telomere length in human remained unknown. Lymphoblastoid cell lines obtained from a patient and from the healthy parents carrying heterozygous RTEL1 mutations displayed telomere shortening, fragility and fusion, and growth defects in culture. Ectopic expression of WT RTEL1 suppressed the telomere shortening and growth defect, confirming the causal role of the RTEL1 mutations in HHS and demonstrating the essential function of human RTEL1 in telomere protection and elongation. Finally, we show that human RTEL1 interacts with the shelterin protein TRF1, providing a potential recruitment mechanism of RTEL1 to telomeres. PMID:23959892

  1. Translational control by the DEAD Box RNA helicase belle regulates ecdysone-triggered transcriptional cascades.

    Directory of Open Access Journals (Sweden)

    Robert J Ihry

    Full Text Available Steroid hormones act, through their respective nuclear receptors, to regulate target gene expression. Despite their critical role in development, physiology, and disease, however, it is still unclear how these systemic cues are refined into tissue-specific responses. We identified a mutation in the evolutionarily conserved DEAD box RNA helicase belle/DDX3 that disrupts a subset of responses to the steroid hormone ecdysone during Drosophila melanogaster metamorphosis. We demonstrate that belle directly regulates translation of E74A, an ets transcription factor and critical component of the ecdysone-induced transcriptional cascade. Although E74A mRNA accumulates to abnormally high levels in belle mutant tissues, no E74A protein is detectable, resulting in misregulation of E74A-dependent ecdysone response genes. The accumulation of E74A mRNA in belle mutant salivary glands is a result of auto-regulation, fulfilling a prediction made by Ashburner nearly 40 years ago. In this model, Ashburner postulates that, in addition to regulating secondary response genes, protein products of primary response genes like E74A also inhibit their own ecdysone-induced transcription. Moreover, although ecdysone-triggered transcription of E74A appears to be ubiquitous during metamorphosis, belle-dependent translation of E74A mRNA is spatially restricted. These results demonstrate that translational control plays a critical, and previously unknown, role in refining transcriptional responses to the steroid hormone ecdysone.

  2. Comparative analyses of reproductive structures in harvestmen (opiliones reveal multiple transitions from courtship to precopulatory antagonism.

    Directory of Open Access Journals (Sweden)

    Mercedes M Burns

    Full Text Available Explaining the rapid, species-specific diversification of reproductive structures and behaviors is a long-standing goal of evolutionary biology, with recent research tending to attribute reproductive phenotypes to the evolutionary mechanisms of female mate choice or intersexual conflict. Progress in understanding these and other possible mechanisms depends, in part, on reconstructing the direction, frequency and relative timing of phenotypic evolution of male and female structures in species-rich clades. Here we examine evolution of reproductive structures in the leiobunine harvestmen or "daddy long-legs" of eastern North America, a monophyletic group that includes species in which males court females using nuptial gifts and other species that are equipped for apparent precopulatory antagonism (i.e., males with long, hardened penes and females with sclerotized pregenital barriers. We used parsimony- and Bayesian likelihood-based analyses to reconstruct character evolution in categorical reproductive traits and found that losses of ancestral gift-bearing penile sacs are strongly associated with gains of female pregenital barriers. In most cases, both events occur on the same internal branch of the phylogeny. These coevolutionary changes occurred at least four times, resulting in clade-specific designs in the penis and pregenital barrier. The discovery of convergent origins and/or enhancements of apparent precopulatory antagonism among closely related species offers an unusual opportunity to investigate how major changes in reproductive morphology have occurred. We propose new hypotheses that attribute these enhancements to changes in ecology or life history that reduce the duration of breeding seasons, an association that is consistent with female choice, sexual conflict, and/or an alternative evolutionary mechanism.

  3. Effect of halloysite nanotubes on the structure and function of important multiple blood components

    International Nuclear Information System (INIS)

    Wu, Keke; Feng, Ru; Jiao, Yanpeng; Zhou, Changren

    2017-01-01

    Many researchers have investigated the application of halloysite nanotubes (HNTs) in biomedicine, because of their special nanoscale hollow tubular structure. Although the cytocompatibility of HNTs has been studied, their blood compatibility has not been systematically investigated. In this work, the effect of HNTs on the structure and function of different blood components has been studied, including the morphology and hemolysis of red blood cells (RBCs). Based on scanning electron microscopy (SEM) observations, optical density test and flow cytometry analysis, we found that HNTs can affect the morphology and membrane integrity of RBCs in phosphate buffered saline (PBS) in a content-dependent way. In particular, based on UV–vis absorption spectra, fluorescence spectra and circular dichroism (CD) spectra, HNTs can alter the secondary structure and conformation of human fibrinogen and γ-globulins. In addition, the detection of biomarker molecules C3a and C5a in plasma suggests that HNTs can trigger complement activation. In the blood clotting assay, HNTs were found to significantly prolong the activated partial thromboplastin time (APTT), shorten the prothrombin time (PT) of platelet-poor plasma (PPP), and change the thromboelastography (TEG) parameters of whole blood coagulation. Furthermore, confocal laser scanning microscopy and flow cytometry analysis were used to test intracellular uptake by macrophages, and the cellular uptake of HNTs in the RAW 264.7 was found to be content-dependent, but not time-dependent. These findings provide insight for the potential use of HNTs as biofriendly nanocontainers for biomaterials in vivo. - Highlights: • Comprehensive study of blood compatibility halloysite nanotubes (HNTs) is processed. • We examine and analyze the effect of HNTs on conformation changes of three plasma proteins. • We prove HNTs can affect blood components at high content but little at low content. • We prove HNTs could be used as biomaterials

  4. Effect of halloysite nanotubes on the structure and function of important multiple blood components.

    Science.gov (United States)

    Wu, Keke; Feng, Ru; Jiao, Yanpeng; Zhou, Changren

    2017-06-01

    Many researchers have investigated the application of halloysite nanotubes (HNTs) in biomedicine, because of their special nanoscale hollow tubular structure. Although the cytocompatibility of HNTs has been studied, their blood compatibility has not been systematically investigated. In this work, the effect of HNTs on the structure and function of different blood components has been studied, including the morphology and hemolysis of red blood cells (RBCs). Based on scanning electron microscopy (SEM) observations, optical density test and flow cytometry analysis, we found that HNTs can affect the morphology and membrane integrity of RBCs in phosphate buffered saline (PBS) in a content-dependent way. In particular, based on UV-vis absorption spectra, fluorescence spectra and circular dichroism (CD) spectra, HNTs can alter the secondary structure and conformation of human fibrinogen and γ-globulins. In addition, the detection of biomarker molecules C3a and C5a in plasma suggests that HNTs can trigger complement activation. In the blood clotting assay, HNTs were found to significantly prolong the activated partial thromboplastin time (APTT), shorten the prothrombin time (PT) of platelet-poor plasma (PPP), and change the thromboelastography (TEG) parameters of whole blood coagulation. Furthermore, confocal laser scanning microscopy and flow cytometry analysis were used to test intracellular uptake by macrophages, and the cellular uptake of HNTs in the RAW 264.7 was found to be content-dependent, but not time-dependent. These findings provide insight for the potential use of HNTs as biofriendly nanocontainers for biomaterials in vivo. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Effect of halloysite nanotubes on the structure and function of important multiple blood components

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Keke; Feng, Ru; Jiao, Yanpeng, E-mail: tjiaoyp@jnu.edu.cn; Zhou, Changren

    2017-06-01

    Many researchers have investigated the application of halloysite nanotubes (HNTs) in biomedicine, because of their special nanoscale hollow tubular structure. Although the cytocompatibility of HNTs has been studied, their blood compatibility has not been systematically investigated. In this work, the effect of HNTs on the structure and function of different blood components has been studied, including the morphology and hemolysis of red blood cells (RBCs). Based on scanning electron microscopy (SEM) observations, optical density test and flow cytometry analysis, we found that HNTs can affect the morphology and membrane integrity of RBCs in phosphate buffered saline (PBS) in a content-dependent way. In particular, based on UV–vis absorption spectra, fluorescence spectra and circular dichroism (CD) spectra, HNTs can alter the secondary structure and conformation of human fibrinogen and γ-globulins. In addition, the detection of biomarker molecules C3a and C5a in plasma suggests that HNTs can trigger complement activation. In the blood clotting assay, HNTs were found to significantly prolong the activated partial thromboplastin time (APTT), shorten the prothrombin time (PT) of platelet-poor plasma (PPP), and change the thromboelastography (TEG) parameters of whole blood coagulation. Furthermore, confocal laser scanning microscopy and flow cytometry analysis were used to test intracellular uptake by macrophages, and the cellular uptake of HNTs in the RAW 264.7 was found to be content-dependent, but not time-dependent. These findings provide insight for the potential use of HNTs as biofriendly nanocontainers for biomaterials in vivo. - Highlights: • Comprehensive study of blood compatibility halloysite nanotubes (HNTs) is processed. • We examine and analyze the effect of HNTs on conformation changes of three plasma proteins. • We prove HNTs can affect blood components at high content but little at low content. • We prove HNTs could be used as biomaterials

  6. First observation of excited structures in neutron-deficient 179Hg : evidence for multiple shape coexistence

    International Nuclear Information System (INIS)

    Kondev, F.G.; Carpenter, M.P.; Janssens, R.V.F.; Lister, C.J.; Abu Saleem, K.; Ahmad, I.; Amro, H.; Caggiano, J.; Davids, C.N.; Heinz, A.; Herskind, B.; Khoo, T.L.; Lauristen, T.; Ma, W.C.; Ressler, J.J.; Reviol, W.; Riedinger, L.L.; Sarantites, D.G.; Seweryniak, D.; Siem, S.; Sonzongni, A.A.; Varmette, P.G.; Wiedenhoever, I.

    2002-01-01

    Excited structures in the neutron-deficient nucleus 179 Hg have been established for the first time using the Gammasphere spectrometer in conjunction with the fragment mass analyzer. Competing states originating from three different minima associated with nearly spherical, oblate, and prolate deformations were found. This result can be contrasted with the situation in heavier odd-mass Hg isotopes where only two minima (oblate and prolate) have been seen. The implications of these three shapes at low spin and excitation energy are discussed in the general context of shape coexistence in this mass region.

  7. Variogram based and Multiple - Point Statistical simulation of shallow aquifer structures in the Upper Salzach valley, Austria

    Science.gov (United States)

    Jandrisevits, Carmen; Marschallinger, Robert

    2014-05-01

    Quarternary sediments in overdeepened alpine valleys and basins in the Eastern Alps bear substantial groundwater resources. The associated aquifer systems are generally geometrically complex with highly variable hydraulic properties. 3D geological models provide predictions of both geometry and properties of the subsurface required for subsequent modelling of groundwater flow and transport. In hydrology, geostatistical Kriging and Kriging based conditional simulations are widely used to predict the spatial distribution of hydrofacies. In the course of investigating the shallow aquifer structures in the Zell basin in the Upper Salzach valley (Salzburg, Austria), a benchmark of available geostatistical modelling and simulation methods was performed: traditional variogram based geostatistical methods, i.e. Indicator Kriging, Sequential Indicator Simulation and Sequential Indicator Co - Simulation were used as well as Multiple Point Statistics. The ~ 6 km2 investigation area is sampled by 56 drillings with depths of 5 to 50 m; in addition, there are 2 geophysical sections with lengths of 2 km and depths of 50 m. Due to clustered drilling sites, indicator Kriging models failed to consistently model the spatial variability of hydrofacies. Using classical variogram based geostatistical simulation (SIS), equally probable realizations were generated with differences among the realizations providing an uncertainty measure. The yielded models are unstructured from a geological point - they do not portray the shapes and lateral extensions of associated sedimentary units. Since variograms consider only two - point spatial correlations, they are unable to capture the spatial variability of complex geological structures. The Multiple Point Statistics approach overcomes these limitations of two point statistics as it uses a Training image instead of variograms. The 3D Training Image can be seen as a reference facies model where geological knowledge about depositional

  8. Power Flow Calculation for Weakly Meshed Distribution Networks with Multiple DGs Based on Generalized Chain-table Storage Structure

    DEFF Research Database (Denmark)

    Chen, Shuheng; Hu, Weihao; Chen, Zhe

    2014-01-01

    Based on generalized chain-table storage structure (GCTSS), a novel power flow method is proposed, which can be used to solve the power flow of weakly meshed distribution networks with multiple distributed generators (DGs). GCTSS is designed based on chain-table technology and its target is to de......Based on generalized chain-table storage structure (GCTSS), a novel power flow method is proposed, which can be used to solve the power flow of weakly meshed distribution networks with multiple distributed generators (DGs). GCTSS is designed based on chain-table technology and its target...... is to describe the topology of radial distribution networks with a clear logic and a small memory size. The strategies of compensating the equivalent currents of break-point branches and the reactive power outputs of PV-type DGs are presented on the basis of superposition theorem. Their formulations...... are simplified to be the final multi-variable linear functions. Furthermore, an accelerating factor is applied to the outer-layer reactive power compensation for improving the convergence procedure. Finally, the proposed power flow method is performed in program language VC++ 6.0, and numerical tests have been...

  9. Evaluating multiple determinants of the structure of plant-animal mutualistic networks.

    Science.gov (United States)

    Vázquez, Diego P; Chacoff, Natacha P; Cagnolo, Luciano

    2009-08-01

    The structure of mutualistic networks is likely to result from the simultaneous influence of neutrality and the constraints imposed by complementarity in species phenotypes, phenologies, spatial distributions, phylogenetic relationships, and sampling artifacts. We develop a conceptual and methodological framework to evaluate the relative contributions of these potential determinants. Applying this approach to the analysis of a plant-pollinator network, we show that information on relative abundance and phenology suffices to predict several aggregate network properties (connectance, nestedness, interaction evenness, and interaction asymmetry). However, such information falls short of predicting the detailed network structure (the frequency of pairwise interactions), leaving a large amount of variation unexplained. Taken together, our results suggest that both relative species abundance and complementarity in spatiotemporal distribution contribute substantially to generate observed network patters, but that this information is by no means sufficient to predict the occurrence and frequency of pairwise interactions. Future studies could use our methodological framework to evaluate the generality of our findings in a representative sample of study systems with contrasting ecological conditions.

  10. Multiple geophysical methods examining neotectonic blind structures in the Maradona valley, Central Precordillera (Argentina)

    Science.gov (United States)

    Lara, Gabriela; Klinger, Federico Lince; Perucca, Laura; Rojo, Guillermo; Vargas, Nicolás; Leiva, Flavia

    2017-08-01

    A high-resolution superficial geophysical study was carried out in an area of the retroarc region of the Andes mountains, located in the southwest of San Juan Province (31°45‧ S, 68°50‧ W), Central Precordillera of Argentina. The main objectives of this study were to confirm the presence of blind neotectonic structures and characterize them by observing variations in magnetic susceptibility, density and p-wave velocities. Geological evidence demonstrates the existence of a neotectonic fault scarps affecting Quaternary alluvial deposits in eastern piedmont of de Las Osamentas range, in addition to direct observation of the cinematic of this feature in several natural exposures. The Maradona valley is characterized by the imbricated eastern-vergence Maradona Fault System that uplifts Neogene sedimentary rocks (Albarracín Formation) over Quaternary (Late Pleistocene-Holocene) alluvial deposits. The combined application of different geophysical methods has allowed the characterization of a blind fault geometry also identified on a natural exposure. The magnetic data added to the gravimetric model, and its integration with a seismic profile clearly shows the existence of an anomalous zone, interpreted as uplifted blocks of Miocene sedimentary rocks of Formation Albarracín displaced over Quaternary deposits. The application and development of different geophysical methods, together with geological studies allow to significantly improving the knowledge of an area affected by Quaternary tectonic activity. Finally, this multidisciplinary study, applied in active blind structures is very relevant for future seismic hazard analysis on areas located very close to populated centers.

  11. Structural dynamics of surfaces by ultrafast electron crystallography: experimental and multiple scattering theory.

    Science.gov (United States)

    Schäfer, Sascha; Liang, Wenxi; Zewail, Ahmed H

    2011-12-07

    Recent studies in ultrafast electron crystallography (UEC) using a reflection diffraction geometry have enabled the investigation of a wide range of phenomena on the femtosecond and picosecond time scales. In all these studies, the analysis of the diffraction patterns and their temporal change after excitation was performed within the kinematical scattering theory. In this contribution, we address the question, to what extent dynamical scattering effects have to be included in order to obtain quantitative information about structural dynamics. We discuss different scattering regimes and provide diffraction maps that describe all essential features of scatterings and observables. The effects are quantified by dynamical scattering simulations and examined by direct comparison to the results of ultrafast electron diffraction experiments on an in situ prepared Ni(100) surface, for which structural dynamics can be well described by a two-temperature model. We also report calculations for graphite surfaces. The theoretical framework provided here allows for further UEC studies of surfaces especially at larger penetration depths and for those of heavy-atom materials. © 2011 American Institute of Physics

  12. Structure studies on 82Kr by means of the multiple Coulomb excitation

    International Nuclear Information System (INIS)

    Bruessermann, S.

    1985-01-01

    With a 82 Kr beam of the energy 4.6 MeV per nucleon a 208 Pb target was irradiated in order to study the Coulomb excitation of 82 Kr. The experiment has been performed at the Society for Heavy Ion Research (GSI) in Darmstadt. The 82 Kr ions backscattered on the 208 Pb target were detected in a position-sensitive parallel-plate avalanche detector. The γ radiation of the excited 82 Kr particles was detected in 4 Ge(Li) detectors in coincidence with the particles. The spectra corrected regarding the Doppler shift contained 16 lines which permitted to determine by means of known mixing and branching ratios 22 electrical quadrupole transition matrix elements. The experimental excitation energies and the transition probabilities determined in this thesis are compared with different nuclear models, like the asymmetric rotator model, the rotational-vibrational model, the harmonic-oscillator model, the nuclear field theory, the SU(5) limit of the IBA-1, and the IBA-2 model. Thereby within the IBA-2 model a criterium for the symmetry of the wavefunction relative to the proton and neutron contributions is elaborated. Because of this criterium to the 2 1 + state a symmetric structure and to the 2 2 + ,3 states an asymmetric structure is assigned. (orig.) [de

  13. Her versus his migraine: multiple sex differences in brain function and structure.

    Science.gov (United States)

    Maleki, Nasim; Linnman, Clas; Brawn, Jennifer; Burstein, Rami; Becerra, Lino; Borsook, David

    2012-08-01

    Migraine is twice as common in females as in males, but the mechanisms behind this difference are still poorly understood. We used high-field magnetic resonance imaging in male and female age-matched interictal (migraine free) migraineurs and matched healthy controls to determine alterations in brain structure. Female migraineurs had thicker posterior insula and precuneus cortices compared with male migraineurs and healthy controls of both sexes. Furthermore, evaluation of functional responses to heat within the migraine groups indicated concurrent functional differences in male and female migraineurs and a sex-specific pattern of functional connectivity of these two regions with the rest of the brain. The results support the notion of a 'sex phenotype' in migraine and indicate that brains are differentially affected by migraine in females compared with males. Furthermore, the results also support the notion that sex differences involve both brain structure as well as functional circuits, in that emotional circuitry compared with sensory processing appears involved to a greater degree in female than male migraineurs.

  14. Mycobacterium smegmatis Lhr Is a DNA-dependent ATPase and a 3'-to-5' DNA translocase and helicase that prefers to unwind 3'-tailed RNA:DNA hybrids.

    Science.gov (United States)

    Ordonez, Heather; Shuman, Stewart

    2013-05-17

    We are interested in the distinctive roster of helicases of Mycobacterium, a genus of the phylum Actinobacteria that includes the human pathogen Mycobacterium tuberculosis and its avirulent relative Mycobacterium smegmatis. Here, we identify and characterize M. smegmatis Lhr as the exemplar of a novel clade of superfamily II helicases, by virtue of its biochemical specificities and signature domain organization. Lhr is a 1507-amino acid monomeric nucleic acid-dependent ATPase that uses the energy of ATP hydrolysis to drive unidirectional 3'-to-5' translocation along single strand DNA and to unwind duplexes en route. The ATPase is more active in the presence of calcium than magnesium. ATP hydrolysis is triggered by either single strand DNA or single strand RNA, yet the apparent affinity for a DNA activator is 11-fold higher than for an RNA strand of identical size and nucleobase sequence. Lhr is 8-fold better at unwinding an RNA:DNA hybrid than it is at displacing a DNA:DNA duplex of identical nucleobase sequence. The truncated derivative Lhr-(1-856) is an autonomous ATPase, 3'-to-5' translocase, and RNA:DNA helicase. Lhr-(1-856) is 100-fold better RNA:DNA helicase than DNA:DNA helicase. Lhr homologs are found in bacteria representing eight different phyla, being especially prevalent in Actinobacteria (including M. tuberculosis) and Proteobacteria (including Escherichia coli).

  15. Associations between proprioceptive neural pathway structural connectivity and balance in people with multiple sclerosis

    Directory of Open Access Journals (Sweden)

    Brett W Fling

    2014-10-01

    Full Text Available Mobility and balance impairments are a hallmark of multiple sclerosis (MS, affecting nearly half of patients at presentation and resulting in decreased activity and participation, falls, injuries, and reduced quality of life. A growing body of work suggests that balance impairments in people with mild MS are primarily the result of deficits in proprioception, the ability to determine body position in space in the absence of vision. A better understanding of the pathophysiology of balance disturbances in MS is needed to develop evidence-based rehabilitation approaches. The purpose of the current study was to 1 map the cortical proprioceptive pathway in-vivo using diffusion weighted imaging and 2 assess associations between proprioceptive pathway white matter microstructural integrity and performance on clinical and behavioral balance tasks. We hypothesized that people with MS (PwMS would have reduced integrity of cerebral proprioceptive pathways, and that reduced white matter microstructure within these tracts would be strongly related to proprioceptive-based balance deficits. We found poorer balance control on proprioceptive-based tasks and reduced white matter microstructural integrity of the cortical proprioceptive tracts in PwMS compared with age-matched healthy controls. Microstructural integrity of this pathway in the right hemisphere was also strongly associated with proprioceptive-based balance control in PwMS and controls. Conversely, while white matter integrity of the right hemisphere’s proprioceptive pathway was significantly correlated with overall balance performance in healthy controls, there was no such relationship in PwMS. These results augment existing literature suggesting that balance control in PwMS may become more dependent upon 1 cerebellar-regulated proprioceptive control, 2 the vestibular system, and/or 3 the visual system.

  16. Alendronate treatment alters bone tissues at multiple structural levels in healthy canine cortical bone.

    Science.gov (United States)

    Acevedo, Claire; Bale, Hrishikesh; Gludovatz, Bernd; Wat, Amy; Tang, Simon Y; Wang, Mingyue; Busse, Björn; Zimmermann, Elizabeth A; Schaible, Eric; Allen, Matthew R; Burr, David B; Ritchie, Robert O

    2015-12-01

    Bisphosphonates are widely used to treat osteoporosis, but have been associated with atypical femoral fractures (AFFs) in the long term, which raises a critical health problem for the aging population. Several clinical studies have suggested that the occurrence of AFFs may be related to the bisphosphonate-induced changes of bone turnover, but large discrepancies in the results of these studies indicate that the salient mechanisms responsible for any loss in fracture resistance are still unclear. Here the role of bisphosphonates is examined in terms of the potential deterioration in fracture resistance resulting from both intrinsic (plasticity) and extrinsic (shielding) toughening mechanisms, which operate over a wide range of length-scales. Specifically, we compare the mechanical properties of two groups of humeri from healthy beagles, one control group comprising eight females (oral doses of saline vehicle, 1 mL/kg/day, 3 years) and one treated group comprising nine females (oral doses of alendronate used to treat osteoporosis, 0.2mg/kg/day, 3 years). Our data demonstrate treatment-specific reorganization of bone tissue identified at multiple length-scales mainly through advanced synchrotron x-ray experiments. We confirm that bisphosphonate treatments can increase non-enzymatic collagen cross-linking at molecular scales, which critically restricts plasticity associated with fibrillar sliding, and hence intrinsic toughening, at nanoscales. We also observe changes in the intracortical architecture of treated bone at microscales, with partial filling of the Haversian canals and reduction of osteon number. We hypothesize that the reduced plasticity associated with BP treatments may induce an increase in microcrack accumulation and growth under cyclic daily loadings, and potentially increase the susceptibility of cortical bone to atypical (fatigue-like) fractures. Published by Elsevier Inc.

  17. Involvement of Subcortical Brain Structures During Olfactory Stimulation in Multiple Chemical Sensitivity.

    Science.gov (United States)

    Alessandrini, Marco; Micarelli, Alessandro; Chiaravalloti, Agostino; Bruno, Ernesto; Danieli, Roberta; Pierantozzi, Mariangela; Genovesi, Giuseppe; Öberg, Johanna; Pagani, Marco; Schillaci, Orazio

    2016-03-01

    Multiple chemical sensitivity (MCS) patients usually react to odour compounds and the majority of neuroimaging studies assessed, especially at the cortical level, many olfactory-related correlates. The purpose of the present study was to depict sub-cortical metabolic changes during a neutral (NC) and pure (OC) olfactory stimulation by using a recently validated (18)F-2-fluoro-2-deoxy-D-glucose (FDG)-positron emission tomography/computer tomography procedure in 26 MCS and 11 healthy (HC) resting subjects undergoing a battery of clinical tests. Twelve subcortical volumes of interest were identified by the automated anatomical labeling library and normalized to thalamus FDG uptake. In both groups, when comparing OC to NC, the within-subjects ANOVA demonstrated a relative decreased metabolism in bilateral putamen and hippocampus and a relative increased metabolism in bilateral amygdala, olfactory cortex (OLF), caudate and pallidum. The between-groups ANOVA demonstrated in MCS a significant higher metabolism in bilateral OLF during NC. As in HC subjects negative correlations were found in OC between FDG uptake in bilateral amygdala and hippocampus and odor pleasantness scale, the latter positively correlated with MCS subjects' bilateral putamen FDG uptake in OC. Besides FDG uptake resemblances in both groups were found, for the first time a relative higher metabolism increase in OLF in MCS subjects at rest with respect to HC was found. When merging this aspect to the different subcortical FDG uptake correlations patterns in the two groups, the present study demonstrated to describe a peculiar metabolic index of behavioral and neurological aspects of MCS complaints.

  18. Discovering perturbation of modular structure in HIV progression by integrating multiple data sources through non-negative matrix factorization.

    Science.gov (United States)

    Ray, Sumanta; Maulik, Ujjwal

    2016-12-20

    Detecting perturbation in modular structure during HIV-1 disease progression is an important step to understand stage specific infection pattern of HIV-1 virus in human cell. In this article, we proposed a novel methodology on integration of multiple biological information to identify such disruption in human gene module during different stages of HIV-1 infection. We integrate three different biological information: gene expression information, protein-protein interaction information and gene ontology information in single gene meta-module, through non negative matrix factorization (NMF). As the identified metamodules inherit those information so, detecting perturbation of these, reflects the changes in expression pattern, in PPI structure and in functional similarity of genes during the infection progression. To integrate modules of different data sources into strong meta-modules, NMF based clustering is utilized here. Perturbation in meta-modular structure is identified by investigating the topological and intramodular properties and putting rank to those meta-modules using a rank aggregation algorithm. We have also analyzed the preservation structure of significant GO terms in which the human proteins of the meta-modules participate. Moreover, we have performed an analysis to show the change of coregulation pattern of identified transcription factors (TFs) over the HIV progression stages.

  19. Integrated analysis of multiple data sources reveals modular structure of biological networks

    International Nuclear Information System (INIS)

    Lu Hongchao; Shi Baochen; Wu Gaowei; Zhang Yong; Zhu Xiaopeng; Zhang Zhihua; Liu Changning; Zhao, Yi; Wu Tao; Wang Jie; Chen Runsheng

    2006-01-01

    It has been a challenging task to integrate high-throughput data into investigations of the systematic and dynamic organization of biological networks. Here, we presented a simple hierarchical clustering algorithm that goes a long way to achieve this aim. Our method effectively reveals the modular structure of the yeast protein-protein interaction network and distinguishes protein complexes from functional modules by integrating high-throughput protein-protein interaction data with the added subcellular localization and expression profile data. Furthermore, we take advantage of the detected modules to provide a reliably functional context for the uncharacterized components within modules. On the other hand, the integration of various protein-protein association information makes our method robust to false-positives, especially for derived protein complexes. More importantly, this simple method can be extended naturally to other types of data fusion and provides a framework for the study of more comprehensive properties of the biological network and other forms of complex networks

  20. Factor structure of the Disability and Impact Profile in patients with multiple sclerosis

    DEFF Research Database (Denmark)

    Cohen, J. L.; Pouwer, F; Pfennings, L E

    1999-01-01

    and their complementary weighted scores share common variance? What is the factor structure of the weighted scores? To what extent do disease-related information and information from psychological questionnaires offer concurrent validity for the factors? Correlations between impairment ratings and the weighted item...... scores were high; for most items the complementary ratings of impact do not supplement information provided by impairment ratings. The DIP weighted scores can be represented to some extent by three independent dimensions: a motor (skeletal movement) or displacement ability factor, a factor relating...... to sensory-cognitive intactness and a psychological well-being factor. A two-factor solution provides a first factor identical to that of the three-factor solution and a second factor representing psychological well-being. The two factors correlate well with instruments measuring disability...

  1. Concurrent topological design of composite structures and materials containing multiple phases of distinct Poisson's ratios

    Science.gov (United States)

    Long, Kai; Yuan, Philip F.; Xu, Shanqing; Xie, Yi Min

    2018-04-01

    Most studies on composites assume that the constituent phases have different values of stiffness. Little attention has been paid to the effect of constituent phases having distinct Poisson's ratios. This research focuses on a concurrent optimization method for simultaneously designing composite structures and materials with distinct Poisson's ratios. The proposed method aims to minimize the mean compliance of the macrostructure with a given mass of base materials. In contrast to the traditional interpolation of the stiffness matrix through numerical results, an interpolation scheme of the Young's modulus and Poisson's ratio using different parameters is adopted. The numerical results demonstrate that the Poisson effect plays a key role in reducing the mean compliance of the final design. An important contribution of the present study is that the proposed concurrent optimization method can automatically distribute base materials with distinct Poisson's ratios between the macrostructural and microstructural levels under a single constraint of the total mass.

  2. Misfortunes never come singly: Structural change, multiple shocks and child malnutrition in rural Senegal.

    Science.gov (United States)

    Lazzaroni, Sara; Wagner, Natascha

    2016-12-01

    This study considers the two most pronounced shocks Senegalese subsistence farmers struggle with, namely increasing purchase prices and droughts. We assess the relationship of these self-reported shocks with child health in a multi-shock approach to account for concomitance of adverse events from the natural, biological, economic and health sphere. We employ a unique farming household panel dataset containing information on children living in poor, rural households in eight regions of Senegal in 2009 and 2011 and account for structural changes occurring between survey periods due to the large scale, national Nutrition Enhancement Program. By zooming in to the micro level we demonstrate that Senegal as a Sahelian country, mainly reliant on subsistence agriculture, is very vulnerable to climate variability and international price developments: According to our conservative estimates, the occurrence of a drought explains 25% of the pooled weight-for-age standard deviation, income losses 31%. Our multi-shock analysis reveals that the shocks are perceived as more severe in 2011 with droughts explaining up to 44% of the standard deviation of child health, increased prices up to 21%. Yet, the concomitance of droughts and increased prices after the structural change, i.e. the Nutrition Enhancement Program, indicates that the health of children experiencing both shocks in 2011 has improved. We argue that these results are driven by the increase in rural household income as theoretically outlined in the agricultural household model. Thus, adequate policy responses to shocks do not only depend on the nature but also on the concomitance of hazardous events. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Genetic structure of Phytophthora infestans populations in China indicates multiple migration events.

    Science.gov (United States)

    Guo, Liyun; Zhu, Xiao-Qiong; Hu, Chia-Hui; Ristaino, Jean Beagle

    2010-10-01

    One hundred isolates of Phytophthora infestans collected from 10 provinces in China between 1998 and 2004 were analyzed for mating type, metalaxyl resistance, mitochondrial DNA (mtDNA) haplotype, allozyme genotype, and restriction fragment length polymorphism (RFLP) with the RG-57 probe. In addition, herbarium samples collected in China, Russia, Australia, and other Asian countries were also typed for mtDNA haplotype. The Ia haplotype was found during the first outbreaks of the disease in China (1938 and 1940), Japan (1901, 1930, and 1931), India (1913), Peninsular Malaysia (1950), Nepal (1954), The Philippines (1910), Australia (1917), Russia (1917), and Latvia (1935). In contrast, the Ib haplotype was found after 1950 in China on both potato and tomato (1952, 1954, 1956, and 1982) and in India (1968 and 1974). Another migration of a genotype found in Siberia called SIB-1 (Glucose-6-phosphate isomerase [Gpi] 100/100, Peptidase [Pep] 100/100, IIa mtDNA haplotype) was identified using RFLP fingerprints among 72% of the isolates and was widely distributed in the north and south of China and has also been reported in Japan. A new genotype named CN-11 (Gpi 100/111, Pep 100/100, IIb mtDNA haplotype), found only in the south of China, and two additional genotypes (Gpi 100/100, Pep 100/100, Ia mtDNA haplotype) named CN-9 and CN-10 were identified. There were more diverse genotypes among isolates from Yunnan province than elsewhere. The SIB-1 (IIa) genotype is identical to those from Siberia, suggesting later migration of this genotype from either Russia or Japan into China. The widespread predominance of SIB-1 suggests that this genotype has enhanced fitness compared with other genotypes found. Movement of the pathogen into China via infected seed from several sources most likely accounts for the distribution of pathogen genotypes observed. MtDNA haplotype evidence and RFLP data suggest multiple migrations of the pathogen into China after the initial introduction of the

  4. Novel structural features in two ZHX homeodomains derived from a systematic study of single and multiple domains

    Directory of Open Access Journals (Sweden)

    Owens Raymond J

    2010-05-01

    Full Text Available Abstract Background Zhx1 to 3 (zinc-fingers and homeoboxes form a set of paralogous genes encoding multi-domain proteins. ZHX proteins consist of two zinc fingers followed by five homeodomains. ZHXs have biological roles in cell cycle control by acting as co-repressors of the transcriptional regulator Nuclear Factor Y. As part of a structural genomics project we have expressed single and multi-domain fragments of the different human ZHX genes for use in structure determination. Results A total of 30 single and multiple domain ZHX1-3 constructs selected from bioinformatics protocols were screened for soluble expression in E. coli using high throughput methodologies. Two homeodomains were crystallized leading to structures for ZHX1 HD4 and ZHX2 HD2. ZHX1 HD4, although closest matched to homeodomains from 'homez' and 'engrailed', showed structural differences, notably an additional C-terminal helix (helix V which wrapped over helix I thereby making extensive contacts. Although ZHX2 HD2-3 was successfully expressed and purified, proteolysis occurred during crystallization yielding crystals of just HD2. The structure of ZHX2 HD2 showed an unusual open conformation with helix I undergoing 'domain-swapping' to form a homodimer. Conclusions Although multiple-domain constructs of ZHX1 selected by bioinformatics studies could be expressed solubly, only single homeodomains yielded crystals. The crystal structure of ZHX1 HD4 showed additional hydrophobic interactions relative to many known homeodomains via extensive contacts formed by the novel C-terminal helix V with, in particular, helix I. Additionally, the replacement of some charged covariant residues (which are commonly observed to form salt bridges in non-homeotherms such as the Drosophila 'engrailed' homeodomain, by apolar residues further increases hydrophobic contacts within ZHX1 HD4, and potentially stability, relative to engrailed homeodomain. ZHX1 HD4 helix V points away from the normally

  5. Key Process Uncertainties in Soil Carbon Dynamics: Comparing Multiple Model Structures and Observational Meta-analysis

    Science.gov (United States)

    Sulman, B. N.; Moore, J.; Averill, C.; Abramoff, R. Z.; Bradford, M.; Classen, A. T.; Hartman, M. D.; Kivlin, S. N.; Luo, Y.; Mayes, M. A.; Morrison, E. W.; Riley, W. J.; Salazar, A.; Schimel, J.; Sridhar, B.; Tang, J.; Wang, G.; Wieder, W. R.

    2016-12-01

    Soil carbon (C) dynamics are crucial to understanding and predicting C cycle responses to global change and soil C modeling is a key tool for understanding these dynamics. While first order model structures have historically dominated this area, a recent proliferation of alternative model structures representing different assumptions about microbial activity and mineral protection is providing new opportunities to explore process uncertainties related to soil C dynamics. We conducted idealized simulations of soil C responses to warming and litter addition using models from five research groups that incorporated different sets of assumptions about processes governing soil C decomposition and stabilization. We conducted a meta-analysis of published warming and C addition experiments for comparison with simulations. Assumptions related to mineral protection and microbial dynamics drove strong differences among models. In response to C additions, some models predicted long-term C accumulation while others predicted transient increases that were counteracted by accelerating decomposition. In experimental manipulations, doubling litter addition did not change soil C stocks in studies spanning as long as two decades. This result agreed with simulations from models with strong microbial growth responses and limited mineral sorption capacity. In observations, warming initially drove soil C loss via increased CO2 production, but in some studies soil C rebounded and increased over decadal time scales. In contrast, all models predicted sustained C losses under warming. The disagreement with experimental results could be explained by physiological or community-level acclimation, or by warming-related changes in plant growth. In addition to the role of microbial activity, assumptions related to mineral sorption and protected C played a key role in driving long-term model responses. In general, simulations were similar in their initial responses to perturbations but diverged over

  6. On functionally-graded crashworthy shape of conical structures for multiple load cases

    International Nuclear Information System (INIS)

    Pang, Tong; Li, Yinfeng; Kang, Hehe; Sun, Guangyong; Li, Qing; Fang, Jianguang

    2017-01-01

    Many studies on energy absorbers have been focused on tapered tubes because they have significant advantages in crashworthiness and provide a desired constant load-deflection response. However, few studies have been reported on tapered tubes with nonlinearly- variable diameters along the longitudinal direction. This paper presents thin-walled Functionally graded tapered tube (FGTT) with a diameter varying nonlinearly subject to axial (0°) and oblique (10°, 20°, 30°) impacts. To explore the advantages of FGTT, conventional Straight/Conical circular tube (SCT/CCT) with the same mass are compared; and FGTTs with a gradient exponent n > 1 are found to be preferable to others in terms of energy absorption capacity under small impact angles. Then, crashworthiness analyses of different crushing distances are conducted and it is found that under a large impact angle (e.g. 20°, 30°), FGTT with a short crushing distance (e.g. 40mm) have a higher mean crashing force than long crushing distance (e.g. 120 mm), especially for n > 1. In addition, the effect of geometric parameters, such as the gradient exponent n and diameter range ΔD between top (incident) and bottom (distal) diameters of FGTTs, are also studied and it is found that the FGTT with ΔD = 40 mm and n > 1 exhibits better crashworthiness than the others under small impact angles (0°, 10°). This paper demonstrates that such FGTT structures have a certain potential to be an energy absorber.

  7. On functionally-graded crashworthy shape of conical structures for multiple load cases

    Energy Technology Data Exchange (ETDEWEB)

    Pang, Tong; Li, Yinfeng [Hunan University, Changsha (China); Kang, Hehe [Chongqing Changan Automobile Co. Ltd., Chongqing (China); Sun, Guangyong; Li, Qing [The University of Sydney, Sydney (Australia); Fang, Jianguang [University of Technology Sydney, Sydney (Australia)

    2017-06-15

    Many studies on energy absorbers have been focused on tapered tubes because they have significant advantages in crashworthiness and provide a desired constant load-deflection response. However, few studies have been reported on tapered tubes with nonlinearly- variable diameters along the longitudinal direction. This paper presents thin-walled Functionally graded tapered tube (FGTT) with a diameter varying nonlinearly subject to axial (0°) and oblique (10°, 20°, 30°) impacts. To explore the advantages of FGTT, conventional Straight/Conical circular tube (SCT/CCT) with the same mass are compared; and FGTTs with a gradient exponent n > 1 are found to be preferable to others in terms of energy absorption capacity under small impact angles. Then, crashworthiness analyses of different crushing distances are conducted and it is found that under a large impact angle (e.g. 20°, 30°), FGTT with a short crushing distance (e.g. 40mm) have a higher mean crashing force than long crushing distance (e.g. 120 mm), especially for n > 1. In addition, the effect of geometric parameters, such as the gradient exponent n and diameter range ΔD between top (incident) and bottom (distal) diameters of FGTTs, are also studied and it is found that the FGTT with ΔD = 40 mm and n > 1 exhibits better crashworthiness than the others under small impact angles (0°, 10°). This paper demonstrates that such FGTT structures have a certain potential to be an energy absorber.

  8. A Preliminary Study on the Multiple Mapping Structure of Classification Systems for Heterogeneous Databases

    Directory of Open Access Journals (Sweden)

    Seok-Hyoung Lee

    2012-06-01

    Full Text Available While science and technology information service portals and heterogeneous databases produced in Korea and other countries are integrated, methods of connecting the unique classification systems applied to each database have been studied. Results of technologists' research, such as, journal articles, patent specifications, and research reports, are organically related to each other. In this case, if the most basic and meaningful classification systems are not connected, it is difficult to achieve interoperability of the information and thus not easy to implement meaningful science technology information services through information convergence. This study aims to address the aforementioned issue by analyzing mapping systems between classification systems in order to design a structure to connect a variety of classification systems used in the academic information database of the Korea Institute of Science and Technology Information, which provides science and technology information portal service. This study also aims to design a mapping system for the classification systems to be applied to actual science and technology information services and information management systems.

  9. A multiple-scaling method of the computation of threaded structures

    International Nuclear Information System (INIS)

    Andrieux, S.; Leger, A.

    1989-01-01

    The numerical computation of threaded structures usually leads to very large finite elements problems. It was therefore very difficult to carry out some parametric studies, especially in non-linear cases involving plasticity or unilateral contact conditions. Nevertheless, these parametric studies are essential in many industrial problems, for instance for the evaluation of various repairing processes of the closure studs of PWR. It is well known that such repairing generally involves several modifications of the thread geometry, of the number of active threads, of the flange clamping conditions, and so on. This paper is devoted to the description of a two-scale method, which easily allows parametric studies. The main idea of this method consists of dividing the problem into a global part, and a local part. The local problem is solved by F.E.M. on the precise geometry of the thread of some elementary loadings. The global one is formulated on the gudgeon scale and is reduced to a monodimensional one. The resolution of this global problem leads to the unsignificant computational cost. Then, a post-processing gives the stress field at the thread scale anywhere in the assembly. After recalling some principles of the two-scales approach, the method is described. The validation by comparison with a direct F.E. computation and some further applications are presented

  10. Multiple structure-intrinsic disorder interactions regulate and coordinate Hox protein function

    Science.gov (United States)

    Bondos, Sarah

    During animal development, Hox transcription factors determine fate of developing tissues to generate diverse organs and appendages. Hox proteins are famous for their bizarre mutant phenotypes, such as replacing antennae with legs. Clearly, the functions of individual Hox proteins must be distinct and reliable in vivo, or the organism risks malformation or death. However, within the Hox protein family, the DNA-binding homeodomains are highly conserved and the amino acids that contact DNA are nearly invariant. These observations raise the question: How do different Hox proteins correctly identify their distinct target genes using a common DNA binding domain? One possible means to modulate DNA binding is through the influence of the non-homeodomain protein regions, which differ significantly among Hox proteins. However genetic approaches never detected intra-protein interactions, and early biochemical attempts were hindered because the special features of ``intrinsically disordered'' sequences were not appreciated. We propose the first-ever structural model of a Hox protein to explain how specific contacts between distant, intrinsically disordered regions of the protein and the homeodomain regulate DNA binding and coordinate this activity with other Hox molecular functions.

  11. Ward identities and consistency relations for the large scale structure with multiple species

    International Nuclear Information System (INIS)

    Peloso, Marco; Pietroni, Massimo

    2014-01-01

    We present fully nonlinear consistency relations for the squeezed bispectrum of Large Scale Structure. These relations hold when the matter component of the Universe is composed of one or more species, and generalize those obtained in [1,2] in the single species case. The multi-species relations apply to the standard dark matter + baryons scenario, as well as to the case in which some of the fields are auxiliary quantities describing a particular population, such as dark matter halos or a specific galaxy class. If a large scale velocity bias exists between the different populations new terms appear in the consistency relations with respect to the single species case. As an illustration, we discuss two physical cases in which such a velocity bias can exist: (1) a new long range scalar force in the dark matter sector (resulting in a violation of the equivalence principle in the dark matter-baryon system), and (2) the distribution of dark matter halos relative to that of the underlying dark matter field

  12. Molecular and Functional Characterization of RecD, a Novel Member of the SF1 Family of Helicases, from Mycobacterium tuberculosis.

    Science.gov (United States)

    Dewhare, Shivendra Singh; Umesh, T G; Muniyappa, K

    2015-05-08

    The annotated whole-genome sequence of Mycobacterium tuberculosis revealed the presence of a putative recD gene; however, the biochemical characteristics of its encoded protein product (MtRecD) remain largely unknown. Here, we show that MtRecD exists in solution as a stable homodimer. Protein-DNA binding assays revealed that MtRecD binds efficiently to single-stranded DNA and linear duplexes containing 5' overhangs relative to the 3' overhangs but not to blunt-ended duplex. Furthermore, MtRecD bound more robustly to a variety of Y-shaped DNA structures having ≥18-nucleotide overhangs but not to a similar substrate containing 5-nucleotide overhangs. MtRecD formed more salt-tolerant complexes with Y-shaped structures compared with linear duplex having 3' overhangs. The intrinsic ATPase activity of MtRecD was stimulated by single-stranded DNA. Site-specific mutagenesis of Lys-179 in motif I abolished the ATPase activity of MtRecD. Interestingly, although MtRecD-catalyzed unwinding showed a markedly higher preference for duplex substrates with 5' overhangs, it could also catalyze significant unwinding of substrates containing 3' overhangs. These results support the notion that MtRecD is a bipolar helicase with strong 5' → 3' and weak 3' → 5' unwinding activities. The extent of unwinding of Y-shaped DNA structures was ∼3-fold lower compared with duplexes with 5' overhangs. Notably, direct interaction between MtRecD and its cognate RecA led to inhibition of DNA strand exchange promoted by RecA. Altogether, these studies provide the first detailed characterization of MtRecD and present important insights into the type of DNA structure the enzyme is likely to act upon during the processes of DNA repair or homologous recombination. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  13. Assessment of the effect of visual impairment on mortality through multiple health pathways: structural equation modeling.

    Science.gov (United States)

    Christ, Sharon L; Lee, David J; Lam, Byron L; Zheng, D Diane; Arheart, Kristopher L

    2008-08-01

    To estimate the direct effects of self-reported visual impairment (VI) on health, disability, and mortality and to estimate the indirect effects of VI on mortality through health and disability mediators. The National Health Interview Survey (NHIS) is a population-based annual survey designed to be representative of the U.S. civilian noninstitutionalized population. The National Death Index of 135,581 NHIS adult participants, 18 years of age and older, from 1986 to 1996 provided the mortality linkage through 2002. A generalized linear structural equation model (GSEM) with latent variable was used to estimate the results of a system of equations with various outcomes. Standard errors and test statistics were corrected for weighting, clustering, and stratification. VI affects mortality, when direct adjustment was made for the covariates. Severe VI increases the hazard rate by a factor of 1.28 (95% CI: 1.07-1.53) compared with no VI, and some VI increases the hazard by a factor of 1.13 (95% CI: 1.07-1.20). VI also affects mortality indirectly through self-rated health and disability. The total effects (direct effects plus mediated effects) on the hazard of mortality of severe VI and some VI relative to no VI are hazard ratio (HR) 1.54 (95% CI: 1.28-1.86) and HR 1.23 (95% CI: 1.16-1.31), respectively. In addition to the direct link between VI and mortality, the effects of VI on general health and disability contribute to an increased risk of death. Ignoring the latter may lead to an underestimation of the substantive impact of VI on mortality.

  14. Nanomechanical microcantilever operated in vibration modes with use of RNA aptamer as receptor molecules for label-free detection of HCV helicase.

    Science.gov (United States)

    Hwang, Kyo Seon; Lee, Sang-Myung; Eom, Kilho; Lee, Jeong Hoon; Lee, Yoon-Sik; Park, Jung Ho; Yoon, Dae Sung; Kim, Tae Song

    2007-11-30

    We report the nanomechanical microcantilevers operated in vibration modes (oscillation) with use of RNA aptamers as receptor molecules for label-free detection of hepatitis C virus (HCV) helicase. The nanomechanical detection principle is that the ligand-receptor binding on the microcantilever surface induces the dynamic response change of microcantilevers. We implemented the label-free detection of HCV helicase in the low concentration as much as 100 pg/ml from measuring the dynamic response change of microcantilevers. Moreover, from the recent studies showing that the ligand-receptor binding generates the surface stress on the microcantilever, we estimate the surface stress, on the oscillating microcantilevers, induced by ligand-receptor binding, i.e. binding between HCV helicase and RNA aptamer. In this article, it is suggested that the oscillating microcantilevers with use of RNA aptamers as receptor molecules may enable one to implement the sensitive label-free detection of very small amount of small-scale proteins.

  15. Multiple-Stage Structure Transformation of Organic-Inorganic Hybrid Perovskite CH3NH3PbI3

    Science.gov (United States)

    Chen, Qiong; Liu, Henan; Kim, Hui-Seon; Liu, Yucheng; Yang, Mengjin; Yue, Naili; Ren, Gang; Zhu, Kai; Liu, Shengzhong; Park, Nam-Gyu; Zhang, Yong

    2016-07-01

    By performing spatially resolved Raman and photoluminescence spectroscopy with varying excitation wavelength, density, and data acquisition parameters, we achieve a unified understanding towards the spectroscopy signatures of the organic-inorganic hybrid perovskite, transforming from the pristine state (CH3NH3PbI3 ) to the fully degraded state (i.e., PbI2 ) for samples with varying crystalline domain size from mesoscopic scale (approximately 100 nm) to macroscopic size (centimeters), synthesized by three different techniques. We show that the hybrid perovskite exhibits multiple stages of structure transformation occurring either spontaneously or under light illumination, with exceptionally high sensitivity to the illumination conditions (e.g., power, illumination time, and interruption pattern). We highlight four transformation stages (stages I-IV, with stage I being the pristine state) along either the spontaneous or photoinduced degradation path exhibiting distinctly different Raman spectroscopy features at each stage, and point out that previously reported Raman spectra in the literature reflect highly degraded structures of either stage III or stage IV. Additional characteristic optical features of partially degraded materials under the joint action of spontaneous and photodegradation are also given. This study offers reliable benchmark results for understanding the intrinsic material properties and structure transformation of this unique category of hybrid materials, and the findings are pertinently important to a wide range of potential applications where the hybrid material is expected to function in greatly different environment and light-matter interaction conditions.

  16. Adaptation of tick-borne encephalitis virus from human brain to different cell cultures induces multiple genomic substitutions.

    Science.gov (United States)

    Ponomareva, Eugenia P; Ternovoi, Vladimir A; Mikryukova, Tamara P; Protopopova, Elena V; Gladysheva, Anastasia V; Shvalov, Alexander N; Konovalova, Svetlana N; Chausov, Eugene V; Loktev, Valery B

    2017-10-01

    The C11-13 strain from the Siberian subtype of tick-borne encephalitis virus (TBEV) was isolated from human brain using pig embryo kidney (PEK), 293, and Neuro-2a cells. Analysis of the complete viral genome of the C11-13 variants during six passages in these cells revealed that the cell-adapted C11-13 variants had multiple amino acid substitutions as compared to TBEV from human brain. Seven out of eight amino acids substitutions in the high-replicating C11-13(PEK) variant mapped to non-structural proteins; 13 out of 14 substitutions in the well-replicating C11-13(293) variant, and all four substitutions in the low-replicating C11-13(Neuro-2a) variant were also localized in non-structural proteins, predominantly in the NS2a (2), NS3 (6) and NS5 (3) proteins. The substitutions NS2a 1067 (Asn → Asp), NS2a 1168 (Leu → Val) in the N-terminus of NS2a and NS3 1745 (His → Gln) in the helicase domain of NS3 were found in all selected variants. We postulate that multiple substitutions in the NS2a, NS3 and NS5 genes play a key role in adaptation of TBEV to different cells.

  17. CMG helicase and DNA polymerase ε form a functional 15-subunit holoenzyme for eukaryotic leading-strand DNA replication.

    Science.gov (United States)

    Langston, Lance D; Zhang, Dan; Yurieva, Olga; Georgescu, Roxana E; Finkelstein, Jeff; Yao, Nina Y; Indiani, Chiara; O'Donnell, Mike E

    2014-10-28

    DNA replication in eukaryotes is asymmetric, with separate DNA polymerases (Pol) dedicated to bulk synthesis of the leading and lagging strands. Pol α/primase initiates primers on both strands that are extended by Pol ε on the leading strand and by Pol δ on the lagging strand. The CMG (Cdc45-MCM-GINS) helicase surrounds the leading strand and is proposed to recruit Pol ε for leading-strand synthesis, but to date a direct interaction between CMG and Pol ε has not been demonstrated. While purifying CMG helicase overexpressed in yeast, we detected a functional complex between CMG and native Pol ε. Using pure CMG and Pol ε, we reconstituted a stable 15-subunit CMG-Pol ε complex and showed that it is a functional polymerase-helicase on a model replication fork in vitro. On its own, the Pol2 catalytic subunit of Pol ε is inefficient in CMG-dependent replication, but addition of the Dpb2 protein subunit of Pol ε, known to bind the Psf1 protein subunit of CMG, allows stable synthesis with CMG. Dpb2 does not affect Pol δ function with CMG, and thus we propose that the connection between Dpb2 and CMG helps to stabilize Pol ε on the leading strand as part of a 15-subunit leading-strand holoenzyme we refer to as CMGE. Direct binding between Pol ε and CMG provides an explanation for specific targeting of Pol ε to the leading strand and provides clear mechanistic evidence for how strand asymmetry is maintained in eukaryotes.

  18. Studies on multiplication effect of noises of PPDs, and a proposal of a new structure to improve the performance

    International Nuclear Information System (INIS)

    Oide, H.; Murase, T.; Otono, H.; Yamashita, S.

    2010-01-01

    Pixelated Photon Detectors (PPDs) are arrayed APDs operated in Geiger-mode. Multi-Pixel Photon Counter (MPPC) is a PPD produced by Hamamatsu Photonics K.K. Test of dark noise rate of a 1600 pixel MPPC as a function of over-voltage at room temperature indicates that the over-voltage is limited up to a few volts because of explosive increase of noise rate. The over-voltage dependence of random noise rate is nevertheless mostly linear. We confirmed this is due to multiplication effect of noises because of after-pulsing and crosstalk. Over-voltage dependence of random noise and photon detection efficiency are qualitatively different. Considering the electric field structure of MPPC (p-on-n type) and Geiger-efficiency as a function of the position of initial pair creation, these characteristics are possible to be understood. One suggestion for p-on-n type PPD from these results is narrowing the depletion layer below the multiplication layer to reduce random noise and after-pulsing. Another proposal is to put additional buffer capacitance parallel to the diode to accomplish higher gain with lower over-voltage simultaneously with lower noise rate.

  19. Studies on multiplication effect of noises of PPDs, and a proposal of a new structure to improve the performance

    Energy Technology Data Exchange (ETDEWEB)

    Oide, H., E-mail: oide@icepp.s.u-tokyo.ac.j [Department of Physics, University of Tokyo, 7-3-1, Hongo, Bunkyo, Tokyo (Japan); Murase, T.; Otono, H. [Department of Physics, University of Tokyo, 7-3-1, Hongo, Bunkyo, Tokyo (Japan); Yamashita, S. [ICEPP, University of Tokyo, 7-3-1, Hongo, Bunkyo, Tokyo (Japan)

    2010-01-21

    Pixelated Photon Detectors (PPDs) are arrayed APDs operated in Geiger-mode. Multi-Pixel Photon Counter (MPPC) is a PPD produced by Hamamatsu Photonics K.K. Test of dark noise rate of a 1600 pixel MPPC as a function of over-voltage at room temperature indicates that the over-voltage is limited up to a few volts because of explosive increase of noise rate. The over-voltage dependence of random noise rate is nevertheless mostly linear. We confirmed this is due to multiplication effect of noises because of after-pulsing and crosstalk. Over-voltage dependence of random noise and photon detection efficiency are qualitatively different. Considering the electric field structure of MPPC (p-on-n type) and Geiger-efficiency as a function of the position of initial pair creation, these characteristics are possible to be understood. One suggestion for p-on-n type PPD from these results is narrowing the depletion layer below the multiplication layer to reduce random noise and after-pulsing. Another proposal is to put additional buffer capacitance parallel to the diode to accomplish higher gain with lower over-voltage simultaneously with lower noise rate.

  20. Studies on multiplication effect of noises of PPD, and a proposal of a new structure to improve the performance

    Energy Technology Data Exchange (ETDEWEB)

    Oide, H., E-mail: oide@icepp.s.u-tokyo.ac.j [Department of Physics, University of Tokyo, 7-3-1 Hongo Bunkyo, Tokyo 113-0033 (Japan); Murase, T.; Otono, H. [Department of Physics, University of Tokyo, 7-3-1 Hongo Bunkyo, Tokyo 113-0033 (Japan); Yamashita, S. [ICEPP, University of Tokyo, 7-3-1 Hongo Bunkyo, Tokyo 113-0033 (Japan)

    2010-11-01

    Pixelated photon detectors (PPDs) are arrayed APDs operated in Geiger-mode. Multi-pixel photon counter (MPPC) is a PPD produced by Hamamatsu Photonics K.K. We performed measurement of total noise rate, random noise rate, after-pulsing, crosstalk, and relative photon detection efficiency for a 1600 px MPPC. The explosive increase of total noise rate to over-voltage is able to be understood of multiplication effect of after-pulsing and crosstalk. Considering the electric field structure of MPPC (p-on-n type) and Geiger-efficiency as a function of the position of initial pair creation, these characteristics are all able to be understood. One suggestion for p-on-n type PPD from these results is narrowing the depletion layer below the multiplication layer to reduce random noise and after-pulsing. Another proposal is to put additional buffer capacitance parallel to the diode to accomplish higher gain with lower over-voltage simultaneously with lower noise rate.

  1. Studies on multiplication effect of noises of PPD, and a proposal of a new structure to improve the performance

    International Nuclear Information System (INIS)

    Oide, H.; Murase, T.; Otono, H.; Yamashita, S.

    2010-01-01

    Pixelated photon detectors (PPDs) are arrayed APDs operated in Geiger-mode. Multi-pixel photon counter (MPPC) is a PPD produced by Hamamatsu Photonics K.K. We performed measurement of total noise rate, random noise rate, after-pulsing, crosstalk, and relative photon detection efficiency for a 1600 px MPPC. The explosive increase of total noise rate to over-voltage is able to be understood of multiplication effect of after-pulsing and crosstalk. Considering the electric field structure of MPPC (p-on-n type) and Geiger-efficiency as a function of the position of initial pair creation, these characteristics are all able to be understood. One suggestion for p-on-n type PPD from these results is narrowing the depletion layer below the multiplication layer to reduce random noise and after-pulsing. Another proposal is to put additional buffer capacitance parallel to the diode to accomplish higher gain with lower over-voltage simultaneously with lower noise rate.

  2. A theoretical study on Love wave sensors in a structure with multiple viscoelastic layers on a piezoelectric substrate

    International Nuclear Information System (INIS)

    Liu, Jiansheng

    2014-01-01

    A theoretical method is used to analyze the performance of Love wave sensors with multiple viscoelastic guiding layers on a piezoelectric substrate. The method is based upon the theoretical model for multi-elastic-layer piezoelectric Love waves and the Maxwell–Weichert model for viscoelastic materials. The relationship between sensor performance and the characteristics of Love waves is discussed. Numerical calculation is completed for a Love wave delay line consisting of a viscoelastic SU-8 layer, an elastic SiO 2 layer, an ST-90°X quartz substrate and two interdigital transducers (IDTs) with a period of 40 μm deposited on the substrate surface. The calculated results prove that a Love wave sensor with such a two-layer structure can achieve better performance than a Love wave sensor with only one (visco)elastic or elastic guiding layer. Some interesting abnormal phenomena, such as an oscillation in mass velocity sensitivity (S mv ), are predicted at the area where tail-raising occurs in the propagation velocity. The method and the numerical results presented in this work may help in the development of a high-performing Love wave sensor with multiple layers. (papers)

  3. A 1D thermomechanical network transition constitutive model coupled with multiple structural relaxation for shape memory polymers

    Science.gov (United States)

    Zeng, Hao; Xie, Zhimin; Gu, Jianping; Sun, Huiyu

    2018-03-01

    A new thermomechanical network transition constitutive model is proposed in the study to describe the viscoelastic behavior of shape memory polymers (SMPs). Based on the microstructure of semi-crystalline SMPs, a new simplified transformation equation is proposed to describe the transform of transient networks. And the generalized fractional Maxwell model is introduced in the paper to estimate the temperature-dependent storage modulus. In addition, a neo-KAHR theory with multiple discrete relaxation processes is put forward to study the structural relaxation of the nonlinear thermal strain in cooling/heating processes. The evolution equations of the time- and temperature-dependent stress and strain response are developed. In the model, the thermodynamical and mechanical characteristics of SMPs in the typical thermomechanical cycle are described clearly and the irreversible deformation is studied in detail. Finally, the typical thermomechanical cycles are simulated using the present constitutive model, and the simulation results agree well with the experimental results.

  4. JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures.

    Science.gov (United States)

    Muth, Thilo; García-Martín, Juan A; Rausell, Antonio; Juan, David; Valencia, Alfonso; Pazos, Florencio

    2012-02-15

    We have implemented in a single package all the features required for extracting, visualizing and manipulating fully conserved positions as well as those with a family-dependent conservation pattern in multiple sequence alignments. The program allows, among other things, to run different methods for extracting these positions, combine the results and visualize them in protein 3D structures and sequence spaces. JDet is a multiplatform application written in Java. It is freely available, including the source code, at http://csbg.cnb.csic.es/JDet. The package includes two of our recently developed programs for detecting functional positions in protein alignments (Xdet and S3Det), and support for other methods can be added as plug-ins. A help file and a guided tutorial for JDet are also available.

  5. B cell follicle-like structures in multiple sclerosis-with focus on the role of B cell activating factor

    DEFF Research Database (Denmark)

    Morten, Haugen; Frederiksen, Jette L; Vinter, Matilda Degn

    2014-01-01

    B lymphocytes play an important role in the pathogenesis of multiple sclerosis (MS). Follicle-like structures (FLS) have recently been found in the subarachnoid space in the leptomeninges in some patients with secondary progressive MS (SPMS). They contain proliferating B lymphocytes, plasma cells......, helper T lymphocytes and a network of follicular dendritic cells. FLS have been shown to correlate with increased cortical demyelination, neuronal loss, meningeal infiltration and central nervous system inflammation, as well as lower age at disease onset and progression to severe disability and death....... In this review, we will discuss the role of FLS in MS pathogenesis and disease course and the possible influence by B cell activating factor (BAFF) and C-X-C motif chemokine 13 (CXCL13)....

  6. Disorder in materials with complex crystal structures: the Non-Local Coherent Potential Approximation for compounds with multiple sublattices

    International Nuclear Information System (INIS)

    Marmodoro, A; Staunton, J B

    2011-01-01

    Over the last few years the Non-Local Coherent Potential Approximation (NL-CPA) has been shown to provide an effective way to describe the electronic structure and related properties of disordered systems, where short-range order (SRO) and other local environment effects are important. Here we present its generalization to materials with multi-atom per unit cell lattices. The method is described using a Green function formalism and illustrated by an implementation for a simplified one-dimensional tight-binding model with substitutional disorder. This development paves the way for a natural reimplementation of the Korringa-Kohn-Rostoker (KKR) multiple scattering solution of Kohn-Sham equations for ab-initio calculations of real materials.

  7. Multiple crossovers between positive and negative magnetoresistance versus field due to fragile spin structure in metallic GdPd3

    Science.gov (United States)

    Pandey, Abhishek; Mazumdar, Chandan; Ranganathan, R.; Johnston, D. C.

    2017-01-01

    Studies on the phenomenon of magnetoresistance (MR) have produced intriguing and application-oriented outcomes for decades–colossal MR, giant MR and recently discovered extremely large MR of millions of percents in semimetals can be taken as examples. We report here the discovery of novel multiple sign changes versus applied magnetic field of the MR in the cubic intermetallic compound GdPd3. Our study shows that a very strong correlation between magnetic, electrical and magnetotransport properties is present in this compound. The magnetic structure in GdPd3 is highly fragile since applied magnetic fields of moderate strength significantly alter the spin arrangement within the system–a behavior that manifests itself in the oscillating MR. Intriguing magnetotransport characteristics of GdPd3 are appealing for field-sensitive device applications, especially if the MR oscillation could materialize at higher temperature by manipulating the magnetic interaction through perturbations caused by chemical substitutions. PMID:28211520

  8. Structural basis for activation of trimeric Gi proteins by multiple growth factor receptors via GIV/Girdin

    Science.gov (United States)

    Lin, Changsheng; Ear, Jason; Midde, Krishna; Lopez-Sanchez, Inmaculada; Aznar, Nicolas; Garcia-Marcos, Mikel; Kufareva, Irina; Abagyan, Ruben; Ghosh, Pradipta

    2014-01-01

    A long-standing issue in the field of signal transduction is to understand the cross-talk between receptor tyrosine kinases (RTKs) and heterotrimeric G proteins, two major and distinct signaling hubs that control eukaryotic cell behavior. Although stimulation of many RTKs leads to activation of trimeric G proteins, the molecular mechanisms behind this phenomenon remain elusive. We discovered a unifying mechanism that allows GIV/Girdin, a bona fide metastasis-related protein and a guanine-nucleotide exchange factor (GEF) for Gαi, to serve as a direct platform for multiple RTKs to activate Gαi proteins. Using a combination of homology modeling, protein–protein interaction, and kinase assays, we demonstrate that a stretch of ∼110 amino acids within GIV C-terminus displays structural plasticity that allows folding into a SH2-like domain in the presence of phosphotyrosine ligands. Using protein–protein interaction assays, we demonstrated that both SH2 and GEF domains of GIV are required for the formation of a ligand-activated ternary complex between GIV, Gαi, and growth factor receptors and for activation of Gαi after growth factor stimulation. Expression of a SH2-deficient GIV mutant (Arg 1745→Leu) that cannot bind RTKs impaired all previously demonstrated functions of GIV—Akt enhancement, actin remodeling, and cell migration. The mechanistic and structural insights gained here shed light on the long-standing questions surrounding RTK/G protein cross-talk, set a novel paradigm, and characterize a unique pharmacological target for uncoupling GIV-dependent signaling downstream of multiple oncogenic RTKs. PMID:25187647

  9. Frequency of Werner helicase 1367 polymorphism and age-related morbidity in an elderly Brazilian population

    Directory of Open Access Journals (Sweden)

    M.A.C. Smith

    2005-07-01

    Full Text Available Werner syndrome (WS is a premature aging disease caused by a mutation in the WRN gene. The gene was identified in 1996 and its product acts as a DNA helicase and exonuclease. Some specific WRN polymorphic variants were associated with increased risk for cardiovascular diseases. The identification of genetic polymorphisms as risk factors for complex diseases affecting older people can improve their prevention, diagnosis and prognosis. We investigated WRN codon 1367 polymorphism in 383 residents in a district of the city of São Paulo, who were enrolled in an Elderly Brazilian Longitudinal Study. Their mean age was 79.70 ± 5.32 years, ranging from 67 to 97. This population was composed of 262 females (68.4% and 121 males (31.6% of European (89.2%, Japanese (3.3%, Middle Eastern (1.81%, and mixed and/or other origins (5.7%. There are no studies concerning this polymorphism in Brazilian population. These subjects were evaluated clinically every two years. The major health problems and morbidities affecting this cohort were cardiovascular diseases (21.7%, hypertension (83.7%, diabetes (63.3%, obesity (41.23%, dementia (8.0%, depression (20.0%, and neoplasia (10.8%. Their prevalence is similar to some urban elderly Brazilian samples. DNA was isolated from blood cells, amplified by PCR and digested with PmaCI. Allele frequencies were 0.788 for the cysteine and 0.211 for the arginine. Genotype distributions were within that expected for the Hardy-Weinberg equilibrium. Female gender was associated with hypertension and obesity. Logistic regression analysis did not detect significant association between the polymorphism and morbidity. These findings confirm those from Europeans and differ from Japanese population.

  10. microRNAs targeting DEAD-box helicases are involved in salinity stress response in rice (Oryza sativa L.