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Sample records for largest ribonucleoprotein particle

  1. X-ray Crystal Structure of the Vault, Largest Ribonucleoprotein Particle, with a Molecular Weight of 10 MDa

    NASA Astrophysics Data System (ADS)

    Tanaka, Hideaki; Kato, Koji; Yamashita, Eiki

    Vaults are among the largest cytoplasmic ribonucleoprotein particles and are found in numerous eukaryotic species. Although roles in multidrug resistance and innate immunity have been suggested, the cellular function remains unclear. We have determined the X-ray structure of rat liver vault at 3.5 Å resolution. A vault particle shell was composed of 78 MVP (Major vault protein) chains with 39-fold dihedral symmetry. The shoulder domain of MVP is structurally similar to SPFH (stomatin/prohibitin/flotillin/HflK/C) domain involved in lipid raft association.

  2. The spliceosomal proteome: at the heart of the largest cellular ribonucleoprotein machine.

    PubMed

    Valadkhan, Saba; Jaladat, Yasaman

    2010-11-01

    Almost all primary transcripts in higher eukaryotes undergo several splicing events and alternative splicing is a major factor in generating proteomic diversity. Thus, the spliceosome, the ribonucleoprotein assembly that performs splicing, is a highly critical cellular machine and as expected, a very complex one. Indeed, the spliceosome is one of the largest, if not the largest, molecular machine in the cell with over 150 different components in human. A large fraction of the spliceosomal proteome is organized into small nuclear ribonucleoprotein particles by associating with one of the small nuclear RNAs, and the function of many spliceosomal proteins revolve around their association or interaction with the spliceosomal RNAs or the substrate pre-messenger RNAs. In addition to the complex web of protein-RNA interactions, an equally complex network of protein-protein interactions exists in the spliceosome, which includes a number of large, conserved proteins with critical functions in the spliceosomal catalytic core. These include the largest conserved nuclear protein, Prp8, which plays a critical role in spliceosomal function in a hitherto unknown manner. Taken together, the large spliceosomal proteome and its dynamic nature has made it a highly challenging system to study, and at the same time, provides an exciting example of the evolution of a proteome around a backbone of primordial RNAs likely dating from the RNA World.

  3. Structural Dynamics of the Vault Ribonucleoprotein Particle

    NASA Astrophysics Data System (ADS)

    Casañas, Arnau; Querol, Jordi; Fita, Ignasi; Verdaguer, Núria

    Vaults are ubiquitous, highly conserved, 13 MDa ribonucleoprotein particles, involved in a diversity of cellular processes, including multidrug resistance, transport mechanisms and signal transmission. There are between 104 and 106 vault particles per mammalian cell and they do not trigger autoimmunity. The vault particle shows a hollow barrel-shaped structure organized in two identical moieties, each consisting of 39 copies of the major vault protein (MVP). Other data indicated that vault halves can dissociate at acidic pH. The high resolution, crystal structure of the of the seven N-terminal domains (R1-R7) of MVP, forming the central vault barrel, together with that of the native vault particle (solved at 8 Å resolution), revealed the interactions governing vault association and suggested a pH-dependent mechanism for a reversible dissociation induced by low pH. Vault particles posses many features making them very promising vehicles for the delivery of therapeutic agents including self-assembly, 100 nm size range, emerging atomic-level structural information, natural presence in humans ensuring biocompability, recombinant production system, existing features for targeting species to the large lumen and a dynamic structure that may be controlled for manipulation of drug release kinetics. All these attributes provide vaults with enormous potential as a drug/gene delivery platform.

  4. Enrichment of processed pseudogene transcripts in L1-ribonucleoprotein particles

    PubMed Central

    Mandal, Prabhat K.; Ewing, Adam D.; Hancks, Dustin C.; Kazazian, Haig H.

    2013-01-01

    Long INterspersed Elements (LINE-1s, L1s) are responsible for over one million retrotransposon insertions and 8000 processed pseudogenes (PPs) in the human genome. An active L1 encodes two proteins (ORF1p and ORF2p) that bind with L1 RNA and form L1-ribonucleoprotein particles (RNPs). Although it is believed that the RNA-binding property of ORF1p is critical to recruit other mobile RNAs to the RNP, the identity of recruited RNAs is largely unknown. Here, we used crosslinking and immunoprecipitation followed by deep sequencing to identify RNA components of L1-RNPs. Our results show that in addition to retrotransposed RNAs [L1, Alu and SINE-VNTR-Alu (SVA)], L1-RNPs are enriched with cellular mRNAs, which have PPs in the human genome. Using purified L1-RNPs, we show that PP-source RNAs preferentially serve as ORF2p templates in a reverse transcriptase assay. In addition, we find that exogenous ORF2p binds endogenous ORF1p, allowing reverse transcription of the same PP-source RNAs. These data demonstrate that interaction of a cellular RNA with the L1-RNP is an inside track to PP formation. PMID:23696454

  5. Functionality of In vitro Reconstituted Group II Intron RmInt1-Derived Ribonucleoprotein Particles

    PubMed Central

    Molina-Sánchez, Maria D.; García-Rodríguez, Fernando M.; Toro, Nicolás

    2016-01-01

    The functional unit of mobile group II introns is a ribonucleoprotein particle (RNP) consisting of the intron-encoded protein (IEP) and the excised intron RNA. The IEP has reverse transcriptase activity but also promotes RNA splicing, and the RNA-protein complex triggers site-specific DNA insertion by reverse splicing, in a process called retrohoming. In vitro reconstituted ribonucleoprotein complexes from the Lactococcus lactis group II intron Ll.LtrB, which produce a double strand break, have recently been studied as a means of developing group II intron-based gene targeting methods for higher organisms. The Sinorhizobium meliloti group II intron RmInt1 is an efficient mobile retroelement, the dispersal of which appears to be linked to transient single-stranded DNA during replication. The RmInt1IEP lacks the endonuclease domain (En) and cannot cut the bottom strand to generate the 3′ end to initiate reverse transcription. We used an Escherichia coli expression system to produce soluble and active RmInt1 IEP and reconstituted RNPs with purified components in vitro. The RNPs generated were functional and reverse-spliced into a single-stranded DNA target. This work constitutes the starting point for the use of group II introns lacking DNA endonuclease domain-derived RNPs for highly specific gene targeting methods. PMID:27730127

  6. The ribonucleoprotein nature of large particles in the meiosporangia of Allomyces.

    PubMed

    ROREM, E S; MACHLIS, L

    1957-11-25

    Particles averaging 3 to 4 micro in diameter, which are called chromospheres and fill the immature meiosporangia of the watermold Allomyces, were isolated and analyzed. The preparations were obtained by repeated centrifugations or by passage of the homogenate into a column of sand saturated with oleic acid, followed by selective elution of the chromospheres with alternate layers of oleic acid and an aqueous solution. The chromospheres contain approximately 12 per cent RNA, no DNA, and 60 per cent protein. It was concluded that they are pure or nearly pure ribonucleoprotein. Analysis of meiosporangia with chromospheres and after the chromospheres have disappeared showed no significant change in RNA or free amino acids. It was concluded that chromosphere disappearance is a fragmentation into small granules. The relation of chromospheres to postmeiotic chromospheres and nuclear caps is discussed. Speculation as to the function of these bodies is presented. PMID:13481022

  7. Classification and purification of proteins of heterogeneous nuclear ribonucleoprotein particles by RNA-binding specificities

    SciTech Connect

    Swanson, M.S.; Dreyfuss, G.

    1988-05-01

    Several proteins of heterogeneous nuclear ribonucleoprotein (hnRNP) particles display very high binding affinities for different ribonucleotide homopolymers. The specificity of some of these proteins at high salt concentrations and in the presence of heparin allows for their rapid one-step purification from HeLa nucleoplasm. The authors show that the hnRNP proteins are poly(U)-binding proteins and compare their specificity to that of the previously described cytoplasmic poly(A)-binding protein. These findings provide a useful tool for the classification and purification of hnRNP proteins from various tissues and organisms and indicate that different hnRNP proteins have different RNA-binding specificities.

  8. Genus-specific recruitment of filovirus ribonucleoprotein complexes into budding particles

    PubMed Central

    Spiegelberg, Larissa; Wahl-Jensen, Victoria; Kolesnikova, Larissa; Feldmann, Heinz; Hoenen, Thomas

    2011-01-01

    The filoviral matrix protein VP40 orchestrates virus morphogenesis and budding. To do this it interacts with both the glycoprotein (GP1,2) and the ribonucleoprotein (RNP) complex components; however, these interactions are still not well understood. Here we show that for efficient VP40-driven formation of transcription and replication-competent virus-like particles (trVLPs), which contain both an RNP complex and GP1,2, the RNP components and VP40, but not GP1,2 and VP40, must be from the same genus. trVLP preparations contained both spherical and filamentous particles, but only the latter were able to infect target cells and to lead to genome replication and transcription. Interestingly, the genus specificity of the VP40–RNP interactions was specific to the formation of filamentous trVLPs, but not to spherical particles. These results not only further our understanding of VP40 interactions, but also suggest that special care is required when using trVLP or VLP systems to model virus morphogenesis. PMID:21900424

  9. Structural Basis for Substrate Placement by an Archaeal Box C/D Ribonucleoprotein Particle

    SciTech Connect

    Xue, Song; Wang, Ruiying; Yang, Fangping; Terns, Rebecca M.; Terns, Michael P.; Zhang, Xinxin; Maxwell, E.Stuart; Li, Hong

    2012-05-09

    Box C/D small nucleolar and Cajal body ribonucleoprotein particles (sno/scaRNPs) direct site-specific 2'-O-methylation of ribosomal and spliceosomal RNAs and are critical for gene expression. Here we report crystal structures of an archaeal box C/D RNP containing three core proteins (fibrillarin, Nop56/58, and L7Ae) and a half-mer box C/D guide RNA paired with a substrate RNA. The structure reveals a guide-substrate RNA duplex orientation imposed by a composite protein surface and the conserved GAEK motif of Nop56/58. Molecular modeling supports a dual C/D RNP structure that closely mimics that recently visualized by electron microscopy. The substrate-bound dual RNP model predicts an asymmetric protein distribution between the RNP that binds and methylates the substrate RNA. The predicted asymmetric nature of the holoenzyme is consistent with previous biochemical data on RNP assembly and provides a simple solution for accommodating base-pairing between the C/D guide RNA and large ribosomal and spliceosomal substrate RNAs.

  10. Identification of two RNA-binding proteins in Balbiani ring premessenger ribonucleoprotein granules and presence of these proteins in specific subsets of heterogeneous nuclear ribonucleoprotein particles.

    PubMed Central

    Wurtz-T; Kiseleva, E; Nacheva, G; Alzhanova-Ericcson, A; Rosén, A; Daneholt, B

    1996-01-01

    Balbiani ring (BR) granules are premessenger ribonucleoprotein particles (RNPs) generated in giant chromosomal puffs, the BRs, in the larval salivary glands of the dipteran chironomus tentans. Monoclonal antibodies were raised against nuclear proteins collected on a single-stranded-DNA-agarose affinity column, and two of them were used to identify RNA-binding proteins in BR granules. First, in Western blots (immunoblots), one of the antibodies recognized a 36-kDa protein and the other recognized a 45-KDa protein. Second, both antibodies bound to the BRs in immunocytological experiments. It was shown in cross-linking experiments that the two proteins are associated with heterogeneous nuclear RNP (hnRNP) complexes extracted from C. tentans nuclei. By immunoelectron microscopy of isolated and partly unfolded BR RNPs, it was specifically demonstrated that the BR granules contain the two proteins and, in addition, that both proteins are distributed frequently along the RNP fiber of the particles. Thus, the 36- and 45-KDa proteins are likely to be abundant, RNA-binding proteins in the BR particles. To elucidate to what extent the two proteins are also present in other hnRNPs, we studied the binding of the antibodies to chromosomal puffs in general. It was observed that many puffs in addition to the BRs harbor the two proteins, but there are also puffs containing only one of the components, either the 36- or the 45-kDa protein. We conclude that the two proteins are not randomly bound to all hnRNPs but that each of them seems to be linked to a specific subset of the particles. PMID:8657116

  11. The 3.2 Angstrom Resolution Structure of the Polymorphic Cowpea Chlorotic Mottle Virus Ribonucleoprotein Particle

    NASA Astrophysics Data System (ADS)

    Speir, Jeffrey Alan

    Structural studies of the polymorphic cowpea chlorotic mottle virus have resulted in high resolution structures for two distinct icosahedral ribonucleoprotein particle conformations dependent upon whether acidic or basic pH conditions prevail. CCMV is stable below pH 6.5, however metal-free particles maintain a 10% increase in hydrodynamic volume at pH >=q 7.5. Identification of this swollen' form of CCMV, which can easily be disrupted with 1M NaCl, led to the first reassembly of an icosahedral virus in vitro from purified viral protein and RNA to form infectious particles, and its assembly has been the subject of biochemical and biophysical investigations for over twenty-five years. Under well defined conditions of pH, ionic strength and divalent metal ion concentration, CCMV capsid protein or capsid protein and RNA will reassemble to form icosahedral particles of various sizes, sheets, tubes, rosettes, and a variety of laminar structures which resemble virion structures from non-related virus families. Analysis of native particles at 3.2A resolution and swollen particles at 28A resolution has suggested that the chemical basis for the formation of polymorphic icosahedral and anisometric structures is: (i) hexamers formed of beta-barrel subunits stabilized by an unusual hexameric parallel beta structure made up of their N-termini, (ii) the location of protein-RNA interactions, (iii) divalent metal cation binding sites that regulate quasi-symmetrical subunit associations, (iv) charge repulsion across the same interfaces when lacking divalent metal ions at basic pH, which induces the formation of sixty 20A diameter portals for RNA release, and (v) a novel, C-terminal-based, subunit dimer assembly unit. The use of C- and N-terminal arms in CCMV has not been observed in other icosahedral RNA virus structures determined at near atomic resolution, however, their detailed interactions and roles in stabilizing the quaternary organization of CCMV are related to that found

  12. Cytoplasmic nonpolysomal ribonucleoprotein particles in sea urchin embryos and their relationship to protein synthesis

    PubMed Central

    Dworkin, Mark B.; Rudensey, Lyle M.; Infante, Anthony A.

    1977-01-01

    We have examined the relationship between the newly synthesized mRNA that enters polysomes in sea urchin embryos and the messengerlike RNA that enters the pool of ribosome-free ribonucleoprotein particles (free RNPs or informosomes). Although the RNA in the free RNPs turns over 25% more rapidly than in the polysomes, labeling kinetics indicate that the RNA containing poly(A) [poly(A)(+)RNA] and the RNA not containing poly(A) [poly(A)(-)RNA] within each cytoplasmic compartment have very similar half-lives. The poly(A)(+)RNA from both free RNPs and polysomes binds ribosomes almost equally well in a reticulocyte lysate, and this binding is sensitive to inhibitors of initiation. The poly(A)(-)RNA from polysomes initiates as well as poly(A)(+)RNA; however, poly(A)(-)RNA from free RNPs is only half as efficient in binding to ribosomes, and by this criterion is only 50% mRNA. We have also examined the size and dynamics of shortening of the poly(A) tails of poly(A)(+)RNA from free RNPs and polysomes. Pulse-labeled poly(A) from both free RNPs and polysomes is about 180 nucleotides in length. Poly(A) shortening is very rapid in polysomes; steady-state labeled polysomal RNA is largely devoid of the 180-nucleotide-long poly(A) segments. Poly(A) shortening in free RNPs is slower; half of the poly(A) derived from steady-state free RNPs is still 180 nucleotides long. Despite this difference in the rates of poly(A) shortening, polysomes and free RNPs have very similar half-lives. There is, then, no obvious relationship between poly(A) shortening and turnover of mRNA in these embryos. The data are interpreted to mean that poly(A)(+)RNA from free RNPs is enriched for a class of mRNA that initiates less frequently in vivo than the bulk of the cellular mRNA. PMID:267921

  13. Functional and structural impact of target uridine substitutions on the H/ACA ribonucleoprotein particle pseudouridine synthase.

    PubMed

    Zhou, Jing; Liang, Bo; Li, Hong

    2010-07-27

    Box H/ACA ribonucleoprotein protein particles catalyze the majority of pseudouridylation in functional RNA. Different from stand alone pseudouridine synthases, the RNP pseudouridine synthase comprises multiple protein subunits and an RNA subunit. Previous studies showed that each subunit, regardless its location, is sensitive to the step of subunit placement at the catalytic center and potentially to the reaction status of the substrate. Here we describe the impact of chemical substitutions of target uridine on enzyme activity and structure. We found that 3-methyluridine in place of uridine inhibited its isomerization while 2'-deoxyuridine or 4-thiouridine did not. Significantly, crystal structures of an archaeal box H/ACA RNP bound with the nonreactive and the two postreactive substrate analogues showed only subtle structural changes throughout the assembly except for a conserved tyrosine and a substrate anchoring loop of Cbf5. Our results suggest a potential role of these elements and the subunit that contacts them in substrate binding and product release.

  14. Structural/functional properties of a mammalian multi-component structure containing all major spliceosomal small nuclear ribonucleoprotein particles.

    PubMed Central

    Moraitou, M; Patrinou-Georgoula, M; Guialis, A

    1998-01-01

    An approx. 40 S multi-component structure, consisting of all major spliceosomal small nuclear ribonucleoprotein particles (snRNP) (U1, U2, U4/U6 and U5) in stable association with a large number of polypeptides, mainly in the range 50-210 kDa, has been reported to exist within rat liver nuclear extracts [Guialis, Moraitou, Patrinou-Georgoula and Dangli (1991) Nucleic Acids Res. 19, 287-296]. Using a new polyclonal antibody recognizing a 63 kDa protein component of the complex, this multi-snRNP assembly was detected within rat liver nuclear extracts as efficiently as with the antibody for the U2 snRNP-specific B' polypeptide. The 63 kDa protein was found to correspond to the 66 kDa subunit of the splicing factor SF3a, a known integral component of the HeLa 17 S U2 snRNP. Anti-2,2,7-trimethylguanosine affinity chromatography was an easy and efficient way of purifying the multi-snRNP complex from rat liver 40 S heterogeneous nuclear ribonucleoprotein particle (hnRNP)-containing sucrose gradient fractions. By subsequent glycerol-gradient sedimentation, all known snRNP forms active in RNA splicing were identified among its constituents. A complex structurally similar to the rat multi-snRNP was also identified in HeLa nuclear extracts. Preservation of hnRNP-snRNP interactions was observed within HeLa 40 S fractions. Moreover, these fractions were capable of restoring splicing activity when applied in reconstitution studies to supplement a micrococcal nuclease-treated splicing extract. PMID:9576861

  15. Particle-bound phytochrome: Association with a ribonucleoprotein fraction from Cucurbita pepo L.

    PubMed

    Quail, P H

    1975-01-01

    In the absence of ethylenediaminetetraacetic acid (EDTA) and added Mg(2+), the phytochrome, RNA, protein, cytochrome c oxidase and NADPH-cytochrome c reductase in 20000 x g pellets from hypocotyl hooks of red-irradiated Cucurbita seedlings are more or less coincident in a single, broad band on linear sucrose gradients. The inclusion of 3 mM EDTA in the extraction, resuspension and gradient media has three major effects: (a) The phytochrome profile splits into two main bands; (b) the main RNA population shifts to a sharp peak which co-sediments with the "lighter" phytochrome band at 31S; (c) the main NADPH-cytochrome c reductase peak shifts to a lower density. This indicates that the EDTA dissociates a rough-endoplasmic-reticulum fraction into separate membrane and ribonucleoprotein (RNP) components, and that part of the phytochrome is associated with the latter. The 31S RNP fraction is 35-40% RNA, has a 260/235 nm absorption ratio of 1.36 and the RNA dissociates into small fragments in sodium dodecyl sulfate. More than 90% of the phytochrome and RNA in the isolated 31S fraction becomes pelletable upon the addition of 10 mM Mg(2+). Higher Mg(2+) levels release the phytochrome and some of the other protein present from the RNA which remains pelletable. The data indicate that the 31S RNP fraction may be degraded ribosomal material with extraneously bound protein, including phytochrome. Several aspects of phytochrome-binding to particulate fractions which have been reported in the literature are consistent with an interaction of Pfr with ribosomal material-degraded or otherwise. PMID:24435122

  16. 3'-end-dependent formation of U6 small nuclear ribonucleoprotein particles in Xenopus laevis oocyte nuclei.

    PubMed

    Terns, M P; Lund, E; Dahlberg, J E

    1992-07-01

    We have identified and characterized a U6 small nuclear (sn) ribonucleoprotein particle (RNP) present in the nuclei of Xenopus laevis oocytes. The structure of this U6 snRNP was investigated by native gel shift analysis and a combination of RNA-protein UV cross-linking, RNase T1 fingerprinting, and immunoprecipitation assays. These analyses demonstrate that certain forms of U6 snRNA associate with the 50-kDa nuclear antigen La both in vivo and in vitro. The La protein binds the stretch of uridylates at the 3' hydroxyl end of newly synthesized U6 snRNA. La does not bind to mature U6 snRNAs that have 2',3'-cyclic phosphate (greater than p) groups at their 3' ends (E. Lund and J. E. Dahlberg, Science 255:327-330, 1992) or to U6 snRNAs in anti-Sm-precipitable U4/U6 snRNPs. We propose that 3'-end modification, including posttranscriptional UMP addition, modulates the binding of La protein to U6 snRNA which, in turn, may affect the function of this RNA. PMID:1535684

  17. A cellular protein phosphorylated by the avian sarcoma virus transforming gene product is associated with ribonucleoprotein particles.

    PubMed Central

    Arrigo, A P; Darlix, J L; Spahr, P F

    1983-01-01

    In chick embryo fibroblasts transformed by Rous sarcoma virus (RSV) the tyrosine phosphorylation of a cellular protein of 34,000 daltons mol. wt. (34 kd) is greatly enhanced; this was shown to be catalyzed by the phosphotransferase activity of RSV transforming protein pp60src. We report here that in cytoplasmic extracts of both normal and transformed cells, in the presence of magnesium ions, the majority of the 34-kd protein is associated with large structures and that a fraction of 34 kd appears to be associated with ribonucleoprotein particles (RNPs). In addition, upon u.v. light cross-linking of RNA to protein in normal or transformed cells, an anti-34 kd serum immunoprecipitates RNA fragments of apparent low sequence complexity as detected by T1 fingerprint analysis. Our results indicate that the 34-kd protein may play a role in the cell at the level of RNPs. Images Fig. 1. Fig. 2. Fig. 3. Fig. 4. Fig. 5. PMID:11894943

  18. Cloning of the cDNA for U1 small nuclear ribonucleoprotein particle 70K protein from Arabidopsis thaliana

    NASA Technical Reports Server (NTRS)

    Reddy, A. S.; Czernik, A. J.; An, G.; Poovaiah, B. W.

    1992-01-01

    We cloned and sequenced a plant cDNA that encodes U1 small nuclear ribonucleoprotein (snRNP) 70K protein. The plant U1 snRNP 70K protein cDNA is not full length and lacks the coding region for 68 amino acids in the amino-terminal region as compared to human U1 snRNP 70K protein. Comparison of the deduced amino acid sequence of the plant U1 snRNP 70K protein with the amino acid sequence of animal and yeast U1 snRNP 70K protein showed a high degree of homology. The plant U1 snRNP 70K protein is more closely related to the human counter part than to the yeast 70K protein. The carboxy-terminal half is less well conserved but, like the vertebrate 70K proteins, is rich in charged amino acids. Northern analysis with the RNA isolated from different parts of the plant indicates that the snRNP 70K gene is expressed in all of the parts tested. Southern blotting of genomic DNA using the cDNA indicates that the U1 snRNP 70K protein is coded by a single gene.

  19. Discovery of Nuclear DNA-like RNA (dRNA, hnRNA) and Ribonucleoproteins Particles Containing hnRNA.

    PubMed

    Georgiev, G P

    2016-01-01

    On August 9-11, 2014, Cold Spring Harbor (USA) hosted a special symposium dedicated to the discovery of messenger or informational RNA and the main events in the subsequent studies of its synthesis, regulation of synthesis, maturation, and transport. The existence of mRNA in bacteria was first suggested in 1961 by Jacob and Monod, based on genetic studies [1]. The same year, Brenner et al. confirmed the hypothesis [2]. Our laboratory played a key role in the discovery of messenger RNA in eukaryotes, as well as in the discovery of the nuclear ribonucleoproteins that contain it and in the elucidation of their structural organization. Therefore, I was invited to represent Russia at the Symposium and deliver a speech on these topics. However, my visa had only been issued after the end of the Symposium, and, therefore, the presentation was delivered by my former colleague G.N. Yenikolopov, who works at Cold Spring Harbor Laboratory. The transcript of the lecture is presented below. PMID:27099780

  20. Conserved Composition of Mammalian Box H/ACA and Box C/D Small Nucleolar Ribonucleoprotein Particles and Their Interaction with the Common Factor Nopp140

    PubMed Central

    Yang, Yunfeng; Isaac, Cynthia; Wang, Chen; Dragon, François; Pogac̆ić, Vanda; Meier, U. Thomas

    2000-01-01

    Small nucleolar ribonucleoprotein particles (snoRNPs) mainly catalyze the modification of rRNA. The two major classes of snoRNPs, box H/ACA and box C/D, function in the pseudouridylation and 2′-O-methylation, respectively, of specific nucleotides. The emerging view based on studies in yeast is that each class of snoRNPs is composed of a unique set of proteins. Here we present a characterization of mammalian snoRNPs. We show that the previously characterized NAP57 is specific for box H/ACA snoRNPs, whereas the newly identified NAP65, the rat homologue of yeast Nop5/58p, is a component of the box C/D class. Using coimmunoprecipitation experiments, we show that the nucleolar and coiled-body protein Nopp140 interacts with both classes of snoRNPs. This interaction is corroborated in vivo by the exclusive depletion of snoRNP proteins from nucleoli in cells transfected with a dominant negative Nopp140 construct. Interestingly, RNA polymerase I transcription is arrested in nucleoli depleted of snoRNPs, raising the possibility of a feedback mechanism between rRNA modification and transcription. Moreover, the Nopp140-snoRNP interaction appears to be conserved in yeast, because depletion of Srp40p, the yeast Nopp140 homologue, in a conditional lethal strain induces the loss of box H/ACA small nucleolar RNAs. We propose that Nopp140 functions as a chaperone of snoRNPs in yeast and vertebrate cells. PMID:10679015

  1. The ribonucleoprotein Csr network.

    PubMed

    Seyll, Ethel; Van Melderen, Laurence

    2013-11-08

    Ribonucleoprotein complexes are essential regulatory components in bacteria. In this review, we focus on the carbon storage regulator (Csr) network, which is well conserved in the bacterial world. This regulatory network is composed of the CsrA master regulator, its targets and regulators. CsrA binds to mRNA targets and regulates translation either negatively or positively. Binding to small non-coding RNAs controls activity of this protein. Expression of these regulators is tightly regulated at the level of transcription and stability by various global regulators (RNAses, two-component systems, alarmone). We discuss the implications of these complex regulations in bacterial adaptation.

  2. The Ribonucleoprotein Csr Network

    PubMed Central

    Seyll, Ethel; Van Melderen, Laurence

    2013-01-01

    Ribonucleoprotein complexes are essential regulatory components in bacteria. In this review, we focus on the carbon storage regulator (Csr) network, which is well conserved in the bacterial world. This regulatory network is composed of the CsrA master regulator, its targets and regulators. CsrA binds to mRNA targets and regulates translation either negatively or positively. Binding to small non-coding RNAs controls activity of this protein. Expression of these regulators is tightly regulated at the level of transcription and stability by various global regulators (RNAses, two-component systems, alarmone). We discuss the implications of these complex regulations in bacterial adaptation. PMID:24217225

  3. Ribonucleoprotein particles of bacterial small non-coding RNA IsrA (IS61 or McaS) and its interaction with RNA polymerase core may link transcription to mRNA fate

    PubMed Central

    van Nues, Rob W.; Castro-Roa, Daniel; Yuzenkova, Yulia; Zenkin, Nikolay

    2016-01-01

    Coupled transcription and translation in bacteria are tightly regulated. Some small RNAs (sRNAs) control aspects of this coupling by modifying ribosome access or inducing degradation of the message. Here, we show that sRNA IsrA (IS61 or McaS) specifically associates with core enzyme of RNAP in vivo and in vitro, independently of σ factor and away from the main nucleic-acids-binding channel of RNAP. We also show that, in the cells, IsrA exists as ribonucleoprotein particles (sRNPs), which involve a defined set of proteins including Hfq, S1, CsrA, ProQ and PNPase. Our findings suggest that IsrA might be directly involved in transcription or can participate in regulation of gene expression by delivering proteins associated with it to target mRNAs through its interactions with transcribing RNAP and through regions of sequence-complementarity with the target. In this eukaryotic-like model only in the context of a complex with its target, IsrA and its associated proteins become active. In this manner, in the form of sRNPs, bacterial sRNAs could regulate a number of targets with various outcomes, depending on the set of associated proteins. PMID:26609136

  4. U1 small nuclear ribonucleoprotein particle-specific proteins interact with the first and second stem-loops of U1 RNA, with the A protein binding directly to the RNA independently of the 70K and Sm proteins.

    PubMed Central

    Patton, J R; Habets, W; van Venrooij, W J; Pederson, T

    1989-01-01

    The U1 small nuclear ribonucleoprotein particle (U1 snRNP), a cofactor in pre-mRNA splicing, contains three proteins, termed 70K, A, and C, that are not present in the other spliceosome-associated snRNPs. We studied the binding of the A and C proteins to U1 RNA, using a U1 snRNP reconstitution system and an antibody-induced nuclease protection technique. Antibodies that reacted with the A and C proteins induced nuclease protection of the first two stem-loops of U1 RNA in reconstituted U1 snRNP. Detailed analysis of the antibody-induced nuclease protection patterns indicated the existence of relatively long-range protein-protein interactions in the U1 snRNP, with the 5' end of U1 RNA and its associated specific proteins interacting with proteins bound to the Sm domain near the 3' end. UV cross-linking experiments in conjunction with an A-protein-specific antibody demonstrated that the A protein bound directly to the U1 RNA rather than assembling in the U1 snRNP exclusively via protein-protein interactions. This conclusion was supported by additional experiments revealing that the A protein could bind to U1 RNA in the absence of bound 70K and Sm core proteins. Images PMID:2529425

  5. Current and future emission estimates of exhaust gases and particles from shipping at the largest port in Korea.

    PubMed

    Song, Sang-Keun; Shon, Zang-Ho

    2014-05-01

    The emissions of exhaust gases (NOx , SO2, VOCs, and CO2) and particles (e.g., PM) from ships traversing Busan Port in Korea were estimated over three different years (the years 2006, 2008, and 2009). This analysis was performed according to the ship operational modes ("at sea," "maneuvering," and "in port") and ship types based on an activity-based method. The ship emissions for current (base year 2009) and future scenarios (years 2020 and 2050) were also compared. The annual emissions of SO2, VOCs, PM, and CO2 were highest (9.6 × 10(3), 374, 1.2 × 10(3), and 5.6 × 10(5) ton year(-1), respectively) in 2008. In contrast, the annual NO x emissions were highest (11.7 × 10(3) ton year(-1)) in 2006 due mainly to the high NO x emission factor. The emissions of air pollutants for each ship operational mode differed considerably, with the largest emission observed in "in port" mode. In addition, the largest fraction (approximately 45-67%) of the emissions of all air pollutants during the study period was emitted from container ships. The future ship emissions of most pollutants (except for SO2 and PM) in 2020 and 2050 are estimated to be 1.4-1.8 and 4.7-6.1 times higher than those in 2009 (base year), respectively. PMID:24497306

  6. Rapid, small scale purification of rice hoja blanca and Echinochloa hoja blanca tenuivirus ribonucleoprotein.

    PubMed

    de Miranda, J R; Espinoza, A M; Hull, R

    1996-01-01

    Highly purified tenuivirus ribonucleoprotein was obtained from small amounts of leaf tissue by sedimenting the ribonucleoprotein particles from debris-free plant extract into a 30% sucrose cushion, in 1.5-mL microfuge tubes. Using this protocol, significant size differences were discovered in the double-stranded forms of the viral genomic RNAs of rice hoja blanca tenuivirus and a tenuivirus isolated from Echinochloa colonum, a common weed of rice cultivation. PMID:8690758

  7. B and T cell immune response to small nuclear ribonucleoprotein particles in lupus mice: autoreactive CD4(+) T cells recognize a T cell epitope located within the RNP80 motif of the 70K protein.

    PubMed

    Monneaux, F; Briand, J P; Muller, S

    2000-08-01

    Systemic lupus erythematosus is characterized by the presence of high titers of autoantibodies reacting with various components of the U1 small nuclear ribonucleoprotein particle (snRNP). It has been suggested that these antibodies are produced by an antigen-driven mechanism under the dependence of antigen-specific T cells. To investigate the role of T cell help in this process, we sought, with 20 overlapping peptides, the Th epitopes on the U1-70K snRNP in unprimed H-2(k) MRL / lpr lupus mice and immunized CBA normal mice. The peptide 131 - 151 was recognized by both IgG autoantibodies and CD4(+) T cells from 7 - 9-week-old MRL / lpr mice. In this test, antigen-presenting cells (APC) from MRL / lpr mice were required; APC from naive CBA mice failed to stimulate CD4(+) cells from MRL / lpr mice. The potential role of MRL / lpr B cells as APC, the expression of MHC class II molecules at their surface and their activation state (expression of CD69, CD80 / B7-1 and CD86 / B7-2 molecules) were studied. Peptide 131 - 151 bound both I-A(k) and I-E(k) class II molecules and favored an IL-2-positive T cell response but not IFN-gamma, IL-6 and IL-10 secretion. Segment 131 - 151 is localized within the RNP80 motif and contains residues that are highly conserved in many nuclear, nucleolar and cytoplasmic RNA binding proteins.

  8. The C-terminal repressor region of herpes simplex virus type 1 ICP27 is required for the redistribution of small nuclear ribonucleoprotein particles and splicing factor SC35; however, these alterations are not sufficient to inhibit host cell splicing.

    PubMed Central

    Sandri-Goldin, R M; Hibbard, M K; Hardwicke, M A

    1995-01-01

    Herpes simplex virus type 1 infection results in a reorganization of antigens associated with the small nuclear ribonucleoprotein particles (snRNPs), resulting in the formation of prominent clusters near the nuclear periphery. In this study, we show that the immediate-early protein ICP27, which is involved in the impairment of host cell splicing and in the changes in the distribution of snRNPs, is also required for reassorting the SR domain splicing factor SC35. Other viral processes, such as adsorption and penetration, shutoff of host protein synthesis, early and late gene expression, and DNA replication, do not appear to play a role in changing the staining pattern of splicing antigens. Furthermore, the C-terminal repressor region of ICP27, which is required for the inhibitory effects on splicing, also is involved in redistributing the snRNPs and SC35. During infection or transfection with five different repressor mutants, the speckled staining pattern characteristic of uninfected cells was seen and the level of a spliced target mRNA was not reduced. Infections in the presence of activator mutants showed a redistributed snRNP pattern and a decreased accumulation of spliced target mRNA. Moreover, two arginine-rich regions in the N-terminal half of ICP27 were not required for the redistribution of snRNPs or SC35. Substitution of these regions with a lysine-rich sequence from simian virus 40 large-T antigen resulted in a redistribution of splicing antigens. Unexpectedly, a repressor mutant with a ts phenotype showed a redistributed staining pattern like that seen with wild-type infected cells. During infections with this ts mutant, splicing was not inhibited, as shown in this and previous studies, confirming its repressor phenotype. Furthermore, both the mutant and the wild-type protein colocalized with snRNPs. Therefore, the redistribution of snRNPs and SC35 correlates with ICP27-mediated impairment of host cell splicing, but these alterations are not sufficient to

  9. Phosphorylation of the C proteins in heterogeneous ribonucleoprotein (hnRNP) particles in HeLa cells: Characterization of in vivo phosphorylation, comparison with in vitro phosphorylation using casein kinase II, and preliminary studies on the effects of phosphorylation on particle structure

    SciTech Connect

    Kleiman, N.J.

    1989-01-01

    Newly formed pre-messenger RNA associates with protein to form heterogeneous ribonucleoprotein (hnRNP) particles. In HeLa cells, hnRNP particles contain six core proteins. Two proteins, termed C{sub 1} and C{sub 2}, are phosphorylated in vitro by casein kinase 11 (CKII). C{sub 1} protein became {sup 32}P-labeled after HeLa cells were incubated with ({sup 32}P)-orthophosphate in vivo (ibid). Because phosphorylation is a ubiquitous regulatory mechanism, C protein phosphorylation was studied in greater detail. C protein phosphorylation in hnRNP particles was investigated in HeLa cells incubated with ({sup 32}P)-orthophosphate in vivo. Immunoblotting in pH 3.5-10 isoelectric focusing (IEF) gels indicated that C proteins focus only at pH 5.0. In pH 4.5-5.5 IEF gels, individually purified C, and 2 proteins resolve into the same four closely spaced, {sup 32}P-labeled bands. A fifth, unlabeled, more basic species was detached when hnRNP particles were purified without NaF. All {sup 32}P-labeled species contained identical amounts of {sup 32}P per unit protein suggesting that charge heterogeneity is not due to differential phosphorylation. Attempts to detect bound carbohydrate were unsuccessful. {sup 32}P-labeled phosphate was readily removed by potato acid phosphatase. E. coli alkaline phosphatase and snake venom phosphodiesterase were ineffective. {sup 32}P-label was found exclusively in phosphoserine. One-dimensional peptide mapping with chymotrypsin and S. aureus protease detected two phosphorylated peptides. C protein phosphorylation was also investigated in vitro. Incubation of hnRNP particles with rabbit liver CKII and {sup 32}P-ATP followed by IEF in pH 4.5-5.5 gels indicated that all four C protein species were {sup 32}P-labeled. {sup 32}P-label was found exclusively in phosphoserine.

  10. Ro small cytoplasmic ribonucleoproteins are a subclass of La ribonucleoproteins: Further characterization of the Ro and La small ribonucleoproteins from uninfected mammalian cells

    SciTech Connect

    Hendrick, J.P.; Wolin, S.L.; Rinke, J.; Lerner, M.R.; Steitz, J.A.

    1981-12-01

    Small ribonucleic acid (RNA)-protein complexes precipitated by anti-Ro and anti-La antibodies from lupus patients have been examined with emphasis on their RNA components. In both ribonucleoprotein (RNP) classes, the numbers of different RNA molecules and their sequences vary between mouse and human cells. The complex mixtures of La RNAs include two previously sequenced 4.5S RNAs from mouse cells and 5S ribosomal RNA-like molecules from both mouse and human cells. All Ro and La RNAs possess 5'-triphosphates. Some La RNAs have internal modifications typical of transfer RNAs. The RoRNPs are quite stable and are localized by immunofluorescence in the cell cytoplasm, whereas the majority of the La RNPs turn over rapidly and reside in the nucleus. Despite these differences, reconstitution experiments show that the Ro particles carry the La as well as the Ro determinant. Studies using a nuclear transcription system demonstrate that most of the La RNAs are synthesized by RNA polymerase III. The possibility that the La protein(s) functions in the transcription or maturation of all RNA polymerase III transcripts is discussed.

  11. Box H/ACA small ribonucleoproteins.

    PubMed

    Kiss, Tamás; Fayet-Lebaron, Eléonore; Jády, Beáta E

    2010-03-12

    Box H/ACA RNAs represent an abundant, evolutionarily conserved class of small noncoding RNAs. All H/ACA RNAs associate with a common set of proteins, and they function as ribonucleoprotein (RNP) enzymes mainly in the site-specific pseudouridylation of ribosomal RNAs (rRNAs) and small nuclear RNAs (snRNAs). Some H/ACA RNPs function in the nucleolytic processing of precursor rRNA (pre-rRNA) and synthesis of telomeric DNA. Thus, H/ACA RNPs are essential for three fundamental cellular processes: protein synthesis, mRNA splicing, and maintenance of genome integrity. Recently, great progress has been made toward understanding of the biogenesis, intracellular trafficking, structure, and function of H/ACA RNPs.

  12. Isolation and Analyses of Axonal Ribonucleoprotein Complexes

    PubMed Central

    Doron-Mandel, Ella; Alber, Stefanie; Oses, Juan A.; Medzihradszky, Katalin F.; Burlingame, Alma L.; Fainzilber, Mike; Twiss, Jeffery L.; Lee, Seung Joon

    2016-01-01

    Cytoskeleton-dependent RNA transport and local translation in axons are gaining increased attention as key processes in the maintenance and functioning of neurons. Specific axonal transcripts have been found to play roles in many aspects of axonal physiology including axon guidance, axon survival, axon to soma communication, injury response and regeneration. This axonal transcriptome requires long-range transport that is achieved by motor proteins carrying transcripts as messenger ribonucleoprotein (mRNP) complexes along microtubules. Other than transport, the mRNP complex plays a major role in the generation, maintenance and regulation of the axonal transcriptome. Identification of axonal RNA binding proteins (RBPs) and analyses of the dynamics of their mRNPs are of high interest to the field. Here we describe methods for the study of interactions between RNA and proteins in axons. First, we describe a protocol for identifying binding proteins for an RNA of interest by using RNA affinity chromatography. Subsequently, we discuss immunoprecipitation (IP) methods allowing the dissection of protein- RNA and protein-protein interactions in mRNPs under various physiological conditions. PMID:26794529

  13. Cotranscriptional recruitment of RNA exosome cofactors Rrp47p and Mpp6p and two distinct Trf-Air-Mtr4 polyadenylation (TRAMP) complexes assists the exonuclease Rrp6p in the targeting and degradation of an aberrant messenger ribonucleoprotein particle (mRNP) in yeast.

    PubMed

    Stuparevic, Igor; Mosrin-Huaman, Christine; Hervouet-Coste, Nadège; Remenaric, Mateja; Rahmouni, A Rachid

    2013-11-01

    The cotranscriptional mRNA processing and packaging reactions that lead to the formation of export-competent messenger ribonucleoprotein particles (mRNPs) are under the surveillance of quality control steps. Aberrant mRNPs resulting from faulty events are retained in the nucleus with ensuing elimination of their mRNA component. The molecular mechanisms by which the surveillance system recognizes defective mRNPs and stimulates their destruction by the RNA degradation machinery are still not completely elucidated. Using an experimental approach in which mRNP formation in yeast is disturbed by the action of the bacterial Rho helicase, we have shown previously that the targeting of Rho-induced aberrant mRNPs is mediated by Rrp6p, which is recruited cotranscriptionally in association with Nrd1p following Rho action. Here we investigated the specific involvement in this quality control process of different cofactors associated with the nuclear RNA degradation machinery. We show that, in addition to the main hydrolytic action of the exonuclease Rrp6p, the cofactors Rrp47p, Mpp6p as well as the Trf-Air-Mtr4 polyadenylation (TRAMP) components Trf4p, Trf5p, and Air2p contribute significantly by stimulating the degradation process upon their cotranscriptional recruitment. Trf4p and Trf5p are apparently recruited in two distinct TRAMP complexes that both contain Air2p as component. Surprisingly, Rrp47p appears to play an important role in mutual protein stabilization with Rrp6p, which highlights a close association between the two partners. Together, our results provide an integrated view of how different cofactors of the RNA degradation machinery cooperate to target and eliminate aberrant mRNPs.

  14. Cotranscriptional Recruitment of RNA Exosome Cofactors Rrp47p and Mpp6p and Two Distinct Trf-Air-Mtr4 Polyadenylation (TRAMP) Complexes Assists the Exonuclease Rrp6p in the Targeting and Degradation of an Aberrant Messenger Ribonucleoprotein Particle (mRNP) in Yeast*

    PubMed Central

    Stuparevic, Igor; Mosrin-Huaman, Christine; Hervouet-Coste, Nadège; Remenaric, Mateja; Rahmouni, A. Rachid

    2013-01-01

    The cotranscriptional mRNA processing and packaging reactions that lead to the formation of export-competent messenger ribonucleoprotein particles (mRNPs) are under the surveillance of quality control steps. Aberrant mRNPs resulting from faulty events are retained in the nucleus with ensuing elimination of their mRNA component. The molecular mechanisms by which the surveillance system recognizes defective mRNPs and stimulates their destruction by the RNA degradation machinery are still not completely elucidated. Using an experimental approach in which mRNP formation in yeast is disturbed by the action of the bacterial Rho helicase, we have shown previously that the targeting of Rho-induced aberrant mRNPs is mediated by Rrp6p, which is recruited cotranscriptionally in association with Nrd1p following Rho action. Here we investigated the specific involvement in this quality control process of different cofactors associated with the nuclear RNA degradation machinery. We show that, in addition to the main hydrolytic action of the exonuclease Rrp6p, the cofactors Rrp47p, Mpp6p as well as the Trf-Air-Mtr4 polyadenylation (TRAMP) components Trf4p, Trf5p, and Air2p contribute significantly by stimulating the degradation process upon their cotranscriptional recruitment. Trf4p and Trf5p are apparently recruited in two distinct TRAMP complexes that both contain Air2p as component. Surprisingly, Rrp47p appears to play an important role in mutual protein stabilization with Rrp6p, which highlights a close association between the two partners. Together, our results provide an integrated view of how different cofactors of the RNA degradation machinery cooperate to target and eliminate aberrant mRNPs. PMID:24047896

  15. Rescue of Infectious Birnavirus from Recombinant Ribonucleoprotein Complexes

    PubMed Central

    Dalton, Romy M.; Rodríguez, José F.

    2014-01-01

    Birnaviruses are unconventional members of the icosahedral double-stranded (dsRNA) RNA virus group. The main differential birnavirus trait is the lack of the inner icosahedral transcriptional core, a ubiquitous structure conserved in all other icosahedral dsRNA viruses, that shelters the genome from cellular dsRNA sensors and provide the enzymatic machinery to produce and extrude mature messenger RNAs. In contrast, birnaviral particles enclose ribonucleoprotein (RNP) complexes formed by the genome segments, the dsRNA-binding VP3 polypeptide and the virus-encoded RNA polymerase (RdRp). The presence of RNPs suggests that the birnavirus replication program might exhibit significant differences with respect to those of prototypal dsRNA viruses. However, experimental evidences supporting this hypothesis are as yet scarce. Of particular relevance for the understanding of birnavirus replication is to determine whether RNPs act as intracellular capsid-independent transcriptional units. Our study was focused to answer this question using the infectious bursal disease virus (IBDV), the best characterized birnavirus, as model virus. Here, we describe the intracellular assembly of functional IBDV RNPs in the absence of the virus-encoded VP2 capsid polypeptide. Recombinant RNPs are generated upon coexpression of the IBDV VP1 and RdRp polypeptides and transfection of purified virus dsRNA. Presented data show that recombinant RNPs direct the expression of the IBDV polypeptide repertoire and the production of infectious virus in culture cells. Results described in this report constitute the first direct experimental evidence showing that birnaviral RNPs are intracellularly active in the absence of the virus capsid. This finding is consistent with presented data indicating that RNP formation precedes virus assembly in IBDV-infected cells, and supports the recently proposed IBDV replication model entailing the release of RNPs during the initial stages of the infection. Indeed

  16. Largest College Endowments, 2011

    ERIC Educational Resources Information Center

    Chronicle of Higher Education, 2012

    2012-01-01

    Of all endowments valued at more than $250-million, the UCLA Foundation had the highest rate of growth over the previous year, at 49 percent. This article presents a table of the largest college endowments in 2011. The table covers the "rank," "institution," "market value as of June 30, 2011," and "1-year change" of institutions participating in…

  17. The elemental composition and origin of fine ambient particles in the largest Polish conurbation: first results from the short-term winter campaign

    NASA Astrophysics Data System (ADS)

    Majewski, Grzegorz; Rogula-Kozłowska, Wioletta

    2016-07-01

    Diurnal (24-h) samples of fine particulate matter (PM2.5, ambient particles with an aerodynamic diameter not greater than 2.5 μm) and soil samples were collected in an urban area in Warsaw, in winter. The samples were analysed for 24 elements with an Epsilon 5 spectrometer (PANalytical). The results were then arranged and compared with the results of research conducted earlier in Poland and other parts of the world. Afterwards, sources of ambient PM2.5 were identified and the share of each in the concentration of PM2.5 was evaluated by means of enrichment factor (EF) analysis, principal component analysis (PCA) and multi-linear regression analysis (MLRA). The results were interpreted using a detailed analysis of correlations between diurnal concentrations of PM2.5, PM2.5-elements, and of changes in meteorological conditions. The winter average ambient concentration of PM2.5 in Warsaw, was 10.7 ± 7.5 μg/m3 and was much lower than in the other sites in Poland. In Warsaw, regardless of the concentration of PM2.5, the concentrations of certain PM2.5-bound elements, mainly toxic, were high, e.g. the average ambient concentrations of PM2.5-bound Se, As, Co, V, Cd and Ni were 12.7 ± 30.5, 10.6 ± 34.4, 9.4 ± 13.7, 15.1 ± 32.7, 9.6 ± 22.2 and 3.5 ± 5.0 ng/m3, respectively. The elemental composition and concentrations of PM2.5 appeared to be influenced mainly by the anthropogenic emissions (energy production based on coal and biomass combustion, whose mean contribution to the concentration of PM2.5 was 18.4 %, and energy production based on oil combustion with a contribution of 9.9 % in PM2.5). A mixture of soil matter and road dust was also identified in PM2.5 (8 %). The mean contribution of traffic (exhaust) emissions to the concentration of PM2.5 in an urban area, selected as representative of the Warsaw conurbation, was assessed at 15.4 %.

  18. Host Factors That Interact with the Pestivirus N-Terminal Protease, Npro, Are Components of the Ribonucleoprotein Complex

    PubMed Central

    Jefferson, Matthew; Donaszi-Ivanov, Andras; Pollen, Sean; Dalmay, Tamas; Saalbach, Gerhard

    2014-01-01

    ABSTRACT The viral N-terminal protease Npro of pestiviruses counteracts cellular antiviral defenses through inhibition of IRF3. Here we used mass spectrometry to identify a new role for Npro through its interaction with over 55 associated proteins, mainly ribosomal proteins and ribonucleoproteins, including RNA helicase A (DHX9), Y-box binding protein (YBX1), DDX3, DDX5, eIF3, IGF2BP1, multiple myeloma tumor protein 2, interleukin enhancer binding factor 3 (IEBP3), guanine nucleotide binding protein 3, and polyadenylate-binding protein 1 (PABP-1). These are components of the translation machinery, ribonucleoprotein particles (RNPs), and stress granules. Significantly, we found that stress granule formation was inhibited in MDBK cells infected with a noncytopathic bovine viral diarrhea virus (BVDV) strain, Kyle. However, ribonucleoproteins binding to Npro did not inhibit these proteins from aggregating into stress granules. Npro interacted with YBX1 though its TRASH domain, since the mutant C112R protein with an inactive TRASH domain no longer redistributed to stress granules. Interestingly, RNA helicase A and La autoantigen relocated from a nuclear location to form cytoplasmic granules with Npro. To address a proviral role for Npro in RNP granules, we investigated whether Npro affected RNA interference (RNAi), since interacting proteins are involved in RISC function during RNA silencing. Using glyceraldehyde-3-phosphate dehydrogenase (GAPDH) silencing with small interfering RNAs (siRNAs) followed by Northern blotting of GAPDH, expression of Npro had no effect on RNAi silencing activity, contrasting with other viral suppressors of interferon. We propose that Npro is involved with virus RNA translation in the cytoplasm for virus particle production, and when translation is inhibited following stress, it redistributes to the replication complex. IMPORTANCE Although the pestivirus N-terminal protease, Npro, has been shown to have an important role in degrading IRF3 to

  19. Saturn's largest ring.

    PubMed

    Verbiscer, Anne J; Skrutskie, Michael F; Hamilton, Douglas P

    2009-10-22

    Most planetary rings in the Solar System lie within a few radii of their host body, because at these distances gravitational accelerations inhibit satellite formation. The best known exceptions are Jupiter's gossamer rings and Saturn's E ring, broad sheets of dust that extend outward until they fade from view at five to ten planetary radii. Source satellites continuously supply the dust, which is subsequently lost in collisions or by radial transport. Here we report that Saturn has an enormous ring associated with its outer moon Phoebe, extending from at least 128R(S) to 207R(S) (Saturn's radius R(S) is 60,330 km). The ring's vertical thickness of 40R(S) matches the range of vertical motion of Phoebe along its orbit. Dynamical considerations argue that these ring particles span the Saturnian system from the main rings to the edges of interplanetary space. The ring's normal optical depth of approximately 2 x 10(-8) is comparable to that of Jupiter's faintest gossamer ring, although its particle number density is several hundred times smaller. Repeated impacts on Phoebe, from both interplanetary and circumplanetary particle populations, probably keep the ring populated with material. Ring particles smaller than centimetres in size slowly migrate inward and many of them ultimately strike the dark leading face of Iapetus.

  20. The largest fossil rodent

    PubMed Central

    Rinderknecht, Andrés; Blanco, R. Ernesto

    2008-01-01

    The discovery of an exceptionally well-preserved skull permits the description of the new South American fossil species of the rodent, Josephoartigasia monesi sp. nov. (family: Dinomyidae; Rodentia: Hystricognathi: Caviomorpha). This species with estimated body mass of nearly 1000 kg is the largest yet recorded. The skull sheds new light on the anatomy of the extinct giant rodents of the Dinomyidae, which are known mostly from isolated teeth and incomplete mandible remains. The fossil derives from San José Formation, Uruguay, usually assigned to the Pliocene–Pleistocene (4–2 Myr ago), and the proposed palaeoenvironment where this rodent lived was characterized as an estuarine or deltaic system with forest communities. PMID:18198140

  1. Mechanical Stability and Reversible Fracture of Vault Particles

    PubMed Central

    Llauró, Aida; Guerra, Pablo; Irigoyen, Nerea; Rodríguez, José F.; Verdaguer, Núria; de Pablo, Pedro J.

    2014-01-01

    Vaults are the largest ribonucleoprotein particles found in eukaryotic cells, with an unclear cellular function and promising applications as vehicles for drug delivery. In this article, we examine the local stiffness of individual vaults and probe their structural stability with atomic force microscopy under physiological conditions. Our data show that the barrel, the central part of the vault, governs both the stiffness and mechanical strength of these particles. In addition, we induce single-protein fractures in the barrel shell and monitor their temporal evolution. Our high-resolution atomic force microscopy topographies show that these fractures occur along the contacts between two major vault proteins and disappear over time. This unprecedented systematic self-healing mechanism, which enables these particles to reversibly adapt to certain geometric constraints, might help vaults safely pass through the nuclear pore complex and potentiate their role as self-reparable nanocontainers. PMID:24507609

  2. The largest bacterium.

    PubMed

    Angert, E R; Clements, K D; Pace, N R

    1993-03-18

    The large, morphologically peculiar microorganism Epulopiscium fishelsoni inhabits the intestinal tract of Acanthurus nigrofuscus, a brown surgeonfish (family Acanthuridae) from the Red Sea. Similar microorganisms have been found in surgeonfish species from the Great Barrier Reef. As these microorganisms have only been seen in surgeonfish and no free-living forms have been found, they are considered to be specific symbionts of surgeonfish, although the nature of the symbiosis is unclear. Initial reports considered them to be eukaryotic protists, based primarily on their size, with individuals being larger than 600 microns by 80 microns. But their cellular morphology in the electron microscope is more like that of bacterial than eukaryotic cells. To resolve the nature of these symbionts, we have isolated the genes encoding the small subunit ribosomal RNA from two morphotypes and used them in a phylogenetic analysis. In situ hybridization with oligonucleotide probes based on the cloned rRNA sequences confirmed the source of the rRNA genes. Our result identify the symbionts as members of the low-(G+C) Gram-positive group of bacteria. They are therefore the largest bacteria to be described so far.

  3. Autoantibodies against small nucleolar ribonucleoprotein complexes and their clinical associations

    PubMed Central

    VAN EENENNAAM, H; VOGELZANGS, J H P; BISSCHOPS, L; TE BOOME, L C J; SEELIG, H P; RENZ, M; DE ROOIJ, D -J; BROUWER, R; PLUK, H; PRUIJN, G J M; VAN VENROOIJ, W J; VAN DEN HOOGEN, F H J

    2002-01-01

    Sera from patients suffering from systemic autoimmune diseases such as systemic lupus erythematosus (SLE) and systemic sclerosis (SSc) have been shown to contain reactivities to nuclear components. Autoantibodies specifically targeting nucleolar antigens are found most frequently in patients suffering from SSc or SSc overlap syndromes. We determined the prevalence and clinical significance of autoantibodies directed to nucleolar RNA-protein complexes, the so-called small nucleolar ribonucleoprotein complexes (snoRNPs). A total of 172 patient sera with antinucleolar antibodies were analysed by immunoprecipitation. From 100 of these patients clinical information was obtained by chart review. Autoantibodies directed to snoRNPs were detected not only in patients suffering from SSc and primary Raynaud's phenomenon (RP), but also in patients suffering from SLE, rheumatoid arthritis (RA) and myositis (PM/DM). Antibodies against box C/D small snoRNPs can be subdivided in antifibrillarin positive and antifibrillarin negative reactivity. Antifibrillarin-positive patient sera were associated with a poor prognosis in comparison with antifibrillarin negative (reactivity with U3 or U8 snoRNP only) patient sera. Anti-Th/To autoantibodies were associated with SSc, primary RP and SLE and were found predominantly in patients suffering from decreased co-diffusion and oesophagus motility and xerophthalmia. For the first time autoantibodies that recognize box H/ACA snoRNPs are described, identifying this class of snoRNPs as a novel autoantigenic activity. Taken together, our data show that antinucleolar patient sera directed to small nucleolar ribonucleoprotein complexes are found frequently in other diseases than SSc and that categorization of diagnoses and clinical manifestations based on autoantibody profiles seems particularly informative in patient sera recognizing box C/D snoRNPs. PMID:12452846

  4. Largest Solar Flare on Record

    NASA Technical Reports Server (NTRS)

    2001-01-01

    The largest solar flare ever recorded occurred at 4:51 p.m. EDT, on Monday, April 2, 2001. as Observed by the Solar and Heliospheric Observatory (SOHO) satellite. Solar flares, among the solar systems mightiest eruptions, are tremendous explosions in the atmosphere of the Sun capable of releasing as much energy as a billion megatons of TNT. Caused by the sudden release of magnetic energy, in just a few seconds, solar flares can accelerate solar particles to very high velocities, almost to the speed of light, and heat solar material to tens of millions of degrees. The recent explosion from the active region near the sun's northwest limb hurled a coronal mass ejection into space at a whopping speed of roughly 7.2 million kilometers per hour. Luckily, the flare was not aimed directly towards Earth. Second to the most severe R5 classification of radio blackout, this flare produced an R4 blackout as rated by the NOAA SEC. This classification measures the disruption in radio communications. Launched December 2, 1995 atop an ATLAS-IIAS expendable launch vehicle, the SOHO is a cooperative effort involving NASA and the European Space Agency (ESA). (Image courtesy NASA Goddard SOHO Project office)

  5. Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA

    SciTech Connect

    Liang, Bo; Zhou, Jing; Kahen, Elliot; Terns, Rebecca M.; Terns, Michael P.; Li, Hong

    2009-09-29

    Box H/ACA small nucleolar and Cajal body ribonucleoprotein particles comprise the most complex pseudouridine synthases and are essential for ribosome and spliceosome maturation. The multistep and multicomponent-mediated enzyme mechanism remains only partially understood. Here we report a crystal structure at 2.35 {angstrom} of a substrate-bound functional archaeal enzyme containing three of the four proteins, Cbf5, Nop10 and L7Ae, and a box H/ACA RNA that reveals detailed information about the protein-only active site. The substrate RNA, containing 5-fluorouridine at the modification position, is fully docked and catalytically rearranged by the enzyme in a manner similar to that seen in two stand-alone pseudouridine synthases. Structural analysis provides a mechanism for plasticity in the diversity of guide RNA sequences used and identifies a substrate-anchoring loop of Cbf5 that also interacts with Gar1 in unliganded structures. Activity analyses of mutated proteins and RNAs support the structural findings and further suggest a role of the Cbf5 loop in regulation of enzyme activity.

  6. Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA.

    PubMed

    Liang, Bo; Zhou, Jing; Kahen, Elliot; Terns, Rebecca M; Terns, Michael P; Li, Hong

    2009-07-01

    Box H/ACA small nucleolar and Cajal body ribonucleoprotein particles comprise the most complex pseudouridine synthases and are essential for ribosome and spliceosome maturation. The multistep and multicomponent-mediated enzyme mechanism remains only partially understood. Here we report a crystal structure at 2.35 A of a substrate-bound functional archaeal enzyme containing three of the four proteins, Cbf5, Nop10 and L7Ae, and a box H/ACA RNA that reveals detailed information about the protein-only active site. The substrate RNA, containing 5-fluorouridine at the modification position, is fully docked and catalytically rearranged by the enzyme in a manner similar to that seen in two stand-alone pseudouridine synthases. Structural analysis provides a mechanism for plasticity in the diversity of guide RNA sequences used and identifies a substrate-anchoring loop of Cbf5 that also interacts with Gar1 in unliganded structures. Activity analyses of mutated proteins and RNAs support the structural findings and further suggest a role of the Cbf5 loop in regulation of enzyme activity.

  7. N-methylation of the heterogeneous nuclear ribonucleoproteins in HeLa cells

    SciTech Connect

    Rieker, J.P.

    1984-01-01

    Several of the core proteins on the 40S heterogeneous nuclear ribonucleoprotein particles (hnRNP) from HeLa cells contain N/sup G/,N/sup G/-dimethyl-L-arginine (uDMA). 3-deazaadenosine (c/sup 3/Ado), an inhibitor of and substrate for s-adenosyl-L-homocysteine hydrolase, has been used to study the methylation patterns of the individual polypeptides. Trimethyllysine and uDMA formation in total cellular protein were inhibited in the presence of the drug while other methylated basic amino acids were unaffected. This inhibition was reversed within 60 min after removal of the drug from the medium. Monolayer HeLa cultures were incubated with (methyl-/sup 3/H)-L-methoinine for 12 hours in the presence of 50 uM c/sup 3/Ado. Purified particles were obtained by centrifugation of nuclear extracts on sucrose density gradients. The core proteins were isolated by two-dimensional gel electrophoresis, acid hydrolyzed and analyzed for radioactivity incorporated into methionine and methylated basic amino acids. The ratio of radioactivity incorporated into uDMA relative to that into methionine for the two major particle proteins with molecular weights of 31,000 (A/sub 1/) and 43,000 (A/sub 2/) was about 2.0 and 0.2 in control cultures. In the presence of c/sup 3/Ado, these ratios were depressed 60 to 80%. Results of pulse-chase experiments suggested that A/sub 1/ and A/sub 2/ are metabolically stable proteins (t/sub 0.5/ > 75 hr), whether or not the proteins were undermethylated. Monomethyl-L-arginine may be a precursor in the formation of u-DMA.

  8. Ribonucleoproteins in Archaeal Pre-rRNA Processing and Modification

    PubMed Central

    Yip, W. S. Vincent; Vincent, Nicholas G.; Baserga, Susan J.

    2013-01-01

    Given that ribosomes are one of the most important cellular macromolecular machines, it is not surprising that there is intensive research in ribosome biogenesis. Ribosome biogenesis is a complex process. The maturation of ribosomal RNAs (rRNAs) requires not only the precise cleaving and folding of the pre-rRNA but also extensive nucleotide modifications. At the heart of the processing and modifications of pre-rRNAs in Archaea and Eukarya are ribonucleoprotein (RNP) machines. They are called small RNPs (sRNPs), in Archaea, and small nucleolar RNPs (snoRNPs), in Eukarya. Studies on ribosome biogenesis originally focused on eukaryotic systems. However, recent studies on archaeal sRNPs have provided important insights into the functions of these RNPs. This paper will introduce archaeal rRNA gene organization and pre-rRNA processing, with a particular focus on the discovery of the archaeal sRNP components, their functions in nucleotide modification, and their structures. PMID:23554567

  9. Maximizing mutagenesis with solubilized CRISPR-Cas9 ribonucleoprotein complexes.

    PubMed

    Burger, Alexa; Lindsay, Helen; Felker, Anastasia; Hess, Christopher; Anders, Carolin; Chiavacci, Elena; Zaugg, Jonas; Weber, Lukas M; Catena, Raul; Jinek, Martin; Robinson, Mark D; Mosimann, Christian

    2016-06-01

    CRISPR-Cas9 enables efficient sequence-specific mutagenesis for creating somatic or germline mutants of model organisms. Key constraints in vivo remain the expression and delivery of active Cas9-sgRNA ribonucleoprotein complexes (RNPs) with minimal toxicity, variable mutagenesis efficiencies depending on targeting sequence, and high mutation mosaicism. Here, we apply in vitro assembled, fluorescent Cas9-sgRNA RNPs in solubilizing salt solution to achieve maximal mutagenesis efficiency in zebrafish embryos. MiSeq-based sequence analysis of targeted loci in individual embryos using CrispRVariants, a customized software tool for mutagenesis quantification and visualization, reveals efficient bi-allelic mutagenesis that reaches saturation at several tested gene loci. Such virtually complete mutagenesis exposes loss-of-function phenotypes for candidate genes in somatic mutant embryos for subsequent generation of stable germline mutants. We further show that targeting of non-coding elements in gene regulatory regions using saturating mutagenesis uncovers functional control elements in transgenic reporters and endogenous genes in injected embryos. Our results establish that optimally solubilized, in vitro assembled fluorescent Cas9-sgRNA RNPs provide a reproducible reagent for direct and scalable loss-of-function studies and applications beyond zebrafish experiments that require maximal DNA cutting efficiency in vivo.

  10. Higher Expression of the Heterogeneous Nuclear Ribonucleoprotein K in Melanoma

    PubMed Central

    Wen, Fushi; Shen, Alex; Shanas, Reneé; Bhattacharyya, Achyut; Lian, Fangru; Hostetter, Galen; Shi, Jiaqi

    2010-01-01

    Background The heterogeneous nuclear ribonucleoprotein (hnRNP) K is an essential RNA and DNA binding protein involved in gene expression and signal transduction. The role of hnRNP K in cancer is relatively understudied. However, several cellular functions strongly indicate that hnRNP K is involved in tumorigenesis. Oncogenes c-Src, c-myc, and eIF4E are regulated by hnRNP K. We have shown an increased cytoplasmic hnRNP K in pancreatic cancer. In the present study, we investigated the altered expression of hnRNP K protein and its correlation with p-ERK in melanoma using human melanoma cell lines and tissue microarray. Materials and Methods The protein levels of hnRNP K and p-ERK in 8 human melanoma cell lines and a melanoma progression tissue microarray containing 80 melanoma, 23 dysplastic nevi, and 14 benign nevi specimens were analyzed using Western blot and immunohistochemistry analysis. hnRNP K was knocked down by siRNA, and its effect on melanoma cells was assessed. Results We showed a higher hnRNP K protein level in both melanoma cell lines and melanoma tissue specimens, which correlated with a higher c-myc expression. An increase in the cytoplasmic hnRNP K and eIF4E protein levels in melanoma cells is also seen. p-ERK level was also higher in dysplastic nevi and melanoma tissues, but did not correlate with hnRNP K protein level. We then demonstrated that knocking down of hnRNP K by siRNA inhibited melanoma cell growth and colony formation, as well as c-myc expression. Conclusions hnRNP K expression correlated with melanoma and may play a role in melanoma tumorigenesis. PMID:20499280

  11. Interaction cloning and characterization of RoBPI, a novel protein binding to human Ro ribonucleoproteins.

    PubMed Central

    Bouffard, P; Barbar, E; Brière, F; Boire, G

    2000-01-01

    Human Ro ribonucleoproteins (RNPs) are autoantigenic particles of unknown function(s) that consist of a 60-kDa protein (Ro60) associated with one hY RNA (hY1-5). Using a modified yeast three-hybrid system, named RNP interaction trap assay (RITA), we cloned a novel Ro RNP-binding protein (RoBPI), based on its property to interact in vivo in yeast with an RNP complex made of recombinant Ro60 (rRo60) protein and hY5 (rhY5) RNA. RoBPI cDNA contains three conserved RNA recognition motifs (RRM) and is present as a family of isoforms differing slightly at their 5' end. The 2.0-kb RoBPI mRNA was detected in all human tissues tested. Highly homologous cDNA sequences were found in banks of expressed sequence tags (ESTs) from mice. Two-hybrid, three-hybrid, and RITA experiments respectively established that 60 kDa RoBPI did not interact in yeast with rRo60 alone, with rhY5 RNA alone, or with bait RNPs consisting of rRo60 and recombinant hY1, hY3, or hY4 RNAs. RoBPI coimmunoprecipitated with Ro RNPs from HeLa cell extracts and partially colocalized with Ro60 in nuclei of cultured cells. Because hY5 RNA and RohY5 RNPs are recent evolutionary additions seen only in primates, but RoBPI seems more conserved, their interaction may represent a gain of function for Ro RNPs. Alternatively, interaction of RohY5 RNPs with RoBPI may have no functional bearing, but may underlie some of the unique biochemical and immunological properties of these RNPs. PMID:10668799

  12. Largest impact craters on Venus

    NASA Technical Reports Server (NTRS)

    Ivanov, B. A.; Weitz, C. M.; Basilevsky, A. T.

    1992-01-01

    High-resolution radar images from the Magellan spacecraft have allowed us to perform a detailed study on 25 large impact craters on Venus with diameters from 70 to 280 km. The dimension of these large craters is comparable with the characteristic thickness of the venusian lithosphere and the atmospheric scale height. Some physical parameters for the largest impact craters on Venus (LICV), such as depth, ring/diameter ratio, and range of ballistic ejecta deposits, have been obtained from the SAR images and the altimetry dataset produced by MIT. Data related to each of these parameters is discussed.

  13. Tissue-specific expression and cDNA cloning of small nuclear ribonucleoprotein-associated polypeptide N

    SciTech Connect

    McAllister, G.; Amara, S.G.; Lerner, M.R. )

    1988-07-01

    Sera from some patients with systemic lupus erythematosus and other autoimmune diseases have antibodies against nuclear antigens. An example is anti-Sm sera, which recognize proteins associated with small nuclear RNA molecules (small nuclear ribonucleoprotein (snRNP) particles). In this paper anti-Sm sera were used to probe immunoblots of various rat tissues. A previously unidentified M{sub r} 28,000 polypeptide was recognized by these anti-Sm sera. This polypeptide, referred to as N, is expressed in a tissue-specific manner, being most abundant in rat brain, less so in heart, and undetectable in the other tissues examined. Immunoprecipitation experiments using antibodies directed against the cap structure of small nuclear RNAs have demonstrated that N is a snRNP-associated polypeptide. Anti-Sm serum was also used to isolate a partial cDNA clone ({lambda}rb91) from a rat brain phage {lambda}gt11 cDNA expression library. A longer cDNA clone was obtained by rescreening the library with {lambda}rb91. In vitro transcription and subsequent translation of this subcloned, longer insert (pGMA2) resulted in a protein product with the same electrophoretic and immunological properties as N, confirming that pGMA2 encodes N. The tissue distribution of N and the involvement of snRNP particles in nuclear pre-mRNA processing may imply a role for N in tissue-specific pre-mRNA splicing.

  14. Rehabilitating China's largest inland river.

    PubMed

    Li, Yiqing; Chen, Yaning; Zhang, Yaoqi; Xia, Yang

    2009-06-01

    Wetlands are particularly important for conserving China's biodiversity but riparian wetlands in the Tarim River basin in western China have been reduced by 46% during the last 3 decades. The world's largest habitat for Populus euphratica, which is in the Tarim River basin, significantly shrank. To protect and restore the deteriorated ecosystems along the Tarim River and its associated wetlands, China's government initiated a multimillion dollar river restoration project to release water from upper dams to the dried-up lower reaches of the Tarim River starting in 2000. We monitored the responses of groundwater and vegetation to water recharge in the lower reaches of the river from 2000 to 2006 by establishing nine 1000-m-long transects perpendicular to the river at intervals of 20-45 km along the 320-km river course below the Daxihaizi Reservoir, the source of water conveyance, to Lake Taitema, the terminus of the Tarim River. Water recharges from the Daxihaizi Reservoir to the lower reaches of the Tarim River significantly increased groundwater levels and vegetation coverage at all monitoring sites along the river. The mean canopy size of the endangered plant species P. euphratica doubled after 6 years of water recharge. Some rare migrating birds returned to rest on the restored wetlands in summer along the lower reaches of the Tarim River. The biggest challenge facing decision makers, however, is to balance water allocation and water rights between agricultural and natural ecosystems in a sustainable way. A large number of inhabitants in the Tarim Basin depend on these limited water resources for a living. At the same time, the endangered ecosystems need to be protected. Given the ecological, socioeconomic, and sociopolitical realities in the Tarim Basin, adaptive water policies and strategies are needed for water allocation in these areas of limited water resources.

  15. Rehabilitating China's largest inland river.

    PubMed

    Li, Yiqing; Chen, Yaning; Zhang, Yaoqi; Xia, Yang

    2009-06-01

    Wetlands are particularly important for conserving China's biodiversity but riparian wetlands in the Tarim River basin in western China have been reduced by 46% during the last 3 decades. The world's largest habitat for Populus euphratica, which is in the Tarim River basin, significantly shrank. To protect and restore the deteriorated ecosystems along the Tarim River and its associated wetlands, China's government initiated a multimillion dollar river restoration project to release water from upper dams to the dried-up lower reaches of the Tarim River starting in 2000. We monitored the responses of groundwater and vegetation to water recharge in the lower reaches of the river from 2000 to 2006 by establishing nine 1000-m-long transects perpendicular to the river at intervals of 20-45 km along the 320-km river course below the Daxihaizi Reservoir, the source of water conveyance, to Lake Taitema, the terminus of the Tarim River. Water recharges from the Daxihaizi Reservoir to the lower reaches of the Tarim River significantly increased groundwater levels and vegetation coverage at all monitoring sites along the river. The mean canopy size of the endangered plant species P. euphratica doubled after 6 years of water recharge. Some rare migrating birds returned to rest on the restored wetlands in summer along the lower reaches of the Tarim River. The biggest challenge facing decision makers, however, is to balance water allocation and water rights between agricultural and natural ecosystems in a sustainable way. A large number of inhabitants in the Tarim Basin depend on these limited water resources for a living. At the same time, the endangered ecosystems need to be protected. Given the ecological, socioeconomic, and sociopolitical realities in the Tarim Basin, adaptive water policies and strategies are needed for water allocation in these areas of limited water resources. PMID:22748091

  16. Isolation of Cognate Cellular and Viral Ribonucleoprotein Complexes of HIV-1 RNA Applicable to Proteomic Discovery and Molecular Investigations.

    PubMed

    Singh, Deepali; Boeras, Ioana; Singh, Gatikrushna; Boris-Lawrie, Kathleen

    2016-01-01

    All decisions affecting the life cycle of human immunodeficiency virus (HIV-1) RNA are executed by ribonucleoprotein complexes (RNPs). HIV-1 RNA cycles through a progression of host RNPs composed of RNA-binding proteins regulating all stages of synthesis, processing, nuclear transport, translation, decay, and co-localization with assembling virions. RNA affinity chromatography is a versatile method to identify RNA-binding proteins to investigate the molecular basis of viral and cellular posttranscriptional control of gene expression. The bait is a HIV-1 RNA motif immobilized on a solid support, typically magnetic or Sepharose beads. The prey is pre-formed RNPs admixed in lysate from cells or concentrated virus particles. The methodology distinguishes high-affinity RNA-protein interactions from low-affinity complexes by increases in ionic strength during progressive elution cycles. Here, we describe RNA affinity chromatography of the 5' untranslated region of HIV-1, obtaining mixtures of high-affinity RNA binding proteins suitable for mass spectrometry and proteome identification.

  17. Heterogeneous nuclear ribonucleoprotein K represses the production of pro-apoptotic Bcl-xS splice isoform.

    PubMed

    Revil, Timothée; Pelletier, Jordan; Toutant, Johanne; Cloutier, Alexandre; Chabot, Benoit

    2009-08-01

    The Bcl-x pre-mRNA is alternatively spliced to produce the anti-apoptotic Bcl-x(L) and the pro-apoptotic Bcl-x(S) isoforms. By performing deletion mutagenesis on a human Bcl-x minigene, we have identified a novel exonic element that controls the use of the 5' splice site of Bcl-x(S). The proximal portion of this element acts as a repressor and is located downstream of an enhancer. Further mutational analysis provided a detailed topological map of the regulatory activities revealing a sharp transition between enhancer and repressor sequences. Portions of the enhancer can function when transplanted in another alternative splicing unit. Chromatography and immunoprecipitation assays indicate that the silencer element interacts with heterogeneous ribonucleoprotein particle (hnRNP) K, consistent with the presence of putative high affinity sites for this protein. Finally, down-regulation of hnRNP K by RNA interference enhanced splicing to Bcl-x(S), an effect seen only when the sequences bound by hnRNP K are present. Our results therefore document a clear role for hnRNP K in preventing the production of the pro-apoptotic Bcl-x(S) splice isoform.

  18. A seasonal trend of single scattering albedo in southern African biomass-burning particles: Implications for satellite products and estimates of emissions for the world's largest biomass-burning source

    NASA Astrophysics Data System (ADS)

    Eck, T. F.; Holben, B. N.; Reid, J. S.; Mukelabai, M. M.; Piketh, S. J.; Torres, O.; Jethva, H. T.; Hyer, E. J.; Ward, D. E.; Dubovik, O.; Sinyuk, A.; Schafer, J. S.; Giles, D. M.; Sorokin, M.; Smirnov, A.; Slutsker, I.

    2013-06-01

    As a representative site of the southern African biomass-burning region, sun-sky data from the 15 year Aerosol Robotic Network (AERONET) deployment at Mongu, Zambia, was analyzed. For the biomass-burning season months (July-November), we investigate seasonal trends in aerosol single scattering albedo (SSA), aerosol size distributions, and refractive indices from almucantar sky scan retrievals. The monthly mean single scattering albedo at 440 nm in Mongu was found to increase significantly from ~0.84 in July to ~0.93 in November (from 0.78 to 0.90 at 675 nm in these same months). There was no significant change in particle size, in either the dominant accumulation or secondary coarse modes during these months, nor any significant trend in the Ångström exponent (440-870 nm; r2 = 0.02). A significant downward seasonal trend in imaginary refractive index (r2 = 0.43) suggests a trend of decreasing black carbon content in the aerosol composition as the burning season progresses. Similarly, burning season SSA retrievals for the Etosha Pan, Namibia AERONET site also show very similar increasing single scattering albedo values and decreasing imaginary refractive index as the season progresses. Furthermore, retrievals of SSA at 388 nm from the Ozone Monitoring Instrument satellite sensor show similar seasonal trends as observed by AERONET and suggest that this seasonal shift is widespread throughout much of southern Africa. A seasonal shift in the satellite retrieval bias of aerosol optical depth from the Moderate Resolution Imaging Spectroradiometer collection 5 dark target algorithm is consistent with this seasonal SSA trend since the algorithm assumes a constant value of SSA. Multi-angle Imaging Spectroradiometer, however, appears less sensitive to the absorption-induced bias.

  19. A Seasonal Trend of Single Scattering Albedo in Southern African Biomass-burning Particles: Implications for Satellite Products and Estimates of Emissions for the World's Largest Biomass-burning Source

    NASA Technical Reports Server (NTRS)

    Eck, T. F.; Holben, B. N.; Reid, J. S.; Mukelabai, M. M.; Piketh, S. J.; Torres, O.; Jethva, H. T.; Hyer, E. J.; Ward, D. E.; Dubovik, O.; Sinyuk, A.; Schafer, J. S.; Giles, D. M.; Sorokin, M.; Smirnov, A.; Slutsker, I.

    2013-01-01

    As a representative site of the southern African biomass-burning region, sun-sky data from the 15 year Aerosol Robotic Network (AERONET) deployment at Mongu, Zambia, was analyzed. For the biomass-burning season months (July-November), we investigate seasonal trends in aerosol single scattering albedo (SSA), aerosol size distributions, and refractive indices from almucantar sky scan retrievals. The monthly mean single scattering albedo at 440 nm in Mongu was found to increase significantly from approx.. 0.84 in July to approx. 0.93 in November (from 0.78 to 0.90 at 675 nm in these same months). There was no significant change in particle size, in either the dominant accumulation or secondary coarse modes during these months, nor any significant trend in the Angstrom exponent (440-870 nm; r(exp 2) = 0.02). A significant downward seasonal trend in imaginary refractive index (r(exp 2) = 0.43) suggests a trend of decreasing black carbon content in the aerosol composition as the burning season progresses. Similarly, burning season SSA retrievals for the Etosha Pan, Namibia AERONET site also show very similar increasing single scattering albedo values and decreasing imaginary refractive index as the season progresses. Furthermore, retrievals of SSA at 388 nm from the Ozone Monitoring Instrument satellite sensor show similar seasonal trends as observed by AERONET and suggest that this seasonal shift is widespread throughout much of southern Africa. A seasonal shift in the satellite retrieval bias of aerosol optical depth from the Moderate Resolution Imaging Spectroradiometer collection 5 dark target algorithm is consistent with this seasonal SSA trend since the algorithm assumes a constant value of SSA. Multi-angle Imaging Spectroradiometer, however, appears less sensitive to the absorption-induced bias.

  20. Autoantibody to Th ribonucleoprotein (nucleolar 7-2 RNA protein particle) in patients with systemic sclerosis

    SciTech Connect

    Okano, Y.; Medsger, T.A. Jr. )

    1990-12-01

    We studied sera of 371 consecutive new patients with systemic sclerosis (SSc; scleroderma) who were first evaluated during 1984-1988. All sera were tested for antinuclear antibodies by immunofluorescence staining using HEp-2 cells as substrate. We excluded 219 sera showing dark nucleoli and screened for antibodies to Th in the remaining 152 sera by immunoprecipitation of a 32P-labeled HeLa cell extract. Fifteen (4.0%) of 371 sera were anti-Th+. Anti-Th antibodies were present in 14 (8.4%) of 167 SSc patients with limited cutaneous involvement, in 1 of 167 with diffuse cutaneous involvement, and in 0 of 37 with SSc overlap syndrome. Among 244 controls with other connective tissue diseases, anti-Th was detected in only 3 patients, all having primary Raynaud's phenomenon of less than 2 years duration. In the subgroup with SSc with limited cutaneous involvement, the 14 anti-Th+ patients had a significantly greater frequency of puffy fingers, small bowel involvement, and hypothyroidism, and a significantly lower frequency of arthralgia and/or arthritis. Their cumulative survival rate from the time of onset of symptoms was lower than that for anti-Th- patients (78% versus 91% at 10 years), primarily due to 3 deaths from pulmonary arterial hypertension (2 from primary pulmonary hypertension and 1 from pulmonary hypertension secondary to pulmonary interstitial fibrosis). Serum anti-Th antibodies are present almost exclusively in patients with SSc with limited cutaneous involvement or in those with primary Raynaud's phenomenon whose disease may evolve to SSc with limited cutaneous involvement, and these antibodies may identify those patients who are at greater risk for reduced survival.

  1. Purification and visualization of influenza a viral ribonucleoprotein complexes.

    PubMed

    Wu, Winco W H; Weaver, Lindsay L; Panté, Nelly

    2009-01-01

    The influenza A viral genome consists of eight negative-sense, single stranded RNA molecules, individually packed with multiple copies of the influenza A nucleoprotein (NP) into viral ribonulceoprotein particles (vRNPs). The influenza vRNPs are enclosed within the viral envelope. During cell entry, however, these vRNP complexes are released into the cytoplasm, where they gain access to the host nuclear transport machinery. In order to study the nuclear import of influenza vRNPs and the replication of the influenza genome, it is useful to work with isolated vRNPs so that other components of the virus do not interfere with these processes. Here, we describe a procedure to purify these vRNPs from the influenza A virus. The procedure starts with the disruption of the influenza A virion with detergents in order to release the vRNP complexes from the enveloped virion. The vRNPs are then separated from the other components of the influenza A virion on a 33-70% discontinuous glycerol gradient by velocity sedimentation. The fractions obtained from the glycerol gradient are then analyzed on via SDS-PAGE after staining with Coomassie blue. The peak fractions containing NP are then pooled together and concentrated by centrifugation. After concentration, the integrity of the vRNPs is verified by visualization of the vRNPs by transmission electron microscopy after negative staining. The glycerol gradient purification is a modification of that from Kemler et al. (1994)(1), and the negative staining has been performed by Wu et al. (2007).(2). PMID:19229188

  2. Identification of a Chloroplast Ribonucleoprotein Complex Containing Trans-splicing Factors, Intron RNA, and Novel Components*

    PubMed Central

    Jacobs, Jessica; Marx, Christina; Kock, Vera; Reifschneider, Olga; Fränzel, Benjamin; Krisp, Christoph; Wolters, Dirk; Kück, Ulrich

    2013-01-01

    Maturation of chloroplast psaA pre-mRNA from the green alga Chlamydomonas reinhardtii requires the trans-splicing of two split group II introns. Several nuclear-encoded trans-splicing factors are required for the correct processing of psaA mRNA. Among these is the recently identified Raa4 protein, which is involved in splicing of the tripartite intron 1 of the psaA precursor mRNA. Part of this tripartite group II intron is the chloroplast encoded tscA RNA, which is specifically bound by Raa4. Using Raa4 as bait in a combined tandem affinity purification and mass spectrometry approach, we identified core components of a multisubunit ribonucleoprotein complex, including three previously identified trans-splicing factors (Raa1, Raa3, and Rat2). We further detected tscA RNA in the purified protein complex, which seems to be specific for splicing of the tripartite group II intron. A yeast-two hybrid screen and co-immunoprecipitation identified chloroplast-localized Raa4-binding protein 1 (Rab1), which specifically binds tscA RNA from the tripartite psaA group II intron. The yeast-two hybrid system provides evidence in support of direct interactions between Rab1 and four trans-splicing factors. Our findings contribute to our knowledge of chloroplast multisubunit ribonucleoprotein complexes and are discussed in support of the generally accepted view that group II introns are the ancestors of the eukaryotic spliceosomal introns. PMID:23559604

  3. Distribution of Ribonucleoprotein and Protein-Only RNase P in Eukarya.

    PubMed

    Lechner, Marcus; Rossmanith, Walter; Hartmann, Roland K; Thölken, Clemens; Gutmann, Bernard; Giegé, Philippe; Gobert, Anthony

    2015-12-01

    RNase P is the endonuclease that removes 5' leader sequences from tRNA precursors. In Eukarya, separate RNase P activities exist in the nucleus and mitochondria/plastids. Although all RNase P enzymes catalyze the same reaction, the different architectures found in Eukarya range from ribonucleoprotein (RNP) enzymes with a catalytic RNA and up to 10 protein subunits to single-subunit protein-only RNase P (PRORP) enzymes. Here, analysis of the phylogenetic distribution of RNP and PRORP enzymes in Eukarya revealed 1) a wealth of novel P RNAs in previously unexplored phylogenetic branches and 2) that PRORP enzymes are more widespread than previously appreciated, found in four of the five eukaryal supergroups, in the nuclei and/or organelles. Intriguingly, the occurrence of RNP RNase P and PRORP seems mutually exclusive in genetic compartments of modern Eukarya. Our comparative analysis provides a global picture of the evolution and diversification of RNase P throughout Eukarya. PMID:26341299

  4. catRAPID signature: identification of ribonucleoproteins and RNA-binding regions

    PubMed Central

    Livi, Carmen Maria; Klus, Petr; Delli Ponti, Riccardo; Tartaglia, Gian Gaetano

    2016-01-01

    Motivation: Recent technological advances revealed that an unexpected large number of proteins interact with transcripts even if the RNA-binding domains are not annotated. We introduce catRAPID signature to identify ribonucleoproteins based on physico-chemical features instead of sequence similarity searches. The algorithm, trained on human proteins and tested on model organisms, calculates the overall RNA-binding propensity followed by the prediction of RNA-binding regions. catRAPID signature outperforms other algorithms in the identification of RNA-binding proteins and detection of non-classical RNA-binding regions. Results are visualized on a webpage and can be downloaded or forwarded to catRAPID omics for predictions of RNA targets. Availability and implementation: catRAPID signature can be accessed at http://s.tartaglialab.com/new_submission/signature. Contact: gian.tartaglia@crg.es or gian@tartaglialab.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26520853

  5. Insulin alters heterogeneous nuclear ribonucleoprotein K protein binding to DNA and RNA

    PubMed Central

    Ostrowski, J.; Kawata, Y.; Schullery, D. S.; Denisenko, O. N.; Higaki, Y.; Abrass, C. K.; Bomsztyk, K.

    2001-01-01

    The interaction of the multimodular heterogeneous nuclear ribonucleoprotein (hnRNP) K protein with many of its protein and nucleic acid partners is regulated by extracellular signals. Acting as a docking platform, K protein could link signal-transduction pathways to DNA- and RNA-directed processes such as transcription, mRNA processing, transport, and translation. Treatment of hepatocyte culture with insulin increased K protein tyrosine phosphorylation. Insulin altered K protein interaction with RNA and DNA in vitro. Administration of insulin into mice had similar effects on K protein in liver. Coimmunoprecipitations of RNA with K protein revealed preferential in vivo K protein binding of a subset of transcripts, including the insulin-inducible c-fos mRNA. These results suggest a class of insulin pathways that signal nucleic acid-directed processes that involve K protein. PMID:11470915

  6. tRNA Core Hypothesis for the Transition from the RNA World to the Ribonucleoprotein World

    PubMed Central

    de Farias, Savio T.; Rêgo, Thais G.; José, Marco V.

    2016-01-01

    Herein we present the tRNA core hypothesis, which emphasizes the central role of tRNAs molecules in the origin and evolution of fundamental biological processes. tRNAs gave origin to the first genes (mRNA) and the peptidyl transferase center (rRNA), proto-tRNAs were at the core of a proto-translation system, and the anticodon and operational codes then arose in tRNAs molecules. Metabolic pathways emerged from evolutionary pressures of the decoding systems. The transitions from the RNA world to the ribonucleoprotein world to modern biological systems were driven by three kinds of tRNAs transitions, to wit, tRNAs leading to both mRNA and rRNA. PMID:27023615

  7. Nuclear dynamics of influenza A virus ribonucleoproteins revealed by live-cell imaging studies

    SciTech Connect

    Loucaides, Eva M.; Kirchbach, Johann C. von; Foeglein, Agnes; Sharps, Jane; Fodor, Ervin; Digard, Paul

    2009-11-10

    The negative sense RNA genome of influenza A virus is transcribed and replicated in the nuclei of infected cells by the viral RNA polymerase. Only four viral polypeptides are required but multiple cellular components are potentially involved. We used fluorescence recovery after photobleaching (FRAP) to characterise the dynamics of GFP-tagged viral ribonucleoprotein (RNP) components in living cells. The nucleoprotein (NP) displayed very slow mobility that significantly increased on formation of transcriptionally active RNPs. Conversely, single or dimeric polymerase subunits showed fast nuclear dynamics that decreased upon formation of heterotrimers, suggesting increased interaction of the full polymerase complex with a relatively immobile cellular component(s). Treatment with inhibitors of cellular transcription indicated that in part, this reflected an interaction with cellular RNA polymerase II. Analysis of mutated influenza virus polymerase complexes further suggested that this was through an interaction between PB2 and RNA Pol II separate from PB2 cap-binding activity.

  8. A structurally plastic ribonucleoprotein complex mediates post-transcriptional gene regulation in HIV-1.

    PubMed

    Fernandes, Jason D; Booth, David S; Frankel, Alan D

    2016-07-01

    HIV replication requires the nuclear export of essential, intron-containing viral RNAs. To facilitate export, HIV encodes the viral accessory protein Rev which binds unspliced and partially spliced viral RNAs and creates a ribonucleoprotein complex that recruits the cellular Chromosome maintenance factor 1 export machinery. Exporting RNAs in this manner bypasses the necessity for complete splicing as a prerequisite for mRNA export, and allows intron-containing RNAs to reach the cytoplasm intact for translation and virus packaging. Recent structural studies have revealed that this entire complex exhibits remarkable plasticity at many levels of organization, including RNA folding, protein-RNA recognition, multimer formation, and host factor recruitment. In this review, we explore each aspect of plasticity from structural, functional, and possible therapeutic viewpoints. WIREs RNA 2016, 7:470-486. doi: 10.1002/wrna.1342 For further resources related to this article, please visit the WIREs website. PMID:26929078

  9. Antibodies to ribosomal ribonucleoprotein. Prevalence in systemic rheumatic diseases and partial characterization of the antigen.

    PubMed

    Cortés, J J; Mendoza, F; Reyes, P A

    1987-08-01

    The prevalence of antibodies to ribosomal ribonucleoproteins (rRNP) was studied in patients with rheumatic diseases. Seven patients had precipitating antibodies against rRNP, 6 had systemic lupus erythematosus, one had primary Sjögren's syndrome. Anti-rRNP was not present in mixed connective tissue disease, rheumatoid arthritis, progressive systemic sclerosis, CREST, primary Raynaud's or normal control sera. A partial immunological identity precipitin line was present between (U1) nRNP and rRNP, but these were distinct in physicochemical properties. Western blot analysis of ribosomal extract using anti-rRNP IgG revealed 2 polypeptides called rA and rB which appear to be the important antigenic determinants.

  10. Aggregation Properties of the Small Nuclear Ribonucleoprotein U1-70K in Alzheimer Disease*

    PubMed Central

    Diner, Ian; Hales, Chadwick M.; Bishof, Isaac; Rabenold, Lake; Duong, Duc M.; Yi, Hong; Laur, Oskar; Gearing, Marla; Troncoso, Juan; Thambisetty, Madhav; Lah, James J.; Levey, Allan I.; Seyfried, Nicholas T.

    2014-01-01

    Recent evidence indicates that U1-70K and other U1 small nuclear ribonucleoproteins are Sarkosyl-insoluble and associate with Tau neurofibrillary tangles selectively in Alzheimer disease (AD). Currently, the mechanisms underlying the conversion of soluble nuclear U1 small nuclear ribonucleoproteins into insoluble cytoplasmic aggregates remain elusive. Based on the biochemical and subcellular distribution properties of U1-70K in AD, we hypothesized that aggregated U1-70K itself or other biopolymers (e.g. proteins or nucleic acids) interact with and sequester natively folded soluble U1-70K into insoluble aggregates. Here, we demonstrate that total homogenates from AD brain induce soluble U1-70K from control brain or recombinant U1-70K to become Sarkosyl-insoluble. This effect was not dependent on RNA and did not correlate with detergent-insoluble Tau levels as AD homogenates with reduced levels of these components were still capable of inducing U1-70K aggregation. In contrast, proteinase K-treated AD homogenates and Sarkosyl-soluble AD fractions were unable to induce U1-70K aggregation, indicating that aggregated proteins in AD brain are responsible for inducing soluble U1-70K aggregation. It was determined that the C terminus of U1-70K, which harbors two disordered low complexity (LC) domains, is necessary for U1-70K aggregation. Moreover, both LC1 and LC2 domains were sufficient for aggregation. Finally, protein cross-linking and mass spectrometry studies demonstrated that a U1-70K fragment harboring the LC1 domain directly interacts with aggregated U1-70K in AD brain. Our results support a hypothesis that aberrant forms of U1-70K in AD can directly sequester soluble forms of U1-70K into insoluble aggregates. PMID:25355317

  11. Diversity of a ribonucleoprotein family in tobacco chloroplasts: two new chloroplast ribonucleoproteins and a phylogenetic tree of ten chloroplast RNA-binding domains.

    PubMed Central

    Ye, L H; Li, Y Q; Fukami-Kobayashi, K; Go, M; Konishi, T; Watanabe, A; Sugiura, M

    1991-01-01

    Two new ribonucleoproteins (RNPs) have been identified from a tobacco chloroplast lysate. These two proteins (cp29A and cp29B) are nuclear-encoded and have a less affinity to single-stranded DNA as compared with three other chloroplast RNPs (cp28, cp31 and cp33) previously isolated. DNA sequencing revealed that both contain two consensus sequence-type homologous RNA-binding domains (CS-RBDs) and a very acidic amino-terminal domain but shorter than that of cp28, cp31 and cp33. Comparison of cp29A and cp29B showed a 19 amino acid insertion in the region separating the two CS-RBDs in cp29B. This insertion results in three tandem repeats of a glycine-rich sequence of 10 amino acids, which is a novel feature in RNPs. The two proteins are encoded by different single nuclear genes and no alternatively spliced transcripts could be identified. We constructed a phylogenetic tree for the ten chloroplast CS-RBDs. These results suggest that there is a sizable RNP family in chloroplasts and the diversity was mainly generated through a series of gene duplications rather than through alternative pre-mRNA splicing. The gene for cp29B contains three introns. The first and second introns interrupt the first CS-RBD and the third intron does the second CS-RBD. The position of the first intron site is the same as that in the human hnRNP A1 protein gene. Images PMID:1721701

  12. Air pollution ranks as largest health risk

    NASA Astrophysics Data System (ADS)

    Wendel, JoAnna

    2014-04-01

    The World Health Organization (WHO) reports that 7 million people died in 2012 from air-pollution-related sicknesses, marking air pollution as the single largest environmental health risk. This finding, a result of better knowledge and assessment of the diseases, is more than double previous estimates of the risk of death from air pollution.

  13. Autoimmune response to U1 small nuclear ribonucleoprotein (U1 snRNP) associated with cytomegalovirus infection.

    PubMed

    Newkirk, M M; van Venrooij, W J; Marshall, G S

    2001-01-01

    The induction of autoantibodies to U1 small nuclear ribonucleoprotein (U1 snRNP) complexes is not well understood. We present evidence that healthy individuals with cytomegalovirus (CMV) infection have an increased frequency and quantity of antibodies to ribonucleoprotein, directed primarily against the U1-70k protein. A significant association between the presence of antibodies to CMV and antibodies to the total RNP targeted by the immune response to the spliceosome (to both the Sm and RNP; Sm/RNP) was found for patients with systemic lupus erythematosus (SLE) but not those with mixed connective-tissue disease. CMV thus may play a role in inducing autoimmune responses in a subset of patients with systemic lupus erythematosus.

  14. Autoimmune response to U1 small nuclear ribonucleoprotein (U1 snRNP) associated with cytomegalovirus infection.

    PubMed

    Newkirk, M M; van Venrooij, W J; Marshall, G S

    2001-01-01

    The induction of autoantibodies to U1 small nuclear ribonucleoprotein (U1 snRNP) complexes is not well understood. We present evidence that healthy individuals with cytomegalovirus (CMV) infection have an increased frequency and quantity of antibodies to ribonucleoprotein, directed primarily against the U1-70k protein. A significant association between the presence of antibodies to CMV and antibodies to the total RNP targeted by the immune response to the spliceosome (to both the Sm and RNP; Sm/RNP) was found for patients with systemic lupus erythematosus (SLE) but not those with mixed connective-tissue disease. CMV thus may play a role in inducing autoimmune responses in a subset of patients with systemic lupus erythematosus. PMID:11438044

  15. Saga is largest commercial submarine ever

    SciTech Connect

    Not Available

    1985-05-01

    The long-range autonomous submarine, Saga, went nuclear last year with an agreement between the French and two Canadian companies. The agreement to convert the prototype from Swedish Stirling closed-cycle combustion engines to a nuclear power supply will make Saga the first non-defense nuclear submarine. With an external hull displacement of 500 tons, Saga will be the largest commercial submarine ever built.

  16. Stellar Astrophysics with the World's largest Telescopes

    NASA Astrophysics Data System (ADS)

    Mikolajewska, Joanna; Olech, Arkadiusz

    The book reviews the most timely and interesting problems of stellar astrophysics, particularly those suitable for studies with the world's largest telescopes, and it can serve as an introduction to such studies. In particular it gives a comprehensive presentation of state-of-the-art research in stellar and planetary system formation, extra-solar planets, final stages of single and binary stellar evolution, and stellar populations in the Local Group of Galaxies, including observational techniques and technologies applicable to those important fields.

  17. Nucleocapsid protein structures from orthobunyaviruses reveal insight into ribonucleoprotein architecture and RNA polymerization

    PubMed Central

    Ariza, Antonio; Tanner, Sian J.; Walter, Cheryl T.; Dent, Kyle C.; Shepherd, Dale A.; Wu, Weining; Matthews, Susan V.; Hiscox, Julian A.; Green, Todd J.; Luo, Ming; Elliott, Richard M.; Fooks, Anthony R.; Ashcroft, Alison E.; Stonehouse, Nicola J.; Ranson, Neil A.; Barr, John N.; Edwards, Thomas A.

    2013-01-01

    All orthobunyaviruses possess three genome segments of single-stranded negative sense RNA that are encapsidated with the virus-encoded nucleocapsid (N) protein to form a ribonucleoprotein (RNP) complex, which is uncharacterized at high resolution. We report the crystal structure of both the Bunyamwera virus (BUNV) N–RNA complex and the unbound Schmallenberg virus (SBV) N protein, at resolutions of 3.20 and 2.75 Å, respectively. Both N proteins crystallized as ring-like tetramers and exhibit a high degree of structural similarity despite classification into different orthobunyavirus serogroups. The structures represent a new RNA-binding protein fold. BUNV N possesses a positively charged groove into which RNA is deeply sequestered, with the bases facing away from the solvent. This location is highly inaccessible, implying that RNA polymerization and other critical base pairing events in the virus life cycle require RNP disassembly. Mutational analysis of N protein supports a correlation between structure and function. Comparison between these crystal structures and electron microscopy images of both soluble tetramers and authentic RNPs suggests the N protein does not bind RNA as a repeating monomer; thus, it represents a newly described architecture for bunyavirus RNP assembly, with implications for many other segmented negative-strand RNA viruses. PMID:23595147

  18. An association between RBMX, a heterogeneous nuclear ribonucleoprotein, and ARTS-1 regulates extracellular TNFR1 release

    SciTech Connect

    Adamik, Barbara; Islam, Aminul; Rouhani, Farshid N.; Hawari, Feras I.; Zhang Jing; Levine, Stewart J.

    2008-07-04

    The type I, 55-kDa tumor necrosis factor receptor (TNFR1) is released to the extracellular space by two mechanisms, the constitutive release of TNFR1 exosome-like vesicles and the inducible proteolytic cleavage of TNFR1 ectodomains. Both pathways appear to be regulated by an interaction between TNFR1 and ARTS-1 (aminopeptidase regulator of TNFR1 shedding). Here, we sought to identify ARTS-1-interacting proteins that modulate TNFR1 release. Co-immunoprecipitation identified an association between ARTS-1 and RBMX (RNA-binding motif gene, X chromosome), a 43-kDa heterogeneous nuclear ribonucleoprotein. RNA interference attenuated RBMX expression, which reduced both the constitutive release of TNFR1 exosome-like vesicles and the IL-1{beta}-mediated inducible proteolytic cleavage of soluble TNFR1 ectodomains. Reciprocally, over-expression of RBMX increased TNFR1 exosome-like vesicle release and the IL-1{beta}-mediated inducible shedding of TNFR1 ectodomains. This identifies RBMX as an ARTS-1-associated protein that regulates both the constitutive release of TNFR1 exosome-like vesicles and the inducible proteolytic cleavage of TNFR1 ectodomains.

  19. High-throughput SHAPE and hydroxyl radical analysis of RNA structure and ribonucleoprotein assembly.

    PubMed

    McGinnis, Jennifer L; Duncan, Caia D S; Weeks, Kevin M

    2009-01-01

    RNA folds to form complex structures vital to many cellular functions. Proteins facilitate RNA folding at both the secondary and tertiary structure levels. An absolute prerequisite for understanding RNA folding and ribonucleoprotein (RNP) assembly reactions is a complete understanding of the RNA structure at each stage of the folding or assembly process. Here we provide a guide for comprehensive and high-throughput analysis of RNA secondary and tertiary structure using SHAPE and hydroxyl radical footprinting. As an example of the strong and sometimes surprising conclusions that can emerge from high-throughput analysis of RNA folding and RNP assembly, we summarize the structure of the bI3 group I intron RNA in four distinct states. Dramatic structural rearrangements occur in both secondary and tertiary structure as the RNA folds from the free state to the active, six-component, RNP complex. As high-throughput and high-resolution approaches are applied broadly to large protein-RNA complexes, other proteins previously viewed as making simple contributions to RNA folding are also likely to be found to exert multifaceted, long-range, cooperative, and nonadditive effects on RNA folding. These protein-induced contributions add another level of control, and potential regulatory function, in RNP complexes.

  20. U1 small nuclear ribonucleoprotein complex and RNA splicing alterations in Alzheimer’s disease

    PubMed Central

    Bai, Bing; Hales, Chadwick M.; Chen, Ping-Chung; Gozal, Yair; Dammer, Eric B.; Fritz, Jason J.; Wang, Xusheng; Xia, Qiangwei; Duong, Duc M.; Street, Craig; Cantero, Gloria; Cheng, Dongmei; Jones, Drew R.; Wu, Zhiping; Li, Yuxin; Diner, Ian; Heilman, Craig J.; Rees, Howard D.; Wu, Hao; Lin, Li; Szulwach, Keith E.; Gearing, Marla; Mufson, Elliott J.; Bennett, David A.; Montine, Thomas J.; Seyfried, Nicholas T.; Wingo, Thomas S.; Sun, Yi E.; Jin, Peng; Hanfelt, John; Willcock, Donna M.; Levey, Allan; Lah, James J.; Peng, Junmin

    2013-01-01

    Deposition of insoluble protein aggregates is a hallmark of neurodegenerative diseases. The universal presence of β-amyloid and tau in Alzheimer’s disease (AD) has facilitated advancement of the amyloid cascade and tau hypotheses that have dominated AD pathogenesis research and therapeutic development. However, the underlying etiology of the disease remains to be fully elucidated. Here we report a comprehensive study of the human brain-insoluble proteome in AD by mass spectrometry. We identify 4,216 proteins, among which 36 proteins accumulate in the disease, including U1-70K and other U1 small nuclear ribonucleoprotein (U1 snRNP) spliceosome components. Similar accumulations in mild cognitive impairment cases indicate that spliceosome changes occur in early stages of AD. Multiple U1 snRNP subunits form cytoplasmic tangle-like structures in AD but not in other examined neurodegenerative disorders, including Parkinson disease and frontotemporal lobar degeneration. Comparison of RNA from AD and control brains reveals dysregulated RNA processing with accumulation of unspliced RNA species in AD, including myc box-dependent-interacting protein 1, clusterin, and presenilin-1. U1-70K knockdown or antisense oligonucleotide inhibition of U1 snRNP increases the protein level of amyloid precursor protein. Thus, our results demonstrate unique U1 snRNP pathology and implicate abnormal RNA splicing in AD pathogenesis. PMID:24023061

  1. A high-throughput pipeline for the production of synthetic antibodies for analysis of ribonucleoprotein complexes.

    PubMed

    Na, Hong; Laver, John D; Jeon, Jouhyun; Singh, Fateh; Ancevicius, Kristin; Fan, Yujie; Cao, Wen Xi; Nie, Kun; Yang, Zhenglin; Luo, Hua; Wang, Miranda; Rissland, Olivia; Westwood, J Timothy; Kim, Philip M; Smibert, Craig A; Lipshitz, Howard D; Sidhu, Sachdev S

    2016-04-01

    Post-transcriptional regulation of mRNAs plays an essential role in the control of gene expression. mRNAs are regulated in ribonucleoprotein (RNP) complexes by RNA-binding proteins (RBPs) along with associated protein and noncoding RNA (ncRNA) cofactors. A global understanding of post-transcriptional control in any cell type requires identification of the components of all of its RNP complexes. We have previously shown that these complexes can be purified by immunoprecipitation using anti-RBP synthetic antibodies produced by phage display. To develop the large number of synthetic antibodies required for a global analysis of RNP complex composition, we have established a pipeline that combines (i) a computationally aided strategy for design of antigens located outside of annotated domains, (ii) high-throughput antigen expression and purification in Escherichia coli, and (iii) high-throughput antibody selection and screening. Using this pipeline, we have produced 279 antibodies against 61 different protein components of Drosophila melanogaster RNPs. Together with those produced in our low-throughput efforts, we have a panel of 311 antibodies for 67 RNP complex proteins. Tests of a subset of our antibodies demonstrated that 89% immunoprecipitate their endogenous target from embryo lysate. This panel of antibodies will serve as a resource for global studies of RNP complexes in Drosophila. Furthermore, our high-throughput pipeline permits efficient production of synthetic antibodies against any large set of proteins.

  2. Effects of stress and aging on ribonucleoprotein assembly and function in the germ line.

    PubMed

    Schisa, Jennifer A

    2014-01-01

    In a variety of cell types, ribonucleoprotein (RNP) complexes play critical roles in regulating RNA metabolism. The germ line contains RNPs found also in somatic cells, such as processing (P) bodies and stress granules, as well as several RNPs unique to the germ line, including germ granules, nuage, Balbiani bodies, P granules, U bodies, and sponge bodies. Recent advances have identified a conserved response of germ line RNPs to environmental stresses such as nutritional stress and heat shock. The RNPs increase significantly in size based on cytology; their morphology and subcellular localization changes, and their composition changes. These dynamic changes are reversible when stresses diminish, and similar changes occur in response to aging or extended meiotic arrest prior to fertilization of oocytes. Intriguing correlations exist between the dynamics of the RNPs and the microtubule cytoskeleton and its motor proteins, suggesting a possible mechanism for the assembly and dissociation of the large RNP granules. Similarly, coordinated changes of the nuclear membrane and endoplasmic reticulum may also help unravel the regulatory mechanisms of RNP dynamics. Based on their composition, the RNPs are thought to regulate mRNA decay and/or translation, and initial support for some of these roles is now at hand. Ultimately, the question of why RNP remodeling occurs to such a large extent during a variety of stresses and aging remains to be fully answered, but a current attractive hypothesis is that the plasticity promotes the maintenance of oocyte quality. PMID:24523207

  3. The expanding universe of ribonucleoproteins: of novel RNA-binding proteins and unconventional interactions.

    PubMed

    Beckmann, Benedikt M; Castello, Alfredo; Medenbach, Jan

    2016-06-01

    Post-transcriptional regulation of gene expression plays a critical role in almost all cellular processes. Regulation occurs mostly by RNA-binding proteins (RBPs) that recognise RNA elements and form ribonucleoproteins (RNPs) to control RNA metabolism from synthesis to decay. Recently, the repertoire of RBPs was significantly expanded owing to methodological advances such as RNA interactome capture. The newly identified RNA binders are involved in diverse biological processes and belong to a broad spectrum of protein families, many of them exhibiting enzymatic activities. This suggests the existence of an extensive crosstalk between RNA biology and other, in principle unrelated, cell functions such as intermediary metabolism. Unexpectedly, hundreds of new RBPs do not contain identifiable RNA-binding domains (RBDs), raising the question of how they interact with RNA. Despite the many functions that have been attributed to RNA, our understanding of RNPs is still mostly governed by a rather protein-centric view, leading to the idea that proteins have evolved to bind to and regulate RNA and not vice versa. However, RNPs formed by an RNA-driven interaction mechanism (RNA-determined RNPs) are abundant and offer an alternative explanation for the surprising lack of classical RBDs in many RNA-interacting proteins. Moreover, RNAs can act as scaffolds to orchestrate and organise protein networks and directly control their activity, suggesting that nucleic acids might play an important regulatory role in many cellular processes, including metabolism.

  4. Hypophosphorylated ASF/SF2 binds TAP and is present in messenger ribonucleoproteins.

    PubMed

    Lai, Ming-Chih; Tarn, Woan-Yuh

    2004-07-23

    Serine/arginine-rich proteins (SR proteins) function in precursor mRNA (pre-mRNA) splicing and may also act as adaptors for mRNA export. SR proteins are dynamically phosphorylated in their RS domain, and differential phosphorylation modulates their splicing activity and subcellular localization. In this study, we investigated the influence of phosphorylation on the function of SR proteins in events occurring during mRNA maturation. Immunoprecipitation experiments showed that the mRNA export receptor TAP associates preferentially with the hypophosphorylated form of shuttling SR proteins, including ASF/SF2. Overexpression of ASF induced subnuclear relocalization of TAP to SR protein-enriched nuclear speckles, suggesting their interaction in vivo. Moreover, the ASF found in a nucleoplasmic fraction rich in heterogeneous nuclear ribonucleoprotein (hnRNP) complexes is hyperphosphorylated, whereas mature messenger RNP (mRNP)-bound ASF is hypophosphorylated. Therefore, hypophosphorylation of ASF in mRNPs coincides with its higher affinity for TAP, suggesting that dephosphorylation of ASF promotes both its incorporation into mRNPs and recruitment of TAP for mRNA export. Thus, the phosphorylation state of RS domains may modulate the function of mammalian shuttling SR proteins during mRNA maturation or export. PMID:15184380

  5. Biogenesis, assembly, and export of viral messenger ribonucleoproteins in the influenza A virus infected cell

    PubMed Central

    York, Ashley; Fodor, Ervin

    2013-01-01

    The flow of genetic information from sites of transcription within the nucleus to the cytoplasmic translational machinery of eukaryotic cells is obstructed by a physical blockade, the nuclear double membrane, which must be overcome in order to adhere to the central dogma of molecular biology, DNA makes RNA makes protein. Advancement in the field of cellular and molecular biology has painted a detailed picture of the molecular mechanisms from transcription of genes to mRNAs and their processing that is closely coupled to export from the nucleus. The rules that govern delivering messenger transcripts from the nucleus must be obeyed by influenza A virus, a member of the Orthomyxoviridae that has adopted a nuclear replication cycle. The negative-sense genome of influenza A virus is segmented into eight individual viral ribonucleoprotein (vRNP) complexes containing the viral RNA-dependent RNA polymerase and single-stranded RNA encapsidated in viral nucleoprotein. Influenza A virus mRNAs fall into three major categories, intronless, intron-containing unspliced and spliced. During evolutionary history, influenza A virus has conceived a way of negotiating the passage of viral transcripts from the nucleus to cytoplasmic sites of protein synthesis. The major mRNA nuclear export NXF1 pathway is increasingly implicated in viral mRNA export and this review considers and discusses the current understanding of how influenza A virus exploits the host mRNA export pathway for replication. PMID:23807439

  6. Active Yeast Telomerase Shares Subunits with Ribonucleoproteins RNase P and RNase MRP.

    PubMed

    Lemieux, Bruno; Laterreur, Nancy; Perederina, Anna; Noël, Jean-François; Dubois, Marie-Line; Krasilnikov, Andrey S; Wellinger, Raymund J

    2016-05-19

    Telomerase is the ribonucleoprotein enzyme that replenishes telomeric DNA and maintains genome integrity. Minimally, telomerase activity requires a templating RNA and a catalytic protein. Additional proteins are required for activity on telomeres in vivo. Here, we report that the Pop1, Pop6, and Pop7 proteins, known components of RNase P and RNase MRP, bind to yeast telomerase RNA and are essential constituents of the telomerase holoenzyme. Pop1/Pop6/Pop7 binding is specific and involves an RNA domain highly similar to a protein-binding domain in the RNAs of RNase P/MRP. The results also show that Pop1/Pop6/Pop7 function to maintain the essential components Est1 and Est2 on the RNA in vivo. Consistently, addition of Pop1 allows for telomerase activity reconstitution with wild-type telomerase RNA in vitro. Thus, the same chaperoning module has allowed the evolution of functionally and, remarkably, structurally distinct RNPs, telomerase, and RNases P/MRP from unrelated progenitor RNAs. PMID:27156450

  7. The expanding universe of ribonucleoproteins: of novel RNA-binding proteins and unconventional interactions.

    PubMed

    Beckmann, Benedikt M; Castello, Alfredo; Medenbach, Jan

    2016-06-01

    Post-transcriptional regulation of gene expression plays a critical role in almost all cellular processes. Regulation occurs mostly by RNA-binding proteins (RBPs) that recognise RNA elements and form ribonucleoproteins (RNPs) to control RNA metabolism from synthesis to decay. Recently, the repertoire of RBPs was significantly expanded owing to methodological advances such as RNA interactome capture. The newly identified RNA binders are involved in diverse biological processes and belong to a broad spectrum of protein families, many of them exhibiting enzymatic activities. This suggests the existence of an extensive crosstalk between RNA biology and other, in principle unrelated, cell functions such as intermediary metabolism. Unexpectedly, hundreds of new RBPs do not contain identifiable RNA-binding domains (RBDs), raising the question of how they interact with RNA. Despite the many functions that have been attributed to RNA, our understanding of RNPs is still mostly governed by a rather protein-centric view, leading to the idea that proteins have evolved to bind to and regulate RNA and not vice versa. However, RNPs formed by an RNA-driven interaction mechanism (RNA-determined RNPs) are abundant and offer an alternative explanation for the surprising lack of classical RBDs in many RNA-interacting proteins. Moreover, RNAs can act as scaffolds to orchestrate and organise protein networks and directly control their activity, suggesting that nucleic acids might play an important regulatory role in many cellular processes, including metabolism. PMID:27165283

  8. Small nuclear ribonucleoprotein associated polypeptide N accelerates cell proliferation in pancreatic adenocarcinoma.

    PubMed

    Ma, Jin; Zhang, Zhuo; Wang, Jiancheng

    2015-10-01

    The spliceosome, the large RNA‑protein molecular complex, is crucial for pre‑mRNA splicing. Several antitumor drugs have been found to tightly bind to the components of the spliceosome and mutations in the spliceosome have been reported in several types of cancer. However, the involvement of the spliceosome in pancreatic adenocarcinoma remains unclear. In the present study, small nuclear ribonucleoprotein associated polypeptide N (SNRPN), a key constituent of spliceosomes, was disrupted in BxPC‑3 pancreatic adenocarcinoma cells using lentivirus‑mediated RNA interference (RNAi). It was found that knockdown of SNRPN reduced the proliferation ability of BxPC‑3 cells, as determined by an MTT assay. Furthermore, cell colony formation was impaired in SNRPN depleted adenocarcinoma cells and cell cycle analysis showed that depletion of SNRPN led to S phase cell cycle arrest and apoptosis. These results suggest that SNRPN is a key player in pancreatic adenocarcinoma cell growth, and targeted loss of SNRPN may be a potential therapeutic method for pancreatic cancer.

  9. The presence of heterogeneous nuclear ribonucleoproteins in frontotemporal lobar degeneration with FUS-positive inclusions.

    PubMed

    Gami-Patel, Priya; Bandopadhyay, Rina; Brelstaff, Jack; Revesz, Tamas; Lashley, Tammaryn

    2016-10-01

    Frontotemporal lobar degeneration with fused in sarcoma-positive inclusions (FTLD-FUS) is a disease with unknown cause. Transportin 1 is abundantly found in FUS-positive inclusions and responsible for the nuclear import of the FET proteins of which FUS is a member. The presence of all FET proteins in pathological inclusions suggests a disturbance of transportin 1-mediated nuclear import. FUS also belongs to the heterogeneous nuclear ribonucleoprotein (hnRNP) protein family. We investigated whether hnRNP proteins are associated with FUS pathology implicating dysfunctional nuclear export in the pathogenesis of FTLD-FUS. hnRNP proteins were investigated in affected brain regions in FTLD-FUS using immunohistochemistry, biochemical analysis, and the expression analysis. We demonstrated the presence of several hnRNP proteins in pathological inclusions including neuronal cytoplasmic inclusions and dystrophic neurites. The biochemical analysis revealed a shift in the location of hnRNP A1 from the nucleus to the cytoplasm. The expression analysis revealed an increase in several hnRNP proteins in FTLD-FUS. These results implicate a wider dysregulation of movement between intracellular compartments, than mechanisms only affecting the nuclear import of FUS proteins. PMID:27500866

  10. Role and molecular mechanism of heterogeneous nuclear ribonucleoprotein K in tumor development and progression

    PubMed Central

    LU, JING; GAO, FENG-HOU

    2016-01-01

    Heterogeneous nuclear ribonucleoprotein K (hnRNP K) is a member of the hnRNP family, which exists in the nucleus and the cytoplasm simultaneously. It is a multifunctional protein that can participate in a variety of regulatory progressions of gene expression and signal transduction, such as chromatin remodeling, transcription, RNA alternative splicing and translation. hnRNP K not only directly binds to the kinases, but also recruits the associated factors regarding transcription, splicing and translation to control gene expression, and therefore, it serves as a docking platform for integrating transduction pathways to nucleic acid-directed processes. Numerous studies also show that abnormal expression of hnRNP K is closely associated with the tumor formation. This protein is overexpressed in numerous types of cancer and its aberrant cytoplasmic localization is also associated with a worse prognosis for patients. These results consistently indicate that hnRNP K has a key role in cancer progression. To understand the hnRNP K pathophysiological process in tumor disease, the previous research results regarding the association between hnRNP K and tumors were reviewed. PMID:27284403

  11. A high-throughput pipeline for the production of synthetic antibodies for analysis of ribonucleoprotein complexes.

    PubMed

    Na, Hong; Laver, John D; Jeon, Jouhyun; Singh, Fateh; Ancevicius, Kristin; Fan, Yujie; Cao, Wen Xi; Nie, Kun; Yang, Zhenglin; Luo, Hua; Wang, Miranda; Rissland, Olivia; Westwood, J Timothy; Kim, Philip M; Smibert, Craig A; Lipshitz, Howard D; Sidhu, Sachdev S

    2016-04-01

    Post-transcriptional regulation of mRNAs plays an essential role in the control of gene expression. mRNAs are regulated in ribonucleoprotein (RNP) complexes by RNA-binding proteins (RBPs) along with associated protein and noncoding RNA (ncRNA) cofactors. A global understanding of post-transcriptional control in any cell type requires identification of the components of all of its RNP complexes. We have previously shown that these complexes can be purified by immunoprecipitation using anti-RBP synthetic antibodies produced by phage display. To develop the large number of synthetic antibodies required for a global analysis of RNP complex composition, we have established a pipeline that combines (i) a computationally aided strategy for design of antigens located outside of annotated domains, (ii) high-throughput antigen expression and purification in Escherichia coli, and (iii) high-throughput antibody selection and screening. Using this pipeline, we have produced 279 antibodies against 61 different protein components of Drosophila melanogaster RNPs. Together with those produced in our low-throughput efforts, we have a panel of 311 antibodies for 67 RNP complex proteins. Tests of a subset of our antibodies demonstrated that 89% immunoprecipitate their endogenous target from embryo lysate. This panel of antibodies will serve as a resource for global studies of RNP complexes in Drosophila. Furthermore, our high-throughput pipeline permits efficient production of synthetic antibodies against any large set of proteins. PMID:26847261

  12. A nuclear F-actin scaffold stabilizes ribonucleoprotein droplets against gravity in large cells.

    PubMed

    Feric, Marina; Brangwynne, Clifford P

    2013-10-01

    The size of a typical eukaryotic cell is of the order of ∼10 μm. However, some cell types grow to very large sizes, including oocytes (immature eggs) of organisms from humans to starfish. For example, oocytes of the frog Xenopus laevis grow to a diameter ≥1 mm. They have a correspondingly large nucleus (germinal vesicle) of ∼450 μm in diameter, which is similar to smaller somatic nuclei, but contains a significantly higher concentration of actin. The form and structure of this nuclear actin remain controversial, and its potential mechanical role within these large nuclei is unknown. Here, we use a microrheology and quantitative imaging approach to show that germinal vesicles contain an elastic F-actin scaffold that mechanically stabilizes these large nuclei against gravitational forces, which are usually considered negligible within cells. We find that on actin disruption, ribonucleoprotein droplets, including nucleoli and histone locus bodies, undergo gravitational sedimentation and fusion. We develop a model that reveals how gravity becomes an increasingly potent force as cells and their nuclei grow larger than ∼10 μm, explaining the requirement for a stabilizing nuclear F-actin scaffold in large Xenopus oocytes. All life forms are subject to gravity, and our results may have broad implications for cell growth and size control.

  13. Targeted Gene Knockin in Porcine Somatic Cells Using CRISPR/Cas Ribonucleoproteins

    PubMed Central

    Park, Ki-Eun; Park, Chi-Hun; Powell, Anne; Martin, Jessica; Donovan, David M.; Telugu, Bhanu P.

    2016-01-01

    The pig is an ideal large animal model for genetic engineering applications. A relatively short gestation interval and large litter size makes the pig a conducive model for generating and propagating genetic modifications. The domestic pig also shares close similarity in anatomy, physiology, size, and life expectancy, making it an ideal animal for modeling human diseases. Often, however, the technical difficulties in generating desired genetic modifications such as targeted knockin of short stretches of sequences or transgenes have impeded progress in this field. In this study, we have investigated and compared the relative efficiency of CRISPR/Cas ribonucleoproteins in engineering targeted knockin of pseudo attP sites downstream of a ubiquitously expressed COL1A gene in porcine somatic cells and generated live fetuses by somatic cell nuclear transfer (SCNT). By leveraging these knockin pseudo attP sites, we have demonstrated subsequent phiC31 integrase mediated integration of green fluorescent protein (GFP) transgene into the site. This work for the first time created an optimized protocol for CRISPR/Cas mediated knockin in porcine somatic cells, while simultaneously creating a stable platform for future transgene integration and generating transgenic animals. PMID:27240344

  14. Effects of stress and aging on ribonucleoprotein assembly and function in the germ line

    PubMed Central

    Schisa, Jennifer A.

    2016-01-01

    In a variety of cell types, ribonucleoprotein (RNP) complexes play critical roles in regulating RNA metabolism. The germ line contains RNPs found also in somatic cells, such as processing (P) bodies and stress granules, as well as several RNPs unique to the germ line, including germ granules, nuage, Balbiani bodies, P granules, U bodies, and sponge bodies. Recent advances have identified a conserved response of germ line RNPs to environmental stresses such as nutritional stress and heat shock. The RNPs increase significantly in size based on cytology; their morphology and subcellular localization changes, and their composition changes. These dynamic changes are reversible when stresses diminish, and similar changes occur in response to aging or extended meiotic arrest prior to fertilization of oocytes. Intriguing correlations exist between the dynamics of the RNPs and the microtubule cytoskeleton and its motor proteins, suggesting a possible mechanism for the assembly and dissociation of the large RNP granules. Similarly, coordinated changes of the nuclear membrane and endoplasmic reticulum may also help unravel the regulatory mechanisms of RNP dynamics. Based on their composition, the RNPs are thought to regulate mRNA decay and/or translation, and initial support for some of these roles is now at hand. Ultimately, the question of why RNP remodeling occurs to such a large extent during a variety of stresses and aging remains to be fully answered, but a current attractive hypothesis is that the plasticity promotes the maintenance of oocyte quality. PMID:24523207

  15. The presence of heterogeneous nuclear ribonucleoproteins in frontotemporal lobar degeneration with FUS-positive inclusions.

    PubMed

    Gami-Patel, Priya; Bandopadhyay, Rina; Brelstaff, Jack; Revesz, Tamas; Lashley, Tammaryn

    2016-10-01

    Frontotemporal lobar degeneration with fused in sarcoma-positive inclusions (FTLD-FUS) is a disease with unknown cause. Transportin 1 is abundantly found in FUS-positive inclusions and responsible for the nuclear import of the FET proteins of which FUS is a member. The presence of all FET proteins in pathological inclusions suggests a disturbance of transportin 1-mediated nuclear import. FUS also belongs to the heterogeneous nuclear ribonucleoprotein (hnRNP) protein family. We investigated whether hnRNP proteins are associated with FUS pathology implicating dysfunctional nuclear export in the pathogenesis of FTLD-FUS. hnRNP proteins were investigated in affected brain regions in FTLD-FUS using immunohistochemistry, biochemical analysis, and the expression analysis. We demonstrated the presence of several hnRNP proteins in pathological inclusions including neuronal cytoplasmic inclusions and dystrophic neurites. The biochemical analysis revealed a shift in the location of hnRNP A1 from the nucleus to the cytoplasm. The expression analysis revealed an increase in several hnRNP proteins in FTLD-FUS. These results implicate a wider dysregulation of movement between intracellular compartments, than mechanisms only affecting the nuclear import of FUS proteins.

  16. Functions of Heterogeneous Nuclear Ribonucleoproteins in Stem Cell Potency and Differentiation

    PubMed Central

    Chen, Qishan; Jin, Min; Zhu, Jianhua; Zhang, Li

    2013-01-01

    Stem cells possess huge importance in developmental biology, disease modelling, cell replacement therapy, and tissue engineering in regenerative medicine because they have the remarkable potential for self-renewal and to differentiate into almost all the cell types in the human body. Elucidation of molecular mechanisms regulating stem cell potency and differentiation is essential and critical for extensive application. Heterogeneous nuclear ribonucleoproteins (hnRNPs) are modular proteins consisting of RNA-binding motifs and auxiliary domains characterized by extensive and divergent functions in nucleic acid metabolism. Multiple roles of hnRNPs in transcriptional and posttranscriptional regulation enable them to be effective gene expression regulators. More recent findings show that hnRNP proteins are crucial factors implicated in maintenance of stem cell self-renewal and pluripotency and cell differentiation. The hnRNPs interact with certain sequences in target gene promoter regions to initiate transcription. In addition, they recognize 3′UTR or 5′UTR of specific gene mRNA forming mRNP complex to regulate mRNA stability and translation. Both of these regulatory pathways lead to modulation of gene expression that is associated with stem cell proliferation, cell cycle control, pluripotency, and committed differentiation. PMID:23984388

  17. The host protein CLUH participates in the subnuclear transport of influenza virus ribonucleoprotein complexes.

    PubMed

    Ando, Tomomi; Yamayoshi, Seiya; Tomita, Yuriko; Watanabe, Shinji; Watanabe, Tokiko; Kawaoka, Yoshihiro

    2016-01-01

    The nucleus is highly compartmentalized yet dynamic. Subnuclear functions are regulated by controlling the subnuclear localization of the nuclear proteins. Influenza viral ribonucleoprotein (vRNP) is replicated in the nucleus and then exported to the cytoplasm. However, the precise subnuclear localization and transport of vRNPs remain unclear. Here, we show that CLUH, a host protein whose cellular function is not well established, plays a key role in the subnuclear transport of vRNP. Viral PB2 and M1 induced CLUH translocation to the nucleoplasm and SC35-positive speckles, respectively, even though CLUH is usually cytoplasmic. CLUH depletion inhibited the translocation of M1 to SC35-positive speckles, but did not interfere with PB2 localization to the nucleoplasm and disrupted the subnuclear transport of vRNP, abolishing vRNP nuclear export without affecting viral RNA or protein expression. Our findings suggest that CLUH plays a role in the subnuclear transport of progeny vRNP. PMID:27573102

  18. Flight performance of the largest volant bird

    NASA Astrophysics Data System (ADS)

    Ksepka, Daniel T.

    2014-07-01

    Pelagornithidae is an extinct clade of birds characterized by bizarre tooth-like bony projections of the jaws. Here, the flight capabilities of pelagornithids are explored based on data from a species with the largest reported wingspan among birds. Pelagornis sandersi sp. nov. is represented by a skull and substantial postcranial material. Conservative wingspan estimates (∼6.4 m) exceed theoretical maximums based on extant soaring birds. Modeled flight properties indicate that lift:drag ratios and glide ratios for P. sandersi were near the upper limit observed in extant birds and suggest that pelagornithids were highly efficient gliders, exploiting a long-range soaring ecology.

  19. Fiji's largest marine reserve benefits reef sharks

    NASA Astrophysics Data System (ADS)

    Goetze, J. S.; Fullwood, L. A. F.

    2013-03-01

    To provide more information about whether sharks benefit from no-take marine reserves, we quantified the relative abundance and biomass of reef sharks inside and outside of Namena, Fiji's largest reserve (60.6 km2). Using stereo baited remote underwater video systems (stereo-BRUVs), we found that the abundance and biomass of sharks was approximately two and four times greater in shallow and deep locations, respectively, within the Namena reserve compared to adjacent fished areas. The greater abundance and biomass of reef sharks inside Namena is likely a result of greater prey availability rather than protection from fishing. This study demonstrates that marine reserves can benefit sharks.

  20. Flight performance of the largest volant bird

    PubMed Central

    Ksepka, Daniel T.

    2014-01-01

    Pelagornithidae is an extinct clade of birds characterized by bizarre tooth-like bony projections of the jaws. Here, the flight capabilities of pelagornithids are explored based on data from a species with the largest reported wingspan among birds. Pelagornis sandersi sp. nov. is represented by a skull and substantial postcranial material. Conservative wingspan estimates (∼6.4 m) exceed theoretical maximums based on extant soaring birds. Modeled flight properties indicate that lift:drag ratios and glide ratios for P. sandersi were near the upper limit observed in extant birds and suggest that pelagornithids were highly efficient gliders, exploiting a long-range soaring ecology. PMID:25002475

  1. Collapse of the world's largest herbivores.

    PubMed

    Ripple, William J; Newsome, Thomas M; Wolf, Christopher; Dirzo, Rodolfo; Everatt, Kristoffer T; Galetti, Mauro; Hayward, Matt W; Kerley, Graham I H; Levi, Taal; Lindsey, Peter A; Macdonald, David W; Malhi, Yadvinder; Painter, Luke E; Sandom, Christopher J; Terborgh, John; Van Valkenburgh, Blaire

    2015-05-01

    Large wild herbivores are crucial to ecosystems and human societies. We highlight the 74 largest terrestrial herbivore species on Earth (body mass ≥100 kg), the threats they face, their important and often overlooked ecosystem effects, and the conservation efforts needed to save them and their predators from extinction. Large herbivores are generally facing dramatic population declines and range contractions, such that ~60% are threatened with extinction. Nearly all threatened species are in developing countries, where major threats include hunting, land-use change, and resource depression by livestock. Loss of large herbivores can have cascading effects on other species including large carnivores, scavengers, mesoherbivores, small mammals, and ecological processes involving vegetation, hydrology, nutrient cycling, and fire regimes. The rate of large herbivore decline suggests that ever-larger swaths of the world will soon lack many of the vital ecological services these animals provide, resulting in enormous ecological and social costs. PMID:26601172

  2. Ribonomic analysis of human DZIP1 reveals its involvement in ribonucleoprotein complexes and stress granules

    PubMed Central

    2014-01-01

    Background DZIP1 (DAZ-interacting protein 1) has been described as a component of the Hh signaling pathway with a putative regulatory role in ciliogenesis. DZIP1 interacts with DAZ RNA binding proteins in embryonic stem cells and human germ cells suggesting a role in mRNA regulation. Results We investigated DZIP1 function in HeLa cells and its involvement in ribonucleoprotein complexes. DZIP1 was predominantly located in granules in the cytoplasm. Under oxidative stress conditions, DZIP1 re-localized to stress granules. DZIP appears to be important for the formation of stress granules during the stress response. We used immunoprecipitation assays with antibodies against DZIP1 and microarray hybridization to identify mRNAs associated with DZIP1. The genetic networks formed by the DZIP1-associated mRNAs were involved in cell cycle and gene expression regulation. DZIP1 is involved in the Hedgehog signaling pathway. We used cyclopamine, a specific inhibitor of this pathway, to analyze the expression of DZIP1 and its associated mRNAs. The abundance of DZIP1-associated mRNAs increased with treatment; however, the silencing or overexpression of DZIP1 in HeLa cells had no effect on the accumulation of the associated mRNAs. Polysomal profile analysis by sucrose gradient centrifugation demonstrated the presence of DZIP1 in the polysomal fraction. Conclusions Our results suggest that DZIP1 is part of an RNP complex that occupies various subcellular locations. The diversity of the mRNAs associated with DZIP1 suggests that this protein is a component of different RNPs associated with translating polysomes and with RNA granules. PMID:24993635

  3. High specificity of Trypanosoma cruzi epimastigote ribonucleoprotein as antigen in serodiagnosis of Chagas' disease.

    PubMed Central

    Solana, M E; Katzin, A M; Umezawa, E S; Miatello, C S

    1995-01-01

    We assessed the performance of an enzyme-linked immunosorbent assay (ELISA) with the Trypanosoma cruzi epimastigote ribosomal fraction (Tulahuen and Y strains) in order to improve the diagnostic specificity of the test. A total of 100 serum samples from patients with chronic Chagas' disease from Brazil and Argentina were studied. Sera from 116 patients, without Chagas' disease, including 10 with active mucocutaneous leishmaniasis and 20 with visceral leishmaniasis, were used as controls. Immunoglobulin G (IgG) antibodies against the ribosomal fraction (ribonucleoproteins [RNPs]) in the ELISA were found in 97% of samples from patients with Chagas' disease. A total of 99% of the sera from patients without the disease were negative, including sera from patients with mucocutaneous and visceral leishmaniases. The distribution of IgG isotypes in randomly chosen serum samples was determined by ELISA; IgG1 and IgG3 were predominant (100% exhibited IgG1 and 85% exhibited IgG3, and 50% also presented the IgG2 isotype. The distribution of the IgG subclasses was confirmed by the Western blot (immunoblot) technique. When total IgG was assayed by Western blot assay, no correlation was found between the pattern of serum reactivity and the clinical features of the patients with Chagas' disease. Therefore, no typical profile of polypeptide recognition could be associated with any clinical form of Chagas' disease (cardiomyopathy or megaviscera). Our results showed that sera from patients with Chagas' disease react with ribosomal antigens and display a typical profile of IgG isotypes (IgG1 plus IgG3).(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7650167

  4. Generation of knock-in primary human T cells using Cas9 ribonucleoproteins

    SciTech Connect

    Schumann, Kathrin; Lin, Steven; Boyer, Eric; Simeonov, Dimitre R.; Subramaniam, Meena; Gate, Rachel E.; Haliburton, Genevieve E.; Ye, Chun J.; Bluestone, Jeffrey A.; Doudna, Jennifer A.; Marson, Alexander

    2015-07-27

    T-cell genome engineering holds great promise for cell-based therapies for cancer, HIV, primary immune deficiencies, and autoimmune diseases, but genetic manipulation of human T cells has been challenging. Improved tools are needed to efficiently “knock out” genes and “knock in” targeted genome modifications to modulate T-cell function and correct disease-associated mutations. CRISPR/Cas9 technology is facilitating genome engineering in many cell types, but in human T cells its efficiency has been limited and it has not yet proven useful for targeted nucleotide replacements. Here we report efficient genome engineering in human CD4+ T cells using Cas9:single-guide RNA ribonucleoproteins (Cas9 RNPs). Cas9 RNPs allowed ablation of CXCR4, a coreceptor for HIV entry. Cas9 RNP electroporation caused up to ~40% of cells to lose high-level cell-surface expression of CXCR4, and edited cells could be enriched by sorting based on low CXCR4 expression. Importantly, Cas9 RNPs paired with homology-directed repair template oligonucleotides generated a high frequency of targeted genome modifications in primary T cells. Targeted nucleotide replacement was achieved in CXCR4 and PD-1 (PDCD1), a regulator of T-cell exhaustion that is a validated target for tumor immunotherapy. Deep sequencing of a target site confirmed that Cas9 RNPs generated knock-in genome modifications with up to ~20% efficiency, which accounted for up to approximately one-third of total editing events. These results establish Cas9 RNP technology for diverse experimental and therapeutic genome engineering applications in primary human T cells.

  5. Generation of knock-in primary human T cells using Cas9 ribonucleoproteins.

    PubMed

    Schumann, Kathrin; Lin, Steven; Boyer, Eric; Simeonov, Dimitre R; Subramaniam, Meena; Gate, Rachel E; Haliburton, Genevieve E; Ye, Chun J; Bluestone, Jeffrey A; Doudna, Jennifer A; Marson, Alexander

    2015-08-18

    T-cell genome engineering holds great promise for cell-based therapies for cancer, HIV, primary immune deficiencies, and autoimmune diseases, but genetic manipulation of human T cells has been challenging. Improved tools are needed to efficiently "knock out" genes and "knock in" targeted genome modifications to modulate T-cell function and correct disease-associated mutations. CRISPR/Cas9 technology is facilitating genome engineering in many cell types, but in human T cells its efficiency has been limited and it has not yet proven useful for targeted nucleotide replacements. Here we report efficient genome engineering in human CD4(+) T cells using Cas9:single-guide RNA ribonucleoproteins (Cas9 RNPs). Cas9 RNPs allowed ablation of CXCR4, a coreceptor for HIV entry. Cas9 RNP electroporation caused up to ∼40% of cells to lose high-level cell-surface expression of CXCR4, and edited cells could be enriched by sorting based on low CXCR4 expression. Importantly, Cas9 RNPs paired with homology-directed repair template oligonucleotides generated a high frequency of targeted genome modifications in primary T cells. Targeted nucleotide replacement was achieved in CXCR4 and PD-1 (PDCD1), a regulator of T-cell exhaustion that is a validated target for tumor immunotherapy. Deep sequencing of a target site confirmed that Cas9 RNPs generated knock-in genome modifications with up to ∼20% efficiency, which accounted for up to approximately one-third of total editing events. These results establish Cas9 RNP technology for diverse experimental and therapeutic genome engineering applications in primary human T cells.

  6. Arabidopsis CML38, a Calcium Sensor That Localizes to Ribonucleoprotein Complexes under Hypoxia Stress1[OPEN

    PubMed Central

    McClintock, Carlee; Li, Tian

    2016-01-01

    During waterlogging and the associated oxygen deprivation stress, plants respond by the induction of adaptive programs, including the redirected expression of gene networks toward the synthesis of core hypoxia-response proteins. Among these core response proteins in Arabidopsis (Arabidopsis thaliana) is the calcium sensor CML38, a protein related to regulator of gene silencing calmodulin-like proteins (rgsCaMs). CML38 transcripts are up-regulated more than 300-fold in roots within 6 h of hypoxia treatment. Transfer DNA insertional mutants of CML38 show an enhanced sensitivity to hypoxia stress, with lowered survival and more severe inhibition of root and shoot growth. By using yellow fluorescent protein (YFP) translational fusions, CML38 protein was found to be localized to cytosolic granule structures similar in morphology to hypoxia-induced stress granules. Immunoprecipitation of CML38 from the roots of hypoxia-challenged transgenic plants harboring CML38pro::CML38:YFP followed by liquid chromatography-tandem mass spectrometry analysis revealed the presence of protein targets associated with messenger RNA ribonucleoprotein (mRNP) complexes including stress granules, which are known to accumulate as messenger RNA storage and triage centers during hypoxia. This finding is further supported by the colocalization of CML38 with the mRNP stress granule marker RNA Binding Protein 47 (RBP47) upon cotransfection of Nicotiana benthamiana leaves. Ruthenium Red treatment results in the loss of CML38 signal in cytosolic granules, suggesting that calcium is necessary for stress granule association. These results confirm that CML38 is a core hypoxia response calcium sensor protein and suggest that it serves as a potential calcium signaling target within stress granules and other mRNPs that accumulate during flooding stress responses. PMID:26634999

  7. Large-Scale Analysis of Kinase Signaling in Yeast Pseudohyphal Development Identifies Regulation of Ribonucleoprotein Granules.

    PubMed

    Shively, Christian A; Kweon, Hye Kyong; Norman, Kaitlyn L; Mellacheruvu, Dattatreya; Xu, Tao; Sheidy, Daniel T; Dobry, Craig J; Sabath, Ivan; Cosky, Eric E P; Tran, Elizabeth J; Nesvizhskii, Alexey; Andrews, Philip C; Kumar, Anuj

    2015-10-01

    Yeast pseudohyphal filamentation is a stress-responsive growth transition relevant to processes required for virulence in pathogenic fungi. Pseudohyphal growth is controlled through a regulatory network encompassing conserved MAPK (Ste20p, Ste11p, Ste7p, Kss1p, and Fus3p), protein kinase A (Tpk2p), Elm1p, and Snf1p kinase pathways; however, the scope of these pathways is not fully understood. Here, we implemented quantitative phosphoproteomics to identify each of these signaling networks, generating a kinase-dead mutant in filamentous S. cerevisiae and surveying for differential phosphorylation. By this approach, we identified 439 phosphoproteins dependent upon pseudohyphal growth kinases. We report novel phosphorylation sites in 543 peptides, including phosphorylated residues in Ras2p and Flo8p required for wild-type filamentous growth. Phosphoproteins in these kinase signaling networks were enriched for ribonucleoprotein (RNP) granule components, and we observe co-localization of Kss1p, Fus3p, Ste20p, and Tpk2p with the RNP component Igo1p. These kinases localize in puncta with GFP-visualized mRNA, and KSS1 is required for wild-type levels of mRNA localization in RNPs. Kss1p pathway activity is reduced in lsm1Δ/Δ and pat1Δ/Δ strains, and these genes encoding P-body proteins are epistatic to STE7. The P-body protein Dhh1p is also required for hyphal development in Candida albicans. Collectively, this study presents a wealth of data identifying the yeast phosphoproteome in pseudohyphal growth and regulatory interrelationships between pseudohyphal growth kinases and RNPs.

  8. Large-Scale Analysis of Kinase Signaling in Yeast Pseudohyphal Development Identifies Regulation of Ribonucleoprotein Granules

    PubMed Central

    Mellacheruvu, Dattatreya; Xu, Tao; Sheidy, Daniel T.; Dobry, Craig J.; Sabath, Ivan; Cosky, Eric E. P.; Tran, Elizabeth J.; Nesvizhskii, Alexey; Andrews, Philip C.; Kumar, Anuj

    2015-01-01

    Yeast pseudohyphal filamentation is a stress-responsive growth transition relevant to processes required for virulence in pathogenic fungi. Pseudohyphal growth is controlled through a regulatory network encompassing conserved MAPK (Ste20p, Ste11p, Ste7p, Kss1p, and Fus3p), protein kinase A (Tpk2p), Elm1p, and Snf1p kinase pathways; however, the scope of these pathways is not fully understood. Here, we implemented quantitative phosphoproteomics to identify each of these signaling networks, generating a kinase-dead mutant in filamentous S. cerevisiae and surveying for differential phosphorylation. By this approach, we identified 439 phosphoproteins dependent upon pseudohyphal growth kinases. We report novel phosphorylation sites in 543 peptides, including phosphorylated residues in Ras2p and Flo8p required for wild-type filamentous growth. Phosphoproteins in these kinase signaling networks were enriched for ribonucleoprotein (RNP) granule components, and we observe co-localization of Kss1p, Fus3p, Ste20p, and Tpk2p with the RNP component Igo1p. These kinases localize in puncta with GFP-visualized mRNA, and KSS1 is required for wild-type levels of mRNA localization in RNPs. Kss1p pathway activity is reduced in lsm1Δ/Δ and pat1Δ/Δ strains, and these genes encoding P-body proteins are epistatic to STE7. The P-body protein Dhh1p is also required for hyphal development in Candida albicans. Collectively, this study presents a wealth of data identifying the yeast phosphoproteome in pseudohyphal growth and regulatory interrelationships between pseudohyphal growth kinases and RNPs. PMID:26447709

  9. M phase phosphoprotein 10 is a human U3 small nucleolar ribonucleoprotein component.

    PubMed

    Westendorf, J M; Konstantinov, K N; Wormsley, S; Shu, M D; Matsumoto-Taniura, N; Pirollet, F; Klier, F G; Gerace, L; Baserga, S J

    1998-02-01

    We have previously developed a novel technique for isolation of cDNAs encoding M phase phosphoproteins (MPPs). In the work described herein, we further characterize MPP10, one of 10 novel proteins that we identified, with regard to its potential nucleolar function. We show that by cell fractionation, almost all MPP10 was found in isolated nucleoli. By immunofluorescence, MPP10 colocalized with nucleolar fibrillarin and other known nucleolar proteins in interphase cells but was not detected in the coiled bodies stained for either fibrillarin or p80 coilin, a protein found only in the coiled body. When nucleoli were separated into fibrillar and granular domains by treatment with actinomycin D, almost all the MPP10 was found in the fibrillar caps, which contain proteins involved in rRNA processing. In early to middle M phase of the cell cycle, MPP10 colocalized with fibrillarin to chromosome surfaces. At telophase, MPP10 was found in cellular structures that resembled nucleolus-derived bodies and prenucleolar bodies. Some of these bodies lacked fibrillarin, a previously described component of nucleolus-derived bodies and prenucleolar bodies, however, and the bulk of MPP10 arrived at the nucleolus later than fibrillarin. To further examine the properties of MPP10, we immunoprecipitated it from cell sonicates. The resulting precipitates contained U3 small nucleolar RNA (snoRNA) but no significant amounts of other box C/D snoRNAs. This association of MPP10 with U3 snoRNA was stable to 400 mM salt and suggested that MPP10 is a component of the human U3 small nucleolar ribonucleoprotein. PMID:9450966

  10. Basal and hydrogen peroxide stimulated sites of phosphorylation in heterogeneous nuclear ribonucleoprotein C1/C2.

    PubMed

    Stone, James R; Maki, Jenny L; Collins, Tucker

    2003-02-11

    Hydrogen peroxide (H2O2) is a recently recognized second messenger, which regulates mammalian cell proliferation and migration. The biochemical mechanisms by which mammalian cells sense and respond to low concentrations of H2O2 are poorly understood. Recently, heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP-C1/C2) was found to be rapidly phosphorylated in response to the application of low concentrations of H2O2 to human endothelial cells. Here, using tandem mass spectrometry, four sites of phosphorylation are identified in hnRNP-C1/C2, all of which are in the acidic C-terminal domain of the protein. Under resting conditions, the protein is phosphorylated at S247 and S286. In response to low concentrations of H2O2, there is increased phosphorylation at S240 and at one of the four contiguous serine residues from S225-S228. Studies using a recombinant acidic C-terminal domain of hnRNP-C overexpressed in Escherichia coli demonstrate that protein kinase CK2 phosphorylates hnRNP-C1/C2 at S247, while protein kinase A and several protein kinase C isoforms fail to phosphorylate the isolated domain. These findings demonstrate that the acidic C-terminal domain of hnRNP-C1/C2 serves as the site for both basal and stimulated phosphorylation, indicating that this domain may play an important role in the regulation of mRNA binding by hnRNP-C1/C2.

  11. Differential requirements for H/ACA ribonucleoprotein components in cell proliferation and response to DNA damage.

    PubMed

    Lin, Ping; Mobasher, Maral E; Hakakian, Yasaman; Kakarla, Veena; Naseem, Anum F; Ziai, Heliya; Alawi, Faizan

    2015-12-01

    H/ACA ribonucleoproteins (RNPs) are comprised of four conserved proteins, dyskerin, NHP2, NOP10, and GAR1, and a function-specifying, noncoding H/ACA RNA. H/ACA RNPs contribute to telomerase assembly and stabilization, and posttranscriptional processing of nascent ribosomal RNA and spliceosomal RNA. However, very little is known about the coordinated action of the four proteins in other biologic processes. As described herein, we observed a differential requirement for the proteins in cell proliferation and identified a possible reliance for these factors in regulation of specific DNA damage biomarkers. In particular, GAR1 expression was upregulated following exposure to all forms of genotoxic stress tested. In contrast, levels of the other proteins were either reduced or unaffected. Only GAR1 showed an altered subcellular localization with a shift from the nucleolus to the nucleoplasm after ultraviolet-C irradiation and doxorubicin treatments. Transient siRNA-mediated depletion of GAR1 and dyskerin arrested cell proliferation, whereas loss of either NHP2 or NOP10 had no effect. Finally, loss of dyskerin, GAR1, NHP2, and NOP10, respectively, limited the accumulation of DNA damage biomarkers. However, the individual responses were dependent upon the specific type of damage incurred. In general, loss of GAR1 had the most suppressive effect on the biomarkers tested. Since the specific responses to genotoxic stress, the contribution of each protein to cell proliferation, and the activation of DNA damage biomarkers were not equivalent, this suggests the possibility that at least some of the proteins, most notably GAR1, may potentially function independently of their respective roles within H/ACA RNP complexes. PMID:26265134

  12. Protein and gene expression characteristics of heterogeneous nuclear ribonucleoprotein H1 in esophageal squamous cell carcinoma

    PubMed Central

    Sun, Yu-Lin; Liu, Fei; Liu, Fang; Zhao, Xiao-Hang

    2016-01-01

    AIM To investigate the expression characteristics of heterogeneous nuclear ribonucleoprotein H1 (HNRNPH1) mRNA and protein in cell lines and tissues of esophageal squamous cell carcinoma (ESCC). METHODS Western blotting was used to assess the expression of HNRNPH1 protein in seven ESCC cell lines and 30 paired fresh tissue specimens. The subcellular localization of HNRNPH1 was determined by immunofluorescence in ESCC cells. The RNA sequencing data from 87 patients with ESCC were obtained from the cancer genome atlas (TCGA), and the expression and clinical characteristics analysis of different transcript variants of HNRNPH1 were evaluated in this dataset. In addition, immunohistochemistry was carried out to detect the expression of HNRNPH1 protein in 125 patients. RESULTS The expression of HNRNPH1 protein varied across different ESCC cell lines. It was exclusively restricted to the nucleus of the ESCC cells. There are two transcript variants of the HNRNPH1 gene. Variant 1 was constitutively expressed, and its expression did not change during tumorigenesis. In contrast, levels of variant 2 were low in non-tumorous tissues and were dramatically increased in ESCC (P = 0.0026). The high levels of variant 2 were associated with poorer differentiated tumors (P = 0.0287). Furthermore, in paired fresh tissue specimens, HNRNPH1 protein was overexpressed in 73.3% (22/30) of neoplastic tissues. HNRNPH1 was significantly upregulated in ESCC, with strong staining in 43.2% (54/125) of tumor tissues and 22.4% (28/125) of matched non-cancerous tissues (P = 0.0005). Positive HNRNPH1 expression was significantly associated with poor tumor differentiation degree (P = 0.0337). CONCLUSION The different alternative transcript variants of HNRNPH1 exhibited different expression changes during tumorigenesis. Its mRNA and protein were overexpressed in ESCC and associated with poorer differentiation of tumor cells. These findings highlight the potential of HNRNPH1 in the therapy and diagnosis

  13. Generation of knock-in primary human T cells using Cas9 ribonucleoproteins

    DOE PAGES

    Schumann, Kathrin; Lin, Steven; Boyer, Eric; Simeonov, Dimitre R.; Subramaniam, Meena; Gate, Rachel E.; Haliburton, Genevieve E.; Ye, Chun J.; Bluestone, Jeffrey A.; Doudna, Jennifer A.; et al

    2015-07-27

    T-cell genome engineering holds great promise for cell-based therapies for cancer, HIV, primary immune deficiencies, and autoimmune diseases, but genetic manipulation of human T cells has been challenging. Improved tools are needed to efficiently “knock out” genes and “knock in” targeted genome modifications to modulate T-cell function and correct disease-associated mutations. CRISPR/Cas9 technology is facilitating genome engineering in many cell types, but in human T cells its efficiency has been limited and it has not yet proven useful for targeted nucleotide replacements. Here we report efficient genome engineering in human CD4+ T cells using Cas9:single-guide RNA ribonucleoproteins (Cas9 RNPs). Cas9more » RNPs allowed ablation of CXCR4, a coreceptor for HIV entry. Cas9 RNP electroporation caused up to ~40% of cells to lose high-level cell-surface expression of CXCR4, and edited cells could be enriched by sorting based on low CXCR4 expression. Importantly, Cas9 RNPs paired with homology-directed repair template oligonucleotides generated a high frequency of targeted genome modifications in primary T cells. Targeted nucleotide replacement was achieved in CXCR4 and PD-1 (PDCD1), a regulator of T-cell exhaustion that is a validated target for tumor immunotherapy. Deep sequencing of a target site confirmed that Cas9 RNPs generated knock-in genome modifications with up to ~20% efficiency, which accounted for up to approximately one-third of total editing events. These results establish Cas9 RNP technology for diverse experimental and therapeutic genome engineering applications in primary human T cells.« less

  14. Protein and gene expression characteristics of heterogeneous nuclear ribonucleoprotein H1 in esophageal squamous cell carcinoma

    PubMed Central

    Sun, Yu-Lin; Liu, Fei; Liu, Fang; Zhao, Xiao-Hang

    2016-01-01

    AIM To investigate the expression characteristics of heterogeneous nuclear ribonucleoprotein H1 (HNRNPH1) mRNA and protein in cell lines and tissues of esophageal squamous cell carcinoma (ESCC). METHODS Western blotting was used to assess the expression of HNRNPH1 protein in seven ESCC cell lines and 30 paired fresh tissue specimens. The subcellular localization of HNRNPH1 was determined by immunofluorescence in ESCC cells. The RNA sequencing data from 87 patients with ESCC were obtained from the cancer genome atlas (TCGA), and the expression and clinical characteristics analysis of different transcript variants of HNRNPH1 were evaluated in this dataset. In addition, immunohistochemistry was carried out to detect the expression of HNRNPH1 protein in 125 patients. RESULTS The expression of HNRNPH1 protein varied across different ESCC cell lines. It was exclusively restricted to the nucleus of the ESCC cells. There are two transcript variants of the HNRNPH1 gene. Variant 1 was constitutively expressed, and its expression did not change during tumorigenesis. In contrast, levels of variant 2 were low in non-tumorous tissues and were dramatically increased in ESCC (P = 0.0026). The high levels of variant 2 were associated with poorer differentiated tumors (P = 0.0287). Furthermore, in paired fresh tissue specimens, HNRNPH1 protein was overexpressed in 73.3% (22/30) of neoplastic tissues. HNRNPH1 was significantly upregulated in ESCC, with strong staining in 43.2% (54/125) of tumor tissues and 22.4% (28/125) of matched non-cancerous tissues (P = 0.0005). Positive HNRNPH1 expression was significantly associated with poor tumor differentiation degree (P = 0.0337). CONCLUSION The different alternative transcript variants of HNRNPH1 exhibited different expression changes during tumorigenesis. Its mRNA and protein were overexpressed in ESCC and associated with poorer differentiation of tumor cells. These findings highlight the potential of HNRNPH1 in the therapy and diagnosis

  15. When the Largest Spiral is Formed

    NASA Astrophysics Data System (ADS)

    Eufrasio, Rafael T.; de Mello, Duília F.; Urrutia-Viscarra, Fernanda; de Oliveira, Claudia Mendes; Dwek, Eli

    2013-03-01

    We used UV-to-IR archival data to investigate the nature of the giant spiral galaxy, NGC 6872, 65 Mpc away. It belongs to the southern Pavo group and is interacting with a small lenticular galaxy, IC4970. GALEX UV images show a very large part of the galaxy not seen before, making it one of the largest spiral galaxies known, with a physical size greater than 150 kpc. The SED of 17 regions (10 kpc of diameter) across the two arms show a remarkable spatial distribution, as if they were mirror images with respect to their stellar population. However, the last 40 kpc of the northeastern arm are much bluer than any other region of the southwestern one. There is a strong spatial correlation between the NUV luminosity and the distance to the nucleus. The UV data supports the scenario of an interaction at 130 Myr which triggered star formation all over the disk of NGC 6872. The tip of the northeastern arm resembles a tidal dwarf galaxy in the process of formation.

  16. The largest volcanic eruptions on Earth

    NASA Astrophysics Data System (ADS)

    Bryan, Scott E.; Peate, Ingrid Ukstins; Peate, David W.; Self, Stephen; Jerram, Dougal A.; Mawby, Michael R.; Marsh, J. S. (Goonie); Miller, Jodie A.

    2010-10-01

    Large igneous provinces (LIPs) are sites of the most frequently recurring, largest volume basaltic and silicic eruptions in Earth history. These large-volume (> 1000 km 3 dense rock equivalent) and large-magnitude (> M8) eruptions produce areally extensive (10 4-10 5 km 2) basaltic lava flow fields and silicic ignimbrites that are the main building blocks of LIPs. Available information on the largest eruptive units are primarily from the Columbia River and Deccan provinces for the dimensions of flood basalt eruptions, and the Paraná-Etendeka and Afro-Arabian provinces for the silicic ignimbrite eruptions. In addition, three large-volume (675-2000 km 3) silicic lava flows have also been mapped out in the Proterozoic Gawler Range province (Australia), an interpreted LIP remnant. Magma volumes of > 1000 km 3 have also been emplaced as high-level basaltic and rhyolitic sills in LIPs. The data sets indicate comparable eruption magnitudes between the basaltic and silicic eruptions, but due to considerable volumes residing as co-ignimbrite ash deposits, the current volume constraints for the silicic ignimbrite eruptions may be considerably underestimated. Magma composition thus appears to be no barrier to the volume of magma emitted during an individual eruption. Despite this general similarity in magnitude, flood basaltic and silicic eruptions are very different in terms of eruption style, duration, intensity, vent configuration, and emplacement style. Flood basaltic eruptions are dominantly effusive and Hawaiian-Strombolian in style, with magma discharge rates of ~ 10 6-10 8 kg s -1 and eruption durations estimated at years to tens of years that emplace dominantly compound pahoehoe lava flow fields. Effusive and fissural eruptions have also emplaced some large-volume silicic lavas, but discharge rates are unknown, and may be up to an order of magnitude greater than those of flood basalt lava eruptions for emplacement to be on realistic time scales (< 10 years). Most

  17. Purification of antigenically intact Ro ribonucleoproteins; biochemical and immunological evidence that the 52-kD protein is not a Ro protein.

    PubMed Central

    Boire, G; Gendron, M; Monast, N; Bastin, B; Ménard, H A

    1995-01-01

    Anti-Ro sera immunoprecipitate Ro ribonucleoproteins (RNPs) from human cell extracts. Ro RNPs are biochemically heterogeneous particles whose functions are unknown and whose exact composition remains controversial. In addition to 60-kD Ro and to La proteins, a 52-kD polypeptide (p52) has been proposed to be a stable component of the Ro RNPs. To confirm the immunological studies supporting this hypothesis, we have biochemically purified Ro RNPs from HeLa cells using non-denaturing conditions. Ro RNPs segregated into three distinct populations, one of which only contained hY5 RNA (RohY5 RNPs). No p52 co-purified with Ro RNPs. Despite the absence of p52, purified Ro RNPs had biochemical and immunological properties identical to those of unfractionated Ro RNPs. Many anti-Ro sera only recognize p52 in immunoblots, and are said to be monospecific anti-p52. Preincubation with purified RohY5 RNPs (free of p52) of all human anti-Ro (including so-called monospecific anti-p52) sera abolished their capacity to immunoprecipitate Ro RNPs from unfractionated HeLa cell extracts. Conversely, preincubation of anti-Ro sera with purified p52 protein specifically inhibited recognition of p52 in immunoblots, but did not interfere with immunoprecipitation of Ro RNPs. Our data demonstrate that anti-p52 antibodies do not target intact Ro RNPs, nor do they target the native 60-kD Ro protein. Contrary to previous reports, p52 protein is not a stable component of antigenically intact Ro RNPs. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 Fig. 5 Fig. 6 PMID:7774061

  18. When the UV Unveils the Largest Spiral

    NASA Astrophysics Data System (ADS)

    Eufrasio, Rafael T.; De Mello, D. F.; Urrutia-Viscarra, F.; Mendes de Oliveira, C.; Dwek, E.

    2013-01-01

    We used archival data GALEX (FUV and NUV), VLT (UBVRI), 2MASS (J,H,K), and Spitzer (IRAC) to investigate the nature of the giant spiral galaxy, NGC 6872, 65 Mpc away. It belongs to the southern Pavo group and is interacting with a small lenticular galaxy, IC4970. GALEX UV images show a very large part of the galaxy not seen before, making it one of the largest spiral galaxies known, with physical size greater than 150 kpc. We have convolved all the images to the same 5.3” FHWM spatial resolution, reprojected them to the same astrometric grid (pixel size of 1.0”) and obtained SED for each pixel. Photometry was performed across the galaxy in circular apertures with diameters of 32”(or 10 kpc at 65 Mpc). When the SEDs are normalized by the 4.5 micron fluxes, the FUV and NUV fluxes span a wide range of a thousand, while the main properties of the normalized SEDs are almost unchanged from the R band to 4.5 micron. We also find an intriguing symmetry between regions in the southwestern and the northeastern arms having nearly identical SEDs. Furthermore, we estimated the metallicity of 12 areas using multi-object spectra taken with Gemini GMOS and we find no clear signature of metallicity gradient, trend supported by numerical simulations (Rupke el at. 2010). As proposed by Mihos et al. (1993) and Horellou & Koribalski (2007), NGC 6872 suffered a major collision with IC 4970 around 130 Myr ago. Our results are consistent with a global mixing of the pre-collision stellar population all over the disk of NGC 6872 at the epoch of the collision and a consequent star formation propagation to the outskirts of the galaxy. This mixing may have contributed to triggering star formation, in agreement with what was predicted by Bastian et al. (2005). The last 40kpc of the northeastern arm is UV-brighter than any region in the other arm, having the youngest population and least contamination of pre-collision stars thrown there by the encounter. There is also a strong UV source at

  19. Characterization of ribonucleoprotein complexes containing an abundant polyadenylated nuclear RNA encoded by Kaposi's sarcoma-associated herpesvirus (human herpesvirus 8).

    PubMed Central

    Zhong, W; Ganem, D

    1997-01-01

    Infection with Kaposi's sarcoma-associated herpesvirus (KSHV) (also called human herpesvirus 8) is strongly linked to all forms of Kaposi's sarcoma. We have previously identified two polyadenylated KSHV transcripts that are actively transcribed in Kaposi's sarcoma (KS) tumors and in KSHV-infected B-lymphoma cells. One of these RNAs (termed T1.1 or nut-1 RNA) is a 1.1-kb transcript present in a subpopulation of KS tumor cells. This RNA is localized to the nucleus of infected cells and has no open reading frames longer than 62 codons, suggesting that it may not function as an mRNA in vivo. Here we demonstrate that nut-1 RNA is a lytic-cycle gene product that is found in high-molecular-weight ribonucleoprotein complexes in infected cell nuclei. The transcript lacks the trimethylguanosine (TMG) cap found in many U-like small nuclear RNAs, but a subpopulation of nut-1 RNAs can associate with Sm protein-containing small nuclear ribonucleoproteins, as judged by immunoprecipitation analyses using monoclonal anti-Sm and anti-TMG antibodies. This interaction does not require other viral gene products, and deletion of the sole candidate Sm binding site on nut-1 RNA does not ablate this association. This finding suggests an indirect interaction with Sm-containing structures, and models for such associations are presented. PMID:8995643

  20. Spitzer/IRAC Photometry Of The Four Largest Uranian Satellites

    NASA Astrophysics Data System (ADS)

    Cartwright, Richard; Emery, J.; Rivkin, A.; Trilling, D.

    2012-10-01

    The surfaces of the four largest Uranian satellites are dominated by water ice and a spectrally neutral constituent that is likely carbonaceous in composition. CO2 ice has been detected on Ariel, Umbriel, and Titania, with no detection on the furthest regular Uranian satellite, Oberon (Grundy et al., 2003, 2006). Whether CO2 ice is primordial or is actively produced in the Uranian system is unclear; however, it seems unlikely that primordial CO2 ice would remain exposed on an icy satellite surface over the age of the Solar System. One possible mechanism for producing CO2 ice is bombardment of water ice and carbonaceous material by charged particles caught in Uranus’ magnetic field. Unlike the other large Uranian satellites, Oberon spends part of its orbit outside the confines of Uranus’ magnetic field, which might help explain why CO2 ice has yet to be detected on Oberon. We are using photometric data gathered by the Infrared Array Camera (IRAC), onboard the Spitzer Space Telescope (SST), in order to search for the signature of CO2 ice on Oberon, and confirm its presence on Ariel, Umbriel, and Titania at longer wavelengths than previous studies. IRAC collects data in four different channels, which are centered roughly at 3.6, 4.5, 5.8, and 8.0 µm. Additionally, we are gathering spectroscopic data using SpeX on IRTF, at similar longitudes to the IRAC observations, in order to characterize the distribution of CO2 ice on these icy satellites over a wide range of near-infrared wavelengths. Our preliminary photometry results for Oberon indicate that there is a steep reduction in reflected solar flux from channel 1 to channel 2, suggesting that surface materials are absorbing photons at wavelengths within the bandpass of channel 2. We will present the results of our photometric analysis of the four largest Uranian moons.

  1. Largest-ever Ozone Hole over Antarctica

    NASA Technical Reports Server (NTRS)

    2002-01-01

    A NASA instrument has detected an Antarctic ozone 'hole' (what scientists call an 'ozone depletion area') that is three times larger than the entire land mass of the United States-the largest such area ever observed. The 'hole' expanded to a record size of approximately 11 million square miles (28.3 million square kilometers) on Sept. 3, 2000. The previous record was approximately 10.5 million square miles (27.2 million square km) on Sept. 19, 1998. The ozone hole's size currently has stabilized, but the low levels in its interior continue to fall. The lowest readings in the ozone hole are typically observed in late September or early October each year. 'These observations reinforce concerns about the frailty of Earth's ozone layer. Although production of ozone-destroying gases has been curtailed under international agreements, concentrations of the gases in the stratosphere are only now reaching their peak. Due to their long persistence in the atmosphere, it will be many decades before the ozone hole is no longer an annual occurrence,' said Dr. Michael J. Kurylo, manager of the Upper Atmosphere Research Program, NASA Headquarters, Washington, DC. Ozone molecules, made up of three atoms of oxygen, comprise a thin layer of the atmosphere that absorbs harmful ultraviolet radiation from the Sun. Most atmospheric ozone is found between approximately six miles (9.5 km) and 18 miles (29 km) above the Earth's surface. Scientists continuing to investigate this enormous hole are somewhat surprised by its size. The reasons behind the dimensions involve both early-spring conditions, and an extremely intense Antarctic vortex. The Antarctic vortex is an upper-altitude stratospheric air current that sweeps around the Antarctic continent, confining the Antarctic ozone hole. 'Variations in the size of the ozone hole and of ozone depletion accompanying it from one year to the next are not unexpected,' said Dr. Jack Kaye, Office of Earth Sciences Research Director, NASA Headquarters

  2. First Light for World's Largest 'Thermometer Camera'

    NASA Astrophysics Data System (ADS)

    2007-08-01

    LABOCA in Service at APEX The world's largest bolometer camera for submillimetre astronomy is now in service at the 12-m APEX telescope, located on the 5100m high Chajnantor plateau in the Chilean Andes. LABOCA was specifically designed for the study of extremely cold astronomical objects and, with its large field of view and very high sensitivity, will open new vistas in our knowledge of how stars form and how the first galaxies emerged from the Big Bang. ESO PR Photo 35a/07 ESO PR Photo 35a/07 LABOCA on APEX "A large fraction of all the gas in the Universe has extremely cold temperatures of around minus 250 degrees Celsius, a mere 20 degrees above absolute zero," says Karl Menten, director at the Max Planck Institute for Radioastronomy (MPIfR) in Bonn, Germany, that built LABOCA. "Studying these cold clouds requires looking at the light they radiate in the submillimetre range, with very sophisticated detectors." Astronomers use bolometers for this task, which are, in essence, thermometers. They detect incoming radiation by registering the resulting rise in temperature. More specifically, a bolometer detector consists of an extremely thin foil that absorbs the incoming light. Any change of the radiation's intensity results in a slight change in temperature of the foil, which can then be registered by sensitive electronic thermometers. To be able to measure such minute temperature fluctuations requires the bolometers to be cooled down to less than 0.3 degrees above absolute zero, that is below minus 272.85 degrees Celsius. "Cooling to such low temperatures requires using liquid helium, which is no simple feat for an observatory located at 5100m altitude," says Carlos De Breuck, the APEX instrument scientist at ESO. Nor is it simple to measure the weak temperature radiation of astronomical objects. Millimetre and submillimetre radiation opens a window into the enigmatic cold Universe, but the signals from space are heavily absorbed by water vapour in the Earth

  3. Comparative study of two box H/ACA ribonucleoprotein pseudouridine-synthases: relation between conformational dynamics of the guide RNA, enzyme assembly and activity.

    PubMed

    Fourmann, Jean-Baptiste; Tillault, Anne-Sophie; Blaud, Magali; Leclerc, Fabrice; Branlant, Christiane; Charpentier, Bruno

    2013-01-01

    Multiple RNA-guided pseudouridine synthases, H/ACA ribonucleoprotein particles (RNPs) which contain a guide RNA and four proteins, catalyze site-specific post-transcriptional isomerization of uridines into pseudouridines in substrate RNAs. In archaeal particles, the guide small RNA (sRNA) is anchored by the pseudouridine synthase aCBF5 and the ribosomal protein L7Ae. Protein aNOP10 interacts with both aCBF5 and L7Ae. The fourth protein, aGAR1, interacts with aCBF5 and enhances catalytic efficiency. Here, we compared the features of two H/ACA sRNAs, Pab21 and Pab91, from Pyrococcus abyssi. We found that aCBF5 binds much more weakly to Pab91 than to Pab21. Surprisingly, the Pab91 sRNP exhibits a higher catalytic efficiency than the Pab21 sRNP. We thus investigated the molecular basis of the differential efficiencies observed for the assembly and catalytic activity of the two enzymes. For this, we compared profiles of the extent of lead-induced cleavages in these sRNAs during a stepwise reconstitution of the sRNPs, and analyzed the impact of the absence of the aNOP10-L7Ae interaction. Such probing experiments indicated that the sRNAs undergo a series of conformational changes upon RNP assembly. These changes were also evaluated directly by circular dichroism (CD) spectroscopy, a tool highly adapted to analyzing RNA conformational dynamics. In addition, our results reveal that the conformation of helix P1 formed at the base of the H/ACA sRNAs is optimized in Pab21 for efficient aCBF5 binding and RNP assembly. Moreover, P1 swapping improved the assembly of the Pab91 sRNP. Nonetheless, efficient aCBF5 binding probably also relies on the pseudouridylation pocket which is not optimized for high activity in the case of Pab21.

  4. Comparative Study of Two Box H/ACA Ribonucleoprotein Pseudouridine-Synthases: Relation between Conformational Dynamics of the Guide RNA, Enzyme Assembly and Activity

    PubMed Central

    Leclerc, Fabrice; Branlant, Christiane; Charpentier, Bruno

    2013-01-01

    Multiple RNA-guided pseudouridine synthases, H/ACA ribonucleoprotein particles (RNPs) which contain a guide RNA and four proteins, catalyze site-specific post-transcriptional isomerization of uridines into pseudouridines in substrate RNAs. In archaeal particles, the guide small RNA (sRNA) is anchored by the pseudouridine synthase aCBF5 and the ribosomal protein L7Ae. Protein aNOP10 interacts with both aCBF5 and L7Ae. The fourth protein, aGAR1, interacts with aCBF5 and enhances catalytic efficiency. Here, we compared the features of two H/ACA sRNAs, Pab21 and Pab91, from Pyrococcus abyssi. We found that aCBF5 binds much more weakly to Pab91 than to Pab21. Surprisingly, the Pab91 sRNP exhibits a higher catalytic efficiency than the Pab21 sRNP. We thus investigated the molecular basis of the differential efficiencies observed for the assembly and catalytic activity of the two enzymes. For this, we compared profiles of the extent of lead-induced cleavages in these sRNAs during a stepwise reconstitution of the sRNPs, and analyzed the impact of the absence of the aNOP10–L7Ae interaction. Such probing experiments indicated that the sRNAs undergo a series of conformational changes upon RNP assembly. These changes were also evaluated directly by circular dichroism (CD) spectroscopy, a tool highly adapted to analyzing RNA conformational dynamics. In addition, our results reveal that the conformation of helix P1 formed at the base of the H/ACA sRNAs is optimized in Pab21 for efficient aCBF5 binding and RNP assembly. Moreover, P1 swapping improved the assembly of the Pab91 sRNP. Nonetheless, efficient aCBF5 binding probably also relies on the pseudouridylation pocket which is not optimized for high activity in the case of Pab21. PMID:23922977

  5. Detail of the largest generator, an Enterprise 5000, also known ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Detail of the largest generator, an Enterprise 5000, also known as "Big Bertha", looking southeast - March Air Force Base, Strategic Air Command, Utility Building, 5220 Riverside Drive, Moreno Valley, Riverside County, CA

  6. Recognition of subsets of the mammalian A/B-type core heterogeneous nuclear ribonucleoprotein polypeptides by novel autoantibodies.

    PubMed Central

    Dangli, A; Plomaritoglou, A; Boutou, E; Vassiliadou, N; Moutsopoulos, H M; Guialis, A

    1996-01-01

    The structurally related A/B-type core heterogeneous nuclear ribonucleoprotein (hnRNP) polypeptides of 34-39 kDa (A1, A2, B1 and B2) belong to a family of RNA-binding proteins that are major components of 40 S hnRNP complexes. By two-dimensional gel electrophoresis and peptide mapping analysis we compared each member of the A/B-type core proteins in the human and rat liver cells. This comparison revealed the unique presence in rat cells of major protein species, referred to as mBx polypeptides, that appeared as three charge isoforms at a position corresponding to the minor HeLa B1b protein spot. In addition, clear differences in the ratios of the A1 polypeptide to the A1b isoform were observed. The detection, in sera of patients with rheumatic autoimmune diseases, of two novel autoantibody specificities, one recognizing solely B2 protein and the second both the B2 and mBx polypeptides, helped to identify mBx proteins as new A/B-type hnRNP components, immunologically related to B2 protein. A common immunoreactive V8 protease peptide of approx. 17 kDa has been identified in B2 and mBx hnRNP polypeptides. mBx protein species are identified in cells of murine origin, and have a ubiquitous tissue distribution and developmental appearance. PMID:9003360

  7. Systemic delivery of siRNA in pumpkin by a plant PHLOEM SMALL RNA-BINDING PROTEIN 1-ribonucleoprotein complex.

    PubMed

    Ham, Byung-Kook; Li, Gang; Jia, Weitao; Leary, Julie A; Lucas, William J

    2014-11-01

    In plants, the vascular system, specifically the phloem, functions in delivery of small RNA (sRNA) to exert epigenetic control over developmental and defense-related processes. Although the importance of systemic sRNA delivery has been established, information is currently lacking concerning the nature of the protein machinery involved in this process. Here, we show that a PHLOEM SMALL-RNA BINDING PROTEIN 1 (PSRP1) serves as the basis for formation of an sRNA ribonucleoprotein complex (sRNPC) that delivers sRNA (primarily 24 nt) to sink organs. Assembly of this complex is facilitated through PSRP1 phosphorylation by a phloem-localized protein kinase, PSRPK1. During long-distance transport, PSRP1-sRNPC is stable against phloem phosphatase activity. Within target tissues, phosphatase activity results in disassembly of PSRP1-sRNPC, a process that is probably required for unloading cargo sRNA into surrounding cells. These findings provide an insight into the mechanism involved in delivery of sRNA associated with systemic gene silencing in plants.

  8. The human 64-kDa polyadenylylation factor contains a ribonucleoprotein-type RNA binding domain and unusual auxiliary motifs.

    PubMed Central

    Takagaki, Y; MacDonald, C C; Shenk, T; Manley, J L

    1992-01-01

    Cleavage stimulation factor is one of the multiple factors required for 3'-end cleavage of mammalian pre-mRNAs. We have shown previously that this factor is composed of three subunits with estimated molecular masses of 77, 64, and 50 kDa and that the 64-kDa subunit can be UV-crosslinked to RNA in a polyadenylylation signal (AAUAAA)-dependent manner. We have now isolated cDNAs encoding the 64-kDa subunit of human cleavage stimulation factor. The 64-kDa subunit contains a ribonucleoprotein-type RNA binding domain in the N-terminal region and a repeat structure in the C-terminal region in which a pentapeptide sequence (consensus MEARA/G) is repeated 12 times and the formation of a long alpha-helix stabilized by salt bridges is predicted. An approximately 270-amino acid segment surrounding this repeat structure is highly enriched in proline and glycine residues (approximately 20% for each). When cloned 64-kDa subunit was expressed in Escherichia coli, an N-terminal fragment containing the RNA binding domain bound to RNAs in a polyadenylylation-signal-independent manner, suggesting that the RNA binding domain is directly involved in the binding of the 64-kDa subunit to pre-mRNAs. Images PMID:1741396

  9. An analytical platform for mass spectrometry-based identification and chemical analysis of RNA in ribonucleoprotein complexes.

    PubMed

    Taoka, Masato; Yamauchi, Yoshio; Nobe, Yuko; Masaki, Shunpei; Nakayama, Hiroshi; Ishikawa, Hideaki; Takahashi, Nobuhiro; Isobe, Toshiaki

    2009-11-01

    We describe here a mass spectrometry (MS)-based analytical platform of RNA, which combines direct nano-flow reversed-phase liquid chromatography (RPLC) on a spray tip column and a high-resolution LTQ-Orbitrap mass spectrometer. Operating RPLC under a very low flow rate with volatile solvents and MS in the negative mode, we could estimate highly accurate mass values sufficient to predict the nucleotide composition of a approximately 21-nucleotide small interfering RNA, detect post-transcriptional modifications in yeast tRNA, and perform collision-induced dissociation/tandem MS-based structural analysis of nucleolytic fragments of RNA at a sub-femtomole level. Importantly, the method allowed the identification and chemical analysis of small RNAs in ribonucleoprotein (RNP) complex, such as the pre-spliceosomal RNP complex, which was pulled down from cultured cells with a tagged protein cofactor as bait. We have recently developed a unique genome-oriented database search engine, Ariadne, which allows tandem MS-based identification of RNAs in biological samples. Thus, the method presented here has broad potential for automated analysis of RNA; it complements conventional molecular biology-based techniques and is particularly suited for simultaneous analysis of the composition, structure, interaction, and dynamics of RNA and protein components in various cellular RNP complexes.

  10. RIP-seq analysis of eukaryotic Sm proteins identifies three major categories of Sm-containing ribonucleoproteins

    PubMed Central

    2014-01-01

    Background Sm proteins are multimeric RNA-binding factors, found in all three domains of life. Eukaryotic Sm proteins, together with their associated RNAs, form small ribonucleoprotein (RNP) complexes important in multiple aspects of gene regulation. Comprehensive knowledge of the RNA components of Sm RNPs is critical for understanding their functions. Results We developed a multi-targeting RNA-immunoprecipitation sequencing (RIP-seq) strategy to reliably identify Sm-associated RNAs from Drosophila ovaries and cultured human cells. Using this method, we discovered three major categories of Sm-associated transcripts: small nuclear (sn)RNAs, small Cajal body (sca)RNAs and mRNAs. Additional RIP-PCR analysis showed both ubiquitous and tissue-specific interactions. We provide evidence that the mRNA-Sm interactions are mediated by snRNPs, and that one of the mechanisms of interaction is via base pairing. Moreover, the Sm-associated mRNAs are mature, indicating a splicing-independent function for Sm RNPs. Conclusions This study represents the first comprehensive analysis of eukaryotic Sm-containing RNPs, and provides a basis for additional functional analyses of Sm proteins and their associated snRNPs outside of the context of pre-mRNA splicing. Our findings expand the repertoire of eukaryotic Sm-containing RNPs and suggest new functions for snRNPs in mRNA metabolism. PMID:24393626

  11. An analytical platform for mass spectrometry-based identification and chemical analysis of RNA in ribonucleoprotein complexes

    PubMed Central

    Taoka, Masato; Yamauchi, Yoshio; Nobe, Yuko; Masaki, Shunpei; Nakayama, Hiroshi; Ishikawa, Hideaki; Takahashi, Nobuhiro; Isobe, Toshiaki

    2009-01-01

    We describe here a mass spectrometry (MS)-based analytical platform of RNA, which combines direct nano-flow reversed-phase liquid chromatography (RPLC) on a spray tip column and a high-resolution LTQ-Orbitrap mass spectrometer. Operating RPLC under a very low flow rate with volatile solvents and MS in the negative mode, we could estimate highly accurate mass values sufficient to predict the nucleotide composition of a ∼21-nucleotide small interfering RNA, detect post-transcriptional modifications in yeast tRNA, and perform collision-induced dissociation/tandem MS-based structural analysis of nucleolytic fragments of RNA at a sub-femtomole level. Importantly, the method allowed the identification and chemical analysis of small RNAs in ribonucleoprotein (RNP) complex, such as the pre-spliceosomal RNP complex, which was pulled down from cultured cells with a tagged protein cofactor as bait. We have recently developed a unique genome-oriented database search engine, Ariadne, which allows tandem MS-based identification of RNAs in biological samples. Thus, the method presented here has broad potential for automated analysis of RNA; it complements conventional molecular biology-based techniques and is particularly suited for simultaneous analysis of the composition, structure, interaction, and dynamics of RNA and protein components in various cellular RNP complexes. PMID:19740761

  12. Rapid isolation and single-molecule analysis of ribonucleoproteins from cell lysate by SNAP-SiMPull.

    PubMed

    Rodgers, Margaret L; Paulson, Joshua; Hoskins, Aaron A

    2015-05-01

    Large macromolecular complexes such as the spliceosomal small nuclear ribonucleoproteins (snRNPs) play a variety of roles within the cell. Despite their biological importance, biochemical studies of snRNPs and other machines are often thwarted by practical difficulties in the isolation of sufficient amounts of material. Studies of the snRNPs as well as other macromolecular machines would be greatly facilitated by new approaches that enable their isolation and biochemical characterization. One such approach is single-molecule pull-down (SiMPull) that combines in situ immunopurification of complexes from cell lysates with subsequent single-molecule fluorescence microscopy experiments. We report the development of a new method, called SNAP-SiMPull, that can readily be applied to studies of splicing factors and snRNPs isolated from whole-cell lysates. SNAP-SiMPull overcomes many of the limitations imposed by conventional SiMPull strategies that rely on fluorescent proteins. We have used SNAP-SiMPull to study the yeast branchpoint bridging protein (BBP) as well as the U1 and U6 snRNPs. SNAP-SiMPull will likely find broad use for rapidly isolating complex cellular machines for single-molecule fluorescence colocalization experiments. PMID:25805862

  13. Identification of heterogeneous nuclear ribonucleoprotein K (hnRNP K) as a repressor of C/EBPbeta-mediated gene activation.

    PubMed

    Miau, L H; Chang, C J; Shen, B J; Tsai, W H; Lee, S C

    1998-04-24

    Transcription factor C/EBPbeta has been known to regulate a wide array of genes including those involved in the acute-phase response. One of the molecular mechanisms underlying transcription activation by C/EBPbeta is through protein-protein interaction with other transcription factors. Here we report the identification and characterization of physical and functional interactions between C/EBPbeta and heterogeneous nuclear ribonucleoprotein (hnRNP) K. This interaction results in the repression of C/EBPbeta-dependent trans-activation of the agp gene. Footprinting assays indicate that hnRNP K cannot bind to the promoter region of agp gene or interfere with the binding of C/EBPbeta to its cognate DNA site. Furthermore, agp gene activation by the synergistic interaction of Nopp140 and C/EBPbeta is abolished by hnRNP K. The kinetics of appearance of C/EBPbeta-hnRNP K complex in the nuclear extract after initiation of acute-phase reaction indicates that hnRNP K functions as a negative regulator of C/EBPbeta-mediated activation of agp gene.

  14. Heterogeneous nuclear ribonucleoprotein K represses transcription from a cytosine/thymidine-rich element in the osteocalcin promoter

    PubMed Central

    2004-01-01

    HnRNP K (heterogeneous nuclear ribonucleoprotein K) was biochemically purified from a screen of proteins co-purifying with binding activity to the osteocalcin promoter. We identify hnRNP K as a novel repressor of osteocalcin gene transcription. Overexpression of hnRNP K lowers the expression of osteocalcin mRNA by 5-fold. Furthermore, luciferase reporter assays demonstrate that overexpression of hnRNP K represses osteocalcin transcription from a CT (cytosine/thymidine)-rich element in the proximal promoter. Electrophoretic mobility-shift analysis reveals that recombinant hnRNP K binds to the CT-rich element, but binds ss (single-stranded), rather than ds (double-stranded) oligonucleotide probes. Accordingly, hnRNP K antibody can supershift a binding activity present in nuclear extracts using ss sense, but not antisense or ds oligonucleotides corresponding to the CT-rich −95 to −47 osteocalcin promoter. Importantly, addition of recombinant hnRNP K to ROS 17/2.8 nuclear extract disrupts formation of a DNA–protein complex on ds CT element oligonucleotides. This action is mutually exclusive with hnRNP K's ability to bind ss DNA. These results demonstrate that hnRNPK, although co-purified with a dsDNA-binding activity, does not itself bind dsDNA. Rather, hnRNP K represses osteocalcin gene transcription by inhibiting the formation of a transcriptional complex on the CT element of the osteocalcin promoter. PMID:15361071

  15. Heterogeneous Nuclear Ribonucleoprotein L is required for the survival and functional integrity of murine hematopoietic stem cells.

    PubMed

    Gaudreau, Marie-Claude; Grapton, Damien; Helness, Anne; Vadnais, Charles; Fraszczak, Jennifer; Shooshtarizadeh, Peiman; Wilhelm, Brian; Robert, François; Heyd, Florian; Möröy, Tarik

    2016-01-01

    The proliferation and survival of hematopoietic stem cells (HSCs) has to be strictly coordinated to ensure the timely production of all blood cells. Here we report that the splice factor and RNA binding protein hnRNP L (heterogeneous nuclear ribonucleoprotein L) is required for hematopoiesis, since its genetic ablation in mice reduces almost all blood cell lineages and causes premature death of the animals. In agreement with this, we observed that hnRNP L deficient HSCs lack both the ability to self-renew and foster hematopoietic differentiation in transplanted hosts. They also display mitochondrial dysfunction, elevated levels of γH2AX, are Annexin V positive and incorporate propidium iodide indicating that they undergo cell death. Lin(-)c-Kit(+) fetal liver cells from hnRNP L deficient mice show high p53 protein levels and up-regulation of p53 target genes. In addition, cells lacking hnRNP L up-regulated the expression of the death receptors TrailR2 and CD95/Fas and show Caspase-3, Caspase-8 and Parp cleavage. Treatment with the pan-caspase inhibitor Z-VAD-fmk, but not the deletion of p53, restored cell survival in hnRNP L deficient cells. Our data suggest that hnRNP L is critical for the survival and functional integrity of HSCs by restricting the activation of caspase-dependent death receptor pathways. PMID:27271479

  16. Heterogeneous nuclear ribonucleoprotein B1 protein impairs DNA repair mediated through the inhibition of DNA-dependent protein kinase activity

    SciTech Connect

    Iwanaga, Kentaro; Sueoka, Naoko; Sato, Akemi; Hayashi, Shinichiro; Sueoka, Eisaburo . E-mail: sueokae@post.saga-med.ac.jp

    2005-08-05

    Heterogeneous nuclear ribonucleoprotein B1, an RNA binding protein, is overexpressed from the early stage of lung cancers; it is evident even in bronchial dysplasia, a premalignant lesion. We evaluated the proteins bound with hnRNP B1 and found that hnRNP B1 interacted with DNA-dependent protein kinase (DNA-PK) complex, and recombinant hnRNP B1 protein dose-dependently inhibited DNA-PK activity in vitro. To test the effect of hnRNP B1 on DNA repair, we performed comet assay after irradiation, using normal human bronchial epithelial (HBE) cells treated with siRNA for hnRNP A2/B1: reduction of hnRNP B1 treated with siRNA for hnRNP A2/B1 induced faster DNA repair in normal HBE cells. Considering these results, we assume that overexpression of hnRNP B1 occurring in the early stage of carcinogenesis inhibits DNA-PK activity, resulting in subsequent accumulation of erroneous rejoining of DNA double-strand breaks, causing tumor progression.

  17. Rapid isolation and single-molecule analysis of ribonucleoproteins from cell lysate by SNAP-SiMPull

    PubMed Central

    Rodgers, Margaret L.; Paulson, Joshua; Hoskins, Aaron A.

    2015-01-01

    Large macromolecular complexes such as the spliceosomal small nuclear ribonucleoproteins (snRNPs) play a variety of roles within the cell. Despite their biological importance, biochemical studies of snRNPs and other machines are often thwarted by practical difficulties in the isolation of sufficient amounts of material. Studies of the snRNPs as well as other macromolecular machines would be greatly facilitated by new approaches that enable their isolation and biochemical characterization. One such approach is single-molecule pull-down (SiMPull) that combines in situ immunopurification of complexes from cell lysates with subsequent single-molecule fluorescence microscopy experiments. We report the development of a new method, called SNAP-SiMPull, that can readily be applied to studies of splicing factors and snRNPs isolated from whole-cell lysates. SNAP-SiMPull overcomes many of the limitations imposed by conventional SiMPull strategies that rely on fluorescent proteins. We have used SNAP-SiMPull to study the yeast branchpoint bridging protein (BBP) as well as the U1 and U6 snRNPs. SNAP-SiMPull will likely find broad use for rapidly isolating complex cellular machines for single-molecule fluorescence colocalization experiments. PMID:25805862

  18. Heterogeneous Nuclear Ribonucleoprotein L is required for the survival and functional integrity of murine hematopoietic stem cells

    PubMed Central

    Gaudreau, Marie-Claude; Grapton, Damien; Helness, Anne; Vadnais, Charles; Fraszczak, Jennifer; Shooshtarizadeh, Peiman; Wilhelm, Brian; Robert, François; Heyd, Florian; Möröy, Tarik

    2016-01-01

    The proliferation and survival of hematopoietic stem cells (HSCs) has to be strictly coordinated to ensure the timely production of all blood cells. Here we report that the splice factor and RNA binding protein hnRNP L (heterogeneous nuclear ribonucleoprotein L) is required for hematopoiesis, since its genetic ablation in mice reduces almost all blood cell lineages and causes premature death of the animals. In agreement with this, we observed that hnRNP L deficient HSCs lack both the ability to self-renew and foster hematopoietic differentiation in transplanted hosts. They also display mitochondrial dysfunction, elevated levels of γH2AX, are Annexin V positive and incorporate propidium iodide indicating that they undergo cell death. Lin-c-Kit+ fetal liver cells from hnRNP L deficient mice show high p53 protein levels and up-regulation of p53 target genes. In addition, cells lacking hnRNP L up-regulated the expression of the death receptors TrailR2 and CD95/Fas and show Caspase-3, Caspase-8 and Parp cleavage. Treatment with the pan-caspase inhibitor Z-VAD-fmk, but not the deletion of p53, restored cell survival in hnRNP L deficient cells. Our data suggest that hnRNP L is critical for the survival and functional integrity of HSCs by restricting the activation of caspase-dependent death receptor pathways. PMID:27271479

  19. A ribonucleoprotein fragment of the 30 S ribosome of E. coli containing two contiguous domains of the 16 S RNA.

    PubMed

    Spitnik-Elson, P; Elson, D; Avital, S; Abramowitz, R

    1982-08-11

    Ribonucleoprotein fragments of the 30 S ribosome of E. coli have been prepared by limited ribonuclease digestion and mild heating of the ribosome in a constant ionic environment. One such fragment has been described previously. A second electrophoretically homogeneous fragment has now been isolated and its RNA and protein moieties have been characterized. It contains the 5' half of the 16 S RNA, encompassing domains I and II except for the extreme 5' terminus and several small gaps. Seven proteins are present: S4, S5, S6, S8, S12, S15 and S20. The RNA binding sites of five of these proteins are known, and all are RNA sequences that are present in the fragment. Published neutron scattering and immuno-electron microscopic data indicate that six of the proteins are clustered together in a cross sectional slice through the center of the subunit. After deproteinization, the RNA moiety gives two bands in gel electrophoresis, one containing domains I and II and the other, essentially only domain II. The former, although larger, migrates faster in gel electrophoresis, indicating that RNA domains I and II interact with each other in such a way as to become more compact than domain II by itself.

  20. Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins

    PubMed Central

    Kim, Sojung; Kim, Daesik; Cho, Seung Woo; Kim, Jungeun; Kim, Jin-Soo

    2014-01-01

    RNA-guided engineered nucleases (RGENs) derived from the prokaryotic adaptive immune system known as CRISPR (clustered, regularly interspaced, short palindromic repeat)/Cas (CRISPR-associated) enable genome editing in human cell lines, animals, and plants, but are limited by off-target effects and unwanted integration of DNA segments derived from plasmids encoding Cas9 and guide RNA at both on-target and off-target sites in the genome. Here, we deliver purified recombinant Cas9 protein and guide RNA into cultured human cells including hard-to-transfect fibroblasts and pluripotent stem cells. RGEN ribonucleoproteins (RNPs) induce site-specific mutations at frequencies of up to 79%, while reducing off-target mutations associated with plasmid transfection at off-target sites that differ by one or two nucleotides from on-target sites. RGEN RNPs cleave chromosomal DNA almost immediately after delivery and are degraded rapidly in cells, reducing off-target effects. Furthermore, RNP delivery is less stressful to human embryonic stem cells, producing at least twofold more colonies than does plasmid transfection. PMID:24696461

  1. Isolation and characterization of the heterogeneous nuclear RNA-ribonucleoprotein complex

    SciTech Connect

    Choi, Y.D.

    1985-01-01

    Exposure of cells to UV light of sufficient intensity brings about crosslinking of RNA to proteins which are in direct contact with it in vivo. The major (/sup 35/S)methionine-labeled proteins which become crosslinked to poly(A)/sup +/hnRNA in HeLa cells are of 120K, 68K, 53K, 43K, 41K, 38K, and 36K (K = kilodaltons). By immunizing mice with UV crosslinked complexes two monoclonal antibodies (2B12 and 4F4) against the C proteins (41K and 43K) and one (3G6) against the 120K protein of the hnRNP complex were obtained. Immunofluorescence microscopy demonstrates that the C proteins and 120K are segregated to the nucleus and are not associated with nucleoli or chromatin. The two C proteins are highly related to each other antigenically. Monoclonal antibody 4F4 identifies the C proteins of the hnRNP complex in widely divergent species from human to lizard. The C proteins are phosphorylated and are in contact with hnRNA in vivo. The hnRNP complex was isolated from vertebrate cell nuclei by immunoprecipitation with these monoclonal antibodies. This complex contains proteins and hnRNA of up to approx.10 kb. The major steady state labeled (/sup 35/S)methionine labeled proteins of the isolated complex from HeLa cells are of 34K, 36K, 36K (A1 and A2), 37K, 38K (B1 and B2), 41K, 43K (C1 and C2) and doublets at 68K and at 120K. These proteins are organized into a 30S particle. Large hnRNP complexes are composed of multiples of 30S particles which are connected by highly nuclease sensitive stretches of hnRNA. It it concluded that the hnRNP structure is an integral component of the mRNA formation pathway in the eukaryotic cell.

  2. Time scale of the largest imaginable magnetic storm

    NASA Astrophysics Data System (ADS)

    Vasyliūnas, V. M.

    2013-01-01

    The depression of the horizontal magnetic field at Earth's equator for the largest imaginable magnetic storm has been estimated (Vasyliūnas, 2011a) as -Dst ~ 2500 nT, from the assumption that the total pressure in the magnetosphere (plasma plus magnetic field perturbation) is limited, in order of magnitude, by the minimum pressure of Earth's dipole field at the location of each flux tube. The obvious related question is how long it would take the solar wind to supply the energy content of this largest storm. The maximum rate of energy input from the solar wind to the magnetosphere can be evaluated on the basis either of magnetotail stress balance or of polar cap potential saturation, giving an estimate of the time required to build up the largest storm, which (for solar-wind and magnetospheric parameter values typical of observed superstorms) is roughly between ~2 and ~6 h.

  3. The Virginia Pipeline: Australia's largest water recycling project.

    PubMed

    Kracman, B; Martin, R; Sztajnbok, P

    2001-01-01

    The need to conserve, reuse and recycle water is becoming increasingly important for both environmental and economic reasons. The Virginia Pipeline is Australia's largest water recycling project. More than half the output from (the capital of South Australia) Adelaide's largest wastewater treatment plant is further treated to achieve a product water quality fit for irrigation of vegetable crops with minimal public health restrictions. The project partners have a vision to achieve total reuse. To achieve this vision, recycled water will need to be stored during cool weather periods when the demand for water is low. Temporary storage of this water in poor quality aquifers is the subject of a major research project.

  4. Protein Kinase C-{delta} mediates down-regulation of heterogeneous nuclear ribonucleoprotein K protein: involvement in apoptosis induction

    SciTech Connect

    Gao, Feng-Hou; Wu, Ying-Li; Zhao, Meng; Chen, Guo-Qiang

    2009-11-15

    We reported previously that NSC606985, a camptothecin analogue, induces apoptosis of acute myeloid leukemia (AML) cells through proteolytic activation of protein kinase C delta ({Delta}PKC-{delta}). By subcellular proteome analysis, heterogeneous nuclear ribonucleoprotein K (hnRNP K) was identified as being significantly down-regulated in NSC606985-treated leukemic NB4 cells. HnRNP K, a docking protein for DNA, RNA, and transcriptional or translational molecules, is implicated in a host of processes involving the regulation of gene expression. However, the molecular mechanisms of hnRNP K reduction and its roles during apoptosis are still not understood. In the present study, we found that, following the appearance of the {Delta}PKC-{delta}, hnRNP K protein was significantly down-regulated in NSC606985, doxorubicin, arsenic trioxide and ultraviolet-induced apoptosis. We further provided evidence that {Delta}PKC-{delta} mediated the down-regulation of hnRNP K protein during apoptosis: PKC-{delta} inhibitor could rescue the reduction of hnRNP K; hnRNP K failed to be decreased in PKC-{delta}-deficient apoptotic KG1a cells; conditional induction of {Delta}PKC-{delta} in U937T cells directly down-regulated hnRNP K protein. Moreover, the proteasome inhibitor also inhibited the down-regulation of hnRNP K protein by apoptosis inducer and the conditional expression of {Delta}PKC-{delta}. More intriguingly, the suppression of hnRNP K with siRNA transfection significantly induced apoptosis. To our knowledge, this is the first demonstration that proteolytically activated PKC-{delta} down-regulates hnRNP K protein in a proteasome-dependent manner, which plays an important role in apoptosis induction.

  5. Cyclophilin E Functions as a Negative Regulator to Influenza Virus Replication by Impairing the Formation of the Viral Ribonucleoprotein Complex

    PubMed Central

    Wang, Zengfu; Liu, Xiaoling; Zhao, Zhendong; Xu, Chongfeng; Zhang, Ke; Chen, Caiwei; Sun, Lei; Gao, George F.; Ye, Xin; Liu, Wenjun

    2011-01-01

    Background The nucleoprotein (NP) of influenza A virus is a multifunctional protein that plays a critical role in the replication and transcription of the viral genome. Therefore, examining host factors that interact with NP may shed light on the mechanism of host restriction barriers and the tissue tropism of influenza A virus. Here, Cyclophilin E (CypE), a member of the peptidyl-propyl cis-trans isomerase (PPIase) family, was found to bind to NP and inhibit viral replication and transcription. Methodology/Principal Findings In the present study, CypE was found to interact with NP but not with the other components of the viral ribonucleoprotein complex (vRNP): PB1, PB2, and PA. Mutagenesis data revealed that the CypE domain comprised of residues 137–186 is responsible for its binding to NP. Functional analysis results indicated that CypE is a negative regulator in the influenza virus life cycle. Furthermore, knock-down of CypE resulted in increased levels of three types of viral RNA, suggesting that CypE negatively affects viral replication and transcription. Moreover, up-regulation of CypE inhibited the activity of influenza viral polymerase. We determined that the molecular mechanism by which CypE negatively regulates influenza virus replication and transcription is by interfering with NP self-association and the NP-PB1 and NP-PB2 interactions. Conclusions/Significance CypE is a host restriction factor that inhibits the functions of NP, as well as viral replication and transcription, by impairing the formation of the vRNP. The data presented here will help us to better understand the molecular mechanisms of host restriction barriers, host adaptation, and tissue tropism of influenza A virus. PMID:21887220

  6. A novel SDS-stable dimer of a heterogeneous nuclear ribonucleoprotein at presynaptic terminals of squid neurons.

    PubMed

    Lico, D T P; Lopes, G S; Brusco, J; Rosa, J C; Gould, R M; De Giorgis, J A; Larson, R E

    2015-08-01

    The presence of mRNAs in synaptic terminals and their regulated translation are important factors in neuronal communication and plasticity. Heterogeneous nuclear ribonucleoprotein (hnRNP) complexes are involved in the translocation, stability, and subcellular localization of mRNA and the regulation of its translation. Defects in these processes and mutations in components of the hnRNP complexes have been related to the formation of cytoplasmic inclusion bodies and neurodegenerative diseases. Despite much data on mRNA localization and evidence for protein synthesis, as well as the presence of translation machinery, in axons and presynaptic terminals, the identity of RNA-binding proteins involved in RNA transport and function in presynaptic regions is lacking. We previously characterized a strongly basic RNA-binding protein (p65), member of the hnRNPA/B subfamily, in squid presynaptic terminals. Intriguingly, in sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), p65 migrated as a 65-kDa protein, whereas members of the hnRNPA/B family typically have molecular masses ranging from 35 to 42kDa. In this report we present further biochemical and molecular characterization that shows endogenous p65 to be an SDS-stable dimer composed of ∼37-kDa hnRNPA/B-like subunits. We cloned and expressed a recombinant protein corresponding to squid hnRNPA/B-like protein and showed its propensity to aggregate and form SDS-stable dimers in vitro. Our data suggest that this unique hnRNPA/B-like protein co-localizes with synaptic vesicle protein 2 and RNA-binding protein ELAV and thus may serve as a link between local mRNA processing and presynaptic function and regulation.

  7. Alterations in polyribosome and messenger ribonucleic acid metabolism and messenger ribonucleoprotein utilization in osmotically stressed plant seedlings

    SciTech Connect

    Mason, H.S.

    1986-01-01

    Polyribosome aggregation state in growing tissues of barley and wheat leaf of stems of pea and squash was studied in relation to seedling growth and water status of the growing tissue in plants at various levels of osmotic stress. It was found to be highly correlated with water potential and osmotic potential of the growing tissue and with leaf of stem elongation rate. Stress rapidly reduced polyribosome content and water status in growing tissues of barley leaves; changes were slow and slight in the non-growing leaf blade. Membrane-bound and free polyribosomes were equally sensitive to stress-induced disaggregation. Incorporation of /sup 32/PO/sub 4//sup 3 -/ into ribosomal RNA was rapidly inhibited by stress, but stability of poly(A)/sup +/RNA relative to ribosomal RNA was similar in stressed and unstressed tissues, with a half-life of about 12 hours. Stress also caused progressive loss of poly(A)/sup +/RNA from these tissues. Quantitation of poly(A) and in vitro messenger template activity in polysome gradient fractions showed a shift of activity from the polysomal region to the region of 20-60 S in stressed plants. Messenger RNA in the 20-60 S region coded for the same peptides as mRNA found in the polysomal fraction. Nonpolysomal and polysome-derived messenger ribonucleoprotein complexes (mRNP) were isolated, and characteristic proteins were found associated with either fraction. Polysomal mRNP from stressed or unstressed plants were translated with similar efficiency in a wheat germ cell-free system. It was concluded that no translational inhibitory activity was associated with nonpolysomal mRNP from barley prepared as described.

  8. MicroRNA-33a disturbs influenza A virus replication by targeting ARCN1 and inhibiting viral ribonucleoprotein activity.

    PubMed

    Hu, Yi; Jiang, Liangzhen; Lai, Wenbin; Qin, Yujie; Zhang, Tinghong; Wang, Shixiong; Ye, Xin

    2016-01-01

    In order to explore the roles of microRNA(s) [miRNA(s)] in the influenza A virus life cycle, we compared the miRNA profiles of 293T and HeLa cell lines, as influenza A virus can replicate efficiently in 293T cells but only poorly in HeLa cells. We analysed differentially expressed miRNAs and identified five, including miR-33a, that could disturb influenza A virus replication significantly. Using TargetScan analysis, we found that ARCN1 could be a potential target of miR-33a. To confirm whether miR-33a could truly target ARCN1, we generated a luciferase reporter for the ARCN1 3' untranslated region (UTR) and performed a luciferase assay. The data indicated that miR-33a could suppress the luciferase activity of the reporter for the ARCN1 3' UTR but not a reporter in which the predicted miR-33a targeting sites on ARCN1 3' UTR were mutated. We performed immunoblotting to confirm that miR-33a could downregulate the protein level of ARCN1. Consistently, the level of ARCN1 protein in HeLa cells was significantly lower than that in 293T cells. We also demonstrated that ectopic expression of ARCN1 could partially rescue the inhibitory effect of miR-33a on virus replication. Furthermore, we demonstrated that miR-33a could impede virus replication at the stage of virus internalization, which was similar to the pattern for knockdown of ARCN1, indicating that miR-33a inhibits influenza virus infection by suppressing ARCN1 expression. In addition, we found that miR-33a could also weaken the viral ribonucleoprotein activity in an ARCN1-independent manner. In conclusion, we found that miR-33a is a novel inhibitory factor for influenza A virus replication. PMID:26498766

  9. Heterogeneous nuclear ribonucleoprotein K upregulates the kinetochore complex component NUF2 and promotes the tumorigenicity of colon cancer cells

    SciTech Connect

    Sugimasa, Hironobu; Taniue, Kenzui; Kurimoto, Akiko; Takeda, Yasuko; Kawasaki, Yoshihiro; Akiyama, Tetsu

    2015-03-27

    Heterogeneous nuclear ribonucleoprotein K (hnRNP K) is a multi-functional protein involved in transcription, mRNA splicing, mRNA stabilization and translation. Although hnRNP K has been suggested to play a role in the development of many cancers, its molecular function in colorectal cancer has remained elusive. Here we show that hnRNP K plays an important role in the mitotic process in HCT116 colon cancer cells. Furthermore, we demonstrate that hnRNP K directly transactivates the NUF2 gene, the product of which is a component of the NDC80 kinetochore complex and which is known to be critical for a stable spindle microtubule-kinetochore attachment. In addition, knockdown of both hnRNP K and NUF2 caused failure in metaphase chromosome alignment and drastic decrease in the growth of colon cancer cells. These results suggest that the hnRNP K-NUF2 axis is important for the mitotic process and proliferation of colon cancer cells and that this axis could be a target for the therapy of colon cancer. - Highlights: • hnRNP K is required for the tumorigenicity of colon cancer cells. • hnRNP K binds to the promoter region of NUF2 and activates its transcription. • NUF2 expression is correlated with hnRNP K expression in colorectal cancer tissue. • hnRNP K and NUF2 are required for metaphase chromosome alignment. • The hnRNP K-NUF2 axis is important for the proliferation of colon cancer cells.

  10. Cassini sheds light on Titan's second largest lake, Ligeia Mare

    NASA Astrophysics Data System (ADS)

    Wendel, JoAnna

    2014-04-01

    Saturn's largest moon, Titan, is known for its dense, planet-like atmosphere and large lakes most likely made of methane and ethane. It has been suggested that Titan's atmosphere and surface are a model of early Earth. Since the early 2000s, NASA's Cassini space probe has been unlocking secrets of the distant moon.

  11. Afterglows from the largest explosions in the universe

    PubMed Central

    Hartmann, Dieter H.

    1999-01-01

    The distinction of “largest explosions in the universe” has been bestowed on cosmic gamma-ray bursts. Their afterglows are brighter than supernovae and therefore are called hypernovae. Photometry and spectroscopy of these afterglows have provided major breakthroughs in our understanding of this mysterious phenomenon. PMID:10220364

  12. Animals as Our Companions: World's Largest Math Event 6.

    ERIC Educational Resources Information Center

    National Council of Teachers of Mathematics, Inc., Reston, VA.

    The World's Largest Math Event 6 (WLME 6) is the National Council of Teachers of Mathematics' (NCTM) celebration of mathematics and mathematics education and is the highlight of Mathematics Education Month. This year's event, slated for April 28, 2000, features the theme "Animals as Our Companions". This theme encourages students to explore the…

  13. The Single Largest Education Donor Comes with Controversy

    ERIC Educational Resources Information Center

    Finkel, Ed

    2012-01-01

    For the last decade, in districts big and small, the Bill & Melinda Gates Foundation has emerged as the largest private funder of educational efforts. This began with an initiative around small schools in the early to mid-2000s, mostly abandoned now, and has gained traction in the past few years in areas such as teacher evaluation, the Common Core…

  14. The Power of Nature. World's Largest Math Event 5.

    ERIC Educational Resources Information Center

    National Council of Teachers of Mathematics, Inc., Reston, VA.

    The theme of the fifth annual World's Largest Math Event (WLME 5) is "The Power of Nature." This theme encourages students to explore natural forces that affect humankind, including phenomena such as hurricanes, earthquakes, and snowstorms, and the mathematics that underlies their study. The 15 activities for WLMES have been grouped into five…

  15. Building Earth's Largest Library: Driving into the Future.

    ERIC Educational Resources Information Center

    Coffman, Steve

    1999-01-01

    Examines the Amazon.com online bookstore as a blueprint for designing the world's largest library. Topics include selection; accessibility and convenience; quality of Web sites and search tools; personalized service; library collection development, including interlibrary loan; library catalogs and catalog records; a circulation system; costs;…

  16. Footprinting analysis of interactions between the largest eukaryotic RNase P/MRP protein Pop1 and RNase P/MRP RNA components.

    PubMed

    Fagerlund, Robert D; Perederina, Anna; Berezin, Igor; Krasilnikov, Andrey S

    2015-09-01

    Ribonuclease (RNase) P and RNase MRP are closely related catalytic ribonucleoproteins involved in the metabolism of a wide range of RNA molecules, including tRNA, rRNA, and some mRNAs. The catalytic RNA component of eukaryotic RNase P retains the core elements of the bacterial RNase P ribozyme; however, the peripheral RNA elements responsible for the stabilization of the global architecture are largely absent in the eukaryotic enzyme. At the same time, the protein makeup of eukaryotic RNase P is considerably more complex than that of the bacterial RNase P. RNase MRP, an essential and ubiquitous eukaryotic enzyme, has a structural organization resembling that of eukaryotic RNase P, and the two enzymes share most of their protein components. Here, we present the results of the analysis of interactions between the largest protein component of yeast RNases P/MRP, Pop1, and the RNA moieties of the enzymes, discuss structural implications of the results, and suggest that Pop1 plays the role of a scaffold for the stabilization of the global architecture of eukaryotic RNase P RNA, substituting for the network of RNA-RNA tertiary interactions that maintain the global RNA structure in bacterial RNase P.

  17. Bayesian Predictive Distribution for the Magnitude of the Largest Aftershock

    NASA Astrophysics Data System (ADS)

    Shcherbakov, R.

    2014-12-01

    Aftershock sequences, which follow large earthquakes, last hundreds of days and are characterized by well defined frequency-magnitude and spatio-temporal distributions. The largest aftershocks in a sequence constitute significant hazard and can inflict additional damage to infrastructure. Therefore, the estimation of the magnitude of possible largest aftershocks in a sequence is of high importance. In this work, we propose a statistical model based on Bayesian analysis and extreme value statistics to describe the distribution of magnitudes of the largest aftershocks in a sequence. We derive an analytical expression for a Bayesian predictive distribution function for the magnitude of the largest expected aftershock and compute the corresponding confidence intervals. We assume that the occurrence of aftershocks can be modeled, to a good approximation, by a non-homogeneous Poisson process with a temporal event rate given by the modified Omori law. We also assume that the frequency-magnitude statistics of aftershocks can be approximated by Gutenberg-Richter scaling. We apply our analysis to 19 prominent aftershock sequences, which occurred in the last 30 years, in order to compute the Bayesian predictive distributions and the corresponding confidence intervals. In the analysis, we use the information of the early aftershocks in the sequences (in the first 1, 10, and 30 days after the main shock) to estimate retrospectively the confidence intervals for the magnitude of the expected largest aftershocks. We demonstrate by analysing 19 past sequences that in many cases we are able to constrain the magnitudes of the largest aftershocks. For example, this includes the analysis of the Darfield (Christchurch) aftershock sequence. The proposed analysis can be used for the earthquake hazard assessment and forecasting associated with the occurrence of large aftershocks. The improvement in instrumental data associated with early aftershocks can greatly enhance the analysis and

  18. Status and ecological effects of the world's largest carnivores.

    PubMed

    Ripple, William J; Estes, James A; Beschta, Robert L; Wilmers, Christopher C; Ritchie, Euan G; Hebblewhite, Mark; Berger, Joel; Elmhagen, Bodil; Letnic, Mike; Nelson, Michael P; Schmitz, Oswald J; Smith, Douglas W; Wallach, Arian D; Wirsing, Aaron J

    2014-01-10

    Large carnivores face serious threats and are experiencing massive declines in their populations and geographic ranges around the world. We highlight how these threats have affected the conservation status and ecological functioning of the 31 largest mammalian carnivores on Earth. Consistent with theory, empirical studies increasingly show that large carnivores have substantial effects on the structure and function of diverse ecosystems. Significant cascading trophic interactions, mediated by their prey or sympatric mesopredators, arise when some of these carnivores are extirpated from or repatriated to ecosystems. Unexpected effects of trophic cascades on various taxa and processes include changes to bird, mammal, invertebrate, and herpetofauna abundance or richness; subsidies to scavengers; altered disease dynamics; carbon sequestration; modified stream morphology; and crop damage. Promoting tolerance and coexistence with large carnivores is a crucial societal challenge that will ultimately determine the fate of Earth's largest carnivores and all that depends upon them, including humans.

  19. Crystal Structure of the Core Region of Hantavirus Nucleocapsid Protein Reveals the Mechanism for Ribonucleoprotein Complex Formation

    PubMed Central

    Guo, Yu; Wang, Wenming; Sun, Yuna; Ma, Chao; Wang, Xu; Wang, Xin; Liu, Pi; Shen, Shu; Li, Baobin; Lin, Jianping; Deng, Fei

    2015-01-01

    ABSTRACT Hantaviruses, which belong to the genus Hantavirus in the family Bunyaviridae, infect mammals, including humans, causing either hemorrhagic fever with renal syndrome (HFRS) or hantavirus cardiopulmonary syndrome (HCPS) in humans with high mortality. Hantavirus encodes a nucleocapsid protein (NP) to encapsidate the genome and form a ribonucleoprotein complex (RNP) together with viral polymerase. Here, we report the crystal structure of the core domains of NP (NPcore) encoded by Sin Nombre virus (SNV) and Andes virus (ANDV), which are two representative members that cause HCPS in the New World. The constructs of SNV and ANDV NPcore exclude the N- and C-terminal portions of full polypeptide to obtain stable proteins for crystallographic study. The structure features an N lobe and a C lobe to clamp RNA-binding crevice and exhibits two protruding extensions in both lobes. The positively charged residues located in the RNA-binding crevice play a key role in RNA binding and virus replication. We further demonstrated that the C-terminal helix and the linker region connecting the N-terminal coiled-coil domain and NPcore are essential for hantavirus NP oligomerization through contacts made with two adjacent protomers. Moreover, electron microscopy (EM) visualization of native RNPs extracted from the virions revealed that a monomer-sized NP-RNA complex is the building block of viral RNP. This work provides insight into the formation of hantavirus RNP and provides an understanding of the evolutionary connections that exist among bunyaviruses. IMPORTANCE Hantaviruses are distributed across a wide and increasing range of host reservoirs throughout the world. In particular, hantaviruses can be transmitted via aerosols of rodent excreta to humans or from human to human and cause HFRS and HCPS, with mortalities of 15% and 50%, respectively. Hantavirus is therefore listed as a category C pathogen. Hantavirus encodes an NP that plays essential roles both in RNP formation and

  20. World's largest TLP moves onto deepwater Norwegian location

    SciTech Connect

    Vielvoye, R.

    1992-05-04

    This paper reports that the world's largest and most sophisticated tension leg platform (TLP) was floated out to Snorre oil field in the Norwegian North Sea last month. The 78,000 ton unit built by Norwegian independent, Sega Petroleum AS, Oslo, was installed in the southern part of block 34/7 and should produce first oil in August, about a month ahead of schedule.

  1. Blueprint of the world`s largest uranium markets

    SciTech Connect

    Bizal, M.R.

    1996-06-01

    This article is a review of two recently released reports: (1) the EURATOM Supply Agency Annual Report for 1995, and (2) the US Energy Information Administration Uranium Industry Annual for 1995. These reports provide myraid information on uranium production, deliveries, contracts, and prices, as well as enrichment market activity during 1995 in the world`s largest nuclear fuel markets: the European Union and the United States.

  2. A local Echo State Property through the largest Lyapunov exponent.

    PubMed

    Wainrib, Gilles; Galtier, Mathieu N

    2016-04-01

    Echo State Networks are efficient time-series predictors, which highly depend on the value of the spectral radius of the reservoir connectivity matrix. Based on recent results on the mean field theory of driven random recurrent neural networks, enabling the computation of the largest Lyapunov exponent of an ESN, we develop a cheap algorithm to establish a local and operational version of the Echo State Property.

  3. Rare gas record in the largest Apollo 15 rock.

    NASA Technical Reports Server (NTRS)

    Marti, K.; Lightner, B. D.

    1972-01-01

    The results obtained from mass-spectrometry analyses of the noble gases He, Ne, Ar, Kr, and Xe in a 182-mg chip of the largest Apollo 15 rock 15555 are presented. The spallation krypton data indicate a well-shielded location through most of the time during which the rock was exposed to cosmic rays. Gas retention ages are estimated. No evidence for the presence of products from plutonium-244 or iodine-129 was found.

  4. What Is the Largest Einstein Radius in the Universe?

    SciTech Connect

    Oguri, Masamune; Blandford, Roger D.

    2008-08-05

    The Einstein radius plays a central role in lens studies as it characterizes the strength of gravitational lensing. In particular, the distribution of Einstein radii near the upper cutoff should probe the probability distribution of the largest mass concentrations in the universe. Adopting a triaxial halo model, we compute expected distributions of large Einstein radii. To assess the cosmic variance, we generate a number of Monte-Carlo realizations of all-sky catalogues of massive clusters. We find that the expected largest Einstein radius in the universe is sensitive to parameters characterizing the cosmological model, especially {sigma}{sub s}: for a source redshift of unity, they are 42{sub -7}{sup +9}, 35{sub -6}{sup +8}, and 54{sub -7}{sup +12} arcseconds (errors denote 1{sigma} cosmic variance), assuming best-fit cosmological parameters of the Wilkinson Microwave Anisotropy Probe five-year (WMAP5), three-year (WMAP3) and one-year (WMAP1) data, respectively. These values are broadly consistent with current observations given their incompleteness. The mass of the largest lens cluster can be as small as {approx} 10{sup 15} M{sub {circle_dot}}. For the same source redshift, we expect in all-sky {approx} 35 (WMAP5), {approx} 15 (WMAP3), and {approx} 150 (WMAP1) clusters that have Einstein radii larger than 2000. For a larger source redshift of 7, the largest Einstein radii grow approximately twice as large. While the values of the largest Einstein radii are almost unaffected by the level of the primordial non-Gaussianity currently of interest, the measurement of the abundance of moderately large lens clusters should probe non-Gaussianity competitively with cosmic microwave background experiments, but only if other cosmological parameters are well-measured. These semi-analytic predictions are based on a rather simple representation of clusters, and hence calibrating them with N-body simulations will help to improve the accuracy. We also find that these 'superlens

  5. Human Heat shock protein 40 (Hsp40/DnaJB1) promotes influenza A virus replication by assisting nuclear import of viral ribonucleoproteins.

    PubMed

    Batra, Jyoti; Tripathi, Shashank; Kumar, Amrita; Katz, Jacqueline M; Cox, Nancy J; Lal, Renu B; Sambhara, Suryaprakash; Lal, Sunil K

    2016-01-01

    A unique feature of influenza A virus (IAV) life cycle is replication of the viral genome in the host cell nucleus. The nuclear import of IAV genome is an indispensable step in establishing virus infection. IAV nucleoprotein (NP) is known to mediate the nuclear import of viral genome via its nuclear localization signals. Here, we demonstrate that cellular heat shock protein 40 (Hsp40/DnaJB1) facilitates the nuclear import of incoming IAV viral ribonucleoproteins (vRNPs) and is important for efficient IAV replication. Hsp40 was found to interact with NP component of IAV RNPs during early stages of infection. This interaction is mediated by the J domain of Hsp40 and N-terminal region of NP. Drug or RNAi mediated inhibition of Hsp40 resulted in reduced nuclear import of IAV RNPs, diminished viral polymerase function and attenuates overall viral replication. Hsp40 was also found to be required for efficient association between NP and importin alpha, which is crucial for IAV RNP nuclear translocation. These studies demonstrate an important role for cellular chaperone Hsp40/DnaJB1 in influenza A virus life cycle by assisting nuclear trafficking of viral ribonucleoproteins. PMID:26750153

  6. Mechanistic and Structural Studies of Protein-Only RNase P Compared to Ribonucleoproteins Reveal the Two Faces of the Same Enzymatic Activity.

    PubMed

    Schelcher, Cédric; Sauter, Claude; Giegé, Philippe

    2016-01-01

    RNase P, the essential activity that performs the 5' maturation of tRNA precursors, can be achieved either by ribonucleoproteins containing a ribozyme present in the three domains of life or by protein-only enzymes called protein-only RNase P (PRORP) that occur in eukaryote nuclei and organelles. A fast growing list of studies has investigated three-dimensional structures and mode of action of PRORP proteins. Results suggest that similar to ribozymes, PRORP proteins have two main domains. A clear functional analogy can be drawn between the specificity domain of the RNase P ribozyme and PRORP pentatricopeptide repeat domain, and between the ribozyme catalytic domain and PRORP N4BP1, YacP-like Nuclease domain. Moreover, both types of enzymes appear to dock with the acceptor arm of tRNA precursors and make specific contacts with the corner of pre-tRNAs. While some clear differences can still be delineated between PRORP and ribonucleoprotein (RNP) RNase P, the two types of enzymes seem to use, fundamentally, the same catalytic mechanism involving two metal ions. The occurrence of PRORP and RNP RNase P represents a remarkable example of convergent evolution. It might be the unique witness of an ongoing replacement of catalytic RNAs by proteins for enzymatic activities. PMID:27348014

  7. The DEAD-Box RNA Helicase DDX3 Associates with Export Messenger Ribonucleoproteins as well asTip-associated Protein and Participates in Translational Control

    PubMed Central

    Lai, Ming-Chih; Lee, Yan-Hwa Wu

    2008-01-01

    Nuclear export of mRNA is tightly linked to transcription, nuclear mRNA processing, and subsequent maturation in the cytoplasm. Tip-associated protein (TAP) is the major nuclear mRNA export receptor, and it acts coordinately with various factors involved in mRNA expression. We screened for protein factors that associate with TAP and identified several candidates, including RNA helicase DDX3. We demonstrate that DDX3 directly interacts with TAP and that its association with TAP as well as mRNA ribonucleoprotein complexes may occur in the nucleus. Depletion of TAP resulted in nuclear accumulation of DDX3, suggesting that DDX3 is, at least in part, exported along with messenger ribonucleoproteins to the cytoplasm via the TAP-mediated pathway. Moreover, the observation that DDX3 localizes transiently in cytoplasmic stress granules under cell stress conditions suggests a role for DDX3 in translational control. Indeed, DDX3 associates with translation initiation complexes. However, DDX3 is probably not critical for general mRNA translation but may instead promote efficient translation of mRNAs containing a long or structured 5′ untranslated region. Given that the DDX3 RNA helicase activity is essential for its involvement in translation, we suggest that DDX3 facilitates translation by resolving secondary structures of the 5′-untranslated region in mRNAs during ribosome scanning. PMID:18596238

  8. Human Heat shock protein 40 (Hsp40/DnaJB1) promotes influenza A virus replication by assisting nuclear import of viral ribonucleoproteins

    PubMed Central

    Batra, Jyoti; Tripathi, Shashank; Kumar, Amrita; Katz, Jacqueline M.; Cox, Nancy J.; Lal, Renu B.; Sambhara, Suryaprakash; Lal, Sunil K.

    2016-01-01

    A unique feature of influenza A virus (IAV) life cycle is replication of the viral genome in the host cell nucleus. The nuclear import of IAV genome is an indispensable step in establishing virus infection. IAV nucleoprotein (NP) is known to mediate the nuclear import of viral genome via its nuclear localization signals. Here, we demonstrate that cellular heat shock protein 40 (Hsp40/DnaJB1) facilitates the nuclear import of incoming IAV viral ribonucleoproteins (vRNPs) and is important for efficient IAV replication. Hsp40 was found to interact with NP component of IAV RNPs during early stages of infection. This interaction is mediated by the J domain of Hsp40 and N-terminal region of NP. Drug or RNAi mediated inhibition of Hsp40 resulted in reduced nuclear import of IAV RNPs, diminished viral polymerase function and attenuates overall viral replication. Hsp40 was also found to be required for efficient association between NP and importin alpha, which is crucial for IAV RNP nuclear translocation. These studies demonstrate an important role for cellular chaperone Hsp40/DnaJB1 in influenza A virus life cycle by assisting nuclear trafficking of viral ribonucleoproteins. PMID:26750153

  9. Mechanistic and Structural Studies of Protein-Only RNase P Compared to Ribonucleoproteins Reveal the Two Faces of the Same Enzymatic Activity

    PubMed Central

    Schelcher, Cédric; Sauter, Claude; Giegé, Philippe

    2016-01-01

    RNase P, the essential activity that performs the 5′ maturation of tRNA precursors, can be achieved either by ribonucleoproteins containing a ribozyme present in the three domains of life or by protein-only enzymes called protein-only RNase P (PRORP) that occur in eukaryote nuclei and organelles. A fast growing list of studies has investigated three-dimensional structures and mode of action of PRORP proteins. Results suggest that similar to ribozymes, PRORP proteins have two main domains. A clear functional analogy can be drawn between the specificity domain of the RNase P ribozyme and PRORP pentatricopeptide repeat domain, and between the ribozyme catalytic domain and PRORP N4BP1, YacP-like Nuclease domain. Moreover, both types of enzymes appear to dock with the acceptor arm of tRNA precursors and make specific contacts with the corner of pre-tRNAs. While some clear differences can still be delineated between PRORP and ribonucleoprotein (RNP) RNase P, the two types of enzymes seem to use, fundamentally, the same catalytic mechanism involving two metal ions. The occurrence of PRORP and RNP RNase P represents a remarkable example of convergent evolution. It might be the unique witness of an ongoing replacement of catalytic RNAs by proteins for enzymatic activities. PMID:27348014

  10. Testing a Parachute for Mars in World's Largest Wind Tunnel

    NASA Technical Reports Server (NTRS)

    2007-01-01

    The team developing the landing system for NASA's Mars Science Laboratory tested the deployment of an early parachute design in mid-October 2007 inside the world's largest wind tunnel, at NASA Ames Research Center, Moffett Field, California.

    In this image, two engineers are dwarfed by the parachute, which holds more air than a 280-square-meter (3,000-square-foot) house and is designed to survive loads in excess of 36,000 kilograms (80,000 pounds).

    The parachute, built by Pioneer Aerospace, South Windsor, Connecticut, has 80 suspension lines, measures more than 50 meters (165 feet) in length, and opens to a diameter of nearly 17 meters (55 feet). It is the largest disk-gap-band parachute ever built and is shown here inflated in the test section with only about 3.8 meters (12.5 feet) of clearance to both the floor and ceiling.

    The wind tunnel, which is 24 meters (80 feet) tall and 37 meters (120 feet) wide and big enough to house a Boeing 737, is part of the National Full-Scale Aerodynamics Complex, operated by the U.S. Air Force, Arnold Engineering Development Center.

    NASA's Jet Propulsion Laboratory, Pasadena, California, is building and testing the Mars Science Laboratory spacecraft for launch in 2009. The mission will land a roving analytical laboratory on the surface of Mars in 2010. JPL is a division of the California Institute of Technology.

  11. Fishing down the largest coral reef fish species.

    PubMed

    Fenner, Douglas

    2014-07-15

    Studies on remote, uninhabited, near-pristine reefs have revealed surprisingly large populations of large reef fish. Locations such as the northwestern Hawaiian Islands, northern Marianas Islands, Line Islands, U.S. remote Pacific Islands, Cocos-Keeling Atoll and Chagos archipelago have much higher reef fish biomass than islands and reefs near people. Much of the high biomass of most remote reef fish communities lies in the largest species, such as sharks, bumphead parrots, giant trevally, and humphead wrasse. Some, such as sharks and giant trevally, are apex predators, but others such as bumphead parrots and humphead wrasse, are not. At many locations, decreases in large reef fish species have been attributed to fishing. Fishing is well known to remove the largest fish first, and a quantitative measure of vulnerability to fishing indicates that large reef fish species are much more vulnerable to fishing than small fish. The removal of large reef fish by fishing parallels the extinction of terrestrial megafauna by early humans. However large reef fish have great value for various ecological roles and for reef tourism.

  12. Fishing down the largest coral reef fish species.

    PubMed

    Fenner, Douglas

    2014-07-15

    Studies on remote, uninhabited, near-pristine reefs have revealed surprisingly large populations of large reef fish. Locations such as the northwestern Hawaiian Islands, northern Marianas Islands, Line Islands, U.S. remote Pacific Islands, Cocos-Keeling Atoll and Chagos archipelago have much higher reef fish biomass than islands and reefs near people. Much of the high biomass of most remote reef fish communities lies in the largest species, such as sharks, bumphead parrots, giant trevally, and humphead wrasse. Some, such as sharks and giant trevally, are apex predators, but others such as bumphead parrots and humphead wrasse, are not. At many locations, decreases in large reef fish species have been attributed to fishing. Fishing is well known to remove the largest fish first, and a quantitative measure of vulnerability to fishing indicates that large reef fish species are much more vulnerable to fishing than small fish. The removal of large reef fish by fishing parallels the extinction of terrestrial megafauna by early humans. However large reef fish have great value for various ecological roles and for reef tourism. PMID:24889317

  13. Methylation pattern of methylene tetrahydrofolate reductase and small nuclear ribonucleoprotein polypeptide N promoters in oligoasthenospermia: a case-control study.

    PubMed

    Botezatu, Anca; Socolov, Razvan; Socolov, Demetra; Iancu, Iulia Virginia; Anton, Gabriela

    2014-02-01

    Alterations in DNA methylation patterns in several genes may lead to abnormal male sexual development and infertility. This study investigated the promoter methylation status of MTHFR and SNRPN in infertile men from Romania by quantitative methylation-specific PCR in order to investigate possible correlations with sperm abnormalities. The study groups included patients (n=27) with a median age of 31 years (range 26-41 years) as well as controls (n=11) with a median age of 30 years (range 24-37 years) recruited from couples seeking advice for infertility. DNA was isolated from sperm samples and promoter methylation was assessed using direct. Significant trends were detected for both genes that indicate a tendency towards promoter hypermethylation in spermatozoa with low motility (MTHFR P=0.0032, r=0.23; SNRPN P=0.0003, r=0.32) and poor morphology (MTHFR P=0.0012, r=0.27; SNRPN P=0.0003, r=0.33) but no trend was found in cases of low sperm count (MTHFR r=0.007; SNRPN r=0.06). The data indicate that the methylation patterns of the promoters of MTHFR and SNRPN are associated with changes in sperm motility and morphology, which could lead to male infertility. A large number of studies are now focused on the causes of male infertility. Among these are epigenetic modifications, which are important contributors to reproductive pathology in the male by providing dynamic changes of the phenotype according to the environmental and metabolic factors. The most known epigenetic modification is DNA methylation and alterations in this pattern in several genes could induce male infertility. The present study aims to investigate the promoter methylation status of the genes for methylene tetrahydrofolate reductase (MTHFR) and small nuclear ribonucleoprotein polypeptide N (SNRPN) in infertile males from Romania, in order to establish a correlation with sperm parameters. MTHFR is an enzyme involved in the folate pathway and in de novo nucleotide biosynthesis but also a good example for

  14. Earth's Largest Meteorite Impact Craters discovered in South America?

    NASA Astrophysics Data System (ADS)

    Kellndorfer, J. M.; Schmidt-Falkenberg, H.

    2014-12-01

    Novel analysis of high resolution InSAR-based digital elevation data from the year 2001 Shuttle Radar Topography Mission combined with a recently produced dataset of pan-tropical vegetation height from ALOS-1 SAR and IceSAT/GLAS Lidar estimates led to the quasi-bald-Earth discovery of four sizable near-perfect circle arcs in South America under dense tropical forests ranging in length from 216 km to 441 km. Terrain elevation profiles of cross-sections across the arcs show a distinct vertical rising and falling in elevations of hundreds of meters over a horizontal distance of tens of kilometers. It is hypothesized that these sizable arcs and associated rim-like topographic terrain features are remnants of huge meteorite impact craters with diameters ranging from 770 km to 1,310 km, thus forming potentially the largest known impact carter structures discovered on Earth today. The potential impact crater rim structures are located north of the eastern Amazon River, in the coastal region of Recife and Natal, and in the Brazilian, Bolivian and Paraguayan border region encompassing the Pantanal. Elevation profiles, hillshades and gray-shaded elevation maps were produced to support the geomorphologic analysis. It is also speculated whether in three of the four potential impact craters, central uplift domes or peaks, which are typical for complex impact crater structures can be identified. The worlds largest iron ore mining area of Carajás in Para, Brazil, falls exactly in the center of the largest hypothesized circular impact crater showing topographic elevations similar to the rim structure discovered 655 km to the north-north-west. Based on the topographic/geomorphologic driven hypothesis, geologic exploration of these topographic features is needed to test whether indeed meteorite impact craters could be verified, what the more exact ellipsoidal shapes of the potential impact craters might be, and to determine when during geologic times the impacts would have taken

  15. RNA gymnastics in mammalian signal recognition particle assembly.

    PubMed

    Wild, Klemens; Sinning, Irmgard

    2014-01-01

    More than one third of the cellular proteome is destined for incorporation into cell membranes or export from the cell. In all domains of life, the signal recognition particle (SRP) delivers these proteins to the membrane and protein traffic falls apart without SRP logistics. With the aid of a topogenic transport signal, SRP retrieves its cargo right at the ribosome, from where they are sorted to the translocation channel. Mammalian SRP is a ribonucleoprotein complex consisting of an SRP RNA of 300 nucleotides and 6 proteins bound to it. Assembly occurs in a hierarchical manner mainly in the nucleolus and only SRP54, which recognizes the signal sequence and regulates the targeting process, is added as the last component in the cytosol. Here we present an update on recent insights in the structure, function and dynamics of SRP RNA in SRP assembly with focus on the S domain, and present SRP as an example for the complex biogenesis of a rather small ribonucleoprotein particle. PMID:25692231

  16. RNA gymnastics in mammalian signal recognition particle assembly

    PubMed Central

    Wild, Klemens; Sinning, Irmgard

    2014-01-01

    Abstract More than one third of the cellular proteome is destined for incorporation into cell membranes or export from the cell. In all domains of life, the signal recognition particle (SRP) delivers these proteins to the membrane and protein traffic falls apart without SRP logistics. With the aid of a topogenic transport signal, SRP retrieves its cargo right at the ribosome, from where they are sorted to the translocation channel. Mammalian SRP is a ribonucleoprotein complex consisting of an SRP RNA of 300 nucleotides and 6 proteins bound to it. Assembly occurs in a hierarchical manner mainly in the nucleolus and only SRP54, which recognizes the signal sequence and regulates the targeting process, is added as the last component in the cytosol. Here we present an update on recent insights in the structure, function and dynamics of SRP RNA in SRP assembly with focus on the S domain, and present SRP as an example for the complex biogenesis of a rather small ribonucleoprotein particle. PMID:25692231

  17. Basal resistance for three of the largest Greenland outlet glaciers

    NASA Astrophysics Data System (ADS)

    Shapero, Daniel R.; Joughin, Ian R.; Poinar, Kristin; Morlighem, Mathieu; Gillet-Chaulet, Fabien

    2016-01-01

    Resistance at the ice-bed interface provides a strong control on the response of ice streams and outlet glaciers to external forcing, yet it is not observable by remote sensing. We used inverse methods constrained by satellite observations to infer the basal resistance to flow underneath three of the Greenland Ice Sheet's largest outlet glaciers. In regions of fast ice flow and high (>250 kPa) driving stresses, ice is often assumed to flow over a strong bed. We found, however, that the beds of these three glaciers provide almost no resistance under the fast-flowing trunk. Instead, resistance to flow is provided by the lateral margins and stronger beds underlying slower-moving ice upstream. Additionally, we found isolated patches of high basal resistivity within the predominantly weak beds. Because these small-scale (<1 ice thickness) features may be artifacts of overfitting our solution to measurement errors, we tested their robustness to different degrees of regularization.

  18. 1. Photocopy of undated wash drawing. The largest building is ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    1. Photocopy of undated wash drawing. The largest building is the Hotel Williams. Next to it is the Williams House (Williams Hotel Annex), HABS No. MI-258 A. Below them are the log cabins built by the American Fur Company (from left to right): Log Building No. 1 (MI-258 C), Log Building No. 2 (MI-258 D), Log Building No. 3 (not documented), Log Building No. 4 (MI-258 E), and Log Building No. 5 (MI-258 F). (Williams Log House, MI-258 B, and Log Building No. 8, MI-258 G, are not shown). The drawing is in the collection of the Michigan Historical Commission. Although it does not have a date, it was painted in the early 20th century after the main building was constructed. - Hotel Williams, Murray Bay, Munising, Alger County, MI

  19. Correlates of species richness in the largest Neotropical amphibian radiation.

    PubMed

    Gonzalez-Voyer, A; Padial, J M; Castroviejo-Fisher, S; de la Riva, I; Vilà, C

    2011-05-01

    Although tropical environments are often considered biodiversity hotspots, it is precisely in such environments where least is known about the factors that drive species richness. Here, we use phylogenetic comparative analyses to study correlates of species richness for the largest Neotropical amphibian radiation: New World direct-developing frogs. Clade-age and species richness were nonsignificantly, negatively correlated, suggesting that clade age alone does not explain among-clade variation in species richness. A combination of ecological and morphological traits explained 65% of the variance in species richness. A more vascularized ventral skin, the ability to colonize high-altitude ranges, encompassing a large variety of vegetation types, correlated significantly with species richness, whereas larger body size was marginally correlated with species richness. Hence, whereas high-altitude ranges play a role in shaping clade diversity in the Neotropics, intrinsic factors, such as skin structures and possibly body size, might ultimately determine which clades are more speciose than others. PMID:21401771

  20. Water, Sanitation, and Hygiene at the World's Largest Mass Gathering.

    PubMed

    Vortmann, Michael; Balsari, Satchit; Holman, Susan R; Greenough, P Gregg

    2015-02-01

    The 2013 Kumbh Mela, a Hindu religious festival and the largest human gathering on earth, drew an estimated 120 million pilgrims to bathe at the holy confluence of the Ganga (Ganges) and Yamuna rivers. To accommodate the massive numbers, the Indian government constructed a temporary city on the flood plains of the two rivers and provided it with roads, electricity, water and sanitation facilities, police stations, and a tiered healthcare system. This phenomenal operation and its impacts have gone largely undocumented. To address this gap, the authors undertook an evaluation and systematic monitoring initiative to study preparedness and response to public health emergencies at the event. This paper describes the water, sanitation, and hygiene components, with particular emphasis on preventive and mitigation strategies; the capacity for surveillance and response to diarrheal disease outbreaks; and the implications of lessons learned for other mass gatherings. PMID:25783442

  1. Opportunities for biodiversity gains under the world's largest reforestation programme.

    PubMed

    Hua, Fangyuan; Wang, Xiaoyang; Zheng, Xinlei; Fisher, Brendan; Wang, Lin; Zhu, Jianguo; Tang, Ya; Yu, Douglas W; Wilcove, David S

    2016-01-01

    Reforestation is a critical means of addressing the environmental and social problems of deforestation. China's Grain-for-Green Program (GFGP) is the world's largest reforestation scheme. Here we provide the first nationwide assessment of the tree composition of GFGP forests and the first combined ecological and economic study aimed at understanding GFGP's biodiversity implications. Across China, GFGP forests are overwhelmingly monocultures or compositionally simple mixed forests. Focusing on birds and bees in Sichuan Province, we find that GFGP reforestation results in modest gains (via mixed forest) and losses (via monocultures) of bird diversity, along with major losses of bee diversity. Moreover, all current modes of GFGP reforestation fall short of restoring biodiversity to levels approximating native forests. However, even within existing modes of reforestation, GFGP can achieve greater biodiversity gains by promoting mixed forests over monocultures; doing so is unlikely to entail major opportunity costs or pose unforeseen economic risks to households. PMID:27598524

  2. The largest Silurian vertebrate and its palaeoecological implications.

    PubMed

    Choo, Brian; Zhu, Min; Zhao, Wenjin; Jia, Liaotao; Zhu, You'an

    2014-06-12

    An apparent absence of Silurian fishes more than half-a-metre in length has been viewed as evidence that gnathostomes were restricted in size and diversity prior to the Devonian. Here we describe the largest pre-Devonian vertebrate (Megamastax amblyodus gen. et sp. nov.), a predatory marine osteichthyan from the Silurian Kuanti Formation (late Ludlow, ~423 million years ago) of Yunnan, China, with an estimated length of about 1 meter. The unusual dentition of the new form suggests a durophagous diet which, combined with its large size, indicates a considerable degree of trophic specialisation among early osteichthyans. The lack of large Silurian vertebrates has recently been used as constraint in palaeoatmospheric modelling, with purported lower oxygen levels imposing a physiological size limit. Regardless of the exact causal relationship between oxygen availability and evolutionary success, this finding refutes the assumption that pre-Emsian vertebrates were restricted to small body sizes.

  3. Opportunities for biodiversity gains under the world's largest reforestation programme

    PubMed Central

    Hua, Fangyuan; Wang, Xiaoyang; Zheng, Xinlei; Fisher, Brendan; Wang, Lin; Zhu, Jianguo; Tang, Ya; Yu, Douglas W.; Wilcove, David S.

    2016-01-01

    Reforestation is a critical means of addressing the environmental and social problems of deforestation. China's Grain-for-Green Program (GFGP) is the world's largest reforestation scheme. Here we provide the first nationwide assessment of the tree composition of GFGP forests and the first combined ecological and economic study aimed at understanding GFGP's biodiversity implications. Across China, GFGP forests are overwhelmingly monocultures or compositionally simple mixed forests. Focusing on birds and bees in Sichuan Province, we find that GFGP reforestation results in modest gains (via mixed forest) and losses (via monocultures) of bird diversity, along with major losses of bee diversity. Moreover, all current modes of GFGP reforestation fall short of restoring biodiversity to levels approximating native forests. However, even within existing modes of reforestation, GFGP can achieve greater biodiversity gains by promoting mixed forests over monocultures; doing so is unlikely to entail major opportunity costs or pose unforeseen economic risks to households. PMID:27598524

  4. The largest Silurian vertebrate and its palaeoecological implications

    PubMed Central

    Choo, Brian; Zhu, Min; Zhao, Wenjin; Jia, Liaotao; Zhu, You'an

    2014-01-01

    An apparent absence of Silurian fishes more than half-a-metre in length has been viewed as evidence that gnathostomes were restricted in size and diversity prior to the Devonian. Here we describe the largest pre-Devonian vertebrate (Megamastax amblyodus gen. et sp. nov.), a predatory marine osteichthyan from the Silurian Kuanti Formation (late Ludlow, ~423 million years ago) of Yunnan, China, with an estimated length of about 1 meter. The unusual dentition of the new form suggests a durophagous diet which, combined with its large size, indicates a considerable degree of trophic specialisation among early osteichthyans. The lack of large Silurian vertebrates has recently been used as constraint in palaeoatmospheric modelling, with purported lower oxygen levels imposing a physiological size limit. Regardless of the exact causal relationship between oxygen availability and evolutionary success, this finding refutes the assumption that pre-Emsian vertebrates were restricted to small body sizes. PMID:24921626

  5. Collapse of the world’s largest herbivores

    PubMed Central

    Ripple, William J.; Newsome, Thomas M.; Wolf, Christopher; Dirzo, Rodolfo; Everatt, Kristoffer T.; Galetti, Mauro; Hayward, Matt W.; Kerley, Graham I. H.; Levi, Taal; Lindsey, Peter A.; Macdonald, David W.; Malhi, Yadvinder; Painter, Luke E.; Sandom, Christopher J.; Terborgh, John; Van Valkenburgh, Blaire

    2015-01-01

    Large wild herbivores are crucial to ecosystems and human societies. We highlight the 74 largest terrestrial herbivore species on Earth (body mass ≥100 kg), the threats they face, their important and often overlooked ecosystem effects, and the conservation efforts needed to save them and their predators from extinction. Large herbivores are generally facing dramatic population declines and range contractions, such that ~60% are threatened with extinction. Nearly all threatened species are in developing countries, where major threats include hunting, land-use change, and resource depression by livestock. Loss of large herbivores can have cascading effects on other species including large carnivores, scavengers, mesoherbivores, small mammals, and ecological processes involving vegetation, hydrology, nutrient cycling, and fire regimes. The rate of large herbivore decline suggests that ever-larger swaths of the world will soon lack many of the vital ecological services these animals provide, resulting in enormous ecological and social costs. PMID:26601172

  6. Venezuela to develop second largest coal mine in South America

    SciTech Connect

    Ridley, R.S.

    1982-09-01

    Venezuela has plans to develop its coal resources in the state of Zulia. The Mino Paso Diablo project includes not only the coal mine but a steel complex and thermal power station. Design by Fluor is expected to be complete by mid-1983; first production is scheduled for 1986. Full production of 6 million tonnes/year will not be reached until the mid-1990s. The entire output is planned for domestic industrial use. At full production the mine will be the second largest coal mine in South America. The coal, which is similar to that of El Cerrejon, Columbia, 250 km away, has a calorific value of 13000 Btu/lb, ash 3%, sulphur 0.5% and free swelling index 5.

  7. The 260: The Largest Solid Rocket Motor Ever Tested

    NASA Technical Reports Server (NTRS)

    Crimmins, P.; Cousineau, M.; Rogers, C.; Shell, V.

    1999-01-01

    Aerojet in the mid 1960s, under contract to NASA, built and static hot fire tested the largest solid rocket motor (SRM) in history for the purpose of demonstrating the feasibility of utilizing large SRMs for space exploration. This program successfully fabricated two high strength steel chambers, loaded each with approximately 1,68 million pounds of propellant, and static test fired these giants with their nozzles up from an underground silo located adjacent to the Florida everglades. Maximum thrust and total impulse in excess of 5,000,000 lbf and 3,470,000,000 lbf-sec were achieved. Flames from the second firing, conducted at night, were seen over eighty miles away. For comparative purposes: the thrust developed was nearly 100 times that of a Minuteman III second stage and the 260 in.-dia cross-section was over 3 times that of the Space Shuttle SRM.

  8. The depths of the largest impact craters on Venus

    NASA Technical Reports Server (NTRS)

    Ivanov, B. A.; Ford, P. G.

    1993-01-01

    The largest impact craters on Venus may be used as evidence of various geological processes within the Venusian crust. We are continuing to construct a data base for the further investigation of large craters on Venus (LCV). We hope to find evidence of crater relaxation that might constrain the thickness and thermal gradient of the crust, as was proposed in an earlier work. The current work concentrates on 27 impact craters with diameters (d) larger than 70 km, i.e., large enough that the footprint of the Magellan altimeter has a good chance of sampling the true crater bottom. All altimeter echoes from points located within (d/2)+70 km from the crater center have been inspected.

  9. Water, Sanitation, and Hygiene at the World's Largest Mass Gathering.

    PubMed

    Vortmann, Michael; Balsari, Satchit; Holman, Susan R; Greenough, P Gregg

    2015-02-01

    The 2013 Kumbh Mela, a Hindu religious festival and the largest human gathering on earth, drew an estimated 120 million pilgrims to bathe at the holy confluence of the Ganga (Ganges) and Yamuna rivers. To accommodate the massive numbers, the Indian government constructed a temporary city on the flood plains of the two rivers and provided it with roads, electricity, water and sanitation facilities, police stations, and a tiered healthcare system. This phenomenal operation and its impacts have gone largely undocumented. To address this gap, the authors undertook an evaluation and systematic monitoring initiative to study preparedness and response to public health emergencies at the event. This paper describes the water, sanitation, and hygiene components, with particular emphasis on preventive and mitigation strategies; the capacity for surveillance and response to diarrheal disease outbreaks; and the implications of lessons learned for other mass gatherings.

  10. Correlates of species richness in the largest Neotropical amphibian radiation.

    PubMed

    Gonzalez-Voyer, A; Padial, J M; Castroviejo-Fisher, S; de la Riva, I; Vilà, C

    2011-05-01

    Although tropical environments are often considered biodiversity hotspots, it is precisely in such environments where least is known about the factors that drive species richness. Here, we use phylogenetic comparative analyses to study correlates of species richness for the largest Neotropical amphibian radiation: New World direct-developing frogs. Clade-age and species richness were nonsignificantly, negatively correlated, suggesting that clade age alone does not explain among-clade variation in species richness. A combination of ecological and morphological traits explained 65% of the variance in species richness. A more vascularized ventral skin, the ability to colonize high-altitude ranges, encompassing a large variety of vegetation types, correlated significantly with species richness, whereas larger body size was marginally correlated with species richness. Hence, whereas high-altitude ranges play a role in shaping clade diversity in the Neotropics, intrinsic factors, such as skin structures and possibly body size, might ultimately determine which clades are more speciose than others.

  11. Supergranulation as the Sun's largest buoyantly driven mode of convection

    NASA Astrophysics Data System (ADS)

    Cossette, Jean-Francois; Rast, Mark

    2016-05-01

    Solar supergranulation has been characterized as horizontally divergent flow motions having a typical scale of 32 Mm using Doppler imaging, granule tracking and helioseismology. Unlike granules, the size of which is comparable to both the thickness of the radiative boundary layer and local scale height at the photosphere, supergranules do not appear to correspond to any particular length scale of the flow. Possible explanations ranging from convection theories involving Helium ionization to spatial correlation or self-organization of granular flows have been proposed as physical mechanisms to explain solar supergranulation. However, its existence remains largely a mystery. Remarkably, horizontal velocity power spectra obtained from Doppler imaging and correlation tracking of flow features at the solar surface reveal the presence of peaks corresponding to granular and supergranular scales, followed by a monotonic decrease in power at scales larger than supergranulation, which suggests that large-scale modes in the deep layers of the convection zone may be suppressed. Using 3D anelastic simulations of solar convection we investigate whether supergranulation may reflect the largest buoyantly driven mode of convection inside the Sun. Results show that the amount of kinetic energy contained in the largest flow scales relative to that associated with supergranular motions is a function of the depth of the transition from a convectively unstable to convectively stable mean stratification inside the simulation. This suggests that the observed monotonic decrease in power at scales larger than supergranulation may be explained by rapid cooling in the subphotospheric layers and an essentially isentropic solar interior, wherein convective driving is effectively suppressed.

  12. Vanillin inhibits translation and induces messenger ribonucleoprotein (mRNP) granule formation in saccharomyces cerevisiae: application and validation of high-content, image-based profiling.

    PubMed

    Iwaki, Aya; Ohnuki, Shinsuke; Suga, Yohei; Izawa, Shingo; Ohya, Yoshikazu

    2013-01-01

    Vanillin, generated by acid hydrolysis of lignocellulose, acts as a potent inhibitor of the growth of the yeast Saccharomyces cerevisiae. Here, we investigated the cellular processes affected by vanillin using high-content, image-based profiling. Among 4,718 non-essential yeast deletion mutants, the morphology of those defective in the large ribosomal subunit showed significant similarity to that of vanillin-treated cells. The defects in these mutants were clustered in three domains of the ribosome: the mRNA tunnel entrance, exit and backbone required for small subunit attachment. To confirm that vanillin inhibited ribosomal function, we assessed polysome and messenger ribonucleoprotein granule formation after treatment with vanillin. Analysis of polysome profiles showed disassembly of the polysomes in the presence of vanillin. Processing bodies and stress granules, which are composed of non-translating mRNAs and various proteins, were formed after treatment with vanillin. These results suggest that vanillin represses translation in yeast cells.

  13. Characterization of the in vitro activity of the RNA-dependent RNA polymerase associated with the ribonucleoproteins of rice hoja blanca tenuivirus.

    PubMed

    Nguyen, M; Ramirez, B C; Goldbach, R; Haenni, A L

    1997-04-01

    An RNA-dependent RNA polymerase (RdRp) activity associated with the ribonucleoproteins of rice hoja blanca tenuivirus (RHBV) was detected and analyzed. Conditions for in vitro RNA synthesis and for coupled RNA synthesis-translation of RHBV were established. In both cases, synthesis of the viral and viral complementary genomic and subgenomic RNA3 and RNA4 were observed, demonstrating that both transcription and replication occurred. Though coupling of RNA synthesis to translation allowed efficient translation of the newly synthesized subgenomic RNAs, studies of the effect of various inhibitors of protein synthesis revealed that RNA synthesis was independent of translation. Primer extension experiments demonstrated that in the presence of capped exogenous RNAs, a stretch of 10 to 16 nonviral nucleotides was added to the 5' end of a population of newly synthesized viral complementary RNA4. It appears that in addition to RdRp activity, RHBV-associated protein(s) also possessed cap-snatching capacity. PMID:9060614

  14. Splicing remodels messenger ribonucleoprotein architecture via eIF4A3-dependent and -independent recruitment of exon junction complex components.

    PubMed

    Zhang, Zuo; Krainer, Adrian R

    2007-07-10

    Pre-mRNA splicing not only removes introns and joins exons to generate spliced mRNA but also results in remodeling of the spliced messenger ribonucleoprotein, influencing various downstream events. This remodeling includes the loading of an exon-exon junction complex (EJC). It is unclear how the spliceosome recruits the EJC onto the mRNA and whether EJC formation or EJC components are required for pre-mRNA splicing. Here we immunodepleted the EJC core component eIF4A3 from HeLa cell nuclear extract and found that eIF4A3 is dispensable for pre-mRNA splicing in vitro. However, eIF4A3 is required for the splicing-dependent loading of the Y14/Magoh heterodimer onto mRNA, and this activity of human eIF4A3 is also present in the Drosophila ortholog. Surprisingly, the loading of six other EJC components was not affected by eIF4A3 depletion, suggesting that their binding to mRNA involves different or redundant pathways. Finally, we found that the assembly of the EJC onto mRNA occurs at the late stages of the splicing reaction and requires the second-step splicing and mRNA-release factor HRH1/hPrp22. The EJC-dependent and -independent recruitment of RNA-binding proteins onto mRNA suggests a role for the EJC in messenger ribonucleoprotein remodeling involving interactions with other proteins already bound to the pre-mRNA, which has implications for nonsense-mediated mRNA decay and other mRNA transactions. PMID:17606899

  15. Cullin 4B is recruited to tristetraprolin-containing messenger ribonucleoproteins and regulates TNF-α mRNA polysome loading.

    PubMed

    Pfeiffer, Jason R; Brooks, Seth A

    2012-02-15

    TNF-α is a central mediator of inflammation and critical for host response to infection and injury. TNF-α biosynthesis is controlled by transcriptional and posttranscriptional mechanisms allowing for rapid, transient production. Tristetraprolin (TTP) is an AU-rich element binding protein that regulates the stability of the TNF-α mRNA. Using a screen to identify TTP-interacting proteins, we identified Cullin 4B (Cul4B), a scaffolding component of the Cullin ring finger ligase family of ubiquitin E3 ligases. Short hairpin RNA knockdown of Cul4B results in a significant reduction in TNF-α protein and mRNA in LPS-stimulated mouse macrophage RAW264.7 cells as well as a reduction in TTP protein. TNF-α message t(1/2) was reduced from 69 to 33 min in LPS-stimulated cells. TNF-3' untranslated region luciferase assays utilizing wild-type and mutant TTP-AA (S52A, S178A) indicate that TTP function is enhanced in Cul4B short hairpin RNA cells. Importantly, the fold induction of TNF-α mRNA polysome loading in response to LPS stimulation is reduced by Cul4B knockdown. Cul4B is present on the polysomes and colocalizes with TTP to exosomes and processing bodies, which are sites of mRNA decay. We conclude that Cul4B licenses the TTP-containing TNF-α messenger ribonucleoprotein for loading onto polysomes, and reduction of Cul4B expression shunts the messenger ribonucleoproteins into the degradative pathway.

  16. Spectral properties of the largest asteroids associated with Taurid Complex

    NASA Astrophysics Data System (ADS)

    Popescu, M.; Birlan, M.; Nedelcu, D. A.; Vaubaillon, J.; Cristescu, C. P.

    2014-12-01

    Context. The Taurid Complex is a massive stream of material in the inner part of the Solar System. It contains objects spanning the range of 10-6-103 m, considered by some authors to have a common cometary origin. The asteroids belonging to Taurid Complex are on Apollo type orbit, with most of them being flagged as potentially hazardous asteroids. In this context, understanding the nature and the origin of this asteroidal population is not only of scientific interest but also of practical importance. Aims: We aim to investigate the surface mineralogy of the asteroids associated with Taurid Complex using visible and near-infrared spectral data. Compositional linking between these asteroids and meteorites can be derived based on the obtained spectra. Methods: We obtained spectra of six of the largest asteroids (2201, 4183, 4486, 5143, 6063, and 269690) associated with Taurid complex. The observations were made with the IRTF telescope equipped with the spectro-imager SpeX. Their taxonomic classification is made using Bus-DeMeo taxonomy. The asteroid spectra are compared with the meteorite spectra from the Relab database. Mineralogical models were applied to determine their surface composition. All the spectral analysis is made in the context of the already published physical data. Results: Five of the objects studied in this paper present spectral characteristics similar to the S taxonomic complex. The spectra of ordinary chondrites (spanning H, L, and LL subtypes) are the best matches for these asteroid spectra. The asteroid (269690) 1996 RG3 presents a flat featureless spectrum which could be associated to a primitive C-type object. The increased reflectance above 2.1 microns constrains its geometrical albedo to a value around 0.03. Conclusions: While there is an important dynamical grouping among the Taurid Complex asteroids, the spectral data of the largest objects do not support a common cometary origin. Furthermore, there are significant variations between the

  17. Holocene dynamics of the Arctic's largest ice shelf.

    PubMed

    Antoniades, Dermot; Francus, Pierre; Pienitz, Reinhard; St-Onge, Guillaume; Vincent, Warwick F

    2011-11-22

    Ice shelves in the Arctic lost more than 90% of their total surface area during the 20th century and are continuing to disintegrate rapidly. The significance of these changes, however, is obscured by the poorly constrained ontogeny of Arctic ice shelves. Here we use the sedimentary record behind the largest remaining ice shelf in the Arctic, the Ward Hunt Ice Shelf (Ellesmere Island, Canada), to establish a long-term context in which to evaluate recent ice-shelf deterioration. Multiproxy analysis of sediment cores revealed pronounced biological and geochemical changes in Disraeli Fiord in response to the formation of the Ward Hunt Ice Shelf and its fluctuations through time. Our results show that the ice shelf was absent during the early Holocene and formed 4,000 years ago in response to climate cooling. Paleoecological data then indicate that the Ward Hunt Ice Shelf remained stable for almost three millennia before a major fracturing event that occurred ∼1,400 years ago. After reformation ∼800 years ago, freshwater was a constant feature of Disraeli Fiord until the catastrophic drainage of its epishelf lake in the early 21st century. PMID:22025693

  18. Largest US oil and gas fields, August 1993

    SciTech Connect

    Not Available

    1993-08-06

    The Largest US Oil and Gas Fields is a technical report and part of an Energy Information Administration (EIA) series presenting distributions of US crude oil and natural gas resources, developed using field-level data collected by EIA`s annual survey of oil and gas proved reserves. The series` objective is to provide useful information beyond that routinely presented in the EIA annual report on crude oil and natural gas reserves. These special reports also will provide oil and gas resource analysts with a fuller understanding of the nature of US crude oil and natural gas occurrence, both at the macro level and with respect to the specific subjects addressed. The series` approach is to integrate EIA`s crude oil and natural gas survey data with related data obtained from other authoritative sources, and then to present illustrations and analyses of interest to a broad spectrum of energy information users ranging from the general public to oil and gas industry personnel.

  19. World's Largest Gold Crystal Studied at Los Alamos

    SciTech Connect

    Vogel, Sven; Nakotte, Heinz

    2014-04-03

    When geologist John Rakovan needed better tools to investigate whether a dazzling 217.78-gram piece of gold was in fact the world's largest single-crystal specimen - a distinguishing factor that would not only drastically increase its market value but also provide a unique research opportunity - he traveled to Los Alamos National Laboratory's Lujan Neutron Scattering Center to peer deep inside the mineral using neutron diffractometry. Neutrons, different from other probes such as X-rays and electrons, are able to penetrate many centimeters deep into most materials. Revealing the inner structure of a crystal without destroying the sample - imperative, as this one is worth an estimated $1.5 million - would allow Rakovan and Lujan Center collaborators Sven Vogel and Heinz Nakotte to prove that this exquisite nugget, which seemed almost too perfect and too big to be real, was a single crystal and hence a creation of nature. Its owner, who lives in the United States, provided the samples to Rakovan to assess the crystallinity of four specimens, all of which had been found decades ago in Venezuela.

  20. LHC World Largest Vacuum Systems Being Commissioned at CERN

    NASA Astrophysics Data System (ADS)

    Jimenez, Jose Miguel

    The CERN Large Hadron Collider (LHC) with its 26.7 km of circumference and three different vacuum systems for the beams and insulation vacuum for magnets and liquid helium transfer lines, will have the world's largest vacuum system operating over a wide range of pressures and employing an impressive array of vacuum technologies. This system is composed by 54 km of UHV vacuum for the circulating beams and 50 km of insulation vacuum. Over the 54 km of UHV beam vacuum, 48 km of this are at cryogenic temperature (1.9 K). The remaining 6 km of beam vacuum containing the insertions for “cleaning” the proton beams, radiofrequency cavities for accelerating the protons as well as beam-monitoring equipment is at ambient temperature and uses non-evaporable getter (NEG) coatings. The noble gases and methane is pumped out by 780 ion pumps. Pressure readings are provided by 170 Bayard-Alpert gauges and 1084 gauges (Pirani and cold cathode Penning). The cryogenic insulation vacuums while technically less demanding, impress by their size (50 km) and volume (15000 m3). Once roughed using mechanical pumps, the vacuum relies on the cryopumping which allows reaching pressure in the 10-4 Pa range.

  1. Developmental origins of the world's largest flowers, Rafflesiaceae.

    PubMed

    Nikolov, Lachezar A; Endress, Peter K; Sugumaran, M; Sasirat, Sawitree; Vessabutr, Suyanee; Kramer, Elena M; Davis, Charles C

    2013-11-12

    Rafflesiaceae, which produce the world's largest flowers, have captivated the attention of biologists for nearly two centuries. Despite their fame, however, the developmental nature of the floral organs in these giants has remained a mystery. Most members of the family have a large floral chamber defined by a diaphragm. The diaphragm encloses the reproductive organs where pollination by carrion flies occurs. In lieu of a functional genetic system to investigate floral development in these highly specialized holoparasites, we used comparative studies of structure, development, and gene-expression patterns to investigate the homology of their floral organs. Our results surprisingly demonstrate that the otherwise similar floral chambers in two Rafflesiaceae subclades, Rafflesia and Sapria, are constructed very differently. In Rafflesia, the diaphragm is derived from the petal whorl. In contrast, in Sapria it is derived from elaboration of a unique ring structure located between the perianth and the stamen whorl, which, although developed to varying degrees among the genera, appears to be a synapomorphy of the Rafflesiaceae. Thus, the characteristic features that define the floral chamber in these closely related genera are not homologous. These differences refute the prevailing hypothesis that similarities between Sapria and Rafflesia are ancestral in the family. Instead, our data indicate that Rafflesia-like and Sapria-like floral chambers represent two distinct derivations of this morphology. The developmental repatterning we identified in Rafflesia, in particular, may have provided architectural reinforcement, which permitted the explosive growth in floral diameter that has arisen secondarily within this subclade. PMID:24167265

  2. Challenges of Computing with FLASH on Largest HPC Platforms

    NASA Astrophysics Data System (ADS)

    Dubey, A.; Daley, C.; Weide, K.

    2010-09-01

    FLASH is a highly capable multiphysics multiscale modular extensible code, originally designed for simulating reactive flows. FLASH consists of interoperable modules that can be combined to generate different applications such as simulations of novae, supernovae, X-Ray bursts, galaxy clusters, weakly compressible turbulence, and many other problems in astrophysics and other fields. FLASH has a wide user base, both within and outside the Flash Center, and is regularly used on largest available HPC platforms. With each new platform we encounter a new set of challenges, because the multiscale multiphysics nature of FLASH simulations exercise the machine's hardware and system software greatly. The increase in the degree of concurrency with each new hardware generation has imposed changes on some of FLASH's parallel algorithms. The pace of change has accelerated with the move towards petascale, and then to exascale. In this work we present some of our scaling hurdles and their solutions. In addition we discuss a more fundamental transition in the code to incorporate a hybrid shared and distributed memory model in preparation for the future million- to billion-way parallelism.

  3. World's Largest Gold Crystal Studied at Los Alamos

    ScienceCinema

    Vogel, Sven; Nakotte, Heinz

    2016-07-12

    When geologist John Rakovan needed better tools to investigate whether a dazzling 217.78-gram piece of gold was in fact the world's largest single-crystal specimen - a distinguishing factor that would not only drastically increase its market value but also provide a unique research opportunity - he traveled to Los Alamos National Laboratory's Lujan Neutron Scattering Center to peer deep inside the mineral using neutron diffractometry. Neutrons, different from other probes such as X-rays and electrons, are able to penetrate many centimeters deep into most materials. Revealing the inner structure of a crystal without destroying the sample - imperative, as this one is worth an estimated $1.5 million - would allow Rakovan and Lujan Center collaborators Sven Vogel and Heinz Nakotte to prove that this exquisite nugget, which seemed almost too perfect and too big to be real, was a single crystal and hence a creation of nature. Its owner, who lives in the United States, provided the samples to Rakovan to assess the crystallinity of four specimens, all of which had been found decades ago in Venezuela.

  4. Benchmark Testing of the Largest Titanium Aluminide Sheet Subelement Conducted

    NASA Technical Reports Server (NTRS)

    Bartolotta, Paul A.; Krause, David L.

    2000-01-01

    To evaluate wrought titanium aluminide (gamma TiAl) as a viable candidate material for the High-Speed Civil Transport (HSCT) exhaust nozzle, an international team led by the NASA Glenn Research Center at Lewis Field successfully fabricated and tested the largest gamma TiAl sheet structure ever manufactured. The gamma TiAl sheet structure, a 56-percent subscale divergent flap subelement, was fabricated for benchmark testing in three-point bending. Overall, the subelement was 84-cm (33-in.) long by 13-cm (5-in.) wide by 8-cm (3-in.) deep. Incorporated into the subelement were features that might be used in the fabrication of a full-scale divergent flap. These features include the use of: (1) gamma TiAl shear clips to join together sections of corrugations, (2) multiple gamma TiAl face sheets, (3) double hot-formed gamma TiAl corrugations, and (4) brazed joints. The structural integrity of the gamma TiAl sheet subelement was evaluated by conducting a room-temperature three-point static bend test.

  5. Characterization of the largest effector gene cluster of Ustilago maydis.

    PubMed

    Brefort, Thomas; Tanaka, Shigeyuki; Neidig, Nina; Doehlemann, Gunther; Vincon, Volker; Kahmann, Regine

    2014-07-01

    In the genome of the biotrophic plant pathogen Ustilago maydis, many of the genes coding for secreted protein effectors modulating virulence are arranged in gene clusters. The vast majority of these genes encode novel proteins whose expression is coupled to plant colonization. The largest of these gene clusters, cluster 19A, encodes 24 secreted effectors. Deletion of the entire cluster results in severe attenuation of virulence. Here we present the functional analysis of this genomic region. We show that a 19A deletion mutant behaves like an endophyte, i.e. is still able to colonize plants and complete the infection cycle. However, tumors, the most conspicuous symptoms of maize smut disease, are only rarely formed and fungal biomass in infected tissue is significantly reduced. The generation and analysis of strains carrying sub-deletions identified several genes significantly contributing to tumor formation after seedling infection. Another of the effectors could be linked specifically to anthocyanin induction in the infected tissue. As the individual contributions of these genes to tumor formation were small, we studied the response of maize plants to the whole cluster mutant as well as to several individual mutants by array analysis. This revealed distinct plant responses, demonstrating that the respective effectors have discrete plant targets. We propose that the analysis of plant responses to effector mutant strains that lack a strong virulence phenotype may be a general way to visualize differences in effector function.

  6. India has the largest number of people infected with HIV.

    PubMed

    Kumar, S

    1999-01-01

    With a population of almost 1 billion people and an estimated 4 million people infected with HIV, India is thought to be the country with the largest number of HIV-infected people in the world. According to UNAIDS, HIV is firmly embedded in India's general population and rapidly spreading into rural areas previously thought to be relatively spared from the epidemic. Almost 500,000 people are infected in Tamil Nadu and the infection rate is 3 times higher in villages than in cities. According to the National AIDS Control Organization, the rate of HIV infection among attendees of STD clinics in Mumbai increased from 23% to 36% in 1 year, and 51% of prostitutes in Mumbai and 55.8% of IV drug users in Manipur are infected. It is estimated that AIDS will cost India US$11 billion cumulatively by 2000, 5% of the country's gross domestic product. Negotiations are underway for the World Bank to loan India $200 million with which to combat HIV/AIDS. Since antiretroviral therapy is too expensive for most Indians, vaccine research must be accelerated in India. HIV infection in India is mainly of HIV-1 subtype C, although subtypes A and B, along with some new recombinant subtypes, have also been reported. HIV-2 has been reported sporadically.

  7. [A Standing Balance Evaluation Method Based on Largest Lyapunov Exponent].

    PubMed

    Liu, Kun; Wang, Hongrui; Xiao, Jinzhuang; Zhao, Qing

    2015-12-01

    In order to evaluate the ability of human standing balance scientifically, we in this study proposed a new evaluation method based on the chaos nonlinear analysis theory. In this method, a sinusoidal acceleration stimulus in forward/backward direction was forced under the subjects' feet, which was supplied by a motion platform. In addition, three acceleration sensors, which were fixed to the shoulder, hip and knee of each subject, were applied to capture the balance adjustment dynamic data. Through reconstructing the system phase space, we calculated the largest Lyapunov exponent (LLE) of the dynamic data of subjects' different segments, then used the sum of the squares of the difference between each LLE (SSDLLE) as the balance capabilities evaluation index. Finally, 20 subjects' indexes were calculated, and compared with evaluation results of existing methods. The results showed that the SSDLLE were more in line with the subjects' performance during the experiment, and it could measure the body's balance ability to some extent. Moreover, the results also illustrated that balance level was determined by the coordinate ability of various joints, and there might be more balance control strategy in the process of maintaining balance. PMID:27079089

  8. Holocene dynamics of the Arctic's largest ice shelf

    PubMed Central

    Antoniades, Dermot; Francus, Pierre; Pienitz, Reinhard; St-Onge, Guillaume; Vincent, Warwick F.

    2011-01-01

    Ice shelves in the Arctic lost more than 90% of their total surface area during the 20th century and are continuing to disintegrate rapidly. The significance of these changes, however, is obscured by the poorly constrained ontogeny of Arctic ice shelves. Here we use the sedimentary record behind the largest remaining ice shelf in the Arctic, the Ward Hunt Ice Shelf (Ellesmere Island, Canada), to establish a long-term context in which to evaluate recent ice-shelf deterioration. Multiproxy analysis of sediment cores revealed pronounced biological and geochemical changes in Disraeli Fiord in response to the formation of the Ward Hunt Ice Shelf and its fluctuations through time. Our results show that the ice shelf was absent during the early Holocene and formed 4,000 years ago in response to climate cooling. Paleoecological data then indicate that the Ward Hunt Ice Shelf remained stable for almost three millennia before a major fracturing event that occurred ∼1,400 years ago. After reformation ∼800 years ago, freshwater was a constant feature of Disraeli Fiord until the catastrophic drainage of its epishelf lake in the early 21st century. PMID:22025693

  9. Largest meteor since Tunguska event explodes above Russian city

    NASA Astrophysics Data System (ADS)

    Showstack, Randy

    2013-02-01

    The meteor that disintegrated in the atmosphere above Chelyabinsk, Russia, on 15 February, injuring more than 1000 people and causing widespread property damage from the shock wave, is the largest such incident since the 1908 Tunguska event in Siberia, according to Paul Chodas, research scientist in the Near-Earth Object (NEO) program office at NASA's Jet Propulsion Laboratory in Pasadena, Calif. During a 15 February teleconference, Chodas said it was an "incredible coincidence" that asteroid DA14 passed safely by Earth on the same day as the Chelyabinsk meteor; the 45-meter-wide asteroid sped by the planet at a distance of just 27,700 kilometers away on its closest approach. He stressed that the meteor was not related to DA14. The meteor "was coming from the wrong direction and at a completely different velocity," he said, noting that the orbit of the meteor went out to the asteroid belt while the orbit of DA14 "is very Earth-like, it does not go out so far."

  10. The dust halo of Saturn's largest icy moon, Rhea.

    PubMed

    Jones, G H; Roussos, E; Krupp, N; Beckmann, U; Coates, A J; Crary, F; Dandouras, I; Dikarev, V; Dougherty, M K; Garnier, P; Hansen, C J; Hendrix, A R; Hospodarsky, G B; Johnson, R E; Kempf, S; Khurana, K K; Krimigis, S M; Krüger, H; Kurth, W S; Lagg, A; McAndrews, H J; Mitchell, D G; Paranicas, C; Postberg, F; Russell, C T; Saur, J; Seiss, M; Spahn, F; Srama, R; Strobel, D F; Tokar, R; Wahlund, J-E; Wilson, R J; Woch, J; Young, D

    2008-03-01

    Saturn's moon Rhea had been considered massive enough to retain a thin, externally generated atmosphere capable of locally affecting Saturn's magnetosphere. The Cassini spacecraft's in situ observations reveal that energetic electrons are depleted in the moon's vicinity. The absence of a substantial exosphere implies that Rhea's magnetospheric interaction region, rather than being exclusively induced by sputtered gas and its products, likely contains solid material that can absorb magnetospheric particles. Combined observations from several instruments suggest that this material is in the form of grains and boulders up to several decimetres in size and orbits Rhea as an equatorial debris disk. Within this disk may reside denser, discrete rings or arcs of material.

  11. New surprises in the largest magnetosphere of our solar system.

    PubMed

    Krupp, Norbert

    2007-10-12

    En route to its ultimate rendezvous with Pluto, the New Horizons spacecraft passed through the magnetic and plasma environment of Jupiter in February 2007. Onboard instruments collected high-resolution images, spectroscopic data, and information about charged particles. The results have revealed unusual structure and variation in Jupiter's plasma and large plasmoids that travel down the magnetotail. Data on Jupiter's aurora provide details of the interaction with the solar wind, and a major volcanic eruption from the moon Io was observed during the encounter.

  12. Cassini RADAR Observes Titan's Kraken Mare, The Largest Extraterrestrial Sea

    NASA Astrophysics Data System (ADS)

    Kirk, R. L.

    2013-12-01

    Synthetic aperture radar (SAR) imaging by Cassini's RADAR instrument beginning in 2006 revealed the presence of hundreds of hydrocarbon lakes and three large seas in Titan's north polar region [1,2]. Kraken Mare appeared to be the largest sea in IR images [3] but only the northern end was imaged by RADAR prior to 2012. High altitude SAR (HiSAR) observations on recent Titan flybys T84, T91, and T92 now provide complete coverage of Kraken and environs to ~50°N, at resolutions of 2-10 km. Backscatter statistics of the sea are 0.002 × 0.04, i.e., any return is substantially less than the noise and much less than typical dry land cross sections of 0.1-1.5. We conclude that Kraken is liquid filled to substantial depth over its entire extent. A surprising result is that the major seas all lie within a 1800 x 900 km 'box' (Fig.1). A third of the area inside this box (0.6 M km2) is sea, whereas the largest lake outside the box is only 0.005 M km2. Kraken's overall shape is complex (lobateness 4.4 vs 2.1 for Ligeia) but its 0.44 M km2 is divided by 20 to 160 km wide straits into 5 sub-basins that are elongated E-W across the box. Numerous straight shoreline segments parallel the edges of the box. Others parallel the 10°, 80°, and 170°W meridians, as do the rectangular drainage patterns mapped by [4]. These alignments suggest a key role for tectonics in creating the depressions occupied by the northern seas. Fensal and Aztlan (the 'lazy H' of dune-filled lows straddling the equator at longitudes 0°-70°W) form a similar pattern of elongated depressions connected by a narrow strait within a rectangular box. In contrast, Titan's small lakes are widely distributed. Multiple depressions with radar-dark floors have been identified near the south pole and hypothesized as former seabeds [5], but though similar in size to the northern seas, they are not aligned with one another or tightly clustered. Thus, the geography of the north and south poles will remain distinct even if

  13. High feeding costs limit dive time in the largest whales.

    PubMed

    Acevedo-Gutiérrez, A; Croll, D A; Tershy, B R

    2002-06-01

    Large body size usually extends dive duration in air-breathing vertebrates. However, the two largest predators on earth, the blue whale (Balaenoptera musculus) and the fin whale (B. physalus), perform short dives for their size. Here, we test the hypothesis that the foraging behavior of these two species (lunge-feeding) is energetically expensive and limits their dive duration. We estimated the cost of lunge-feeding in both species using an approach that combined attaching time/depth recorders to seven blue whales and eight fin whales and comparing the collected dive information with predictions made by optimality models of dive behavior. We show that the rate at which whales recovered from a foraging dive was twice that of a non-foraging dive and that the cost of foraging relative to the cost of travel to and from the prey patch was 3.15 in blue whales (95 % CI 2.58-3.72) and 3.60 in fin whales (95 % CI 2.35-4.85). Whales foraged in small areas (<1 km(2)) and foraging bouts lasted more than one dive, indicating that prey did not disperse and thus that prey dispersal could not account for the limited dive durations of the whales. Despite the enormous size of blue whales and fin whales, the high energetic costs of lunge-feeding confine them to short durations of submergence and to areas with dense prey aggregations. As a corollary, because of their limited foraging time under water, these whales may be particularly vulnerable to perturbations in prey abundance.

  14. Global assessment of nutrient loads to the world's largest lakes

    NASA Astrophysics Data System (ADS)

    Fink, Gabriel; Reder, Klara; Malsy, Marcus; Eisner, Stephanie; Flörke, Martina

    2015-04-01

    Lakes are essential resources of drinking water for a large part of mankind. Even so, most of the industrial and domestic waste water is discharged - often untreated - into rivers and streams that are finally the tributaries of these important freshwater bodies. Additionally, diffuse nutrient sources such as fertilizer and atmospheric deposition exacerbate existing algal blooms and low oxygen concentrations in rivers, lakes, and reservoirs. In this tense atmosphere of competing water uses, it is necessary to analyze all sources of pollution as well as their total contributions in order to protect these water bodies against deterioration. Finally, this is a general and urgently needed basis for developing recommendations for involved stakeholders and decision makers. Therefore, the project eartH2Observe, initiated and financed by the European Commission, creates the necessary and underlying quantitative and qualitative hydrological and water use data. In this context, information for global as well as for regional water resource assessments is being prepared based on new earth observations and an ensemble of global hydrological models. As a member of this ensemble, WaterGAP3 provides global estimates of lake water quality relevant parameters on a 5 arc minutes grid, namely total phosphorus and total nitrogen. These nutrient loads to lakes from different sources such as industrial fertilizer, organic fertilizer, domestic loads, atmospheric deposition, and urban surface runoff are estimated for the period 1990 to 2010 in a monthly time step. Whereas nutrient loads and their changes into numerous lakes worldwide are calculated, a special focus is set on nutrient loads into the large and shallow Lake Peipus, which is located between Estonia and Russia and subject to blooms of harmful cyanobacteria. We present estimates, trends, as well as sources of present nutrient loads (TN and TP) to the world's largest lakes with detailed insights to the Lake Peipus situation

  15. Liver Retransplantation in Adults: The Largest Multicenter Italian Study

    PubMed Central

    Maggi, Umberto; Andorno, Enzo; Rossi, Giorgio; De Carlis, Luciano; Cillo, Umberto; Bresadola, Fabrizio; Mazzaferro, Vincenzo; Risaliti, Andrea; Bertoli, Paolo; Consonni, Dario; Barretta, Francesco; De Feo, Tullia; Scalamogna, Mario

    2012-01-01

    This study is the largest Italian survey on liver retransplantations (RET). Data report on 167 adult patients who received 2 grafts, 16 who received 3 grafts, and one who received 4 grafts over a 11 yr period. There was no statistically significant difference in graft survival after the first or the second RET (52, 40, and 29% vs 44, 36, and 18% at 1,5,and 10 yr, respectively: Log-Rank test, p = 0.30). Survivals at 1, 5, and 10 years of patients who underwent 2 (n = 151) or 3 (n = 15) RETs, were 65, 48,and 39% vs 59, 44, and 30%, respectively (p = 0.59). Multivariate analysis of survival showed that only the type of graft (whole vs reduced) was associated with a statistically significant difference (HR = 3.77, Wald test p = 0. 05); the donor age appeared to be a relevant factor as well, although the difference was not statistically significant (HR = 1.91, Wald test p = 0.08). Though late RETs have better results on long term survival relative to early RETs, no statistically significant difference can be found in early results, till three years after RET. Considering late first RETs (interval>30 days from previous transplantation) with whole grafts the difference in graft survival in RETs due to HCV recurrence (n = 17) was not significantly different from RETs due to other causes (n = 53) (65–58 and 31% vs 66–57 and 28% respectively at 1–5 and 10 years, p = 0.66). PMID:23071604

  16. The dust halo of Saturn's largest icy moon, Rhea.

    PubMed

    Jones, G H; Roussos, E; Krupp, N; Beckmann, U; Coates, A J; Crary, F; Dandouras, I; Dikarev, V; Dougherty, M K; Garnier, P; Hansen, C J; Hendrix, A R; Hospodarsky, G B; Johnson, R E; Kempf, S; Khurana, K K; Krimigis, S M; Krüger, H; Kurth, W S; Lagg, A; McAndrews, H J; Mitchell, D G; Paranicas, C; Postberg, F; Russell, C T; Saur, J; Seiss, M; Spahn, F; Srama, R; Strobel, D F; Tokar, R; Wahlund, J-E; Wilson, R J; Woch, J; Young, D

    2008-03-01

    Saturn's moon Rhea had been considered massive enough to retain a thin, externally generated atmosphere capable of locally affecting Saturn's magnetosphere. The Cassini spacecraft's in situ observations reveal that energetic electrons are depleted in the moon's vicinity. The absence of a substantial exosphere implies that Rhea's magnetospheric interaction region, rather than being exclusively induced by sputtered gas and its products, likely contains solid material that can absorb magnetospheric particles. Combined observations from several instruments suggest that this material is in the form of grains and boulders up to several decimetres in size and orbits Rhea as an equatorial debris disk. Within this disk may reside denser, discrete rings or arcs of material. PMID:18323452

  17. GIS learning tool for world's largest earthquakes and their causes

    NASA Astrophysics Data System (ADS)

    Chatterjee, Moumita

    The objective of this thesis is to increase awareness about earthquakes among people, especially young students by showing the five largest and two most predictable earthquake locations in the world and their plate tectonic settings. This is a geographic based interactive tool which could be used for learning about the cause of great earthquakes in the past and the safest places on the earth in order to avoid direct effect of earthquakes. This approach provides an effective way of learning for the students as it is very user friendly and more aligned to the interests of the younger generation. In this tool the user can click on the various points located on the world map which will open a picture and link to the webpage for that point, showing detailed information of the earthquake history of that place including magnitude of quake, year of past quakes and the plate tectonic settings that made this place earthquake prone. Apart from knowing the earthquake related information students will also be able to customize the tool to suit their needs or interests. Students will be able to add/remove layers, measure distance between any two points on the map, select any place on the map and know more information for that place, create a layer from this set to do a detail analysis, run a query, change display settings, etc. At the end of this tool the user has to go through the earthquake safely guidelines in order to be safe during an earthquake. This tool uses Java as programming language and uses Map Objects Java Edition (MOJO) provided by ESRI. This tool is developed for educational purpose and hence its interface has been kept simple and easy to use so that students can gain maximum knowledge through it instead of having a hard time to install it. There are lots of details to explore which can help more about what a GIS based tool is capable of. Only thing needed to run this tool is latest JAVA edition installed in their machine. This approach makes study more fun and

  18. Smart-Geology for the World's largest fossil oyster reef

    NASA Astrophysics Data System (ADS)

    Dorninger, Peter; Nothegger, Clemens; Djuricic, Ana; Rasztovits, Sascha; Harzhauser, Mathias

    2014-05-01

    The geo-edutainment park "Fossilienwelt Weinviertel" at Stetten in Lower Austria exposes the world's largest fossil oyster biostrome. In the past decade, significant progress has been made in 3D digitizing sensor technology. To cope with the high amount of data, processing methods have been automated to a high degree. Consequently, we formulated the hypothesis that appropriate application of state-of-the-art 3D digitizing, data processing, and visualization technologies allows for a significant automation in paleontological prospection, making an evaluation of huge areas commercially feasible in both time and costs. We call the necessary processing steps "Smart Geology", being characterized by automation and large volumes of data. The Smart Geology project (FWF P 25883-N29) investigates three topics, 3D digitizing, automated geological and paleontological analysis and interpretation and finally investigating the applicability of smart devices for on-site accessibility of project data in order to support the two scientific hypotheses concerning the emerging process of the shell bed, i.e. was it formed by a tsunami or a major storm, and does it preserve pre- and post-event features. This contribution concentrates on the innovative and sophisticated 3D documentation and visualization processes being applied to virtualise approximately 15.000 fossil oysters at the approximately 25 by 17 m accessible shell bad. We decided to use a Terrestrial Laserscanner (TLS) for the determination of the geometrical 3D structures. The TLS achieves about 2 mm single point measurement accuracy. The scanning campaign provides a "raw" point cloud of approximately 1 bio. points at the respective area. Due to the scanning configuration used, the occurrence of occluded ares is minimized hence the full 3D structure of this unique site can be modelled. In addition, approximately 300 photos were taken with a nominal resolution of 0.6 mm per pixel. Sophisticated artificial lightning (close to

  19. The Largest Holocene Eruption of the Central Andes Found

    NASA Astrophysics Data System (ADS)

    Fernandez-Turiel, J.; Rodriguez-Gonzalez, A.; Saavedra, J.; Perez-Torrado, F.; Carracedo, J.; Osterrieth, M.; Carrizo, J.; Esteban, G.

    2013-12-01

    We present new data and interpretation about a major eruption -spreading ˜110 km3 ashes over 440.000 km2- long thought to have occurred around 4200 years ago in the Cerro Blanco Volcanic Complex (CBVC) in NW Argentina. This eruption may be the biggest during the past five millennia in the Central Volcanic Zone of the Andes, and possibly one of the largest Holocene eruptions in the world. The environmental effects of this voluminous eruption are still noticeable, as evidenced by the high content of arsenic and other trace elements in the groundwaters of the Chacopampean Plain. The recognition of this significant volcanic event may shed new light on interpretations of critical changes observed in the mid-Holocene paleontological and archaeological records, and offers researchers an excellent, extensive regional chronostratigraphic marker for reconstructing mid-Holocene geological history over a wide geographical area of South America. More than 100 ashes were sampled in Argentina, Chile and Uruguay during different field campaigns. Ash samples were characterized by scanning electron microscope (SEM), X-ray diffraction (XRD), grain size distributions laser diffraction, and geochemically by electron microprobe (EMPA) and laser ablation-HR-ICP-MS. New and published 14C ages were calibrated to calendar years BP. The age of the most recent CBVC eruption is 4407-4093 cal y BP, indirectly dated by 14C of associated organic sediment within the lower part of a proximal fall deposit of this event (26°53'16.05"S-67°44'48.68"W). This is the youngest record of a major volcanic event in the Southern Puna. This age is consistent with other radiocarbon dates of organic matter in palaeosols underlying or overlying distal ash fall deposits. Based on their products, all of rhyolitic composition, we have distinguished 8 main episodes during the evolution of the most recent CBVC eruption: 1) the eruption began with a white rhyolite lava dome extrusion; 2) followed by a Plinian

  20. Watching the Creation of Southern California's Largest Reservoir

    NASA Technical Reports Server (NTRS)

    2001-01-01

    The new Diamond Valley Lake Reservoir near the city of Hemet in Riverside County is billed as the largest earthworks construction project in U.S.history. Construction began in 1995 and involved 31 million cubic meters of foundation excavation and 84 million cubic meters of embankment construction. This set of MISR images captures the most recent phase in the reservoir's activation. At the upper left is a natural-color view acquired by the instrument's vertical-viewing (nadir) camera on March 14, 2000 (Terra orbit 1273), shortly after the Metropolitan Water District began filling the reservoir with water from the Colorado River and Northern California. Water appears darker than the surrounding land. The image at the upper right was acquired nearly one year later on March 1, 2001 (Terra orbit 6399), and shows a clear increase in the reservoir's water content. When full, the lake will hold nearly a trillion liters of water.

    According to the Metropolitan Water District, the 7 kilometer x 3 kilometer reservoir nearly doubles Southern California's above-groundwater storage capacity. In addition to routine water management, Diamond Valley Lake is designed to provide protection against drought and a six-month emergency supply in the event of earthquake damage to a major aqueduct. In the face of electrical power shortages, it is also expected to reduce dependence on the pumping of water from northern mountains during the high-demand summer months. An unexpected result of site excavation was the uncovering of mastodon and mammoth skeletons along with bones from extinct species not previously thought to have been indigenous to the area, such as the giant long-horned bison and North American lion. A museum and interpretive center is being built to protect these finds.

    The lower MISR image, from May 20, 2001 (Terra orbit 7564), is a false-color view combining data from the instrument's 26-degree forward view (displayed as blue) with data from the 26-degree backward

  1. Drilling the Bushveld Complex- the world's largest layered mafic intrusion

    NASA Astrophysics Data System (ADS)

    Ashwal, L. D.; Webb, S. J.; Trumbull, R. B.

    2013-12-01

    The fact that surprising new discoveries can be made in layered mafic intrusions (e.g., subtle 100-150 m cyclicity in apparently homogeneous cumulates over 1000s of m) means that we are still in the first-order characterization phase of understanding these objects. Accordingly, we have secured funding from ICDP for a planning workshop to be held in Johannesburg in early 2014, aimed at scientific drilling of the Bushveld Complex, the world's largest layered mafic intrusion. Science objectives include, but are not limited to: 1. Magma chamber processes & melt evolution. How many melts/magmas/mushes were involved, what were their compositions and how did they interact? What, if anything, is missing from the Complex, and where did it go? Did Bushveld magmatism have an effect upon Earth's atmosphere at 2 Ga? 2. Crust-mantle interactions & origin of Bushveld granitoids. Are Bushveld granites & rhyolites crustal melts, differentiates from the mafic magmas or products of immiscibility? How can the evolved isotopic signatures in the mafic rocks (e.g., epsilon Nd to -8) be understood? 3. Origin of ore deposits. What were the relative roles of gravity settling, magma mixing, immiscibility and hydrothermal fluid transport in producing the PGE, Cr and V deposits? We have identified 3 potential drilling targets representing a total of ~12 km of drill core. Exact locations of drill sites are to be discussed at the workshop. Target A- East-Central Bushveld Complex. We propose 3 overlapping 3 km boreholes that will provide the first roof-to-floor continuous coverage of the Rustenburg Layered Suite. These boreholes will represent a curated, internationally available reference collection of Bushveld material for present and future research. Target B- Southeastern Bushveld Complex. We propose a single borehole of ~2 km depth, collared in Rooiberg felsite, and positioned to intersect the Roof Zone, Upper Zone, Main Zone and floor of the Complex. Amongst other things, this site will

  2. ALMA Partners Break Ground on World's Largest Millimeter Wavelength Telescope

    NASA Astrophysics Data System (ADS)

    2003-11-01

    Scientists and dignitaries from North America, Europe, and Chile broke ground today (Thursday, November 6, 2003) on what will be the world's largest, most sensitive radio telescope operating at millimeter wavelengths. ALMA - the Atacama Large Millimeter Array - will be a single instrument composed of 64 high-precision antennas located on the Chajnantor plain of the Chilean Andes in the District of San Pedro de Atacama, 16,500 feet (5,000 meters) above sea level. ALMA's primary function will be to observe and image with unprecedented clarity the enigmatic cold regions of the Universe, which are optically dark, yet shine brightly in the millimeter portion of the electromagnetic spectrum. ALMA Array Artist's Conception of ALMA Array in Compact Configuration (Click on Image for Larger Version) Other Images Available: Artist's conception of the antennas for the Atacama Large Millimeter Array Moonrise over ALMA test equipment near Cerro Chajnantor, Chile VertexRSI antenna at the VLA test site The Atacama Large Millimeter Array is an international astronomy facility. ALMA is an equal partnership between Europe and North America, in cooperation with the Republic of Chile, and is funded in North America by the U.S. National Science Foundation (NSF) in cooperation with the National Research Council of Canada (NRC), and in Europe by the European Southern Observatory (ESO) and Spain. ALMA construction and operations are led on behalf of North America by the National Radio Astronomy Observatory (NRAO), which is managed by Associated Universities, Inc. (AUI), and on behalf of Europe by ESO. "The U.S. National Science Foundation joins today with our North American partner, Canada, and with the European Southern Observatory, Spain, and Chile to prepare for a spectacular new instrument," said Dr. Rita Colwell, director of the U.S. National Science Foundation. "The Atacama Large Millimeter Array will expand our vision of the Universe with "eyes" that pierce the shrouded mantles of

  3. Time-Resolved Visualisation of Nearly-Native Influenza A Virus Progeny Ribonucleoproteins and Their Individual Components in Live Infected Cells.

    PubMed

    Avilov, Sergiy; Magnus, Julie; Cusack, Stephen; Naffakh, Nadia

    2016-01-01

    Influenza viruses are a global health concern because of the permanent threat of novel emerging strains potentially capable of causing pandemics. Viral ribonucleoproteins (vRNPs) containing genomic RNA segments, nucleoprotein oligomers, and the viral polymerase, play a central role in the viral replication cycle. Our knowledge about critical events such as vRNP assembly and interactions with other viral and cellular proteins is poor and could be substantially improved by time lapse imaging of the infected cells. However, such studies are limited by the difficulty to achieve live-cell compatible labeling of active vRNPs. Previously we designed the first unimpaired recombinant influenza WSN-PB2-GFP11 virus allowing fluorescent labeling of the PB2 subunit of the viral polymerase (Avilov et al., J.Virol. 2012). Here, we simultaneously labeled the viral PB2 protein using the above-mentioned strategy, and virus-encoded progeny RNPs through spontaneous incorporation of transiently expressed NP-mCherry fusion proteins during RNP assembly in live infected cells. This dual labeling enabled us to visualize progeny vRNPs throughout the infection cycle and to characterize independently the mobility, oligomerization status and interactions of vRNP components in the nuclei of live infected cells. PMID:26978069

  4. Heterogeneous nuclear ribonucleoprotein K and nucleolin as transcriptional activators of the vascular endothelial growth factor promoter through interaction with secondary DNA structures

    PubMed Central

    Uribe, Diana J.; Guo, Kexiao; Shin, Yoon-Joo; Sun, Daekyu

    2011-01-01

    The human vascular endothelial growth factor (VEGF) promoter contains a polypurine/polypyrimidine (pPu/pPy) tract that is known to play a critical role in its transcriptional regulation. This pPu/pPy tract undergoes a conformational transition between B-DNA, single stranded DNA and atypical secondary DNA structures such as G-quadruplexes and i-motifs. We studied the interaction of the cytosine-rich (C-rich) and guanine-rich (G-rich) strands of this tract with transcription factors heterogeneous nuclear ribonucleoprotein (hnRNP) K and nucleolin, respectively, both in vitro and in vivo and their potential role in the transcriptional control of VEGF. Using chromatin immunoprecipitation (ChIP) assay for our in vivo studies and electrophoretic mobility shift assay (EMSA) for our in vitro studies, we demonstrated that both nucleolin and hnRNP K bind selectively to the G- and C-rich sequences, respectively, in the pPu/pPy tract of the VEGF promoter. The small interfering RNA (siRNA)-mediated silencing of either nucleolin or hnRNP K resulted in the down-regulation of basal VEGF gene, suggesting that they act as activators of VEGF transcription. Taken together, the identification of transcription factors that can recognize and bind to atypical DNA structures within the pPu/pPy tract will provide new insight into mechanisms of transcriptional regulation of the VEGF gene. PMID:21466159

  5. Time-Resolved Visualisation of Nearly-Native Influenza A Virus Progeny Ribonucleoproteins and Their Individual Components in Live Infected Cells

    PubMed Central

    Avilov, Sergiy; Magnus, Julie; Cusack, Stephen; Naffakh, Nadia

    2016-01-01

    Influenza viruses are a global health concern because of the permanent threat of novel emerging strains potentially capable of causing pandemics. Viral ribonucleoproteins (vRNPs) containing genomic RNA segments, nucleoprotein oligomers, and the viral polymerase, play a central role in the viral replication cycle. Our knowledge about critical events such as vRNP assembly and interactions with other viral and cellular proteins is poor and could be substantially improved by time lapse imaging of the infected cells. However, such studies are limited by the difficulty to achieve live-cell compatible labeling of active vRNPs. Previously we designed the first unimpaired recombinant influenza WSN-PB2-GFP11 virus allowing fluorescent labeling of the PB2 subunit of the viral polymerase (Avilov et al., J.Virol. 2012). Here, we simultaneously labeled the viral PB2 protein using the above-mentioned strategy, and virus-encoded progeny RNPs through spontaneous incorporation of transiently expressed NP-mCherry fusion proteins during RNP assembly in live infected cells. This dual labeling enabled us to visualize progeny vRNPs throughout the infection cycle and to characterize independently the mobility, oligomerization status and interactions of vRNP components in the nuclei of live infected cells. PMID:26978069

  6. Solution Structure of the HIV-1 Intron Splicing Silencer and Its Interactions with the UP1 Domain of Heterogeneous Nuclear Ribonucleoprotein (hnRNP) A1.

    PubMed

    Jain, Niyati; Morgan, Christopher E; Rife, Brittany D; Salemi, Marco; Tolbert, Blanton S

    2016-01-29

    Splicing patterns in human immunodeficiency virus type 1 (HIV-1) are maintained through cis regulatory elements that recruit antagonistic host RNA-binding proteins. The activity of the 3' acceptor site A7 is tightly regulated through a complex network of an intronic splicing silencer (ISS), a bipartite exonic splicing silencer (ESS3a/b), and an exonic splicing enhancer (ESE3). Because HIV-1 splicing depends on protein-RNA interactions, it is important to know the tertiary structures surrounding the splice sites. Herein, we present the NMR solution structure of the phylogenetically conserved ISS stem loop. ISS adopts a stable structure consisting of conserved UG wobble pairs, a folded 2X2 (GU/UA) internal loop, a UU bulge, and a flexible AGUGA apical loop. Calorimetric and biochemical titrations indicate that the UP1 domain of heterogeneous nuclear ribonucleoprotein A1 binds the ISS apical loop site-specifically and with nanomolar affinity. Collectively, this work provides additional insights into how HIV-1 uses a conserved RNA structure to commandeer a host RNA-binding protein. PMID:26607354

  7. Heterogenous ribonucleoprotein A18 (hnRNP A18) promotes tumor growth by increasing protein translation of selected transcripts in cancer cells.

    PubMed

    Chang, Elizabeth T; Parekh, Palak R; Yang, Qingyuan; Nguyen, Duc M; Carrier, France

    2016-03-01

    The heterogenous ribonucleoprotein A18 (hnRNP A18) promotes tumor growth by coordinating the translation of selected transcripts associated with proliferation and survival. hnRNP A18 binds to and stabilizes the transcripts of pro-survival genes harboring its RNA signature motif in their 3'UTRs. hnRNP A18 binds to ATR, RPA, TRX, HIF-1α and several protein translation factor mRNAs on polysomes and increases de novo protein translation under cellular stress. Most importantly, down regulation of hnRNP A18 decreases proliferation, invasion and migration in addition to significantly reducing tumor growth in two mouse xenograft models, melanoma and breast cancer. Moreover, tissue microarrays performed on human melanoma, prostate, breast and colon cancer indicate that hnRNP A18 is over expressed in 40 to 60% of these malignant tissue as compared to normal adjacent tissue. Immunohistochemistry data indicate that hnRNP A18 is over expressed in the stroma and hypoxic areas of human tumors. These data thus indicate that hnRNP A18 can promote tumor growth in in vivo models by coordinating the translation of pro-survival transcripts to support the demands of proliferating cells and increase survival under cellular stress. hnRNP A18 therefore represents a new target to selectively inhibit protein translation in tumor cells. PMID:26824423

  8. U1 small nuclear ribonucleoproteins (snRNPs) aggregate in Alzheimer’s disease due to autosomal dominant genetic mutations and trisomy 21

    PubMed Central

    2014-01-01

    Background We recently identified U1 small nuclear ribonucleoprotein (snRNP) tangle-like aggregates and RNA splicing abnormalities in sporadic Alzheimer’s disease (AD). However little is known about snRNP biology in early onset AD due to autosomal dominant genetic mutations or trisomy 21 in Down syndrome. Therefore we investigated snRNP biochemical and pathologic features in these disorders. Findings We performed quantitative proteomics and immunohistochemistry in postmortem brain from genetic AD cases. Electron microscopy was used to characterize ultrastructural features of pathologic aggregates. U1-70k and other snRNPs were biochemically enriched in the insoluble fraction of human brain from subjects with presenilin 1 (PS1) mutations. Aggregates of U1 snRNP-immunoreactivity formed cytoplasmic tangle-like structures in cortex of AD subjects with PS1 and amyloid precursor protein (APP) mutations as well as trisomy 21. Ultrastructural analysis with electron microscopy in an APP mutation case demonstrated snRNP immunogold labeling of paired helical filaments (PHF). Conclusions These studies identify U1 snRNP pathologic changes in brain of early onset genetic forms of AD. Since dominant genetic mutations and trisomy 21 result in dysfunctional amyloid processing, the findings suggest that aberrant β-amyloid processing may influence U1 snRNP aggregate formation. PMID:24773620

  9. Uncovering the stoichiometry of Pyrococcus furiosus RNase P, a multi-subunit catalytic ribonucleoprotein complex, by surface-induced dissociation and ion mobility mass spectrometry.

    PubMed

    Ma, Xin; Lai, Lien B; Lai, Stella M; Tanimoto, Akiko; Foster, Mark P; Wysocki, Vicki H; Gopalan, Venkat

    2014-10-20

    We demonstrate that surface-induced dissociation (SID) coupled with ion mobility mass spectrometry (IM-MS) is a powerful tool for determining the stoichiometry of a multi-subunit ribonucleoprotein (RNP) complex assembled in a solution containing Mg(2+). We investigated Pyrococcus furiosus (Pfu) RNase P, an archaeal RNP that catalyzes tRNA 5' maturation. Previous step-wise, Mg(2+)-dependent reconstitutions of Pfu RNase P with its catalytic RNA subunit and two interacting protein cofactor pairs (RPP21⋅RPP29 and POP5⋅RPP30) revealed functional RNP intermediates en route to the RNase P enzyme, but provided no information on subunit stoichiometry. Our native MS studies with the proteins showed RPP21⋅RPP29 and (POP5⋅RPP30)2 complexes, but indicated a 1:1 composition for all subunits when either one or both protein complexes bind the cognate RNA. These results highlight the utility of SID and IM-MS in resolving conformational heterogeneity and yielding insights on RNP assembly.

  10. Overexpression of an Arabidopsis heterogeneous nuclear ribonucleoprotein gene, AtRNP1, affects plant growth and reduces plant tolerance to drought and salt stresses.

    PubMed

    Wang, Zhenyu; Zhao, Xiuyang; Wang, Bing; Liu, Erlong; Chen, Ni; Zhang, Wei; Liu, Heng

    2016-04-01

    Heterogeneous nuclear ribonucleoproteins (hnRNPs) participate in diverse regulations of plant growth and environmental stress responses. In this work, an Arabidopsis hnRNP of unknown function, AtRNP1, was investigated. We found that AtRNP1 gene is highly expressed in rosette and cauline leaves, and slightly induced under drought, salt, osmotic and ABA stresses. AtRNP1 protein is localized to both the nucleus and cytoplasm. We performed homologous overexpression of AtRNP1 and found that the transgenic plants showed shortened root length and plant height, and accelerated flowering. In addition, the transgenic plants also showed reduced tolerance to drought, salt, osmotic and ABA stresses. Further studies revealed that under both normal and stress conditions, the proline contents in the transgenic plants are markedly decreased, associated with reduced expression levels of a proline synthase gene and several stress-responsive genes. These results suggested that the overexpression of AtRNP1 negatively affects plant growth and abiotic stress tolerance. PMID:26923071

  11. Activation of Akt is essential for the propagation of mitochondrial respiratory stress signaling and activation of the transcriptional coactivator heterogeneous ribonucleoprotein A2.

    PubMed

    Guha, Manti; Fang, Ji-Kang; Monks, Robert; Birnbaum, Morris J; Avadhani, Narayan G

    2010-10-15

    Mitochondrial respiratory stress (also called mitochondrial retrograde signaling) activates a Ca(2+)/calcineurin-mediated signal that culminates in transcription activation/repression of a large number of nuclear genes. This signal is propagated through activation of the regulatory proteins NFκB c-Rel/p50, C/EBPδ, CREB, and NFAT. Additionally, the heterogeneous ribonucleoprotein A2 (hnRNPA2) functions as a coactivator in up-regulating the transcription of Cathepsin L, RyR1, and Glut-4, the target genes of stress signaling. Activation of IGF1R, which causes a metabolic switch to glycolysis, cell invasiveness, and resistance to apoptosis, is a phenotypic hallmark of C2C12 myoblasts subjected to mitochondrial stress. In this study, we report that mitochondrial stress leads to increased expression, activation, and nuclear localization of Akt1. Mitochondrial respiratory stress also activates Akt1-gene expression, which involves hnRNPA2 as a coactivator, indicating a complex interdependency of these two factors. Using Akt1(-/-) mouse embryonic fibroblasts and Akt1 mRNA-silenced C2C12 cells, we show that Akt1-mediated phosphorylation is crucial for the activation and recruitment of hnRNPA2 to the enhanceosome complex. Akt1 mRNA silencing in mtDNA-depleted cells resulted in reversal of the invasive phenotype, accompanied by sensitivity to apoptotic stimuli. These results show that Akt1 is an important regulator of the nuclear transcriptional response to mitochondrial stress.

  12. Heterogeneous ribonucleoprotein R regulates arylalkylamine N-acetyltransferase synthesis via internal ribosomal entry site-mediated translation in a circadian manner.

    PubMed

    Lee, Hwa-Rim; Kim, Tae-Don; Kim, Hyo-Jin; Jung, Youngseob; Lee, Dohyun; Lee, Kyung-Ha; Kim, Do-Yeon; Woo, Kyung-Chul; Kim, Kyong-Tai

    2015-11-01

    Rhythmic arylalkylamine N-acetyltransferase (AANAT) synthesis is a prominent circadian-controlled response that occurs in most mammals. AANAT is the core enzyme in melatonin production; because melatonin participates in many physiological processes, the regulation of AANAT is an important research topic. In this study, we focused on the role of heterogeneous ribonucleoprotein R (hnRNP R) in the translation of AANAT. A novel RNA-binding protein hnRNP R widely interacted with the 5' untranslated region (UTR) of AANAT mRNA and contributed to translation through an internal ribosomal entry site (IRES). Fine-tuning of AANAT protein synthesis occurred in response to knockdown and overexpression of hnRNP R. Nocturnal elevation of AANAT protein was dependent on the rhythmic changes of hnRNP R, whose levels are elevated in the pineal gland during nighttime. Increases in hnRNP R additionally improved AANAT production in rat pinealocytes under norepinephrine (NE) treatment. These results suggest that cap-independent translation of AANAT mRNA plays a role in the rhythmic synthesis of melatonin through the recruitment of translational machinery to hnRNP R-bound AANAT mRNA.

  13. Morphological details in bloodstain particles.

    PubMed

    De Wael, K; Lepot, L

    2015-01-01

    During the commission of crimes blood can be transferred to the clothing of the offender or on other crime related objects. Bloodstain particles are sub-millimetre sized flakes that are lost from dried bloodstains. The nature of these red particles is easily confirmed using spectroscopic methods. In casework, bloodstain particles showing highly detailed morphological features were observed. These provided a rationale for a series of experiments described in this work. It was found that the "largest" particles are shed from blood deposited on polyester and polyamide woven fabrics. No particles are lost from the stains made on absorbent fabrics and from those made on knitted fabrics. The morphological features observed in bloodstain particles can provide important information on the substrates from which they were lost. PMID:25437904

  14. A comprehensive analysis of 3′ end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation

    PubMed Central

    Gruber, Andreas J.; Schmidt, Ralf; Gruber, Andreas R.; Martin, Georges; Ghosh, Souvik; Belmadani, Manuel; Keller, Walter

    2016-01-01

    Alternative polyadenylation (APA) is a general mechanism of transcript diversification in mammals, which has been recently linked to proliferative states and cancer. Different 3′ untranslated region (3′ UTR) isoforms interact with different RNA-binding proteins (RBPs), which modify the stability, translation, and subcellular localization of the corresponding transcripts. Although the heterogeneity of pre-mRNA 3′ end processing has been established with high-throughput approaches, the mechanisms that underlie systematic changes in 3′ UTR lengths remain to be characterized. Through a uniform analysis of a large number of 3′ end sequencing data sets, we have uncovered 18 signals, six of which are novel, whose positioning with respect to pre-mRNA cleavage sites indicates a role in pre-mRNA 3′ end processing in both mouse and human. With 3′ end sequencing we have demonstrated that the heterogeneous ribonucleoprotein C (HNRNPC), which binds the poly(U) motif whose frequency also peaks in the vicinity of polyadenylation (poly(A)) sites, has a genome-wide effect on poly(A) site usage. HNRNPC-regulated 3′ UTRs are enriched in ELAV-like RBP 1 (ELAVL1) binding sites and include those of the CD47 gene, which participate in the recently discovered mechanism of 3′ UTR–dependent protein localization (UDPL). Our study thus establishes an up-to-date, high-confidence catalog of 3′ end processing sites and poly(A) signals, and it uncovers an important role of HNRNPC in regulating 3′ end processing. It further suggests that U-rich elements mediate interactions with multiple RBPs that regulate different stages in a transcript's life cycle. PMID:27382025

  15. Heterogeneous nuclear ribonucleoprotein K (hnRNP K) is a tissue biomarker for detection of early Hepatocellular carcinoma in patients with cirrhosis

    PubMed Central

    2012-01-01

    Background Hepatocellular carcinoma (HCC) is one of the most common malignant tumors occurring mainly in patients with chronic liver disease. Detection of early HCC is critically important for treatment of these patients. Methods We employed a proteomic profiling approach to identify potential biomarker for early HCC detection. Based on Barcelona Clinic Liver Cancer (BCLC) staging classification, 15 early HCC and 25 late HCC tissue samples from post-operative HCC patients and their clinicopathological data were used for the discovery of biomarkers specific for the detection of early HCC. Differential proteins among cirrhotic, early, and late tissue samples were separated by two-dimensional gel electrophoresis (2-DE) and subsequently identified by mass spectrometry (MS). Receiver operating characteristic (ROC) curves analysis were performed to find potential biomarkers associated with early HCC. Diagnosis performance of the biomarker was obtained from diagnosis test. Results Protein spot SSP2215 was found to be significantly overexpressed in HCC, particularly in early HCC, and identified as heterogeneous nuclear ribonucleoprotein K (hnRNP K) by tandem mass spectrometry (MALDI TOF/TOF). The overexpression in HCC was subsequently validated by western blot and immunohistochemistry. ROC curve analysis showed that hnRNP K intensity could detect early HCC at 66.67 % sensitivity and 84 % specificity, which was superior to serum α-fetoprotein (AFP) in detection of early HCC. Furthermore, the diagnosis test demonstrated, when combined with hnRNP K and serum AFP as biomarker panel to detect early HCC at different cut-off value, the sensitivity and specificity could be enhanced to 93.33 % and 96 %, respectively. Conclusions hnRNP K is a potential tissue biomarker, either alone or in combination with serum AFP, for detection of early HCC. High expression of hnRNP K could be helpful to discriminate early HCC from a nonmalignant nodule, especially for patients with liver

  16. Heterogeneous nuclear ribonucleoproteins A1 and A2 modulate expression of Tid1 isoforms and EGFR signaling in non-small cell lung cancer.

    PubMed

    Chen, Chi-Yuan; Jan, Chia-Ing; Pi, Wen-Chieh; Wang, Wen-Lung; Yang, Pan-Chyr; Wang, Tong-Hong; Karni, Rotem; Wang, Tzu-Chien V

    2016-03-29

    The Tid1 protein is a DnaJ co-chaperone that has two alternative splicing isoforms: Tid1 long form (Tid1-L) and Tid1 short form (Tid1-S). Recent studies have shown that Tid1-L functions as a tumor suppressor by decreasing EGFR signaling in various cancers, including head and neck cancer and non-small cell lung cancer (NSCLC). However, the molecular mechanism responsible for regulating the alternative splicing of Tid1 is not yet known. Two splicing factors, heterogeneous nuclear ribonucleoproteins (hnRNP) A1 and A2, participate in alternative splicing and are known to be overexpressed in lung cancers. In this work, we examined if hnRNP A1 and A2 could regulate the alternative splicing of Tid1 to modulate tumorigenesis in NSCLC. We report that RNAi-mediated depletion of both hnRNP A1/A2 (but not single depletion of either) increased Tid1-L expression, inhibited cell proliferation and attenuated EGFR signaling. Analyses of the expression levels of hnRNP A1, hnRNP A2, EGFR and Tid1-L in NSCLC tissues revealed that hnRNP A1 and A2 are positively correlated with EGFR, but negatively correlated with Tid1-L. NSCLC patients with high-level expression of hnRNP A1, hnRNP A2 and EGFR combined with low-level expression of Tid1-L were associated with poor overall survival. Taken together, our results suggest that hnRNP A1 or A2 are both capable of facilitating the alternative splicing of exon 11 in the Tid1 pre-mRNA, thereby suppressing the expression of Tid1-L and allowing EGFR-related signaling to facilitate NSCLC tumorigenesis. PMID:26919236

  17. A comprehensive analysis of 3' end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation.

    PubMed

    Gruber, Andreas J; Schmidt, Ralf; Gruber, Andreas R; Martin, Georges; Ghosh, Souvik; Belmadani, Manuel; Keller, Walter; Zavolan, Mihaela

    2016-08-01

    Alternative polyadenylation (APA) is a general mechanism of transcript diversification in mammals, which has been recently linked to proliferative states and cancer. Different 3' untranslated region (3' UTR) isoforms interact with different RNA-binding proteins (RBPs), which modify the stability, translation, and subcellular localization of the corresponding transcripts. Although the heterogeneity of pre-mRNA 3' end processing has been established with high-throughput approaches, the mechanisms that underlie systematic changes in 3' UTR lengths remain to be characterized. Through a uniform analysis of a large number of 3' end sequencing data sets, we have uncovered 18 signals, six of which are novel, whose positioning with respect to pre-mRNA cleavage sites indicates a role in pre-mRNA 3' end processing in both mouse and human. With 3' end sequencing we have demonstrated that the heterogeneous ribonucleoprotein C (HNRNPC), which binds the poly(U) motif whose frequency also peaks in the vicinity of polyadenylation (poly(A)) sites, has a genome-wide effect on poly(A) site usage. HNRNPC-regulated 3' UTRs are enriched in ELAV-like RBP 1 (ELAVL1) binding sites and include those of the CD47 gene, which participate in the recently discovered mechanism of 3' UTR-dependent protein localization (UDPL). Our study thus establishes an up-to-date, high-confidence catalog of 3' end processing sites and poly(A) signals, and it uncovers an important role of HNRNPC in regulating 3' end processing. It further suggests that U-rich elements mediate interactions with multiple RBPs that regulate different stages in a transcript's life cycle. PMID:27382025

  18. Heterogeneous nuclear ribonucleoproteins A1 and A2 modulate expression of Tid1 isoforms and EGFR signaling in non-small cell lung cancer

    PubMed Central

    Chen, Chi-Yuan; Jan, Chia-Ing; Pi, Wen-Chieh; Wang, Wen-Lung; Yang, Pan-Chyr; Wang, Tong-Hong; Karni, Rotem; Wang, Tzu-Chien V.

    2016-01-01

    The Tid1 protein is a DnaJ co-chaperone that has two alternative splicing isoforms: Tid1 long form (Tid1-L) and Tid1 short form (Tid1-S). Recent studies have shown that Tid1-L functions as a tumor suppressor by decreasing EGFR signaling in various cancers, including head and neck cancer and non-small cell lung cancer (NSCLC). However, the molecular mechanism responsible for regulating the alternative splicing of Tid1 is not yet known. Two splicing factors, heterogeneous nuclear ribonucleoproteins (hnRNP) A1 and A2, participate in alternative splicing and are known to be overexpressed in lung cancers. In this work, we examined if hnRNP A1 and A2 could regulate the alternative splicing of Tid1 to modulate tumorigenesis in NSCLC. We report that RNAi-mediated depletion of both hnRNP A1/A2 (but not single depletion of either) increased Tid1-L expression, inhibited cell proliferation and attenuated EGFR signaling. Analyses of the expression levels of hnRNP A1, hnRNP A2, EGFR and Tid1-L in NSCLC tissues revealed that hnRNP A1 and A2 are positively correlated with EGFR, but negatively correlated with Tid1-L. NSCLC patients with high-level expression of hnRNP A1, hnRNP A2 and EGFR combined with low-level expression of Tid1-L were associated with poor overall survival. Taken together, our results suggest that hnRNP A1 or A2 are both capable of facilitating the alternative splicing of exon 11 in the Tid1 pre-mRNA, thereby suppressing the expression of Tid1-L and allowing EGFR-related signaling to facilitate NSCLC tumorigenesis. PMID:26919236

  19. RNA-Free and Ribonucleoprotein-Associated Influenza Virus Polymerases Directly Bind the Serine-5-Phosphorylated Carboxyl-Terminal Domain of Host RNA Polymerase II

    PubMed Central

    Martínez-Alonso, Mónica; Hengrung, Narin

    2016-01-01

    ABSTRACT Influenza viruses subvert the transcriptional machinery of their hosts to synthesize their own viral mRNA. Ongoing transcription by cellular RNA polymerase II (Pol II) is required for viral mRNA synthesis. By a process known as cap snatching, the virus steals short 5′ capped RNA fragments from host capped RNAs and uses them to prime viral transcription. An interaction between the influenza A virus RNA polymerase and the C-terminal domain (CTD) of the large subunit of Pol II has been established, but the molecular details of this interaction remain unknown. We show here that the influenza virus ribonucleoprotein (vRNP) complex binds to the CTD of transcriptionally engaged Pol II. Furthermore, we provide evidence that the viral polymerase binds directly to the serine-5-phosphorylated form of the Pol II CTD, both in the presence and in the absence of viral RNA, and show that this interaction is conserved in evolutionarily distant influenza viruses. We propose a model in which direct binding of the viral RNA polymerase in the context of vRNPs to Pol II early in infection facilitates cap snatching, while we suggest that binding of free viral polymerase to Pol II late in infection may trigger Pol II degradation. IMPORTANCE Influenza viruses cause yearly epidemics and occasional pandemics that pose a threat to human health, as well as represent a large economic burden to health care systems globally. Existing vaccines are not always effective, as they may not exactly match the circulating viruses. Furthermore, there are a limited number of antivirals available, and development of resistance to these is a concern. New measures to combat influenza are needed, but before they can be developed, it is necessary to better understand the molecular interactions between influenza viruses and their host cells. By providing further insights into the molecular details of how influenza viruses hijack the host transcriptional machinery, we aim to uncover novel targets for

  20. Assembly of Functional Ribonucleoprotein Complexes by AU-rich Element RNA-binding Protein 1 (AUF1) Requires Base-dependent and -independent RNA Contacts*

    PubMed Central

    Zucconi, Beth E.; Wilson, Gerald M.

    2013-01-01

    AU-rich element RNA-binding protein 1 (AUF1) regulates the stability and/or translational efficiency of diverse mRNA targets, including many encoding products controlling the cell cycle, apoptosis, and inflammation by associating with AU-rich elements residing in their 3′-untranslated regions. Previous biochemical studies showed that optimal AUF1 binding requires 33–34 nucleotides with a strong preference for U-rich RNA despite observations that few AUF1-associated cellular mRNAs contain such extended U-rich domains. Using the smallest AUF1 isoform (p37AUF1) as a model, we employed fluorescence anisotropy-based approaches to define thermodynamic parameters describing AUF1 ribonucleoprotein (RNP) complex formation across a panel of RNA substrates. These data demonstrated that 15 nucleotides of AU-rich sequence were sufficient to nucleate high affinity p37AUF1 RNP complexes within a larger RNA context. In particular, p37AUF1 binding to short AU-rich RNA targets was significantly stabilized by interactions with a 3′-purine residue and largely base-independent but non-ionic contacts 5′ of the AU-rich site. RNP stabilization by the upstream RNA domain was associated with an enhanced negative change in heat capacity consistent with conformational changes in protein and/or RNA components, and fluorescence resonance energy transfer-based assays demonstrated that these contacts were required for p37AUF1 to remodel local RNA structure. Finally, reporter mRNAs containing minimal high affinity p37AUF1 target sequences associated with AUF1 and were destabilized in a p37AUF1-dependent manner in cells. These findings provide a mechanistic explanation for the diverse population of AUF1 target mRNAs but also suggest how AUF1 binding could regulate protein and/or microRNA binding events at adjacent sites. PMID:23940053

  1. Radiosensitization and downregulation of heterogeneous nuclear ribonucleoprotein K (hnRNP K) upon inhibition of mitogen/extracellular signal-regulated kinase (MEK) in malignant melanoma cells

    PubMed Central

    Eder, Stefan; Lamkowski, Andreas; Priller, Markus; Port, Matthias; Steinestel, Konrad

    2015-01-01

    Background Heterogeneous nuclear ribonucleoprotein K (hnRNP K) is an important cofactor in the p53-mediated DNA damage response pathway upon ionizing radiation (IR) and exerts anti-apoptotic effects also independent of p53 pathway activation. Furthermore, hnRNP K is overexpressed in various neoplasms including malignant melanoma (MM). Here, we investigate the role of hnRNP K in the radioresistance of MM cells. Methods and results Our results show cytoplasmic expression of hnRNP K in human MM surgical specimens, but not in benign nevi, and a quick dose- and time-dependent upregulation in response to IR accompanied by cytoplasmic redistribution of the protein in the IPC-298 cellular tumor model carrying an activating NRAS mutation (p.Q61L). SiRNA-based knockdown of hnRNP K induced a delayed decline in γH2AX/53BP1-positive DNA repair foci upon IR. Pharmacological interference with MAPK signaling abrogated ERK phosphorylation, diminished cellular hnRNP K levels, impaired γH2AX/53BP1-foci repair and proliferative capability and increased apoptosis comparable to the observed hnRNP K knockdown phenotype in IPC-298 cells. Conclusion Our results indicate that pharmacological interference with MAPK signaling increases vulnerability of NRAS-mutant malignant melanoma cells to ionizing radiation along with downregulation of endogenous hnRNP K and point towards a possible use for combined MEK inhibition and localized radiation therapy of MM in the NRAS-mutant setting where BRAF inhibitors offer no clinical benefit. PMID:26136337

  2. SPF30 is an essential human splicing factor required for assembly of the U4/U5/U6 tri-small nuclear ribonucleoprotein into the spliceosome.

    PubMed

    Rappsilber, J; Ajuh, P; Lamond, A I; Mann, M

    2001-08-17

    Spliceosome assembly involves the sequential recruitment of small nuclear ribonucleoproteins (snRNPs) onto a pre-mRNA substrate. Although several non-snRNP proteins function during the binding of U1 and U2 snRNPs, little is known about the subsequent binding of the U4/U5/U6 tri-snRNP. A recent proteomic analysis of the human spliceosome identified SPF30 (Neubauer, G., King, A., Rappsilber, J., Calvio, C., Watson, M., Ajuh, P., Sleeman, J., Lamond, A., and Mann, M. (1998) Nat. Genet. 20, 46-50), a homolog of the survival of motor neurons (SMN) protein, as a spliceosome factor. We show here that SPF30 is a nuclear protein that associates with both U4/U5/U6 and U2 snRNP components. In the absence of SPF30, the preformed tri-snRNP fails to assemble into the spliceosome. Mass spectrometric analysis shows that a recombinant glutathione S-transferase-SPF30 fusion protein associates with complexes containing core Sm and U4/U5/U6 tri-snRNP proteins when added to HeLa nuclear extract, most strongly to U4/U6-90. The data indicate that SPF30 is an essential human splicing factor that may act to dock the U4/U5/U6 tri-snRNP to the A complex during spliceosome assembly or, alternatively, may act as a late assembly factor in both the tri-snRNP and the A-complex. PMID:11331295

  3. Gas, Dust, and Nuclei: Cometary Types in the Largest IR Survey of Comets.

    NASA Astrophysics Data System (ADS)

    Bauer, James; Kramer, Emily; Mainzer, Amy; Grav, Tommy; Masiero, Joseph; Stevenson, Rachel; Nugent, Carrie; Sonnett, Sarah

    2015-08-01

    Space-based infrared (IR) surveys of objects have the potential to yield rich data sets for any particular class of small body. Thermal IR measurements often yield the most fundamental of astrophysical properties, the object’s size. When these data are synergistically combined with shorter-wavelength observations, the albedos of these bodies can be determined. The interpretation of IR observations of cometary bodies are more complicated, since their activity may obscure the bare surfaces of their nuclei. Yet space-based IR surveys provide the opportunity to observe this emitted dust and gas at wavelengths and sensitivities not possible from the ground.With the 163 comets detected during the WISE prime mission, and the more than 60 comets seen in the first year of data since the NEOWISE reactivated mission, the combined sample represents the largest survey of comets in the mid-IR. These data of over 200 comets provide dust particle size constraints and dust reflectance measurements, as well as nucleus size measurements. They are sensitive to the presence of the rarely observed gas species, CO2, directly detectable only from above the Earth’s atmosphere, and to the presence of CO emission, which is difficult to view from the ground. The data contain large samples of major cometary types (long-period and short-period comets), as well as smaller samples of Halley-type comets, Main Belt comets, and Near Earth comets, observed at multiple epochs, and so provide an unprecedentedly comprehensive view of the different comet populations.

  4. Deletion of small nuclear ribonucleoprotein polypeptide N (SNRPN) in Prader-Willi syndrome detected by fluorescence in situ hybridization: Two sibs with the typical phenotype without a cytogenetic deletion in chromosome 15q

    SciTech Connect

    Ishikawa, Tatsuya; Kibe, Tetsuya; Wada, Yoshiro

    1996-04-24

    The small nuclear ribonucleoprotein polypeptide N (SNRPN) gene is regarded as one of the candidates for Prader-Willi syndrome (PWS). We describe two sibs with typical PWS presenting deletion of SNRPN detected by fluorescence in situ hybridization (FISH). Neither a cytogenetically detectable 15q12 deletion nor a deletion for the D15S11, D15S10, and GABRB3 cosmid probes were found in either patient. This implies a smaller deletion limited to the PWS critical region. FISH with a SNRPN probe will permit analysis of PWS patients with limited deletions not detectable with other probes. 22 refs., 1 fig.

  5. Rare particles

    SciTech Connect

    Kutschera, W.

    1984-01-01

    The use of Accelerator Mass Spectrometry (AMS) to search for hypothetical particles and known particles of rare processes is discussed. The hypothetical particles considered include fractionally charged particles, anomalously heavy isotopes, and superheavy elements. The known particles produced in rare processes discussed include doubly-charged negative ions, counting neutrino-produced atoms in detectors for solar neutrino detection, and the spontaneous emission of /sup 14/C from /sup 223/Ra. 35 references. (WHK)

  6. Cosmology and Particle Physics

    NASA Astrophysics Data System (ADS)

    Steigman, G.

    1982-01-01

    The cosmic connections between physics on the very largest and very smallest scales are reviewed with an emphasis on the symbiotic relation between elementary particle physics and cosmology. After a review of the early Universe as a cosmic accelerator, various cosmological and astrophysical constraints on models of particle physics are outlined. To illustrate this approach to particle physics via cosmology, reference is made to several areas of current research: baryon non-conservation and baryon asymmetry; free quarks, heavy hadrons and other exotic relics; primordial nucleosynthesis and neutrino masses. In the last few years we have witnessed the birth and growth to healthy adolescence of a new collaboration between astrophysicists and particle physicists. The most notable success of this cooperative effort has been to provide the framework for understanding, within the context of GUTs and the hot big-bang cosmology, the universal baryon asymmetry. The most exciting new predictions this effort has spawned are that exotic relics may exist in detectable abundances. In particular, we may live in a neutrino-dominated Universe. In the next few years, accummulating laboratory data (for example proton decay, neutrino masses and oscillations) coupled with theoritical work in particle physics and cosmology will ensure the growth to maturity of this joint effort.

  7. Mutagenesis of SNM1, Which Encodes a Protein Component of the Yeast RNase MRP, Reveals a Role for This Ribonucleoprotein Endoribonuclease in Plasmid Segregation

    PubMed Central

    Cai, Ti; Reilly, Tracey R.; Cerio, Michael; Schmitt, Mark E.

    1999-01-01

    RNase MRP is a ribonucleoprotein endoribonuclease that has been shown to have roles in both mitochondrial DNA replication and nuclear 5.8S rRNA processing. SNM1 encodes an essential 22.5-kDa protein that is a component of yeast RNase MRP. It is an RNA binding protein that binds the MRP RNA specifically. This 198-amino-acid protein can be divided into three structural regions: a potential leucine zipper near the amino terminus, a binuclear zinc cluster in the middle region, and a serine- and lysine-rich region near the carboxy terminus. We have performed PCR mutagenesis of the SNM1 gene to produce 17 mutants that have a conditional phenotype for growth at different temperatures. Yeast strains carrying any of these mutations as the only copy of snm1 display an rRNA processing defect identical to that in MRP RNA mutants. We have characterized these mutant proteins for RNase MRP function by examining 5.8S rRNA processing, MRP RNA binding in vivo, and the stability of the RNase MRP RNA. The results indicate two separate functional domains of the protein, one responsible for binding the MRP RNA and a second that promotes substrate cleavage. The Snm1 protein appears not to be required for the stability of the MRP RNA, but very low levels of the protein are required for processing of the 5.8S rRNA. Surprisingly, a large number of conditional mutations that resulted from nonsense and frameshift mutations throughout the coding regions were identified. The most severe of these was a frameshift at amino acid 7. These mutations were found to be undergoing translational suppression, resulting in a small amount of full-length Snm1 protein. This small amount of Snm1 protein was sufficient to maintain enough RNase MRP activity to support viability. Translational suppression was accomplished in two ways. First, CEN plasmid missegregation leads to plasmid amplification, which in turn leads to SNM1 mRNA overexpression. Translational suppression of a small amount of the superabundant

  8. Particle separation

    NASA Technical Reports Server (NTRS)

    Moosmuller, Hans (Inventor); Chakrabarty, Rajan K. (Inventor); Arnott, W. Patrick (Inventor)

    2011-01-01

    Embodiments of a method for selecting particles, such as based on their morphology, is disclosed. In a particular example, the particles are charged and acquire different amounts of charge, or have different charge distributions, based on their morphology. The particles are then sorted based on their flow properties. In a specific example, the particles are sorted using a differential mobility analyzer, which sorts particles, at least in part, based on their electrical mobility. Given a population of particles with similar electrical mobilities, the disclosed process can be used to sort particles based on the net charge carried by the particle, and thus, given the relationship between charge and morphology, separate the particles based on their morphology.

  9. Particle separation

    DOEpatents

    Moosmuller, Hans; Chakrabarty, Rajan K.; Arnott, W. Patrick

    2011-04-26

    Embodiments of a method for selecting particles, such as based on their morphology, is disclosed. In a particular example, the particles are charged and acquire different amounts of charge, or have different charge distributions, based on their morphology. The particles are then sorted based on their flow properties. In a specific example, the particles are sorted using a differential mobility analyzer, which sorts particles, at least in part, based on their electrical mobility. Given a population of particles with similar electrical mobilities, the disclosed process can be used to sort particles based on the net charge carried by the particle, and thus, given the relationship between charge and morphology, separate the particles based on their morphology.

  10. The structure of Escherichia coli signal recognition particle revealed by scanning transmission electron microscopy.

    PubMed

    Mainprize, Iain L; Beniac, Daniel R; Falkovskaia, Elena; Cleverley, Robert M; Gierasch, Lila M; Ottensmeyer, F Peter; Andrews, David W

    2006-12-01

    Structural studies on various domains of the ribonucleoprotein signal recognition particle (SRP) have not converged on a single complete structure of bacterial SRP consistent with the biochemistry of the particle. We obtained a three-dimensional structure for Escherichia coli SRP by cryoscanning transmission electron microscopy and mapped the internal RNA by electron spectroscopic imaging. Crystallographic data were fit into the SRP reconstruction, and although the resulting model differed from previous models, they could be rationalized by movement through an interdomain linker of Ffh, the protein component of SRP. Fluorescence resonance energy transfer experiments determined interdomain distances that were consistent with our model of SRP. Docking our model onto the bacterial ribosome suggests a mechanism for signal recognition involving interdomain movement of Ffh into and out of the nascent chain exit site and suggests how SRP could interact and/or compete with the ribosome-bound chaperone, trigger factor, for a nascent chain during translation.

  11. Particle generator

    DOEpatents

    Hess, Wayne P.; Joly, Alan G.; Gerrity, Daniel P.; Beck, Kenneth M.; Sushko, Peter V.; Shlyuger, Alexander L.

    2005-06-28

    Energy tunable solid state sources of neutral particles are described. In a disclosed embodiment, a halogen particle source includes a solid halide sample, a photon source positioned to deliver photons to a surface of the halide, and a collimating means positioned to accept a spatially defined plume of hyperthermal halogen particles emitted from the sample surface.

  12. The nuclear matrix protein p255 is a highly phosphorylated form of RNA polymerase II largest subunit which associates with spliceosomes.

    PubMed Central

    Vincent, M; Lauriault, P; Dubois, M F; Lavoie, S; Bensaude, O; Chabot, B

    1996-01-01

    The monoclonal antibody CC-3 recognizes a phosphodependent epitope on a 255 kDa nuclear matrix protein (p255) recently shown to associate with splicing complexes as part of the [U4/U6.U5] tri-snRNP particle [Chabot et al. (1995) Nucleic Acids Res. 23, 3206-3213]. In mouse and Drosophila cultured cells the electrophoretic mobility of p255, faster in the latter species, was identical to that of the hyperphosphorylated form of RNA polymerase II largest subunit (IIo). The CC-3 immunoreactivity of p255 was abolished by 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole, which is known to cause the dephosphorylation of the C-terminal domain of subunit IIo by inhibiting the TFIIH-associated kinase. The identity of p255 was confirmed by showing that CC-3-immunoprecipitated p255 was recognized by POL3/3 and 8WG16, two antibodies specific to RNA polymerase II largest subunit. Lastly, the recovery of RNA polymerase II largest subunit from HeLa splicing mixtures was compromised by EDTA, which prevents the interaction of p255 with splicing complexes and inhibits splicing. Our results indicate that p255 represents a highly phosphorylated form of RNA polymerase II largest subunit physically associated with spliceosomes and possibly involved in coupling transcription to RNA processing. PMID:8972849

  13. Reduced IgG anti-small nuclear ribonucleoprotein autoantibody production in systemic lupus erythematosus patients with positive IgM anti-cytomegalovirus antibodies

    PubMed Central

    Palafox Sánchez, Claudia Azucena; Satoh, Minoru; Chan, Edward KL; Carcamo, Wendy C; Muñoz Valle, José Francisco; Orozco Barocio, Gerardo; Oregon Romero, Edith; Navarro Hernández, Rosa Elena; Salazar Páramo, Mario; Cabral Castañeda, Antonio; Vázquez del Mercado, Mónica

    2009-01-01

    Introduction Systemic lupus erythematosus is characterized by production of autoantibodies to RNA or DNA–protein complexes such as small nuclear ribonucleoproteins (snRNPs). A role of Epstein–Barr virus in the pathogenesis has been suggested. Similar to Epstein–Barr virus, cytomegalovirus (CMV) infects the majority of individuals at a young age and establishes latency with a potential for reactivation. Homology of CMV glycoprotein B (UL55) with the U1snRNP-70 kDa protein (U1–70 k) has been described; however, the role of CMV infection in production of anti-snRNPs is controversial. We investigated the association of CMV serology and autoantibodies in systemic lupus erythematosus. Methods Sixty-one Mexican patients with systemic lupus erythematosus were tested for CMV and Epstein–Barr virus serology (viral capsid antigen, IgG, IgM) and autoantibodies by immunoprecipitation and ELISA (IgG and IgM class, U1RNP/Sm, U1–70 k, P peptide, rheumatoid factor, dsDNA, β2-glycoprotein I). Results IgG anti-CMV and IgM anti-CMV were positive in 95% (58/61) and 33% (20/61), respectively, and two cases were negative for both. Clinical manifestation and autoantibodies in the IgM anti-CMV(+) group (n = 20) versus the IgM anti-CMV(-)IgG (+) (n = 39) group were compared. Most (19/20) of the IgM anti-CMV(+) cases were IgG anti-CMV(+), consistent with reactivation or reinfection. IgM anti-CMV was unrelated to rheumatoid factor or IgM class autoantibodies and none was positive for IgM anti-Epstein–Barr virus–viral capsid antigen, indicating that this is not simply due to false positive results caused by rheumatoid factor or nonspecific binding by certain IgM. The IgM anti-CMV(+) group has significantly lower levels of IgG anti-U1RNP/Sm and IgG anti-U1–70 k (P = 0.0004 and P = 0.0046, respectively). This finding was also confirmed by immunoprecipitation. Among the IgM anti-CMV(-) subset, anti-Su was associated with anti-U1RNP and anti-Ro (P < 0.05). High levels of Ig

  14. Solar Energetic Particle Variations

    NASA Technical Reports Server (NTRS)

    Reames, D. V.

    2003-01-01

    In the largest solar energetic-particle (SEP) events, acceleration occurs at shock waves driven out from the Sun by coronal mass ejections (CMEs). In fact, the highest proton intensities directly measured near Earth at energies up to approximately 1 GeV occur at the time of passage of shocks, which arrive about a day after the CMEs leave the Sun. CME-driven shocks expanding across magnetic fields can fill over half of the heliosphere with SEPs. Proton-generated Alfven waves trap particles near the shock for efficient acceleration but also throttle the intensities at Earth to the streaming limit early in the events. At high energies, particles begin to leak from the shock and the spectrum rolls downward to form an energy-spectral 'knee' that can vary in energy from approximately 1 MeV to approximately 1 GeV in different events. All of these factors affect the radiation dose as a function of depth and latitude in the Earth's atmosphere and the risk to astronauts and equipment in space. SEP ionization of the polar atmosphere produces nitrates that precipitate to become trapped in the polar ice. Observations of nitrate deposits in ice cores reveal individual large SEP events and extend back approximately 400 years. Unlike sunspots, SEP events follow the approximately 80-100-year Gleissberg cycle rather faithfully and are now at a minimum in that cycle. The largest SEP event in the last 400 years appears to be related to the flare observed by Carrington in 1859, but the probability of SEP events with such large fluences falls off sharply because of the streaming limit.

  15. Structure and sequence of the gene for the largest subunit of trypanosomal RNA polymerase III.

    PubMed Central

    Köck, J; Evers, R; Cornelissen, A W

    1988-01-01

    As the first step in the analysis of the transcription process in the African trypanosome, Trypanosoma brucei, we have started to characterise the trypanosomal RNA polymerases. We have previously described the gene encoding the largest subunit of RNA polymerase II and found that two almost identical RNA polymerase II genes are encoded within the genome of T. brucei. Here we present the identification, cloning and sequence analysis of the gene encoding the largest subunit of RNA polymerase III. This gene contains a single open reading frame encoding a polypeptide with a Mr of 170 kD. In total, eight encoding a polypeptide with a Mr of 170 kD. In total, eight highly conserved regions with significant homology to those previously reported in other eukaryotic RNA polymerase largest subunits were identified. Some of these domains contain functional sites, which are conserved among all eukaryotic largest subunit genes analysed thus far. Since these domains make up a large part of each polypeptide, independent of the RNA polymerase class, these data strongly support the hypothesis that these domains provide a major part of the transcription machinery of the RNA polymerase complex. The additional domains which are uniquely present in the largest subunit of RNA polymerase I and II, respectively, two large hydrophylic insertions and a C-terminal extension, might be a determining factor in specific transcription of the gene classes. Images PMID:3174432

  16. The Multivariate Largest Lyapunov Exponent as an Age-Related Metric of Quiet Standing Balance

    PubMed Central

    Liu, Kun; Wang, Hongrui; Xiao, Jinzhuang

    2015-01-01

    The largest Lyapunov exponent has been researched as a metric of the balance ability during human quiet standing. However, the sensitivity and accuracy of this measurement method are not good enough for clinical use. The present research proposes a metric of the human body's standing balance ability based on the multivariate largest Lyapunov exponent which can quantify the human standing balance. The dynamic multivariate time series of ankle, knee, and hip were measured by multiple electrical goniometers. Thirty-six normal people of different ages participated in the test. With acquired data, the multivariate largest Lyapunov exponent was calculated. Finally, the results of the proposed approach were analysed and compared with the traditional method, for which the largest Lyapunov exponent and power spectral density from the centre of pressure were also calculated. The following conclusions can be obtained. The multivariate largest Lyapunov exponent has a higher degree of differentiation in differentiating balance in eyes-closed conditions. The MLLE value reflects the overall coordination between multisegment movements. Individuals of different ages can be distinguished by their MLLE values. The standing stability of human is reduced with the increment of age. PMID:26064182

  17. Particle therapy

    SciTech Connect

    Raju, M.R.

    1993-09-01

    Particle therapy has a long history. The experimentation with particles for their therapeutic application got started soon after they were produced in the laboratory. Physicists played a major role in proposing the potential applications in radiotherapy as well as in the development of particle therapy. A brief review of the current status of particle radiotherapy with some historical perspective is presented and specific contributions made by physicists will be pointed out wherever appropriate. The rationale of using particles in cancer treatment is to reduce the treatment volume to the target volume by using precise dose distributions in three dimensions by using particles such as protons and to improve the differential effects on tumors compared to normal tissues by using high-LET radiations such as neutrons. Pions and heavy ions combine the above two characteristics.

  18. Particle astrophysics

    NASA Technical Reports Server (NTRS)

    Sadoulet, Bernard; Cronin, James; Aprile, Elena; Barish, Barry C.; Beier, Eugene W.; Brandenberger, Robert; Cabrera, Blas; Caldwell, David; Cassiday, George; Cline, David B.

    1991-01-01

    The following scientific areas are reviewed: (1) cosmology and particle physics (particle physics and the early universe, dark matter, and other relics); (2) stellar physics and particles (solar neutrinos, supernovae, and unconventional particle physics); (3) high energy gamma ray and neutrino astronomy; (4) cosmic rays (space and ground observations). Highest scientific priorities for the next decade include implementation of the current program, new initiatives, and longer-term programs. Essential technological developments, such as cryogenic detectors of particles, new solar neutrino techniques, and new extensive air shower detectors, are discussed. Also a certain number of institutional issues (the funding of particle astrophysics, recommended funding mechanisms, recommended facilities, international collaborations, and education and technology) which will become critical in the coming decade are presented.

  19. Magnetic particles

    NASA Technical Reports Server (NTRS)

    Chang, Manchium (Inventor); Colvin, Michael S. (Inventor)

    1989-01-01

    Magnetic polymer particles are formed by swelling porous, polymer particles and impregnating the particles with an aqueous solution of precursor magnetic metal salt such as an equimolar mixture of ferrous chloride and ferric chloride. On addition of a basic reagent such as dilute sodium hydroxide, the metal salts are converted to crystals of magnetite which are uniformly contained througout the pores of the polymer particle. The magnetite content can be increased and neutral buoyancy achieved by repetition of the impregnaton and neutralization steps to adjust the magnetite content to a desired level.

  20. The Host RNAs in Retroviral Particles.

    PubMed

    Telesnitsky, Alice; Wolin, Sandra L

    2016-01-01

    As they assemble, retroviruses encapsidate both their genomic RNAs and several types of host RNA. Whereas limited amounts of messenger RNA (mRNA) are detectable within virion populations, the predominant classes of encapsidated host RNAs do not encode proteins, but instead include endogenous retroelements and several classes of non-coding RNA (ncRNA), some of which are packaged in significant molar excess to the viral genome. Surprisingly, although the most abundant host RNAs in retroviruses are also abundant in cells, unusual forms of these RNAs are packaged preferentially, suggesting that these RNAs are recruited early in their biogenesis: before associating with their cognate protein partners, and/or from transient or rare RNA populations. These RNAs' packaging determinants differ from the viral genome's, and several of the abundantly packaged host ncRNAs serve cells as the scaffolds of ribonucleoprotein particles. Because virion assembly is equally efficient whether or not genomic RNA is available, yet RNA appears critical to the structural integrity of retroviral particles, it seems possible that the selectively encapsidated host ncRNAs might play roles in assembly. Indeed, some host ncRNAs appear to act during replication, as some transfer RNA (tRNA) species may contribute to nuclear import of human immunodeficiency virus 1 (HIV-1) reverse transcription complexes, and other tRNA interactions with the viral Gag protein aid correct trafficking to plasma membrane assembly sites. However, despite high conservation of packaging for certain host RNAs, replication roles for most of these selectively encapsidated RNAs-if any-have remained elusive. PMID:27548206

  1. The Host RNAs in Retroviral Particles

    PubMed Central

    Telesnitsky, Alice; Wolin, Sandra L.

    2016-01-01

    As they assemble, retroviruses encapsidate both their genomic RNAs and several types of host RNA. Whereas limited amounts of messenger RNA (mRNA) are detectable within virion populations, the predominant classes of encapsidated host RNAs do not encode proteins, but instead include endogenous retroelements and several classes of non-coding RNA (ncRNA), some of which are packaged in significant molar excess to the viral genome. Surprisingly, although the most abundant host RNAs in retroviruses are also abundant in cells, unusual forms of these RNAs are packaged preferentially, suggesting that these RNAs are recruited early in their biogenesis: before associating with their cognate protein partners, and/or from transient or rare RNA populations. These RNAs’ packaging determinants differ from the viral genome’s, and several of the abundantly packaged host ncRNAs serve cells as the scaffolds of ribonucleoprotein particles. Because virion assembly is equally efficient whether or not genomic RNA is available, yet RNA appears critical to the structural integrity of retroviral particles, it seems possible that the selectively encapsidated host ncRNAs might play roles in assembly. Indeed, some host ncRNAs appear to act during replication, as some transfer RNA (tRNA) species may contribute to nuclear import of human immunodeficiency virus 1 (HIV-1) reverse transcription complexes, and other tRNA interactions with the viral Gag protein aid correct trafficking to plasma membrane assembly sites. However, despite high conservation of packaging for certain host RNAs, replication roles for most of these selectively encapsidated RNAs—if any—have remained elusive. PMID:27548206

  2. Particle preconcentrator

    SciTech Connect

    Linker, K.L.; Conrad, F.J.; Custer, C.A.; Rhykerd, C.L. Jr

    2000-07-11

    An apparatus and method are disclosed for preconcentrating particles and vapors. The preconcentrator apparatus permits detection of highly diluted amounts of particles in a main gas stream, such as a stream of ambient air. A main gas stream having airborne particles entrained therein is passed through a previous screen. The particles accumulate upon the screen, as the screen acts as a sort of selective particle filter. The flow of the main gas stream is then interrupted by diaphragm shutter valves, whereupon a cross-flow of carrier gas stream is blown parallel past the faces of the screen to dislodge the accumulated particles and carry them to a particle or vapor detector, such as an ion mobility spectrometer. The screen may be heated, such as by passing an electrical current there through, to promote desorption of particles therefrom during the flow of the carrier gas. Various types of screens are disclosed. The apparatus and method of the invention may find particular utility in the fields of narcotics, explosives detection and chemical agents.

  3. Particle preconcentrator

    DOEpatents

    Linker, Kevin L.; Conrad, Frank J.; Custer, Chad A.; Rhykerd, Jr., Charles L.

    1998-01-01

    An apparatus and method for preconcentrating particles and vapors. The preconcentrator apparatus permits detection of highly diluted amounts of particles in a main gas stream, such as a stream of ambient air. A main gas stream having airborne particles entrained therein is passed through a pervious screen. The particles accumulate upon the screen, as the screen acts as a sort of selective particle filter. The flow of the main gas stream is then interrupted by diaphragm shutter valves, whereupon a cross-flow of carrier gas stream is blown parallel past the faces of the screen to dislodge the accumulated particles and carry them to a particle or vapor detector, such as an ion mobility spectrometer. The screen may be heated, such as by passing an electrical current there through, to promote desorption of particles therefrom during the flow of the carrier gas. Various types of screens are disclosed. The apparatus and method of the invention may find particular utility in the fields of narcotics, explosives detection and chemical agents.

  4. Particle preconcentrator

    DOEpatents

    Linker, Kevin L.; Conrad, Frank J.; Custer, Chad A.; Rhykerd, Jr., Charles L.

    2000-01-01

    An apparatus and method for preconcentrating particles and vapors. The preconcentrator apparatus permits detection of highly diluted amounts of particles in a main gas stream, such as a stream of ambient air. A main gas stream having airborne particles entrained therein is passed through a pervious screen. The particles accumulate upon the screen, as the screen acts as a sort of selective particle filter. The flow of the main gas stream is then interrupted by diaphragm shutter valves, whereupon a cross-flow of carrier gas stream is blown parallel past the faces of the screen to dislodge the accumulated particles and carry them to a particle or vapor detector, such as an ion mobility spectrometer. The screen may be heated, such as by passing an electrical current there through, to promote desorption of particles therefrom during the flow of the carrier gas. Various types of screens are disclosed. The apparatus and method of the invention may find particular utility in the fields of narcotics, explosives detection and chemical agents.

  5. Particle preconcentrator

    DOEpatents

    Linker, Kevin L.; Conrad, Frank J.; Custer, Chad A.; Rhykerd, Jr., Charles L.

    2005-09-20

    An apparatus and method for preconcentrating particles and vapors. The preconcentrator apparatus permits detection of highly diluted amounts of particles in a main gas stream, such as a stream of ambient air. A main gas stream having airborne particles entrained therein is passed through a pervious screen. The particles accumulate upon the screen, as the screen acts as a sort of selective particle filter. The flow of the main gas stream is then interrupted by diaphragm shutter valves, whereupon a cross-flow of carrier gas stream is blown parallel past the faces of the screen to dislodge the accumulated particles and carry them to a particle or vapor detector, such as an ion mobility spectrometer. The screen may be heated, such as by passing an electrical current there through, to promote desorption of particles therefrom during the flow of the carrier gas. Various types of screens are disclosed. The apparatus and method of the invention may find particular utility in the fields of narcotics, explosives detection and chemical agents.

  6. Particle preconcentrator

    DOEpatents

    Linker, K.L.; Conrad, F.J.; Custer, C.A.; Rhykerd, C.L. Jr.

    1998-12-29

    An apparatus and method are disclosed for preconcentrating particles and vapors. The preconcentrator apparatus permits detection of highly diluted amounts of particles in a main gas stream, such as a stream of ambient air. A main gas stream having airborne particles entrained therein is passed through a pervious screen. The particles accumulate upon the screen, as the screen acts as a sort of selective particle filter. The flow of the main gas stream is then interrupted by diaphragm shutter valves, whereupon a cross-flow of carrier gas stream is blown parallel past the faces of the screen to dislodge the accumulated particles and carry them to a particle or vapor detector, such as an ion mobility spectrometer. The screen may be heated, such as by passing an electrical current there through, to promote desorption of particles therefrom during the flow of the carrier gas. Various types of screens are disclosed. The apparatus and method of the invention may find particular utility in the fields of narcotics, explosives detection and chemical agents. 3 figs.

  7. Deep, diverse and definitely different: unique attributes of the world's largest ecosystem

    NASA Astrophysics Data System (ADS)

    Ramirez-Llodra, E.; Brandt, A.; Danovaro, R.; de Mol, B.; Escobar, E.; German, C. R.; Levin, L. A.; Martinez Arbizu, P.; Menot, L.; Buhl-Mortensen, P.; Narayanaswamy, B. E.; Smith, C. R.; Tittensor, D. P.; Tyler, P. A.; Vanreusel, A.; Vecchione, M.

    2010-09-01

    The deep sea, the largest biome on Earth, has a series of characteristics that make this environment both distinct from other marine and land ecosystems and unique for the entire planet. This review describes these patterns and processes, from geological settings to biological processes, biodiversity and biogeographical patterns. It concludes with a brief discussion of current threats from anthropogenic activities to deep-sea habitats and their fauna. Investigations of deep-sea habitats and their fauna began in the late 19th century. In the intervening years, technological developments and stimulating discoveries have promoted deep-sea research and changed our way of understanding life on the planet. Nevertheless, the deep sea is still mostly unknown and current discovery rates of both habitats and species remain high. The geological, physical and geochemical settings of the deep-sea floor and the water column form a series of different habitats with unique characteristics that support specific faunal communities. Since 1840, 28 new habitats/ecosystems have been discovered from the shelf break to the deep trenches and discoveries of new habitats are still happening in the early 21st century. However, for most of these habitats the global area covered is unknown or has been only very roughly estimated; an even smaller - indeed, minimal - proportion has actually been sampled and investigated. We currently perceive most of the deep-sea ecosystems as heterotrophic, depending ultimately on the flux on organic matter produced in the overlying surface ocean through photosynthesis. The resulting strong food limitation thus shapes deep-sea biota and communities, with exceptions only in reducing ecosystems such as inter alia hydrothermal vents or cold seeps. Here, chemoautolithotrophic bacteria play the role of primary producers fuelled by chemical energy sources rather than sunlight. Other ecosystems, such as seamounts, canyons or cold-water corals have an increased

  8. Deep, diverse and definitely different: unique attributes of the world's largest ecosystem

    NASA Astrophysics Data System (ADS)

    Ramirez-Llodra, E.; Brandt, A.; Danovaro, R.; Escobar, E.; German, C. R.; Levin, L. A.; Martinez Arbizu, P.; Menot, L.; Buhl-Mortensen, P.; Narayanaswamy, B. E.; Smith, C. R.; Tittensor, D. P.; Tyler, P. A.; Vanreusel, A.; Vecchione, M.

    2010-04-01

    The deep sea, the largest biome on Earth, has a series of characteristics that make this environment both distinct from other marine and land ecosystems and unique for the entire planet. This review describes these patterns and processes, from geological settings to biological processes, biodiversity and biogeographical patterns. It concludes with a brief discussion of current threats from anthropogenic activities to deep-sea habitats and their fauna. Investigations of deep-sea habitats and their fauna began in the late 19th Century. In the intervening years, technological developments and stimulating discoveries have promoted deep-sea research and changed our way of understanding life on the planet. Nevertheless, the deep sea is still mostly unknown and current discovery rates of both habitats and species remain high. The geological, physical and geochemical settings of the deep-sea floor and the water column form a series of different habitats with unique characteristics that support specific faunal communities. Since 1840, 27 new habitats/ecosystems have been discovered from the shelf break to the deep trenches and discoveries of new habitats are still happening in the early 21st Century. However, for most of these habitats, the global area covered is unknown or has been only very roughly estimated; an even smaller - indeed, minimal - proportion has actually been sampled and investigated. We currently perceive most of the deep-sea ecosystems as heterotrophic, depending ultimately on the flux on organic matter produced in the overlying surface ocean through photosynthesis. The resulting strong food limitation, thus, shapes deep-sea biota and communities, with exceptions only in reducing ecosystems such as inter alia hydrothermal vents or cold seeps, where chemoautolithotrophic bacteria play the role of primary producers fuelled by chemical energy sources rather than sunlight. Other ecosystems, such as seamounts, canyons or cold-water corals have an increased

  9. Assessment of the Relative Largest Earthquake Hazard Level in the NW Himalaya and its Adjacent Region

    NASA Astrophysics Data System (ADS)

    Tsapanos, Theodoros M.; Yadav, R. B. S.; Olasoglou, Efthalia M.; Singh, Mayshree

    2016-04-01

    In the present study, the level of the largest earthquake hazard is assessed in 28 seismic zones of the NW Himalaya and its vicinity, which is a highly seismically active region of the world. Gumbel's third asymptotic distribution (hereafter as GIII) is adopted for the evaluation of the largest earthquake magnitudes in these seismic zones. Instead of taking in account any type of Mmax, in the present study we consider the ω value which is the largest earthquake magnitude that a region can experience according to the GIII statistics. A function of the form Θ(ω, RP6.0) is providing in this way a relatively largest earthquake hazard scale defined by the letter K(K index). The return periods for the ω values (earthquake magnitudes) 6 or larger (RP6.0) are also calculated. According to this index, the investigated seismic zones are classified into five groups and it is shown that seismic zones 3 (Quetta of Pakistan), 11 (Hindukush), 15 (northern Pamirs), and 23 (Kangra, Himachal Pradesh of India) correspond to a "very high" K index which is 6.

  10. Map and Aerial Photo Collections in the United States: Survey of the Seventy Largest Collections.

    ERIC Educational Resources Information Center

    Stevens, Stanley D.

    1981-01-01

    Data gathered from 56 libraries, agencies, and other institutions holding large collections of maps and aerial photographs are reported, including such areas as personnel, equipment, acquisitions, floor space, promotion, and use of computers. The 70 largest collections are ranked and profiled, and a sample questionnaire is provided. (FM)

  11. Pterosaur from the latest cretaceous of west Texas: discovery of the largest flying creature.

    PubMed

    Lawson, D A

    1975-03-14

    Three partial skeletons of a large pterosaur have been found in the latest Cretaceous nonmarine rock of West Texas. This flying reptile had thin, elongate, perhaps toothless jaws and a long neck similar to Pterodaustro and Pterodactylus. With an estimated wingspan of 15.5 meters, it is undoutbtedly the largest flying creature presently known.

  12. 78 FR 23624 - Determination and Certification Under the Foreign Assistance Act Relating to the Largest...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-19

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF STATE Determination and Certification Under the Foreign Assistance Act Relating to the Largest Exporting and Importing Countries of Certain Precursor Chemicals Pursuant to Section 490(b)(1)(A) of the Foreign Assistance Act...

  13. Profile of a Woman Officer; Findings of a Study of Executives in America's 1300 Largest Companies.

    ERIC Educational Resources Information Center

    1978

    The typical woman officer from the nation's largest industrial, banking, retail and utility companies is married, at least 50 years of age, has had some college, was born into a family of low or lower middle class income, and has a work salary of less than $30,000. While the number of women officers in leading business organizations is small, the…

  14. The 2003 Music in Our School's Month and World's Largest Concert Teacher's Guide.

    ERIC Educational Resources Information Center

    Music Educators National Conference, Reston, VA.

    On March 13, 2003 millions of school children, teachers, and citizens from around the world participate simultaneously in the "World's Largest Concert" (WLC). This concert, a sing-along program, is broadcast on PBS and the Armed Forces Radio and Television Network overseas. Participating in the WLC is a way to celebrate Music in Our Schools Month.…

  15. NAFTA: The World's Largest Trading Zone Turns 20

    ERIC Educational Resources Information Center

    Ferrarini, Tawni Hunt; Day, Stephen

    2014-01-01

    Everyone under the age of 20 who has grown up in North America has lived in the common market created by NAFTA--the North American Free Trade Agreement. In a zone linking the United States, Canada, and Mexico, most goods and investments flow freely across borders to users, consumers, and investors. In 1994, NAFTA created the largest relatively…

  16. Phase space reconstruction and estimation of the largest Lyapunov exponent for gait kinematic data

    SciTech Connect

    Josiński, Henryk; Świtoński, Adam; Michalczuk, Agnieszka; Wojciechowski, Konrad

    2015-03-10

    The authors describe an example of application of nonlinear time series analysis directed at identifying the presence of deterministic chaos in human motion data by means of the largest Lyapunov exponent. The method was previously verified on the basis of a time series constructed from the numerical solutions of both the Lorenz and the Rössler nonlinear dynamical systems.

  17. 12 CFR 1501.3 - Comparable ratings requirement for national banks among the second 50 largest insured banks.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... banks among the second 50 largest insured banks. 1501.3 Section 1501.3 Banks and Banking DEPARTMENT OF... national banks among the second 50 largest insured banks. (a) Scope and purpose. Section 5136A of the Revised Statutes permits a national bank that is within the second 50 largest insured banks to own...

  18. 12 CFR 1501.3 - Comparable ratings requirement for national banks among the second 50 largest insured banks.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... banks among the second 50 largest insured banks. 1501.3 Section 1501.3 Banks and Banking DEPARTMENT OF... national banks among the second 50 largest insured banks. (a) Scope and purpose. Section 5136A of the Revised Statutes permits a national bank that is within the second 50 largest insured banks to own...

  19. 12 CFR 1501.3 - Comparable ratings requirement for national banks among the second 50 largest insured banks.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... banks among the second 50 largest insured banks. 1501.3 Section 1501.3 Banks and Banking DEPARTMENT OF... national banks among the second 50 largest insured banks. (a) Scope and purpose. Section 5136A of the Revised Statutes permits a national bank that is within the second 50 largest insured banks to own...

  20. 12 CFR 1501.3 - Comparable ratings requirement for national banks among the second 50 largest insured banks.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... banks among the second 50 largest insured banks. 1501.3 Section 1501.3 Banks and Banking DEPARTMENT OF... national banks among the second 50 largest insured banks. (a) Scope and purpose. Section 5136A of the Revised Statutes permits a national bank that is within the second 50 largest insured banks to own...

  1. Polyribosomes are molecular 3D nanoprinters that orchestrate the assembly of vault particles.

    PubMed

    Mrazek, Jan; Toso, Daniel; Ryazantsev, Sergey; Zhang, Xing; Zhou, Z Hong; Fernandez, Beatriz Campo; Kickhoefer, Valerie A; Rome, Leonard H

    2014-11-25

    Ribosomes are molecular machines that function in polyribosome complexes to translate genetic information, guide the synthesis of polypeptides, and modulate the folding of nascent proteins. Here, we report a surprising function for polyribosomes as a result of a systematic examination of the assembly of a large ribonucleoprotein complex, the vault particle. Structural and functional evidence points to a model of vault assembly whereby the polyribosome acts like a 3D nanoprinter to direct the ordered translation and assembly of the multi-subunit vault homopolymer, a process which we refer to as polyribosome templating. Structure-based mutagenesis and cell-free in vitro expression studies further demonstrated the critical importance of the polyribosome in vault assembly. Polyribosome templating prevents chaos by ensuring efficiency and order in the production of large homopolymeric protein structures in the crowded cellular environment and might explain the origin of many polyribosome-associated molecular assemblies inside the cell.

  2. Magnetic particles

    NASA Technical Reports Server (NTRS)

    Chang, Manchium (Inventor); Colvin, Michael S. (Inventor); Rembaum, Alan (Inventor); Richards, Gil F. (Inventor)

    1987-01-01

    Metal oxide containing polymers and particularly styrene, acrylic or protein polymers containing fine, magnetic iron oxide particles are formed by combining a NO.sub.2 -substituted polymer with an acid such as hydrochloric acid in the presence of metal, particularly iron particles. The iron is oxidized to fine, black Fe.sub.3 O.sub.4 particles which deposit selectively on the polymer particles. Nitrated polymers are formed by reacting functionally substituted, nitrated organic compounds such as trinitrobenzene sulfonate or dinitrofluoro benzene with a functionally coreactive polymer such as an amine modified acrylic polymer or a protein. Other transition metals such as cobalt can also be incorporated into polymers using this method.

  3. Auroral particles

    NASA Technical Reports Server (NTRS)

    Evans, David S.

    1987-01-01

    The problems concerning the aurora posed prior to the war are now either solved in principle or were restated in a more fundamental form. The pre-war hypothesis concerning the nature of the auroral particles and their energies was fully confirmed, with the exception that helium and oxygen ions were identified as participating in the auroral particle precipitation in addition to the protons. The nature of the near-Earth energization processes affecting auroral particles was clarified. Charged particle trajectories in various electric field geometries were modeled. The physical problems have now moved from determining the nature and geometry of the electric fields, which accelerate charged particles near the Earth, to accounting for the existence of these electric fields as a natural consequence of the solar wind's interaction with Earth. Ultimately the reward in continuing the work in auroral and magnetospheric particle dynamics will be a deeper understanding of the subtleties of classical electricity and magnetism as applied to situations not blessed with well-defined and invariant geometries.

  4. THE BRIGHTEST CLUSTER GALAXY IN A85: THE LARGEST CORE KNOWN SO FAR

    SciTech Connect

    López-Cruz, O.; Añorve, C.; Ibarra-Medel, H. J.; Birkinshaw, M.; Worrall, D. M.; Barkhouse, W. A.; Torres-Papaqui, J. P.

    2014-11-10

    We have found that the brightest cluster galaxy (BCG) in A85, Holm 15A, displays the largest core known so far. Its cusp radius, r {sub γ} = 4.57 ± 0.06 kpc (4.''26 ± 0.''06), is more than 18 times larger than the mean for BCGs and ≳ 1 kpc larger than A2261-BCG, hitherto the largest-cored BCG. Holm 15A hosts the luminous amorphous radio source 0039-095B and has the optical signature of a LINER. Scaling laws indicate that this core could host a supermassive black hole (SMBH) of mass M {sub •} ∼ (10{sup 9}-10{sup 11}) M {sub ☉}. We suggest that cores this large represent a relatively short phase in the evolution of BCGs, whereas the masses of their associated SBMH might be set by initial conditions.

  5. A method for reducing the largest relative errors in Monte Carlo iterated-fission-source calculations

    SciTech Connect

    Hunter, J. L.; Sutton, T. M.

    2013-07-01

    In Monte Carlo iterated-fission-source calculations relative uncertainties on local tallies tend to be larger in lower-power regions and smaller in higher-power regions. Reducing the largest uncertainties to an acceptable level simply by running a larger number of neutron histories is often prohibitively expensive. The uniform fission site method has been developed to yield a more spatially-uniform distribution of relative uncertainties. This is accomplished by biasing the density of fission neutron source sites while not biasing the solution. The method is integrated into the source iteration process, and does not require any auxiliary forward or adjoint calculations. For a given amount of computational effort, the use of the method results in a reduction of the largest uncertainties relative to the standard algorithm. Two variants of the method have been implemented and tested. Both have been shown to be effective. (authors)

  6. Distribution of the largest event in the critical epidemic-type aftershock-sequence model

    NASA Astrophysics Data System (ADS)

    Vere-Jones, David; Zhuang, Jiancang

    2008-10-01

    This Brief Report corrects and extends the results of Zhuang and Ogata [Phys. Rev. E 73, 046134 (2006)] on the asymptotic behavior of the largest event in the epidemic-type aftershock-sequence model for earthquake occurrence. We show that, in the special case that the underlying branching process is critical, there exists a previously unnoticed mode of behavior, which occurs when the expected family size grows relatively slowly.

  7. Disruption of largest subunit RNA polymerase II genes in Trypanosoma brucei.

    PubMed Central

    Chung, H M; Lee, M G; Dietrich, P; Huang, J; Van der Ploeg, L H

    1993-01-01

    Two types of largest subunit RNA polymerase II (pol II) genes (pol IIA and pol IIB), differing in 3 amino acid substitutions, are encoded in the Trypanosoma brucei (stock 427-60) genome. As a result, the alpha-amanitin-resistant transcription of the procyclic acidic repetitive protein (PARP) and variant surface glycoprotein (VSG) genes was proposed to involve a modified, alpha-amanitin-resistant form of the largest subunit of pol II. Alternatively, pol I could transcribe the PARP and VSG genes. To discriminate between these two models, we deleted the N-terminal domain (about one-third of the polypeptide), which encodes the amino acid substitutions which discriminated the pol IIA and pol IIB genes, at both pol IIB alleles. The pol IIB- trypanosomes still transcribe the PARP genes and the VSG gene promoter region in insect-form trypanosomes by alpha-amanitin-resistant RNA polymerases, while control housekeeping genes are transcribed in an alpha-amanitin-sensitive manner, presumably by pol IIA. We conclude that the alpha-amanitin-resistant transcription of protein coding genes in T. brucei is not mediated by a diverged form of the largest subunit of pol II and that the presence of both the pol IIA and pol IIB genes is not essential for trypanosome viability. This conclusion was further supported by the finding that individual trypanosome variants exhibited allelic heterogeneity for the previously identified amino acid substitutions and that various permutations of the polymorphic amino acids generate at least four different types of largest subunit pol II genes. The expression of the PARP genes and the VSG gene promoter region by alpha-amanitin-resistant RNA polymerases in the pol IIB- trypanosomes provides evidence for transcription of these genes by pol I. Images PMID:8497277

  8. Rapid Deposition Technology Holds the Key for the World's Largest Solar Manufacturer (Fact Sheet)

    SciTech Connect

    Not Available

    2010-10-01

    Thanks in part to years of collaboration with the National Renewable Energy Laboratory (NREL), a manufacturer of thin-film solar modules has grown from a small garage-type operation to become the world's largest manufacturer of solar modules. First Solar, Inc. now manufactures cadmium telluride (CdTe) solar modules throughout the world, but it began in Ohio as a small company called Solar Cells, Inc.

  9. Distribution of the largest event in the critical epidemic-type aftershock-sequence model.

    PubMed

    Vere-Jones, David; Zhuang, Jiancang

    2008-10-01

    This Brief Report corrects and extends the results of Zhuang and Ogata [Phys. Rev. E 73, 046134 (2006)] on the asymptotic behavior of the largest event in the epidemic-type aftershock-sequence model for earthquake occurrence. We show that, in the special case that the underlying branching process is critical, there exists a previously unnoticed mode of behavior, which occurs when the expected family size grows relatively slowly.

  10. THE CHALLENGE OF THE LARGEST STRUCTURES IN THE UNIVERSE TO COSMOLOGY

    SciTech Connect

    Park, Changbom; Choi, Yun-Young; Kim, Sungsoo S.; Kim, Kap-Sung; Kim, Juhan; Gott III, J. Richard

    2012-11-01

    Large galaxy redshift surveys have long been used to constrain cosmological models and structure formation scenarios. In particular, the largest structures discovered observationally are thought to carry critical information on the amplitude of large-scale density fluctuations or homogeneity of the universe, and have often challenged the standard cosmological framework. The Sloan Great Wall (SGW) recently found in the Sloan Digital Sky Survey (SDSS) region casts doubt on the concordance cosmological model with a cosmological constant (i.e., the flat {Lambda}CDM model). Here we show that the existence of the SGW is perfectly consistent with the {Lambda}CDM model, a result that only our very large cosmological N-body simulation (the Horizon Run 2, HR2) could supply. In addition, we report on the discovery of a void complex in the SDSS much larger than the SGW, and show that such size of the largest void is also predicted in the {Lambda}CDM paradigm. Our results demonstrate that an initially homogeneous isotropic universe with primordial Gaussian random phase density fluctuations growing in accordance with the general relativity can explain the richness and size of the observed large-scale structures in the SDSS. Using the HR2 simulation we predict that a future galaxy redshift survey about four times deeper or with 3 mag fainter limit than the SDSS should reveal a largest structure of bright galaxies about twice as big as the SGW.

  11. Experimental Particle Physics

    SciTech Connect

    Rosenfeld, Carl; Mishra, Sanjib R.; Petti, Roberto; Purohit, Milind V.

    2014-08-31

    , which collected data at SLAC until 2008. They continued to analyze the voluminous BaBar data with an emphasis on precision tests of Quantum Chromodynamics and on properties of the "eta_B," a bottom quark paired in a meson with a strange quark. The ATLAS experiment became the principal research focus for Purohit. One of the world's largest pieces of scientific equipment, ATLAS observes particle collisions at the highest-energy particle accelerator ever built, the Large Hadron Collider (LHC) at CERN. Our efforts on ATLAS included participation in the commissioning, calibration, and installation of components called "CSCs". The unprecedented energy of 14 TeV enabled the ATLAS and CMS collaborations to declare discovery of the famous Higgs particle in 2012.

  12. Particle Sizer

    NASA Technical Reports Server (NTRS)

    1987-01-01

    Microspheres are tiny plastic beads that represent the first commercial products manufactured in orbit. An example of how they are used is a new aerodynamic particle sizer designated APS 33B produced by TSI Incorporated. TSI purchased the microspheres from the National Bureau of Standards which certified their exact size and the company uses them in calibration of the APS 33B* instrument, latest in a line of TSI systems for generating counting and weighing minute particles of submicron size. Instruments are used for evaluating air pollution control devices, quantifying environments, meteorological research, testing filters, inhalation, toxicology and other areas where generation or analysis of small airborne particles is required. * The APS 33B is no longer being manufactured. An improved version, APS 3320, is now being manufactured. 2/28/97

  13. Carbon particles

    DOEpatents

    Hunt, Arlon J.

    1984-01-01

    A method and apparatus whereby small carbon particles are made by pyrolysis of a mixture of acetylene carried in argon. The mixture is injected through a nozzle into a heated tube. A small amount of air is added to the mixture. In order to prevent carbon build-up at the nozzle, the nozzle tip is externally cooled. The tube is also elongated sufficiently to assure efficient pyrolysis at the desired flow rates. A key feature of the method is that the acetylene and argon, for example, are premixed in a dilute ratio, and such mixture is injected while cool to minimize the agglomeration of the particles, which produces carbon particles with desired optical properties for use as a solar radiant heat absorber.

  14. Deep, diverse and definitely different: unique attributes of the world's largest ecosystem

    NASA Astrophysics Data System (ADS)

    Ramirez-Llodra, E.; Brandt, A.; Danovaro, R.; Escobar, E.; German, C. R.; Levin, L. A.; Martinez Arbizu, P.; Menot, L.; Buhl-Mortensen, P.; Narayanaswamy, B. E.; Smith, C. R.; Tittensor, D. P.; Tyler, P. A.; Vanreusel, A.; Vecchione, M.

    2010-04-01

    The deep sea, the largest biome on Earth, has a series of characteristics that make this environment both distinct from other marine and land ecosystems and unique for the entire planet. This review describes these patterns and processes, from geological settings to biological processes, biodiversity and biogeographical patterns. It concludes with a brief discussion of current threats from anthropogenic activities to deep-sea habitats and their fauna. Investigations of deep-sea habitats and their fauna began in the late 19th Century. In the intervening years, technological developments and stimulating discoveries have promoted deep-sea research and changed our way of understanding life on the planet. Nevertheless, the deep sea is still mostly unknown and current discovery rates of both habitats and species remain high. The geological, physical and geochemical settings of the deep-sea floor and the water column form a series of different habitats with unique characteristics that support specific faunal communities. Since 1840, 27 new habitats/ecosystems have been discovered from the shelf break to the deep trenches and discoveries of new habitats are still happening in the early 21st Century. However, for most of these habitats, the global area covered is unknown or has been only very roughly estimated; an even smaller - indeed, minimal - proportion has actually been sampled and investigated. We currently perceive most of the deep-sea ecosystems as heterotrophic, depending ultimately on the flux on organic matter produced in the overlying surface ocean through photosynthesis. The resulting strong food limitation, thus, shapes deep-sea biota and communities, with exceptions only in reducing ecosystems such as inter alia hydrothermal vents or cold seeps, where chemoautolithotrophic bacteria play the role of primary producers fuelled by chemical energy sources rather than sunlight. Other ecosystems, such as seamounts, canyons or cold-water corals have an increased

  15. Deep, diverse and definitely different: unique attributes of the world's largest ecosystem

    NASA Astrophysics Data System (ADS)

    Ramirez-Llodra, E.; Brandt, A.; Danovaro, R.; de Mol, B.; Escobar, E.; German, C. R.; Levin, L. A.; Martinez Arbizu, P.; Menot, L.; Buhl-Mortensen, P.; Narayanaswamy, B. E.; Smith, C. R.; Tittensor, D. P.; Tyler, P. A.; Vanreusel, A.; Vecchione, M.

    2010-09-01

    The deep sea, the largest biome on Earth, has a series of characteristics that make this environment both distinct from other marine and land ecosystems and unique for the entire planet. This review describes these patterns and processes, from geological settings to biological processes, biodiversity and biogeographical patterns. It concludes with a brief discussion of current threats from anthropogenic activities to deep-sea habitats and their fauna. Investigations of deep-sea habitats and their fauna began in the late 19th century. In the intervening years, technological developments and stimulating discoveries have promoted deep-sea research and changed our way of understanding life on the planet. Nevertheless, the deep sea is still mostly unknown and current discovery rates of both habitats and species remain high. The geological, physical and geochemical settings of the deep-sea floor and the water column form a series of different habitats with unique characteristics that support specific faunal communities. Since 1840, 28 new habitats/ecosystems have been discovered from the shelf break to the deep trenches and discoveries of new habitats are still happening in the early 21st century. However, for most of these habitats the global area covered is unknown or has been only very roughly estimated; an even smaller - indeed, minimal - proportion has actually been sampled and investigated. We currently perceive most of the deep-sea ecosystems as heterotrophic, depending ultimately on the flux on organic matter produced in the overlying surface ocean through photosynthesis. The resulting strong food limitation thus shapes deep-sea biota and communities, with exceptions only in reducing ecosystems such as inter alia hydrothermal vents or cold seeps. Here, chemoautolithotrophic bacteria play the role of primary producers fuelled by chemical energy sources rather than sunlight. Other ecosystems, such as seamounts, canyons or cold-water corals have an increased

  16. Determinations of microbial loads associated with microscopic-size particles of Kennedy Space Center soil.

    PubMed

    Ruschmeyer, O R; Pflug, I J

    1977-01-01

    Plate counts for six fractions, of micrometer-size, of Kennedy Space Center soil provided estimates of aerobic, mesophilic, heterotrophic, microbial loads on single soil particles. Analyses included unheated particles, particles subjected to wet heat at 80 degrees C for 20 min, and particles subjected to dry heat at 110 degrees C for 1 hr. Unheated particles yielded mean counts ranging from 6 colonies per particle for the smallest (44-53 micrometers) soil fraction to approximately 55 colonies per particle for the largest size (105-125 micrometers) soil fraction tested. Mean counts for heat-resistant forms ranged from 2 colonies per particle for the smaller particles to 12-15 colonies for the largest particles analyzed.

  17. Particle Beam Radiography

    NASA Astrophysics Data System (ADS)

    Peach, Ken; Ekdahl, Carl

    2014-02-01

    Particle beam radiography, which uses a variety of particle probes (neutrons, protons, electrons, gammas and potentially other particles) to study the structure of materials and objects noninvasively, is reviewed, largely from an accelerator perspective, although the use of cosmic rays (mainly muons but potentially also high-energy neutrinos) is briefly reviewed. Tomography is a form of radiography which uses multiple views to reconstruct a three-dimensional density map of an object. There is a very wide range of applications of radiography and tomography, from medicine to engineering and security, and advances in instrumentation, specifically the development of electronic detectors, allow rapid analysis of the resultant radiographs. Flash radiography is a diagnostic technique for large high-explosive-driven hydrodynamic experiments that is used at many laboratories. The bremsstrahlung radiation pulse from an intense relativistic electron beam incident onto a high-Z target is the source of these radiographs. The challenge is to provide radiation sources intense enough to penetrate hundreds of g/cm2 of material, in pulses short enough to stop the motion of high-speed hydrodynamic shocks, and with source spots small enough to resolve fine details. The challenge has been met with a wide variety of accelerator technologies, including pulsed-power-driven diodes, air-core pulsed betatrons and high-current linear induction accelerators. Accelerator technology has also evolved to accommodate the experimenters' continuing quest for multiple images in time and space. Linear induction accelerators have had a major role in these advances, especially in providing multiple-time radiographs of the largest hydrodynamic experiments.

  18. Particle blender

    DOEpatents

    Willey, Melvin G.

    1981-01-01

    An infinite blender that achieves a homogeneous mixture of fuel microspheres is provided. Blending is accomplished by directing respective groups of desired particles onto the apex of a stationary coaxial cone. The particles progress downward over the cone surface and deposit in a space at the base of the cone that is described by a flexible band provided with a wide portion traversing and in continuous contact with the circumference of the cone base and extending upwardly therefrom. The band, being attached to the cone at a narrow inner end thereof, causes the cone to rotate on its arbor when the band is subsequently pulled onto a take-up spool. As a point at the end of the wide portion of the band passes the point where it is tangent to the cone, the blended particles are released into a delivery tube leading directly into a mold, and a plate mounted on the lower portion of the cone and positioned between the end of the wide portion of the band and the cone assures release of the particles only at the tangent point.

  19. Analysis of the largest tandemly repeated DNA families in the human genome

    PubMed Central

    Warburton, Peter E; Hasson, Dan; Guillem, Flavia; Lescale, Chloe; Jin, Xiaoping; Abrusan, Gyorgy

    2008-01-01

    Background Tandemly Repeated DNA represents a large portion of the human genome, and accounts for a significant amount of copy number variation. Here we present a genome wide analysis of the largest tandem repeats found in the human genome sequence. Results Using Tandem Repeats Finder (TRF), tandem repeat arrays greater than 10 kb in total size were identified, and classified into simple sequence e.g. GAATG, classical satellites e.g. alpha satellite DNA, and locus specific VNTR arrays. Analysis of these large sequenced regions revealed that several "simple sequence" arrays actually showed complex domain and/or higher order repeat organization. Using additional methods, we further identified a total of 96 additional arrays with tandem repeat units greater than 2 kb (the detection limit of TRF), 53 of which contained genes or repeated exons. The overall size of an array of tandem 12 kb repeats which spanned a gap on chromosome 8 was found to be 600 kb to 1.7 Mbp in size, representing one of the largest non-centromeric arrays characterized. Several novel megasatellite tandem DNA families were observed that are characterized by repeating patterns of interspersed transposable elements that have expanded presumably by unequal crossing over. One of these families is found on 11 different chromosomes in >25 arrays, and represents one of the largest most widespread megasatellite DNA families. Conclusion This study represents the most comprehensive genome wide analysis of large tandem repeats in the human genome, and will serve as an important resource towards understanding the organization and copy number variation of these complex DNA families. PMID:18992157

  20. Health Benefits of Particle Filtration

    SciTech Connect

    Fisk, William J.

    2013-10-01

    The evidence of health benefits of particle filtration in homes and commercial buildings is reviewed. Prior reviews of papers published before 2000 are summarized. The results of 16 more recent intervention studies are compiled and analyzed. Also, reviewed are four studies that modeled health benefits of using filtration to reduce indoor exposures to particles from outdoors. Prior reviews generally concluded that particle filtration is, at best, a source of small improvements in allergy and asthma health effects; however, many early studies had weak designs. A majority of recent intervention studies employed strong designs and more of these studies report statistically significant improvements in health symptoms or objective health outcomes, particularly for subjects with allergies or asthma. The percent age improvement in health outcomes is typically modest, for example, 7percent to 25percent. Delivery of filtered air to the breathing zone of sleeping allergic or asthmatic persons may be more consistently effective in improving health than room air filtration. Notable are two studies that report statistically significant improvements, with filtration, in markers that predict future adverse coronary events. From modeling, the largest potential benefits of indoor particle filtration may be reductions in morbidity and mortality from reducing indoor exposures to particles from outdoor air.

  1. Health Benefits of Particle Filtration

    SciTech Connect

    Fisk, William J.

    2013-10-01

    The evidence of health benefits of particle filtration in homes and commercial buildings is reviewed. Prior reviews of papers published before 2000 are summarized. The results of 16 more recent intervention studies are compiled and analyzed. Also reviewed are four studies that modeled health benefits of using filtration to reduce indoor exposures to particles from outdoors. Prior reviews generally concluded that particle filtration is, at best, a source of small improvements in allergy and asthma health effects; however, many early studies had weak designs. A majority of recent intervention studies employed strong designs and more of these studies report statistically significant improvements in health symptoms or objective health outcomes, particularly for subjects with allergies or asthma. The percentage improvement in health outcomes is typically modest, e.g., 7percent to 25percent. Delivery of filtered air to the breathing zone of sleeping allergic or asthmatic persons may be more consistently effective in improving health than room air filtration. Notable are two studies that report statistically significant improvements, with filtration, in markers that predict future adverse coronary events. From modeling, the largest potential benefits of indoor particle filtration may be reductions in morbidity and mortality from reducing indoor exposures to particles from outdoor air.

  2. The Genome Russia project: closing the largest remaining omission on the world Genome map.

    PubMed

    Oleksyk, Taras K; Brukhin, Vladimir; O'Brien, Stephen J

    2015-01-01

    We are witnessing the great era of genome exploration of the world, as genetic variation in people is being detailed across multiple varied world populations in an effort unprecedented since the first human genome sequence appeared in 2001. However, these efforts have yet to produce a comprehensive mapping of humankind, because important regions of modern human civilization remain unexplored. The Genome Russia Project promises to fill one of the largest gaps, the expansive regions across the Russian Federation, informing not just medical genomics of the territories, but also the migration settlements  of historic and pre-historic Eurasian peoples.

  3. Mesophotic fishes of the Abrolhos Shelf, the largest reef ecosystem in the South Atlantic.

    PubMed

    Simon, T; Pinheiro, H T; Moura, R L; Carvalho-Filho, A; Rocha, L A; Martins, A S; Mazzei, E; Francini-Filho, R B; Amado-Filho, G M; Joyeux, J-C

    2016-07-01

    Fishes inhabiting rhodolith beds and reefs at mesophotic depths on the Abrolhos Shelf, which encompasses the largest and richest coral reef formation in the South Atlantic Ocean, were assessed through technical diving and remotely operated vehicles (ROVs). A total of 74 fish species were recorded, including at least one new species, one new record for the south-western Atlantic and six new records for the Abrolhos region. Overfishing, mining and port activities are already threatening many endangered and commercially important species recorded on the mesophotic reefs of Abrolhos Shelf, and the establishment of marine protected areas and off-reserve fisheries regulations are urgently needed. PMID:27094882

  4. Venezuelan projects advance to develop world`s largest heavy oil reserves

    SciTech Connect

    Croft, G.; Stauffer, K.

    1996-07-08

    A number of joint venture projects at varying stages of progress promise to greatly increase Venezuela`s production of extra heavy oil. Units of Conoco, Chevron, Total, Arco, and Mobil have either signed agreements or are pursuing negotiations with affiliates of state-owned Petroleos de Venezuela SA on the development of huge reserves of 8--10{degree} gravity crude. Large heavy oil resources are present in the oil producing areas of eastern and western Venezuela, and the largest are in eastern Venezuela`s Orinoco heavy oil belt. The paper discusses the Orinoco heavy oil belt geology and several joint ventures being implemented.

  5. Mitochondrial genome of Micrura bella (Nemertea: Heteronemertea), the largest mitochondrial genome known to phylum Nemertea.

    PubMed

    Shen, Chunyang; Shi-Chun, Sun

    2016-07-01

    The complete mitochondrial genome (mitogenome) of Micrura bella was sequenced and analyzed. Being the largest mitogenome known to phylum Nemertea, the genome is 16 847 bp in length. It encodes 37 genes typical to metazoan mitogenomes and has the same gene arrangement with the other Heteronemertea mitogenomes sequenced to date. The genome has the maximal number of non-coding nucleotides (2037 bp at 25 sites) in Nemertea mitogenomes, among which two large non-coding regions were found (507 and 508 bp, respectively).

  6. Cluster-Void Degeneracy Breaking: Dark Energy, Planck, and the Largest Cluster and Void

    NASA Astrophysics Data System (ADS)

    Sahlén, Martin; Zubeldía, Íñigo; Silk, Joseph

    2016-03-01

    Combining galaxy cluster and void abundances breaks the degeneracy between mean matter density {{{Ω }}}{{m}} and power-spectrum normalization {σ }8. For the first time for voids, we constrain {{{Ω }}}{{m}}=0.21+/- 0.10 and {σ }8=0.95+/- 0.21 for a flat Λ CDM universe, using extreme-value statistics on the claimed largest cluster and void. The Planck-consistent results detect dark energy with two objects, independently of other dark energy probes. Cluster-void studies are also complementary in scale, density, and nonlinearity, and are of particular interest for testing modified-gravity models.

  7. Mesophotic fishes of the Abrolhos Shelf, the largest reef ecosystem in the South Atlantic.

    PubMed

    Simon, T; Pinheiro, H T; Moura, R L; Carvalho-Filho, A; Rocha, L A; Martins, A S; Mazzei, E; Francini-Filho, R B; Amado-Filho, G M; Joyeux, J-C

    2016-07-01

    Fishes inhabiting rhodolith beds and reefs at mesophotic depths on the Abrolhos Shelf, which encompasses the largest and richest coral reef formation in the South Atlantic Ocean, were assessed through technical diving and remotely operated vehicles (ROVs). A total of 74 fish species were recorded, including at least one new species, one new record for the south-western Atlantic and six new records for the Abrolhos region. Overfishing, mining and port activities are already threatening many endangered and commercially important species recorded on the mesophotic reefs of Abrolhos Shelf, and the establishment of marine protected areas and off-reserve fisheries regulations are urgently needed.

  8. An unusual symbiont from the gut of surgeonfishes may be the largest known prokaryote.

    PubMed Central

    Clements, K D; Bullivant, S

    1991-01-01

    Symbionts first reported from the gut of a Red Sea surgeonfish, Acanthurus nigrofuscus (family Acanthuridae), were subsequently described as Epulopiscium fishelsoni. The taxonomic position of this very large (up to 576 microns in length) microorganism has previously been designated in the literature as either uncertain or eukaryotic. We suggest that similar symbionts from Great Barrier Reef surgeonfish may be prokaryotes, which together with E. fishelsoni from the Red Sea may represent the largest known forms of this cell type. Features identifying the symbionts as prokaryotes include the presence of bacterial-type flagella and a bacterial nucleoid and the absence of a nucleus or any other membrane-bound organelle. Images PMID:1885516

  9. THE MASS OF (4) VESTA DERIVED FROM ITS LARGEST GRAVITATIONAL EFFECTS

    SciTech Connect

    Kuzmanoski, Mike; Novakovic, Bojan; Apostolovska, Gordana E-mail: bojan@matf.bg.ac.r

    2010-09-15

    In this paper, we present a recalculated value of the mass of (4) Vesta, derived from its largest gravitational perturbations on selected asteroids during their mutual close encounters. This was done by using a new method for mass determination, which is based on the linking of pre-encounter observations to the orbit determined from post-encounter ones. The estimated weighted mean of the mass of (4) Vesta is (1.300 {+-} 0.001) x 10{sup -10} M{sub sun}.

  10. The Largest Response Component in the Motor Cortex Reflects Movement Timing but Not Movement Type

    PubMed Central

    Sussillo, David; Ryu, Stephen I.

    2016-01-01

    Abstract Neural activity in monkey motor cortex (M1) and dorsal premotor cortex (PMd) can reflect a chosen movement well before that movement begins. The pattern of neural activity then changes profoundly just before movement onset. We considered the prediction, derived from formal considerations, that the transition from preparation to movement might be accompanied by a large overall change in the neural state that reflects when movement is made rather than which movement is made. Specifically, we examined “components” of the population response: time-varying patterns of activity from which each neuron’s response is approximately composed. Amid the response complexity of individual M1 and PMd neurons, we identified robust response components that were “condition-invariant”: their magnitude and time course were nearly identical regardless of reach direction or path. These condition-invariant response components occupied dimensions orthogonal to those occupied by the “tuned” response components. The largest condition-invariant component was much larger than any of the tuned components; i.e., it explained more of the structure in individual-neuron responses. This condition-invariant response component underwent a rapid change before movement onset. The timing of that change predicted most of the trial-by-trial variance in reaction time. Thus, although individual M1 and PMd neurons essentially always reflected which movement was made, the largest component of the population response reflected movement timing rather than movement type. PMID:27761519

  11. Impact of closing Canada's largest point-source of mercury emissions on local atmospheric mercury concentrations.

    PubMed

    Eckley, Chris S; Parsons, Matthew T; Mintz, Rachel; Lapalme, Monique; Mazur, Maxwell; Tordon, Robert; Elleman, Robert; Graydon, Jennifer A; Blanchard, Pierrette; St Louis, Vincent

    2013-09-17

    The Flin Flon, Manitoba copper smelter was Canada's largest point source of mercury emissions until its closure in 2010 after ~80 years of operation. The objective of this study was to understand the variables controlling the local ground-level air mercury concentrations before and after this major point source reduction. Total gaseous mercury (TGM) in air, mercury in precipitation, and other ancillary meteorological and air quality parameters were measured pre- and postsmelter closure, and mercury speciation measurements in air were collected postclosure. The results showed that TGM was significantly elevated during the time period when the smelter operated (4.1 ± 3.7 ng m(-3)), decreased only 20% during the year following its closure, and remained ~2-fold above background levels. Similar trends were observed for mercury concentrations in precipitation. Several lines of evidence indicated that while smelter stack emissions would occasionally mix down to the surface resulting in large spikes in TGM concentrations (up to 61 ng m(-3)), the largest contributor to elevated TGM concentrations before and after smelter closure was from surface-air fluxes from mercury-enriched soils and/or tailings. These findings highlight the ability of legacy mercury, deposited to local landscapes over decades from industrial activities, to significantly affect local air concentrations via emissions/re-emissions. PMID:23978035

  12. Approximating natural connectivity of scale-free networks based on largest eigenvalue

    NASA Astrophysics Data System (ADS)

    Tan, S.-Y.; Wu, J.; Li, M.-J.; Lu, X.

    2016-06-01

    It has been recently proposed that natural connectivity can be used to efficiently characterize the robustness of complex networks. The natural connectivity has an intuitive physical meaning and a simple mathematical formulation, which corresponds to an average eigenvalue calculated from the graph spectrum. However, as a network model close to the real-world system that widely exists, the scale-free network is found difficult to obtain its spectrum analytically. In this article, we investigate the approximation of natural connectivity based on the largest eigenvalue in both random and correlated scale-free networks. It is demonstrated that the natural connectivity of scale-free networks can be dominated by the largest eigenvalue, which can be expressed asymptotically and analytically to approximate natural connectivity with small errors. Then we show that the natural connectivity of random scale-free networks increases linearly with the average degree given the scaling exponent and decreases monotonically with the scaling exponent given the average degree. Moreover, it is found that, given the degree distribution, the more assortative a scale-free network is, the more robust it is. Experiments in real networks validate our methods and results.

  13. Metagenomic Characterisation of the Viral Community of Lough Neagh, the Largest Freshwater Lake in Ireland.

    PubMed

    Skvortsov, Timofey; de Leeuwe, Colin; Quinn, John P; McGrath, John W; Allen, Christopher C R; McElarney, Yvonne; Watson, Catherine; Arkhipova, Ksenia; Lavigne, Rob; Kulakov, Leonid A

    2016-01-01

    Lough Neagh is the largest and the most economically important lake in Ireland. It is also one of the most nutrient rich amongst the world's major lakes. In this study, 16S rRNA analysis of total metagenomic DNA from the water column of Lough Neagh has revealed a high proportion of Cyanobacteria and low levels of Actinobacteria, Acidobacteria, Chloroflexi, and Firmicutes. The planktonic virome of Lough Neagh has been sequenced and 2,298,791 2×300 bp Illumina reads analysed. Comparison with previously characterised lakes demonstrates that the Lough Neagh viral community has the highest level of sequence diversity. Only about 15% of reads had homologs in the RefSeq database and tailed bacteriophages (Caudovirales) were identified as a major grouping. Within the Caudovirales, the Podoviridae and Siphoviridae were the two most dominant families (34.3% and 32.8% of the reads with sequence homology to the RefSeq database), while ssDNA bacteriophages constituted less than 1% of the virome. Putative cyanophages were found to be abundant. 66,450 viral contigs were assembled with the largest one being 58,805 bp; its existence, and that of another 34,467 bp contig, in the water column was confirmed. Analysis of the contigs confirmed the high abundance of cyanophages in the water column. PMID:26927795

  14. Public health preparedness for the world's largest mass gathering: 2010 World Exposition in Shanghai, China.

    PubMed

    Yi, He; Zheng'an, Yuan; Fan, Wu; Xiang, Guo; Chen, Dong; Yongchao, He; Xiaodong, Sun; Hao, Pan; Mahany, Mollie; Keim, Mark

    2012-12-01

    The 2010 World Exposition in Shanghai China (Expo) was the largest mass gathering in world history, attracting a record 72 million visitors. More than 190 countries participated in the Expo, along with more than 50 international organizations. The 2010 Expo was six months in duration (May 1 through October 30, 2010), and the size of the venue site comprised 5.28 square kilometers. Great challenges were imposed on the public health system in Shanghai due to the high number and density of visitors, long duration of the event, and other risk factors such as high temperatures, typhoon, etc. As the major metropolitan public health agency in Shanghai, the Shanghai Municipal Center for Disease Control and Prevention (SCDC) implemented a series of actions in preparing for, and responding to, the potential health impact of the world's largest mass gathering to date, which included partnerships for capacity building, enhancement of internal organizational structure, risk assessment, strengthened surveillance, disaster planning and exercises, laboratory management, vaccination campaign, health education, health intervention, risk communication and mass media surveillance, and technical support for health inspection. The clear-cut organizational structures and job responsibilities, as well as comprehensive operational and scientific preparations, were key elements to ensure the success of the 2010 World Exposition. PMID:22995587

  15. Metagenomic Characterisation of the Viral Community of Lough Neagh, the Largest Freshwater Lake in Ireland

    PubMed Central

    Skvortsov, Timofey; de Leeuwe, Colin; Quinn, John P.; McGrath, John W.; Allen, Christopher C. R.; McElarney, Yvonne; Watson, Catherine; Arkhipova, Ksenia; Lavigne, Rob; Kulakov, Leonid A.

    2016-01-01

    Lough Neagh is the largest and the most economically important lake in Ireland. It is also one of the most nutrient rich amongst the world’s major lakes. In this study, 16S rRNA analysis of total metagenomic DNA from the water column of Lough Neagh has revealed a high proportion of Cyanobacteria and low levels of Actinobacteria, Acidobacteria, Chloroflexi, and Firmicutes. The planktonic virome of Lough Neagh has been sequenced and 2,298,791 2×300 bp Illumina reads analysed. Comparison with previously characterised lakes demonstrates that the Lough Neagh viral community has the highest level of sequence diversity. Only about 15% of reads had homologs in the RefSeq database and tailed bacteriophages (Caudovirales) were identified as a major grouping. Within the Caudovirales, the Podoviridae and Siphoviridae were the two most dominant families (34.3% and 32.8% of the reads with sequence homology to the RefSeq database), while ssDNA bacteriophages constituted less than 1% of the virome. Putative cyanophages were found to be abundant. 66,450 viral contigs were assembled with the largest one being 58,805 bp; its existence, and that of another 34,467 bp contig, in the water column was confirmed. Analysis of the contigs confirmed the high abundance of cyanophages in the water column. PMID:26927795

  16. Supergranulation as the Largest Buoyantly Driven Convective Scale of the Sun

    NASA Astrophysics Data System (ADS)

    Cossette, Jean-Francois; Rast, Mark P.

    2016-09-01

    The origin of solar supergranulation remains a mystery. Unlike granulation, the size of which is comparable to both the thickness of the radiative boundary layer and local scale-height in the photosphere, supergranulation does not reflect any obvious length scale of the solar convection zone. Moreover, recent observations of flows in the photosphere using Doppler imaging or correlation or feature tracking show a monotonic decrease in horizontal flow power at scales larger than supergranulation. Both local area and global spherical shell simulations of solar convection by contrast show the opposite, an increase in horizontal flow amplitudes to a low wavenumber. We examine these disparities and investigate how the solar supergranulation may arise as a consequence of nonlocal heat transport by cool diving plumes. Using three-dimensional anelastic simulations with surface driving, we show that the kinetic energy of the largest convective scales in the upper layers of a stratified domain reflects the depth of transition from strong buoyant driving to adiabatic stratification below caused by the dilution of the granular downflows. This depth is quite shallow because of the rapid increase of the mean density below the photosphere. We interpret the observed monotonic decrease in solar convective power at scales larger than supergranulation to be a consequence of this rapid transition, with the supergranular scale the largest buoyantly driven mode of convection in the Sun.

  17. Constraining gravity at the largest scales through CMB lensing and galaxy velocities

    NASA Astrophysics Data System (ADS)

    Pullen, Anthony R.; Alam, Shadab; He, Siyu; Ho, Shirley

    2016-08-01

    We demonstrate a new method to constrain gravity on the largest cosmological scales by combining measurements of cosmic microwave background (CMB) lensing and the galaxy velocity field. EG is a statistic, constructed from a gravitational lensing tracer and a measure of velocities such as redshift-space distortions (RSD), that can discriminate between gravity models while being independent of clustering bias and σ8. While traditionally, the lensing field for EG has been probed through galaxy lensing, CMB lensing has been proposed as a more robust tracer of the lensing field for EG at higher redshifts while avoiding intrinsic alignments. We perform the largest-scale measurement of EG ever, up to 150 Mpc h-1, by cross-correlating the Planck CMB lensing map with the Sloan Digital Sky Survey III (SDSS-III) CMASS galaxy sample and combining this with our measurement of the CMASS auto-power spectrum and the RSD parameter β. We report EG(z = 0.57) = 0.243 ± 0.060 (stat) ± 0.013 (sys), a measurement in tension with the general relativity (GR) prediction at a level of 2.6σ. Note that our EG measurement deviates from GR only at scales greater than 80 Mpc h-1, scales which have not been probed by previous EG tests. Upcoming surveys, which will provide an order-of-magnitude reduction in statistical errors, can significantly constrain alternative gravity models when combined with better control of systematics.

  18. Sequencing of tsunami waves: Why the first wave is not always the largest

    NASA Astrophysics Data System (ADS)

    Okal, Emile; Synolakis, Costas

    2015-04-01

    In many instances, the largest wave to hit a coastline during a tsunami is not the first one. Classical examples include the arrivals of the 1960 Chilean tsunami in Hilo, Hawaii, and of the 1964 Alaskan tsunami in Crescent City, California, where most casualties took place during later arrivals. This situation can be socially treacherous, since residents and civil defense authorities are led to believe that the worst is over after a first, relatively mild arrival, and to give an early "all clear" before the true largest wave, as was the case in Papeete, Tahiti during the 2011 Tohoku tsunami. We research this problem by using a number of simple models for which analytical solutions are available, as well as more realistic simulations of the large earthquake tsunamis of the past decade, and compare their results to a catalog of waveforms obtained at DART buoys spread over the Pacific Basin. Preliminary results indicate a transition from a regime of Maximum First Wave to one of Delayed Maximum when distance is increased, azimuth to receiver is moved away from the normal to fault strike, and/or source size is reduced.

  19. Population genetic structure of Earth's largest fish, the whale shark (Rhincodon typus).

    PubMed

    Castro, A L F; Stewart, B S; Wilson, S G; Hueter, R E; Meekan, M G; Motta, P J; Bowen, B W; Karl, S A

    2007-12-01

    Large pelagic vertebrates pose special conservation challenges because their movements generally exceed the boundaries of any single jurisdiction. To assess the population structure of whale sharks (Rhincodon typus), we sequenced complete mitochondrial DNA control regions from individuals collected across a global distribution. We observed 51 single site polymorphisms and 8 regions with indels comprising 44 haplotypes in 70 individuals, with high haplotype (h = 0.974 +/- 0.008) and nucleotide diversity (pi = 0.011 +/- 0.006). The control region has the largest length variation yet reported for an elasmobranch (1143-1332 bp). Phylogenetic analyses reveal no geographical clustering of lineages and the most common haplotype was distributed globally. The absence of population structure across the Indian and Pacific basins indicates that oceanic expanses and land barriers in Southeast Asia are not impediments to whale shark dispersal. We did, however, find significant haplotype frequency differences (AMOVA, Phi(ST) = 0.107, P < 0.001) principally between the Atlantic and Indo-Pacific populations. In contrast to other recent surveys of globally distributed sharks, we find much less population subdivision and no evidence for cryptic evolutionary partitions. Discovery of the mating and pupping areas of whale sharks is key to further population genetic studies. The global pattern of shared haplotypes in whale sharks provides a compelling argument for development of broad international approaches for management and conservation of Earth's largest fish.

  20. Evaluation of nonlinear properties of epileptic activity using largest Lyapunov exponent

    NASA Astrophysics Data System (ADS)

    Medvedeva, Tatiana M.; Lüttjohann, Annika; van Luijtelaar, Gilles; Sysoev, Ilya V.

    2016-04-01

    Absence seizures are known to be highly non-linear large amplitude oscillations with a well pronounced main time scale. Whilst the appearance of the main frequency is usually considered as a transition from noisy complex dynamics of baseline EEG to more regular absence activity, the dynamical properties of this type of epileptiformic activity in genetic absence models was not studied precisely. Here, the estimation of the largest Lyapunov exponent from intracranial EEGs of 10 WAG/Rij rats (genetic model of absence epilepsy) was performed. Fragments of 10 seizures and 10 episodes of on-going EEG each of 4 s length were used for each animal, 3 cortical and 2 thalamic channels were analysed. The method adapted for short noisy data was implemented. The positive values of the largest Lyapunov exponent were found as for baseline as for spike wave discharges (SWDs), with values for SWDs being significantly less than for on-going activity. Current findings may indicate that SWD is a chaotic process with a well pronounced main timescale rather than a periodic regime. Also, the absence activity was shown to be less chaotic than the baseline one.

  1. Metagenomic Characterisation of the Viral Community of Lough Neagh, the Largest Freshwater Lake in Ireland.

    PubMed

    Skvortsov, Timofey; de Leeuwe, Colin; Quinn, John P; McGrath, John W; Allen, Christopher C R; McElarney, Yvonne; Watson, Catherine; Arkhipova, Ksenia; Lavigne, Rob; Kulakov, Leonid A

    2016-01-01

    Lough Neagh is the largest and the most economically important lake in Ireland. It is also one of the most nutrient rich amongst the world's major lakes. In this study, 16S rRNA analysis of total metagenomic DNA from the water column of Lough Neagh has revealed a high proportion of Cyanobacteria and low levels of Actinobacteria, Acidobacteria, Chloroflexi, and Firmicutes. The planktonic virome of Lough Neagh has been sequenced and 2,298,791 2×300 bp Illumina reads analysed. Comparison with previously characterised lakes demonstrates that the Lough Neagh viral community has the highest level of sequence diversity. Only about 15% of reads had homologs in the RefSeq database and tailed bacteriophages (Caudovirales) were identified as a major grouping. Within the Caudovirales, the Podoviridae and Siphoviridae were the two most dominant families (34.3% and 32.8% of the reads with sequence homology to the RefSeq database), while ssDNA bacteriophages constituted less than 1% of the virome. Putative cyanophages were found to be abundant. 66,450 viral contigs were assembled with the largest one being 58,805 bp; its existence, and that of another 34,467 bp contig, in the water column was confirmed. Analysis of the contigs confirmed the high abundance of cyanophages in the water column.

  2. Particle acceleration

    NASA Technical Reports Server (NTRS)

    Vlahos, L.; Machado, M. E.; Ramaty, R.; Murphy, R. J.; Alissandrakis, C.; Bai, T.; Batchelor, D.; Benz, A. O.; Chupp, E.; Ellison, D.

    1986-01-01

    Data is compiled from Solar Maximum Mission and Hinothori satellites, particle detectors in several satellites, ground based instruments, and balloon flights in order to answer fundamental questions relating to: (1) the requirements for the coronal magnetic field structure in the vicinity of the energization source; (2) the height (above the photosphere) of the energization source; (3) the time of energization; (4) transistion between coronal heating and flares; (5) evidence for purely thermal, purely nonthermal and hybrid type flares; (6) the time characteristics of the energization source; (7) whether every flare accelerates protons; (8) the location of the interaction site of the ions and relativistic electrons; (9) the energy spectra for ions and relativistic electrons; (10) the relationship between particles at the Sun and interplanetary space; (11) evidence for more than one acceleration mechanism; (12) whether there is single mechanism that will accelerate particles to all energies and also heat the plasma; and (13) how fast the existing mechanisms accelerate electrons up to several MeV and ions to 1 GeV.

  3. Purification of Drosophila snRNPs and characterization of two populations of functional U1 particles.

    PubMed Central

    Labourier, E; Rio, D C

    2001-01-01

    U1 snRNP is required at an early stage during assembly of the spliceosome, the dynamic ribonucleoprotein (RNP) complex that performs nuclear pre-mRNA splicing. Here, we report the purification of U1 snRNP particles from Drosophila nuclear extracts and the characterization of their biochemical properties, polypeptide contents, and splicing activities. On the basis of their antigenicity, apparent molecular weight, and by peptide sequencing, the Drosophila 70K, SNF, B, U1-C, D1, D2, D3, E, F, and G proteins are shown to be integral components of these particles. Sequence database searches revealed that both the U1-specific and the Sm proteins are extensively conserved between human and Drosophila snRNPs. Furthermore, both species possess a conserved intrinsic U1-associated kinase activity with identical substrate specificity in vitro. Finally, our results demonstrate that a second type of functional U1 particle, completely lacking the U1/U2-specific protein SNF and the associated protein kinase activity, can be isolated from cultured Kc cell or Canton S embryonic nuclear extracts. This work describes the first characterization of a purified Drosophila snRNP particle and reinforces the view that their activity and composition, with the exception of the atypical bifunctional U1-A/U2-B" SNF protein, are highly conserved in metazoans. PMID:11333025

  4. Rapid Deposition Technology Holds the Key for the World's Largest Manufacturer of Thin-Film Solar Modules (Fact Sheet)

    SciTech Connect

    Not Available

    2013-08-01

    First Solar, Inc. has been collaborating with NREL since 1991, advancing its thin-film cadmium telluride solar technology to grow from a startup company to become one of the world's largest manufacturers of solar modules, and the world's largest manufacturer of thin-film solar modules.

  5. Structural diversity of signal recognition particle RNAs in plastids.

    PubMed

    Rosenblad, Magnus Alm; Träger, Chantal; Schünemann, Danja

    2013-10-01

    One of the pathways for protein targeting to the plasma membrane in bacteria utilizes the co-translationally acting signal recognition particle (SRP), a universally conserved ribonucleoprotein complex consisting of a 54 kDa protein and a functional RNA. An interesting exception is the higher plant chloroplast SRP, which lacks the otherwise essential RNA component. Furthermore, green plant chloroplasts have an additional post-translational SRP-dependent transport system in which the chloroplast-specific cpSRP43 protein binds to imported substrate proteins and to the conserved 54 kDa SRP subunit (cpSRP54). While homologs to the bacterial SRP protein and RNA component previously have been identified in genome sequences of red algae and diatoms, a recent study investigated the evolution of the green plant SRP system.1 Analysis of hundreds of plastid and nuclear genomes showed a surprising pattern of multiple losses of the plastid SRP RNA during evolution and a widespread presence in all non-spermatophyte plants and green algae. Contrary to expectations, all green organisms that have an identified cpSRP RNA also contain a cpSRP43. Notably, the structure of the plastid SRP RNAs is much more diverse than that of bacterial SRP RNAs. The apical GNRA tetraloop is only conserved in organisms of the red lineage and basal organisms of the green lineage, whereas further chloroplast SRP RNAs are characterized by atypical, mostly enlarged apical loops.

  6. In Search of the Largest Possible Tsunami: An Example Following the 2011 Japan Tsunami

    NASA Astrophysics Data System (ADS)

    Geist, E. L.; Parsons, T.

    2012-12-01

    Many tsunami hazard assessments focus on estimating the largest possible tsunami: i.e., the worst-case scenario. This is typically performed by examining historic and prehistoric tsunami data or by estimating the largest source that can produce a tsunami. We demonstrate that worst-case assessments derived from tsunami and tsunami-source catalogs are greatly affected by sampling bias. Both tsunami and tsunami sources are well represented by a Pareto distribution. It is intuitive to assume that there is some limiting size (i.e., runup or seismic moment) for which a Pareto distribution is truncated or tapered. Likelihood methods are used to determine whether a limiting size can be determined from existing catalogs. Results from synthetic catalogs indicate that several observations near the limiting size are needed for accurate parameter estimation. Accordingly, the catalog length needed to empirically determine the limiting size is dependent on the difference between the limiting size and the observation threshold, with larger catalog lengths needed for larger limiting-threshold size differences. Most, if not all, tsunami catalogs and regional tsunami source catalogs are of insufficient length to determine the upper bound on tsunami runup. As an example, estimates of the empirical tsunami runup distribution are obtained from the Miyako tide gauge station in Japan, which recorded the 2011 Tohoku-oki tsunami as the largest tsunami among 51 other events. Parameter estimation using a tapered Pareto distribution is made both with and without the Tohoku-oki event. The catalog without the 2011 event appears to have a low limiting tsunami runup. However, this is an artifact of undersampling. Including the 2011 event, the catalog conforms more to a pure Pareto distribution with no confidence in estimating a limiting runup. Estimating the size distribution of regional tsunami sources is subject to the same sampling bias. Physical attenuation mechanisms such as wave breaking

  7. Largest Laplacian eigenvalue predicts the emergence of costly punishment in the evolutionary ultimatum game on networks

    NASA Astrophysics Data System (ADS)

    Li, Xiang; Cao, Lang

    2009-12-01

    In recent years, there has been a growing interest in studying the role of costly punishment in promoting altruistic behaviors among selfish individuals. Rejections in ultimatum bargaining as a metaphor exemplify costly punishment, where the division of a sum of resources proposed by one side may be rejected by the other side, and both sides get nothing. Under a setting of the network of contacts among players, we find that the largest Laplacian eigenvalue of the network determines the critical division of players’ proposals, below which pure punishers who never accept any offers will emerge as a phase transition in the system. The critical division of offers that predicts the emergence of costly punishment is termed as the selfishness tolerance of a network within evolutionary ultimatum game, and extensive numerical simulations on the data of the science collaboration network, and computer-generated small-world/scale-free networks support the analytical findings.

  8. Microbial life in the Lake Medee, the largest deep-sea salt-saturated formation.

    PubMed

    Yakimov, Michail M; La Cono, Violetta; Slepak, Vladlen Z; La Spada, Gina; Arcadi, Erika; Messina, Enzo; Borghini, Mireno; Monticelli, Luis S; Rojo, David; Barbas, Coral; Golyshina, Olga V; Ferrer, Manuel; Golyshin, Peter N; Giuliano, Laura

    2013-01-01

    Deep-sea hypersaline anoxic lakes (DHALs) of the Eastern Mediterranean represent some of the most hostile environments on our planet. We investigated microbial life in the recently discovered Lake Medee, the largest DHAL found to-date. Medee has two unique features: a complex geobiochemical stratification and an absence of chemolithoautotrophic Epsilonproteobacteria, which usually play the primary role in dark bicarbonate assimilation in DHALs interfaces. Presumably because of these features, Medee is less productive and exhibits reduced diversity of autochthonous prokaryotes in its interior. Indeed, the brine community almost exclusively consists of the members of euryarchaeal MSBL1 and bacterial KB1 candidate divisions. Our experiments utilizing cultivation and [(14)C]-assimilation, showed that these organisms at least partially rely on reductive cleavage of osmoprotectant glycine betaine and are engaged in trophic cooperation. These findings provide novel insights into how prokaryotic communities can adapt to salt-saturated conditions and sustain active metabolism at the thermodynamic edge of life. PMID:24352146

  9. Mauna Loa--history, hazards and risk of living with the world's largest volcano

    USGS Publications Warehouse

    Trusdell, Frank A.

    2012-01-01

    Mauna Loa on the Island Hawaiʻi is the world’s largest volcano. People residing on its flanks face many hazards that come with living on or near an active volcano, including lava flows, explosive eruptions, volcanic smog, damaging earthquakes, and local tsunami (giant seawaves). The County of Hawaiʻi (Island of Hawaiʻi) is the fastest growing County in the State of Hawaii. Its expanding population and increasing development mean that risk from volcano hazards will continue to grow. U.S. Geological Survey (USGS) scientists at the Hawaiian Volcano Observatory (HVO) closely monitor and study Mauna Loa Volcano to enable timely warning of hazardous activity and help protect lives and property.

  10. Induced Seismicity: What is the Size of the Largest Expected Earthquake?

    NASA Astrophysics Data System (ADS)

    Zoeller, G.; Holschneider, M.

    2014-12-01

    The injections of fluids is a well-known origin for the triggering of earthquake sequences. The growing number of projects related to enhanced geothermal systems, fracking and others has led to the question, which maximum earthquake magnitude can be expected as a consequence of fluid injection. This question is addressed from the perspective of statistical analysis. Using basic empirical laws of earthquake statistics, we estimate the magnitude MT of the maximum expected earthquake in a pre-defined future time window T. A case study of the fluid injection site at Paradox Valley, Colorado, USA, demonstrates that the magnitude m=4.3 of the largest observed earthquake on 27 May 2000 is lying very well within the expectation from past seismicity without adjusting any parameters. Vice versa, for a given maximum tolerable earthquake at an injection site, we can constrain the corresponding amount of injected fluids that must not be exceeded within pre-defined confidence bounds.

  11. Contamination Control Assessment of the World's Largest Space Environment Simulation Chamber

    NASA Technical Reports Server (NTRS)

    Snyder, Aaron; Henry, Michael W.; Grisnik, Stanley P.; Sinclair, Stephen M.

    2012-01-01

    The Space Power Facility s thermal vacuum test chamber is the largest chamber in the world capable of providing an environment for space simulation. To improve performance and meet stringent requirements of a wide customer base, significant modifications were made to the vacuum chamber. These include major changes to the vacuum system and numerous enhancements to the chamber s unique polar crane, with a goal of providing high cleanliness levels. The significance of these changes and modifications are discussed in this paper. In addition, the composition and arrangement of the pumping system and its impact on molecular back-streaming are discussed in detail. Molecular contamination measurements obtained with a TQCM and witness wafers during two recent integrated system tests of the chamber are presented and discussed. Finally, a concluding remarks section is presented.

  12. Largest Laplacian eigenvalue predicts the emergence of costly punishment in the evolutionary ultimatum game on networks.

    PubMed

    Li, Xiang; Cao, Lang

    2009-12-01

    In recent years, there has been a growing interest in studying the role of costly punishment in promoting altruistic behaviors among selfish individuals. Rejections in ultimatum bargaining as a metaphor exemplify costly punishment, where the division of a sum of resources proposed by one side may be rejected by the other side, and both sides get nothing. Under a setting of the network of contacts among players, we find that the largest Laplacian eigenvalue of the network determines the critical division of players' proposals, below which pure punishers who never accept any offers will emerge as a phase transition in the system. The critical division of offers that predicts the emergence of costly punishment is termed as the selfishness tolerance of a network within evolutionary ultimatum game, and extensive numerical simulations on the data of the science collaboration network, and computer-generated small-world/scale-free networks support the analytical findings.

  13. Fifteen Years of Operation at NASA's National Transonic Facility with the World's Largest Adjustable Speed Drive

    NASA Technical Reports Server (NTRS)

    Sydnor, George H.; Bhatia, Ram; Krattiger, Hansueli; Mylius, Justus; Schafer, D.

    2012-01-01

    In September 1995, a project was initiated to replace the existing drive line at NASA's most unique transonic wind tunnel, the National Transonic Facility (NTF), with a single 101 MW synchronous motor driven by a Load Commutated Inverter (LCI). This Adjustable Speed Drive (ASD) system also included a custom four-winding transformer, harmonic filter, exciter, switch gear, control system, and feeder cable. The complete system requirements and design details have previously been presented and published [1], as well as the commissioning and acceptance test results [2]. The NTF was returned to service in December 1997 with the new drive system powering the fan. Today, this installation still represents the world s largest horizontal single motor/drive combination. This paper describes some significant events that occurred with the drive system during the first 15 years of service. These noteworthy issues are analyzed and root causes presented. Improvements that have substantially increased the long term viability of the system are given.

  14. Deoxygenation alters bacterial diversity and community composition in the ocean’s largest oxygen minimum zone

    NASA Astrophysics Data System (ADS)

    Beman, J. Michael; Carolan, Molly T.

    2013-10-01

    Oceanic oxygen minimum zones (OMZs) have a central role in biogeochemical cycles and are expanding as a consequence of climate change, yet how deoxygenation will affect the microbial communities that control these cycles is unclear. Here we sample across dissolved oxygen gradients in the oceans’ largest OMZ and show that bacterial richness displays a unimodal pattern with decreasing dissolved oxygen, reaching maximum values on the edge of the OMZ and decreasing within it. Rare groups on the OMZ margin are abundant at lower dissolved oxygen concentrations, including sulphur-cycling Chromatiales, for which 16S rRNA was amplified from extracted RNA. Microbial species distribution models accurately replicate community patterns based on multivariate environmental data, demonstrate likely changes in distributions and diversity in the eastern tropical North Pacific Ocean, and highlight the sensitivity of key bacterial groups to deoxygenation. Through these mechanisms, OMZ expansion may alter microbial composition, competition, diversity and function, all of which have implications for biogeochemical cycling in OMZs.

  15. Microbial life in the Lake Medee, the largest deep-sea salt-saturated formation

    PubMed Central

    Yakimov, Michail M.; La Cono, Violetta; Slepak, Vladlen Z.; La Spada, Gina; Arcadi, Erika; Messina, Enzo; Borghini, Mireno; Monticelli, Luis S.; Rojo, David; Barbas, Coral; Golyshina, Olga V.; Ferrer, Manuel; Golyshin, Peter N.; Giuliano, Laura

    2013-01-01

    Deep-sea hypersaline anoxic lakes (DHALs) of the Eastern Mediterranean represent some of the most hostile environments on our planet. We investigated microbial life in the recently discovered Lake Medee, the largest DHAL found to-date. Medee has two unique features: a complex geobiochemical stratification and an absence of chemolithoautotrophic Epsilonproteobacteria, which usually play the primary role in dark bicarbonate assimilation in DHALs interfaces. Presumably because of these features, Medee is less productive and exhibits reduced diversity of autochthonous prokaryotes in its interior. Indeed, the brine community almost exclusively consists of the members of euryarchaeal MSBL1 and bacterial KB1 candidate divisions. Our experiments utilizing cultivation and [14C]-assimilation, showed that these organisms at least partially rely on reductive cleavage of osmoprotectant glycine betaine and are engaged in trophic cooperation. These findings provide novel insights into how prokaryotic communities can adapt to salt-saturated conditions and sustain active metabolism at the thermodynamic edge of life. PMID:24352146

  16. Assembling the Largest, Most Distant Sample of Halo Wide Binaries for Galactic Structure and Dynamics

    NASA Astrophysics Data System (ADS)

    Coronado, J.; Chanamé, J.

    2015-10-01

    Samples of wide binaries (agtrsim \\ 100\\ AU) are a gold mine for Galactic studies. They have been used on a large list of applications in a diversity of fields. In the dynamical arena, wide binaries provided the first meaningful constraints on the mass and nature of disk dark matter and, more recently, they were used to close the remaining parameter space of MACHO-like halo dark matter not accessible to the micro-lensing campaigns. All these applications were possible when samples of these objects became large enough to not be dominated by random, chance alignments of two unrelated stars projected on the sky. Nevertheless, still today the largest available sample of the particularly valuable halo wide binaries free from selection biases, contains not much more than 100 systems, and conclusions on dark matter are very sensitive to this fact.

  17. Truth hurts--hard lessons from Australia's largest mass casualty exercise with contaminated patients.

    PubMed

    Edwards, Nicholas A; Caldicott, David G E; Eliseo, Tony; Pearce, Andrew

    2006-04-01

    In response to the increasing threat of a mass casualty incident involving chemical, biological or radiological agents, and concern over the preparedness of our hospital system to cope with patients from such an incident, we conducted the largest hospital-based field exercise involving contaminated patients that has been held in Australia. In the present paper, we outline the background to, and methodology of, Exercise Supreme Truth, and the efforts made to increase its realism. We focus our discussion on three issues highlighted by the exercise, which we believe have enormous implications for the development of hospital chemical, biological or radiological plans and the likelihood of their success--hospital security, crowd control and decontamination.

  18. From Pushing Paper to Pushing Dirt - Canada's Largest LLRW Cleanup Gets Underway - 13111

    SciTech Connect

    Veen, Walter van; Lawrence, Dave

    2013-07-01

    The Port Hope Project is the larger of the two projects in the Port Hope Area Initiative (PHAI), Canada's largest low level radioactive waste (LLRW) cleanup. With a budget of approximately $1 billion, the Port Hope Project includes a broad and complex range of remedial elements from a state of the art water treatment plant, an engineered waste management facility, municipal solid waste removal, remediation of 18 major sites within the Municipality of Port Hope (MPH), sediment dredging and dewatering, an investigation of 4,800 properties (many of these homes) to identify LLRW and remediation of approximately 450 of these properties. This paper discusses the status of the Port Hope Project in terms of designs completed and regulatory approvals received, and sets out the scope and schedule for the remaining studies, engineering designs and remediation contracts. (authors)

  19. Microbial life in the Lake Medee, the largest deep-sea salt-saturated formation

    NASA Astrophysics Data System (ADS)

    Yakimov, Michail M.; La Cono, Violetta; Slepak, Vladlen Z.; La Spada, Gina; Arcadi, Erika; Messina, Enzo; Borghini, Mireno; Monticelli, Luis S.; Rojo, David; Barbas, Coral; Golyshina, Olga V.; Ferrer, Manuel; Golyshin, Peter N.; Giuliano, Laura

    2013-12-01

    Deep-sea hypersaline anoxic lakes (DHALs) of the Eastern Mediterranean represent some of the most hostile environments on our planet. We investigated microbial life in the recently discovered Lake Medee, the largest DHAL found to-date. Medee has two unique features: a complex geobiochemical stratification and an absence of chemolithoautotrophic Epsilonproteobacteria, which usually play the primary role in dark bicarbonate assimilation in DHALs interfaces. Presumably because of these features, Medee is less productive and exhibits reduced diversity of autochthonous prokaryotes in its interior. Indeed, the brine community almost exclusively consists of the members of euryarchaeal MSBL1 and bacterial KB1 candidate divisions. Our experiments utilizing cultivation and [14C]-assimilation, showed that these organisms at least partially rely on reductive cleavage of osmoprotectant glycine betaine and are engaged in trophic cooperation. These findings provide novel insights into how prokaryotic communities can adapt to salt-saturated conditions and sustain active metabolism at the thermodynamic edge of life.

  20. A protein kinase from wheat germ that phosphorylates the largest subunit of RNA polymerase II.

    PubMed Central

    Guilfoyle, T J

    1989-01-01

    A protein kinase from wheat germ that phosphorylates the largest subunit of RNA polymerase IIA has been partially purified and characterized. The kinase has a native molecular weight of about 200 kilodaltons. This kinase utilizes Mg2+ and ATP and transfers about 20 phosphates to the heptapeptide repeats Pro-Thr-Ser-Pro-Ser-Tyr-Ser in the carboxyl-terminal domain of the 220-kilodalton subunit of soybean RNA polymerase II. This phosphorylation results in a mobility shift of the 220-kilodalton subunits of a variety of eukaryotic RNA polymerases to polypeptides ranging in size from greater than 220 kilodaltons to 240 kilodaltons on sodium dodecyl sulfate-polyacrylamide gels. The phosphorylation is highly specific to the heptapeptide repeats since a degraded subunit polypeptide of 180 kilodaltons that lacks the heptapeptide repeats is poorly phosphorylated. Synthetic heptapeptide repeat multimers inhibit the phosphorylation of the 220-kilodalton subunit. PMID:2535525

  1. Legionella pneumophila, armed to the hilt: justifying the largest arsenal of effectors in the bacterial world.

    PubMed

    Ensminger, Alexander W

    2016-02-01

    Many bacterial pathogens use dedicated translocation systems to deliver arsenals of effector proteins to their hosts. Once inside the host cytosol, these effectors modulate eukaryotic cell biology to acquire nutrients, block microbial degradation, subvert host defenses, and enable pathogen transmission to other hosts. Among all bacterial pathogens studied to date, the gram-negative pathogen, Legionella pneumophila, maintains the largest arsenal of effectors, with over 330 effector proteins translocated by the Dot/Icm type IVB translocation system. In this review, I will discuss some of the recent work on understanding the consequences of this large arsenal. I will also present several models that seek to explain how L. pneumophila has acquired and subsequently maintained so many more effectors than its peers.

  2. The Trypanosoma brucei protein phosphatase gene: polycistronic transcription with the RNA polymerase II largest subunit gene.

    PubMed Central

    Evers, R; Cornelissen, A W

    1990-01-01

    We have previously described the trypanosomal gene encoding the largest subunit of RNA polymerase II (RNAP II) and found that two almost identical genes are encoded within the Trypanosoma brucei genome. Here we show by Southern analyses that the 5' breakpoint between both loci is located approximately 7.5 kb upstream of the RNAP II genes. Northern analyses revealed that the 5' duplicated segment contains at least four other genes, which are transcribed in both bloodstream and procyclic trypanosomes. The gene located immediately upstream of the RNAP II gene in both loci was characterized by sequence analyses. The deduced amino acid sequences show a high degree of similarity to the catalytic subunit of protein phosphatase class 1 (PP1) genes. S1 mapping provided strong evidence in support of the fact that the PP1 and RNAP II genes belong to a single transcription unit. Images PMID:2169604

  3. Complete mitochondrial genome of the largest living fish: whale shark Rhincodon typus (Orectolobiformes: Rhincodontidae).

    PubMed

    Chen, Xiao; Ai, Weiming; Pan, Lianghao; Shi, Xiaofang

    2016-01-01

    The whale shark Rhincodon typus (Pisces: Chondrichthyes, Orectolobiformes, Rhincodontidae) is the largest living fish on Earth. In this study, we presented its complete mitogenome. It is 16,928 bp in length, contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and one control region with the typical gene order and transcriptional direction in the vertebrates. Overall base composition of the R. typus mitogenome is 33.5% A, 24.3% C, 12.8% G and 29.5% T. Two start codon (GTG and ATG) and two stop codon patterns (TAG and TAA/T) were found in protein-coding genes. The tRNA-Ser2 could not be folded into the typical cloverleaf secondary structure because of the replacement of its dihydrouridine arm by a simple loop. A termination associated sequences (TAS) and three conserved sequence blocks (CSB1-3) were identified in the control region.

  4. Rupture propagation behavior and the largest possible earthquake induced by fluid injection into deep reservoirs

    NASA Astrophysics Data System (ADS)

    Gischig, Valentin S.

    2015-09-01

    Earthquakes caused by fluid injection into deep underground reservoirs constitute an increasingly recognized risk to populations and infrastructure. Quantitative assessment of induced seismic hazard, however, requires estimating the maximum possible magnitude earthquake that may be induced during fluid injection. Here I seek constraints on an upper limit for the largest possible earthquake using source-physics simulations that consider rate-and-state friction and hydromechanical interaction along a straight homogeneous fault. Depending on the orientation of the pressurized fault in the ambient stress field, different rupture behaviors can occur: (1) uncontrolled rupture-front propagation beyond the pressure front or (2) rupture-front propagation arresting at the pressure front. In the first case, fault properties determine the earthquake magnitude, and the upper magnitude limit may be similar to natural earthquakes. In the second case, the maximum magnitude can be controlled by carefully designing and monitoring injection and thus restricting the pressurized fault area.

  5. Dramatic inundation changes of China's two largest freshwater lakes linked to the Three Gorges Dam.

    PubMed

    Feng, Lian; Hu, Chuanmin; Chen, Xiaoling; Zhao, Xi

    2013-09-01

    Ever since its planning in the 1990s, the Three Gorges Dam (TGD) caused endless debate in China on its potential impacts on the environment and humans. However, to date, synoptic assessment of environmental changes and their potential linkage with the TGD is still lacking. Here, we combine remote sensing, meteorological, and hydrological observations to investigate the potential influence of the TGD on the downstream freshwater lakes. A 10 year Moderate Resolution Imaging Spectroradiometer (MODIS) time series from 2000 to 2009 revealed significantly decreasing trends (3.3 and 3.6%/year) in the inundation areas of the two largest freshwater lakes of China (Poyang Lake and Dongting Lake) downstream of the TGD since its impoundment in 2003, after which both relative humidity and surface runoff coefficient of the lakes' drainages also dropped dramatically. These environmental changes appear to be linked to the TGD.

  6. Evaluation of several priority pollutants in zebra mussels (Dreissena polymorpha) in the largest Italian subalpine lakes.

    PubMed

    Riva, Consuelo; Binelli, Andrea; Provini, Alfredo

    2008-02-01

    Zebra mussel (Dreissena polymorpha) has been used for the biomonitoring of several POPs (PCBs, DDTs, HCB and HCHs) in the largest Italian subalpine great lakes (Lake Maggiore, Garda, Como, Iseo and Lugano). Samplings were carried out in April 2003 at 15 locations selected according to industrial and anthropic levels of lakes. Results have pointed out high DDT levels in D. polymorpha specimens from Lake Maggiore (700-1400 ng/g lipids, 5-9 times higher than those measured in mussels of other Italian lakes), due to a contamination from a chemical plant located on one of the main lake inlet that occurred in 1996. On the contrary, PCB levels (400-2509 ng/g lipids) highlighted an overall pollution, with some sporadic peaks of contamination. Data showed a moderate increase trend compared to those found in a previous monitoring campaign carried out in 1996. Future monitoring is needed in order to confirm this tendency.

  7. Where did the money go? The cost and performance of the largest commercial sector DSM program

    SciTech Connect

    Eto, J.; Kito, S.; Shown, L.; Sonnenblick, R.

    1995-12-01

    We calculate the total resource cost (TRC) of energy savings for 40 of the largest 1992 commercial sector DSM programs. The calculation includes the participating customer`s cost contribution to energy saving measures and all utility costs, including incentives received by customers, program administrative and overhead costs, measurement and evaluation costs, and shareholder incentives paid to the utility. All savings are based on post-program savings evaluations. We find that, on a savings-weighted basis, the programs have saved energy at a cost of 3.2 {cents}/kWh. Taken as a whole, the programs have been highly cost effective when compared to the avoided costs faced by the utilities when the programs were developed. We investigate reasons for differences in program costs and examine uncertainties in current utility practices for reporting costs and evaluating savings.

  8. Perspectives from the world's largest Alzheimer's disease research conference: Stockholm, Sweden, July 2002.

    PubMed

    Ward Robinson, Jennie; Halderman, Sally

    2002-10-01

    The 8th International Conference on Alzheimer's Disease and Related Disorders, held in Stockholm, Sweden from July 20 to 25, 2002, provided an exciting forum for nearly 3700 researchers from 78 countries to present and discuss advances in dementia research on a worldwide stage. Hosted by the Alzheimer's Association (Chicago, IL), this largest dementia research conference ever held united experienced researchers and relative newcomers to the field to learn from one another, challenge one another's thinking, and explore new possibilities for collaboration. The 12-fold growth in attendance, up from 300 scientists at the 1st International Research Conference in 1988, signals the increasing global importance of Alzheimer's disease in the research community as well as among policy makers and the general public. In fact, a recent survey of older Americans by the National Council on the Aging revealed that future memory loss was the number one health worry of the American elderly population.

  9. Genetic and marine cyclonic eddy analyses on the largest macroalgal bloom in the world.

    PubMed

    Lin, Hanzhi; Jiang, Peng; Zhang, Jiaxu; Wang, Jinfeng; Qin, Song; Sun, Song

    2011-07-15

    In 2008, a massive Ulva prolifera bloom, with a 3-million-ton biomass covering an area of 1.29 × 10(4) km(2) at its largest, suddenly appeared from May to July in South Yellow Sea. The mechanism behind the rapid growth of these seaweeds was investigated. Molecular phylogenetic analysis of free-floating algal samples from the Yellow Sea suggested that U. prolifera belong to one population, and that temporary cyclonic eddies in the Yellow Sea in late spring and early summer may help promote the proliferation of this bloom by providing seaweeds with sufficient growth time, abundant nutrition, and favorable habitats. The initial investigation on the relationship between marine cyclonic eddies and the route of free-floating algae extends our knowledge on how the emergence of free-floating macroalgal blooms in coastal areas could yield a large biomass.

  10. Dramatic inundation changes of China's two largest freshwater lakes linked to the Three Gorges Dam.

    PubMed

    Feng, Lian; Hu, Chuanmin; Chen, Xiaoling; Zhao, Xi

    2013-09-01

    Ever since its planning in the 1990s, the Three Gorges Dam (TGD) caused endless debate in China on its potential impacts on the environment and humans. However, to date, synoptic assessment of environmental changes and their potential linkage with the TGD is still lacking. Here, we combine remote sensing, meteorological, and hydrological observations to investigate the potential influence of the TGD on the downstream freshwater lakes. A 10 year Moderate Resolution Imaging Spectroradiometer (MODIS) time series from 2000 to 2009 revealed significantly decreasing trends (3.3 and 3.6%/year) in the inundation areas of the two largest freshwater lakes of China (Poyang Lake and Dongting Lake) downstream of the TGD since its impoundment in 2003, after which both relative humidity and surface runoff coefficient of the lakes' drainages also dropped dramatically. These environmental changes appear to be linked to the TGD. PMID:23919680

  11. Role of macroscopic particles in deep-sea oxygen consumption.

    PubMed

    Bochdansky, Alexander B; van Aken, Hendrik M; Herndl, Gerhard J

    2010-05-01

    Macroscopic particles (>500 mum), including marine snow, large migrating zooplankton, and their fast-sinking fecal pellets, represent primary vehicles of organic carbon flux from the surface to the deep sea. In contrast, freely suspended microscopic particles such as bacteria and protists do not sink, and they contribute the largest portion of metabolism in the upper ocean. In bathy- and abyssopelagic layers of the ocean (2,000-6,000 m), however, microscopic particles may not dominate oxygen consumption. In a section across the tropical Atlantic, we show that macroscopic particle peaks occurred frequently in the deep sea, whereas microscopic particles were barely detectable. In 10 of 17 deep-sea profiles (>2,000 m depth), macroscopic particle abundances were more strongly cross-correlated with oxygen deficits than microscopic particles, suggesting that biomass bound to large particles dominates overall deep-sea metabolism.

  12. Risk Factors and Prevalence of Helicobacter pylori in Five Largest Islands of Indonesia: A Preliminary Study

    PubMed Central

    Makmun, Dadang; Nusi, Iswan Abbas; Zain, Lukman Hakim; Zulkhairi; Akil, Fardah; Uswan, Willi Brodus; Simanjuntak, David; Uchida, Tomohisa; Adi, Pangestu; Utari, Amanda Pitarini; Rezkitha, Yudith Annisa Ayu; Subsomwong, Phawinee; Nasronudin; Suzuki, Rumiko; Yamaoka, Yoshio

    2015-01-01

    The prevalence of Helicobacter pylori infection in Indonesia is still controversial and mainly investigated in the largest ethnic group, Javanese. We examined the prevalence of H. pylori infection using four different tests including culture, histology confirmed by immunohistochemistry and rapid urease test. We also analyzed risk factors associated with H. pylori infection in five largest islands in Indonesia. From January 2014–February 2015 we consecutively recruited a total of 267 patients with dyspeptic symptoms in Java, Papua, Sulawesi, Borneo and Sumatera Island. Overall, the prevalence of H. pylori infection was 22.1% (59/267). Papuan, Batak and Buginese ethnics had higher risk for H. pylori infection than Javanese, Dayak and Chinese ethnics (OR = 30.57, 6.31, 4.95; OR = 28.39, 5.81, 4.61 and OR = 23.23, 4.76, 3.77, respectively, P <0.05). The sensitivity and specificity for RUT and culture were 90.2%, 92.9% and 80.5%, 98.2%, respectively. The patients aged 50–59 years group had significantly higher H. pylori infection than 30–39 years group (OR 2.98, P = 0.05). Protestant had significantly higher H. pylori infection rate than that among Catholic (OR 4.42, P = 0.008). It was also significantly lower among peoples who used tap water as source of drinking water than from Wells/river (OR 9.67, P = 0.03). However only ethnics as become independent risk factors for H. pylori infection. Although we confirmed low prevalence of H. pylori in Javanese; predominant ethnic in Indonesia, several ethnic groups had higher risk of H. pylori infection. The age, religion and water source may implicate as a risk factor for H. pylori infection in Indonesia. PMID:26599790

  13. The Roseau Tuff: Redefining the Largest Quaternary Eruption in the Caribbean

    NASA Astrophysics Data System (ADS)

    Howe, T. M.; Lindsay, J. M.; Shane, P. A.; Schmitt, A. K.

    2012-12-01

    Although activity is the Lesser Antilles is generally characterized by dome-forming eruptions, pyroclastic flow deposits on the island of Dominica indicate that a series of Plinian eruptions occurred 20-30 ka ago. The largest pyroclastic deposit, the Roseau Tuff, outcrops on the western side of the island. Although sub-aerial material from this eruption has an estimated volume of only 3 km3 (Sigurdsson 1972), Carey and Sigurdsson (1980) correlated tephra and pyroclastic flow deposits from 26 deep sea cores to the Roseau Tuff and calculated a total erupted tephra volume of 58 km3. Based on this estimate, the Roseau Tuff eruption is considered the largest Quaternary eruption in the Caribbean. New evidence based on major and trace element whole rock data and mineral chemistry suggests that the homogeneity of eruptive deposits from southern Dominica may result in ambiguous correlations. Microprobe analyses from orthopyroxenes (En52-58), clinopyroxenes (En64-69), plagioclases (An54-92), Fe-Ti oxides, and amphiboles were used to characterize the Roseau Tuff and other pyroclastic deposits across the island. Although the data show significant differences between eruptions of different centres, multiple eruptions from individual centres appear homogenous over time spans of up to 20 ka. The homogenous character of the mineral populations implies a long-lived magma reservoir beneath each centre. However, equilibrium constraints show that mineral populations in individual eruptions are not in equilibrium. This suggests that either some mineral populations are xenocrystic or a significant amount of magma mixing occurred just prior to eruption. While the homogenous character of the eruptive deposits provides insight into the nature of andesitic volcanism in island arcs, it also limits the potential for stratigraphic correlation and calls into question the original volume estimate of the Roseau Tuff eruption.

  14. Mapping Biomass for REDD in the Largest Forest of Central Africa: the Democratic Republic of Congo

    NASA Astrophysics Data System (ADS)

    Shapiro, Aurelie; Saatchi, Sassan

    2014-05-01

    With the support of the International Climate Initiative (ICI) of the Federal Ministry of the Environment, Conservation, and Nuclear Security, the implementation of the German Development Bank KfW, the World Wide Fund for Nature (WWF) Germany, the University of California Los Angeles (UCLA) and local DRC partners will produce a national scale biomass map for the entire forest coverage of the Democratic Republic of Congo (DRC) along with feasibility assessments of different forest protection measures within a framework of a REDD+ model project. The « Carbon Map and Model (CO2M&M) » project will produce a national forest biomass map for the DRC, which will enable quantitative assessments of carbon stocks and emissions in the largest forest of the Congo Basin. This effort will support the national REDD (Reducing Emissions from Deforestation and Degradation) program in DRC, which plays a major role in sustainable development and poverty alleviation. This map will be developed from field data, complemented by airborne LiDAR (Light Detection and Ranging) and aerial photos, systematically sampled throughout the forests of the DRC and up-scaled to satellite images to accurately estimate carbon content in all forested areas. The second component of the project is to develop specific approaches for model REDD projects in key landscapes. This project represents the largest LiDAR-derived mapping effort in Africa, under unprecedented logistical constraints, which will provide one of the poorest nations in the world with the richest airborne and satellites derived datasets for analyzing forest structure, biomass and biodiversity.

  15. Ceres In Context: What the Rest of the Asteroid Population Tells Us About Its Largest Member

    NASA Astrophysics Data System (ADS)

    Rivkin, A.

    2015-12-01

    Ceres is famously the largest object in the asteroid belt. Over the course of the last 215 years it has been considered everything from a unique protoplanet (or indeed full-fledged "planet") to a large but run-of-the-mill piece of rock. Over the last decade, models of Ceres' thermal history and shape measurements based on HST imagery have led to the recognition that Ceres is a differentiated object, and likely an ice-rich one. In the last year the Dawn spacecraft has provided unprecedented views of Ceres' surface and combined with data from observational facilities like Herschel and countless telescopes it has shown the varied nature of its geology and ongoing processes. Even given these recent results, Ceres remains an inhabitant of the asteroid belt, existing in the ambient environment and affected by impactors, micrometeorites, solar wind, and other factors. While we only have spacecraft imagery from a very small number of targets, we do have a wealth of Earth-based data from the objects that have shared space with Ceres for billions of years. The insights gained from studying these objects can be applied to Ceres to understand its context and nature. Similarly, what we learn at Ceres will be applicable in many ways to other objects, particularly the twenty or so largest asteroids, which tend to be low-albedo, water-rich bodies. I will discuss our current understanding of the asteroids, particularly those that share important characteristics with Ceres, and focus on what we can learn about Ceres from these bodies.

  16. Climate-driven changes in riverine inputs affecting the stoichiometry of Earth's largest lake

    NASA Astrophysics Data System (ADS)

    Sterner, R.; Small, G. E.

    2014-12-01

    Lake Superior, Earth's largest lake by area, has seen a steady increase in nitrate levels over the past century, while phosphorus remains exceedingly low, resulting in an increasingly imbalanced stoichiometry. Although its ratio of watershed area:lake area is relatively small, rivers emptying into Lake Superior could be important drivers of long-term changes in lake stoichiometry. To better assess how the Lake Superior watershed affects its stoichiometry, we examined the chemistry of two of its largest tributaries, the Saint Louis River and the Nipigon River, at their confluences with Lake Superior. Both of these rivers have high dissolved organic carbon (DOC) but low nitrate (NO3) concentrations relative to the lake. Using simple mixing models, we found these nearshore confluences to create sinks of lake NO3 as a result of relatively high rates of denitrification. Climate change is altering the amounts and patterns of delivery of materials from land to lakes and we also examined the plume from a June, 2012 100-year flood in the Saint Louis River. Three days after this historic rain event, we found elevated chlorophyll levels throughout the plume, up to 5-fold higher than in the open lake. Combining our samples with satellite imagery, we conservatively estimate that this plume contained 598,000 kg of phosphorus in dissolved and particulate form, or 40% of the average annual P input to the lake. If storm events such as this occur with increasing frequency as predicted in climate change scenarios, the lake's productivity may increase and stoichiometry could become more balanced, through greater P input and increased N retention due to sedimentation and denitrification.

  17. Ages and Loads of Riverine Carbon of the Five Largest Rivers in South Korea

    NASA Astrophysics Data System (ADS)

    Lee, E. J.; Shin, Y.; Oh, N. H.

    2015-12-01

    Understanding the quantity and quality of riverine carbon is crucial to predict the changes of the regional carbon cycle and to efficiently manage drinking water quality. We investigated both the loads and ages of carbon exported by the five largest rivers in South Korea using seasonal sampling and dual carbon isotope analysis for 2012 - 2013. Annually a total of 581 Gg of carbon (DIC, DOC, and POC combined) was transported to the ocean through the five rivers, releasing 7.6, 1.7, and 0.8 g-C m-2 yr-1 of DIC, DOC, and POC, respectively, which accounted for 80%, 14%, and 6% of the annual loads of riverine carbon, respectively. About 37-45% of annual riverine DIC loads, 37-51% of DOC loads, and 33-47% of POC loads were released from the basins during the summer monsoon (June - August) indicating strong effects of precipitation in the riverine carbon export. Modern to ~1,020 years old carbon was released from the five river basins. The δDI13C and ΔDI14C showed a negative correlation in each river whereas no consistent correlation was observed between δDO13C and ΔDO14C, suggesting a large variation in DOC sources. Riverine POC load increased sharply after a typhoon and ΔPO14C was higher in summer than winter in the five rivers. The results suggested that both quantity and quality of riverine carbon released from the five largest basins could be strongly influenced by the Asian monsoon climates and that relatively young dissolved carbon could be predominantly released as the intensity and frequency of storms increase.

  18. Risk Factors and Prevalence of Helicobacter pylori in Five Largest Islands of Indonesia: A Preliminary Study.

    PubMed

    Syam, Ari Fahrial; Miftahussurur, Muhammad; Makmun, Dadang; Nusi, Iswan Abbas; Zain, Lukman Hakim; Zulkhairi; Akil, Fardah; Uswan, Willi Brodus; Simanjuntak, David; Uchida, Tomohisa; Adi, Pangestu; Utari, Amanda Pitarini; Rezkitha, Yudith Annisa Ayu; Subsomwong, Phawinee; Nasronudin; Suzuki, Rumiko; Yamaoka, Yoshio

    2015-01-01

    The prevalence of Helicobacter pylori infection in Indonesia is still controversial and mainly investigated in the largest ethnic group, Javanese. We examined the prevalence of H. pylori infection using four different tests including culture, histology confirmed by immunohistochemistry and rapid urease test. We also analyzed risk factors associated with H. pylori infection in five largest islands in Indonesia. From January 2014-February 2015 we consecutively recruited a total of 267 patients with dyspeptic symptoms in Java, Papua, Sulawesi, Borneo and Sumatera Island. Overall, the prevalence of H. pylori infection was 22.1% (59/267). Papuan, Batak and Buginese ethnics had higher risk for H. pylori infection than Javanese, Dayak and Chinese ethnics (OR = 30.57, 6.31, 4.95; OR = 28.39, 5.81, 4.61 and OR = 23.23, 4.76, 3.77, respectively, P <0.05). The sensitivity and specificity for RUT and culture were 90.2%, 92.9% and 80.5%, 98.2%, respectively. The patients aged 50-59 years group had significantly higher H. pylori infection than 30-39 years group (OR 2.98, P = 0.05). Protestant had significantly higher H. pylori infection rate than that among Catholic (OR 4.42, P = 0.008). It was also significantly lower among peoples who used tap water as source of drinking water than from Wells/river (OR 9.67, P = 0.03). However only ethnics as become independent risk factors for H. pylori infection. Although we confirmed low prevalence of H. pylori in Javanese; predominant ethnic in Indonesia, several ethnic groups had higher risk of H. pylori infection. The age, religion and water source may implicate as a risk factor for H. pylori infection in Indonesia.

  19. Risk Factors and Prevalence of Helicobacter pylori in Five Largest Islands of Indonesia: A Preliminary Study.

    PubMed

    Syam, Ari Fahrial; Miftahussurur, Muhammad; Makmun, Dadang; Nusi, Iswan Abbas; Zain, Lukman Hakim; Zulkhairi; Akil, Fardah; Uswan, Willi Brodus; Simanjuntak, David; Uchida, Tomohisa; Adi, Pangestu; Utari, Amanda Pitarini; Rezkitha, Yudith Annisa Ayu; Subsomwong, Phawinee; Nasronudin; Suzuki, Rumiko; Yamaoka, Yoshio

    2015-01-01

    The prevalence of Helicobacter pylori infection in Indonesia is still controversial and mainly investigated in the largest ethnic group, Javanese. We examined the prevalence of H. pylori infection using four different tests including culture, histology confirmed by immunohistochemistry and rapid urease test. We also analyzed risk factors associated with H. pylori infection in five largest islands in Indonesia. From January 2014-February 2015 we consecutively recruited a total of 267 patients with dyspeptic symptoms in Java, Papua, Sulawesi, Borneo and Sumatera Island. Overall, the prevalence of H. pylori infection was 22.1% (59/267). Papuan, Batak and Buginese ethnics had higher risk for H. pylori infection than Javanese, Dayak and Chinese ethnics (OR = 30.57, 6.31, 4.95; OR = 28.39, 5.81, 4.61 and OR = 23.23, 4.76, 3.77, respectively, P <0.05). The sensitivity and specificity for RUT and culture were 90.2%, 92.9% and 80.5%, 98.2%, respectively. The patients aged 50-59 years group had significantly higher H. pylori infection than 30-39 years group (OR 2.98, P = 0.05). Protestant had significantly higher H. pylori infection rate than that among Catholic (OR 4.42, P = 0.008). It was also significantly lower among peoples who used tap water as source of drinking water than from Wells/river (OR 9.67, P = 0.03). However only ethnics as become independent risk factors for H. pylori infection. Although we confirmed low prevalence of H. pylori in Javanese; predominant ethnic in Indonesia, several ethnic groups had higher risk of H. pylori infection. The age, religion and water source may implicate as a risk factor for H. pylori infection in Indonesia. PMID:26599790

  20. Carbonaceous Particles Production in a Sputtering Discharge

    SciTech Connect

    Dominique, Claire; Sant, Marco; Arnas, Cecile

    2005-10-31

    Spherical dust particles have been produced in argon glow discharge by sputtering of a graphite cathode. Their size varies from 40 to 200 nm depending on the distance between the two electrodes and the largest ones have a cauliflower shape. Simulations giving the evolution of the energy distribution of sputtered carbon atoms suggest a mechanism of growth by carbon vapour condensation. The chemical composition and structure of particles have been investigated by infrared spectroscopy and appear to be a complex arrangement of the carbon atoms and hetero-atoms.

  1. The ash deposits of the 4200 BP Cerro Blanco eruption: the largest Holocene eruption of the Central Andes

    NASA Astrophysics Data System (ADS)

    Fernandez-Turiel, Jose-Luis; Saavedra, Julio; Perez-Torrado, Francisco-Jose; Rodriguez-Gonzalez, Alejandro; Carracedo, Juan-Carlos; Lobo, Agustin; Rejas, Marta; Gallardo, Juan-Fernando; Osterrieth, Margarita; Carrizo, Julieta; Esteban, Graciela; Martinez, Luis-Dante; Gil, Raul-Andres; Ratto, Norma; Baez, Walter

    2015-04-01

    We present new data about a major eruption -spreading approx. 110 km3 ashes over 440.000 km2- long thought to have occurred around 4200 years ago in the Cerro Blanco Volcanic Complex (CBVC) in the Central Andes of NW Argentina (Southern Puna, 26°45' S, 67°45' W). This eruption may be the biggest during the past five millennia in the Central Volcanic Zone of the Andes, and possibly one of the largest Holocene eruptions in the world. Discrimination and correlation of pyroclastic deposits of this eruption of Cerro Blanco was conducted comparing samples of proximal (domes, pyroclastic flow and fall deposits) with distal ash fall deposits (up to 400 km from de vent). They have been characterized using optical and electron microscopy (SEM), X-ray diffraction, particle-size distribution by laser diffraction and electron microprobe and HR-ICP-MS with laser ablation for major and trace element composition of glass, feldspars and biotite. New and published 14C ages were calibrated using Bayesian statistics. An one-at-a-time inversion method was used to reconstruct the eruption conditions using the Tephra2 code (Bonadonna et al. 2010, https://vhub.org/resources/tephra2). This method allowed setting the main features of the eruption that explains the field observations in terms of thickness and grain size distributions of the ash fall deposit. The main arguments that justify the correlation are four: 1) Compositional coincidence for glass, feldspars, and biotite in proximal and distal materials; 2) Stratigraphic and geomorphological relationships, including structure and thickness variation of the distal deposits; 3) Geochronological consistency, matching proximal and distal ages; and 4) Geographical distribution of correlated outcrops in relation to the eruption centre at the coordinates of Cerro Blanco. With a magnitude of 7.0 and a volcanic explosivity index or VEI 7, this eruption of ~4200 BP at Cerro Blanco is the largest in the last five millennia known in the Central

  2. The largest caldera-forming eruptions in Kamchatka: geochronology, definition, volumes, and petrologic and isotopic investigation

    NASA Astrophysics Data System (ADS)

    Bindeman, I. N.; Leonov, V.; Shipley, N. K.

    2012-12-01

    The continental arc of Kamchatka has the highest magma production rates in the world and arguably the largest number of calderas per unit arc length, which are in response to rapid head-on collision at a subduction angle of ~45°. Kamchatkan caldera sizes and volumes of ignimbrite eruptions some of the world's largest, but rapid volcanic and tectonic uplift and burial, rapid erosion rates, and bulldozing effects of multiple glaciations have reshaped Pleistocene and older calderas. This has left behind remnants of isolated, yet thick, often intracaldera-only ignimbrite sequences. While the contribution of Kamchatkan arc volcanism to global Pleistocene volcanism and oscillating Pleistocene climate is of prime importance, the combination of harsh climate, remoteness, poor road infrastructure, and heavy vegetation cover make fieldwork and recognition of caldera volcanics challenging. We present new results of geologic, geochronologic, geochemical and isotopic investigation of two of the largest caldera in Kamchatka - Pauzhetka (27x18km, 0.44Ma) and Karymshina (30x16km, 1.78 Ma). In both places large-volume climactic ignimbrites are represented by quartz-, zircon-, and biotite- bearing, but sanidine-free rhyolitic to high-silica rhyolitic tuffs. These compositional characteristics and evolved trace elemental ratios indicate a high degree of differentiation rarely achieved in other silicic rocks of the Kamchatka arc and worldwide. Crystallinity of ignimbrites ranges from high (35%) to relatively low (10%). Preliminary investigation of chemical and isotopic variations in pre-caldera sequences in both calderas demonstrates diverse peripheral eruptions of basaltic to dacitic compositions, with predominance of the former. The search for the precursor high-silica rhyolite continues. At Karymshina, pre-caldera magmas have a greater diversity of Sr (0,703283-0,703552) and Nd (0,513046- 0,512962) ratios, and moderately diverse and elevated δ18O values (5.5-7.5‰). In contrast

  3. Foundations and Public Information: Sunshine or Shadow? Preliminary Findings from a Study of the Public Information Accountability of the Country's Largest Foundations.

    ERIC Educational Resources Information Center

    Bruce, Ellen; And Others

    The types of written information that the largest foundations in the United States voluntarily make available to the public were studied. Of the 208 foundations contacted, 150 were the largest grant-making foundations, 30 were the largest community foundations, and 28 were the largest corporate foundations. The response rate to written and…

  4. A Search for Free Fractional Electric Charge Elementary Particles

    SciTech Connect

    Halyo, Valerie

    2000-12-04

    A direct search was carried out in bulk matter for free fractional electric charge elementary particles using the largest mass single sample ever studied--about 17.4 mg of silicone oil. The search used an improved and highly automated Millikan oil drop technique. No evidence for fractional charge particles was found. The concentration of particles with fractional charge more than 0.16 e (e being the magnitude of the electron charge) from the nearest integer charge is less than 4.71 x 10{sup -22} particles per nucleon with 95% confidence.

  5. A Search for Free Fractional Electric Charge Elementary Particles

    SciTech Connect

    Halyo, Valerie

    2000-12-04

    A direct search was carried out in bulk matter for free fractional electric charge elementary particles using the largest mass single sample ever studied| about 17.4 mg of silicone oil. The search used an improved and highly automated Millikan oil drop technique. No evidence for fractional charge particles was found. The concentration of particles with fractional charge more than 0.16 e (e being the magnitude of the electron charge) from the nearest integer charge is less than 4.71 x 10{sup -22} particles per nucleon with 95% confidence.

  6. Search for free fractional electric charge elementary particles

    SciTech Connect

    Halyo, V.

    1999-10-29

    The authors have carried out a direct search in bulk matter for free fractional electric charge elementary particles using the largest mass single sample ever studied--about 17.4 mg of silicone oil. The search used an improved and highly automated Millikan oil drop technique. No evidence for fractional charge particles was found. The concentration of particles with fractional charge more than 0.16 e (e being the magnitude of the electron charge) from the nearest integer charge is less than 4.71 x 10{sup {minus}22} particles per nucleon with 95% confidence.

  7. The Million-Body Problem: Particle Simulations in Astrophysics

    ScienceCinema

    Rasio, Fred [Northwestern University

    2016-07-12

    Computer simulations using particles play a key role in astrophysics. They are widely used to study problems across the entire range of astrophysical scales, from the dynamics of stars, gaseous nebulae, and galaxies, to the formation of the largest-scale structures in the universe. The 'particles' can be anything from elementary particles to macroscopic fluid elements, entire stars, or even entire galaxies. Using particle simulations as a common thread, this talk will present an overview of computational astrophysics research currently done in our theory group at Northwestern. Topics will include stellar collisions and the gravothermal catastrophe in dense star clusters.

  8. Particle Acceleration by Cme-driven Shock Waves

    NASA Technical Reports Server (NTRS)

    Reames, Donald V.

    1999-01-01

    In the largest solar energetic particle (SEP) events, acceleration occurs at shock waves driven out from the Sun by coronal mass ejections (CMEs). Peak particle intensities are a strong function of CME speed, although the intensities, spectra, and angular distributions of particles escaping the shock are highly modified by scattering on Alfven waves produced by the streaming particles themselves. Element abundances vary in complex ways because ions with different values of Q/A resonate with different parts of the wave spectrum, which varies with space and time. Just recently, we have begun to model these systematic variations theoretically and to explore other consequences of proton-generated waves.

  9. Lessons From the Largest Historic Floods Documented by the U.S. Geological Survey

    NASA Astrophysics Data System (ADS)

    Costa, J. E.

    2003-12-01

    A recent controversy over the flood risk downstream from a USGS streamgaging station in southern California that recorded a large debris flow led to the decision to closely examine a sample of the largest floods documented in the US. Twenty-nine floods that define the envelope curve of the largest rainfall-runoff floods were examined in detail, including field visits. These floods have a profound impact on local, regional, and national interpretations of potential peak discharges and flood risk. These 29 floods occured throughout the US from the northern Chesapeake Bay in Maryland to Kauai, Hawaii, and over time from 1935-1978. Methods used to compute peak discharges were slope-area (21/29), culvert computations (2/29), measurements lost or not available for study (2/29), bridge contraction, culvert flow, and flow over road (1/29), rating curve extension (1/29), current meter measurement (1/29), and rating curve and current meter measurement (1/29). While field methods and tools have improved significantly over the last 70 years (e.g. total stations, GPS, GIS, hydroacoustics, digital plotters and computer programs like SAC and CAP), the primary methods of hydraulic analysis for indirect measurements of outstanding floods has not changed: today flow is still assumed to be 1-D and gradually varied. Unsteady or multi-dimensional flow models are rarely if ever used to determine peak discharges. Problems identified in this sample of 29 floods include debris flows misidentified as water floods, small drainage areas determined from small-scale maps and mislocated sites, high-water marks set by transient hydraulic phenomena, possibility of disconnected flow surfaces, scour assumptions in sand channels, poor site selection, incorrect approach angle for road overflow, and missing or lost records. Each published flood magnitude was checked by applying modern computer models with original field data, or by re-calculating computations. Four of 29 floods in this sample were

  10. Hydraulics and basin morphometry of the largest flash floods in the conterminous United States

    USGS Publications Warehouse

    Costa, J.E.

    1987-01-01

    The maximum rainfall-runoff floods measured by indirect methods in small basins (0.39-370 km2) in the conterminous United States are examined. This analysis identified twelve floods that were the largest ever measured. These floods all occurred in semiarid to arid areas. For eleven of the twelve largest rainfall-runoff floods measured in small basins by the slope-area method, values of hydraulic depth; hydraulic radius; width-depth ratio; n value; mean velocity; velocity-head coefficient; Froude number; water-surface, energy, and channel slopes; shear stress; and unit stream power are tabulated. Estimated composite n values weighted by subsection conveyance range from 0.028 to 0.048 with a mean of 0.038. Mean velocities ranged from 3.47 to 9.97 m s-1. Froude numbers ranged from 0.81 to 2.49, with 9 of 12 floods having values greater than 1.00. Water-surface, energy, and channel slopes vary considerably for each flood. Energy slope always was less than water-surface slope by values of 1-104%. Channel slope was greater than energy slope in eight floods. Shear stresses ranged between 61 and 855 N m-2, and unit stream power from 212 to 8131 w m-1. Floods in these small basins produced shear stresses and unit stream powers several hundred times greater than floods in large rivers. Floods on other small streams, with smaller unit discharges, produced greater shear stresses and stream powers. This indicates that the force of a flood is controlled by the depth-slope product, not absolute discharge. In the twelve watersheds studied, basin relief ranged from 165 to 1280 m, elongation ratios ranged from 0.55 to 0.80, the number of first-order streams (basin magnitude) ranged from 10 to 4297, drainage density ranged from 4.1 to 10.9 km km-2, basin slope ranged from 0.0043 to 0.2486, relief ratio ranged from 0.0097 to 0.34, ruggedness number ranged from 0.69 to 7.17, and first-order channel frequency ranged from 5.1 to 38.6 km-2. Elongation ratios were larger, and drainage

  11. Genesis of the largest Amazonian wetland in northern Brazil inferred by morphology and gravity anomalies

    NASA Astrophysics Data System (ADS)

    Rossetti, Dilce de Fátima; Cassola Molina, Eder; Cremon, Édipo Henrique

    2016-08-01

    The Pantanal Setentrional (PS) is the second largest wetland in Brazil, occurring in a region of northern Amazonia previously regarded as part of the intracratonic Solimões Basin. However, while Paleozoic to Neogene strata are recorded in this basin, the PS constitutes a broad region with an expressive record of only Late Pleistocene and Holocene deposits. The hypothesis investigated in the present work is if these younger deposits were formed within a sedimentary basin having a geological history separated from the Solimões Basin. Due to the location in a remote region of low accessibility, the sedimentary fill of the PS wetland remains largely unknown in subsurface. In the present work, we combine geomorphological and gravity data acquired on a global basis by several satellite gravity missions to approach the geological context of this region. The results revealed a wetland characterized in surface by a low-lying terrain with wedge shape and concave-up geometry that is in sharp contact with highland areas of Precambrian rocks of the Guiana Shield. Such contact is defined by a series of mainly NE- or NW-trending straight lineaments that eventually extend into both the Guiana Shield and the PS wetland. Also of relevance is that a great part of the PS wetland sedimentary cover consists of dominantly sandy deposits preserved as residual paleo-landforms with triangular shapes previously related to megafan depositional systems. These are distributed radially at the northern margin of the PS, with axis toward basement rocks and fringes toward the wetland's center, the latter containing the largest megafan landform. The analysis of gravity anomaly data revealed a main NNE-trending chain ∼500 km in length defined by high gravity values (i.e., up to 60 mGal); these are bounded by negative anomalies as low as -90 mGal. The chain with positive gravity anomaly marks the center of a subsiding area having a geological evolution that differs from the adjacent intracratonic

  12. Demobilization of the World's Largest Decontamination and Decommissioning Project Project Closeout of three Gaseous Diffusion Plants for Re-industrialization

    SciTech Connect

    Stevens, J.L.; Miller, JA.

    2006-07-01

    This paper describes the challenges and lessons learned from the demobilization of the world' largest, and first, successfully decontaminated and decommissioned project. These gaseous diffusion plants are the first plants to be successfully decommissioned in the United States. (authors)

  13. Paramyxovirus Glycoprotein Incorporation, Assembly and Budding: A Three Way Dance for Infectious Particle Production

    PubMed Central

    El Najjar, Farah; Schmitt, Anthony P.; Dutch, Rebecca Ellis

    2014-01-01

    Paramyxoviruses are a family of negative sense RNA viruses whose members cause serious diseases in humans, such as measles virus, mumps virus and respiratory syncytial virus; and in animals, such as Newcastle disease virus and rinderpest virus. Paramyxovirus particles form by assembly of the viral matrix protein, the ribonucleoprotein complex and the surface glycoproteins at the plasma membrane of infected cells and subsequent viral budding. Two major glycoproteins expressed on the viral envelope, the attachment protein and the fusion protein, promote attachment of the virus to host cells and subsequent virus-cell membrane fusion. Incorporation of the surface glycoproteins into infectious progeny particles requires coordinated interplay between the three viral structural components, driven primarily by the matrix protein. In this review, we discuss recent progress in understanding the contributions of the matrix protein and glycoproteins in driving paramyxovirus assembly and budding while focusing on the viral protein interactions underlying this process and the intracellular trafficking pathways for targeting viral components to assembly sites. Differences in the mechanisms of particle production among the different family members will be highlighted throughout. PMID:25105277

  14. The global distribution of largest, deepest, and most intense precipitation systems

    NASA Astrophysics Data System (ADS)

    Liu, Chuntao; Zipser, Edward J.

    2015-05-01

    By grouping the contiguous precipitating area detected by the precipitation radar on board the Global Precipitation Mission (GPM) core satellite, snapshots of precipitation systems are summarized as precipitation features (PFs), and their properties are cataloged from 1 year GPM observations. These PFs are categorized by their area and depth and convective intensity based on the 20 and 40 dBZ radar echo tops, respectively. The largest PFs are found mainly over ocean at the mid-high latitudes, especially over southern ocean. The deepest PFs are mainly over tropical land, the West Pacific Warm Pool, and the Great Plains of the United States and Argentina. The most convectively intense PFs are dominant over land regions, including midlatitude and high latitude. The zonal precipitation contribution from extremely large precipitation systems is greater in midlatitude and high latitude than in the tropics. These extreme precipitation systems are rare but contribute significantly to the global precipitation. It is important to include their impacts in global climate models to correctly describe the global water cycle.

  15. Epidemiological study of hepatitis A, B and C in the largest Afro-Brazilian isolated community.

    PubMed

    Matos, Márcia A D; Reis, Nádia Rúbia S; Kozlowski, Aline G; Teles, Sheila A; Motta-Castro, Ana Rita C; Mello, Francisco C A; Gomes, Selma A; Martins, Regina M B

    2009-09-01

    This study was conducted to estimate the prevalence and molecular epidemiological features of viral hepatitis A, B and C in the Kalunga population, which represents the largest Afro-Brazilian isolated community. Among 878 individuals studied, the overall prevalence of anti-hepatitis A virus antibodies was 80.9%, with a significant rise from 44.8% to near 100% between the first and fourth decade of life. Rates for hepatitis B surface antigen (HBsAg) and antibody to hepatitis B core antigen (anti-HBc) of 1.8% and 35.4%, respectively, were found. Increasing age, male gender, illiteracy and history of multiple sexual partners were associated with hepatitis B virus (HBV) infection. An occult HBV infection rate of 1.7% (5/295) was found among anti-HBc-positive individuals. HBV genotype A (subtype Aa) was dominant in this community. Only 5/878 individuals (0.6%) were positive for anti-hepatitis C virus (HCV). HCV RNA was detected in three of them, who were infected with genotype 1 (subtype 1a). These findings point out high, intermediate and low endemicity for hepatitis A, B and C, respectively, in the Kalunga community in Brazil. Circulation of HBV genotype A (subtype Aa) in this Afro-Brazilian isolated community indicates the introduction of this virus during the slave trade from Africa to Brazil.

  16. Fire carbon emissions over maritime southeast Asia in 2015 largest since 1997.

    PubMed

    Huijnen, V; Wooster, M J; Kaiser, J W; Gaveau, D L A; Flemming, J; Parrington, M; Inness, A; Murdiyarso, D; Main, B; van Weele, M

    2016-01-01

    In September and October 2015 widespread forest and peatland fires burned over large parts of maritime southeast Asia, most notably Indonesia, releasing large amounts of terrestrially-stored carbon into the atmosphere, primarily in the form of CO2, CO and CH4. With a mean emission rate of 11.3 Tg CO2 per day during Sept-Oct 2015, emissions from these fires exceeded the fossil fuel CO2 release rate of the European Union (EU28) (8.9 Tg CO2 per day). Although seasonal fires are a frequent occurrence in the human modified landscapes found in Indonesia, the extent of the 2015 fires was greatly inflated by an extended drought period associated with a strong El Niño. We estimate carbon emissions from the 2015 fires to be the largest seen in maritime southeast Asia since those associated with the record breaking El Niño of 1997. Compared to that event, a much better constrained regional total carbon emission estimate can be made for the 2015 fires through the use of present-day satellite observations of the fire's radiative power output and atmospheric CO concentrations, processed using the modelling and assimilation framework of the Copernicus Atmosphere Monitoring Service (CAMS) and combined with unique in situ smoke measurements made on Kalimantan. PMID:27241616

  17. Ticks associated with the three largest wild ruminant species in southern Africa.

    PubMed

    Horak, I G; Golezardy, H; Uys, A C

    2007-09-01

    The objective of this study was to assess the host status of the three largest southern African wild ruminants, namely giraffes, Giraffa camelopardalis, African buffaloes, Syncerus caffer, and eland, Taurotragus oryx for ixodid ticks. To this end recently acquired unpublished data are added here to already published findings on the tick burdens of these animals, and the total numbers and species of ticks recorded on 12 giraffes, 18 buffaloes and 36 eland are summarized and discussed. Twenty-eight ixodid tick species were recovered. All stages of development of ten species, namely Amblyomma hebraeum, Rhipicephalus (Boophilus) decoloratus, Haemaphysalis silacea, Ixodes pilosus group, Margaropus winthemi, Rhipicephalus appendiculatus, Rhipicephalus evertsi evertsi, Rhipicephalus glabroscutatum, Rhipicephalus maculatus and Rhipicephalus muehlensi were collected. The adults of 13 species, of which the immature stages use small mammals as hosts, namely Haemaphysalis aciculifer, Hyalomma glabrum, Hyalomma marginatum rufipes, Hyalomma truncatum, Ixodes rubicundus, Rhipicephalus capensis, Rhipicephalus exophthalmos, Rhipicephalus follis, Rhipicephalus gertrudae, Rhipicephalus lounsburyi, Rhipicephalus lunulatus, Rhipicephalus pravus group and Rhipicephalus simus, were also collected.

  18. Sustained Presence of Cutaneous Leishmaniasis in Urban Manaus, the Largest Human Settlement in the Amazon.

    PubMed

    Benício, Ednelza; Cordeiro, Mayara; Monteiro, Hannah; Saboia Moura, Marco Antônio; Oliveira, Cintia; Nunes Gadelha, Ellen Pricilla; Chrusciak-Talhari, Anette; Talhari, Carolina; de Lima Ferreira, Luiz Carlos; Mira, Marcelo Távora; Lima Machado, Paulo Roberto; Talhari, Sinésio; Schriefer, Albert

    2015-12-01

    The Amazon is responsible for approximately 40% of the American tegumentary leishmaniasis (ATL) in Brazil. Herein the sustained presence of ATL in Manaus, the largest settlement in the Amazon, was investigated. Records of notification of historic cases, and data from cases prospectively enrolled in the Tropical Medicine Foundation of the Amazonas State were used. Geographic coordinates of prospective patients' living sites were used to detect inner-city clusters of ATL. Infecting Leishmania species was determined by polymerase chain reaction. Among prospectively enrolled subjects, 94.8% were infected with Leishmania (Viannia) guyanensis, 76.7% were male, 30.2% were 0-20 years old, and 69.8% had an urban residence. Historic cases showed a profile similar to that of prospectively enrolled subjects. Several clusters of ATL, widely distributed within the city of Manaus, could be detected. In conclusion, there was a high frequency of disease in young age groups and cases clustered in urban neighborhoods. It cannot be determined from these data whether transmission of these cases occurred within or outside the city of Manaus.

  19. Unveiling the formation route of the largest galaxies in the Universe

    NASA Astrophysics Data System (ADS)

    Perea, Jaime D.; Solanes, José M.

    2016-09-01

    Observational evidence indicates that the role of gas is secondary to that of gravity in the formation of the most luminous spheroids inhabiting the centres of galaxy associations, as originally conjectured in the late 80s/early 90s. However, attempts to explain the origin of the Fundamental Plane (FP) of massive early-type galaxies (ETGs) - a tilted version of the scaling relation connecting the size, velocity dispersion and mass of virialized homologous systems - based on sequences of pairwise mergers, have systematically concluded that dissipation cannot be ignored. We use controlled simulations of the pre-virialization stage of galaxy groups to show that multiple collisionless merging is capable of creating realistic first-ranked galaxies. Our mock remnants define a thin FP that perfectly fits data from all kinds of giant ETGs in the local volume, showing the existence of a unified relationship for these systems. High-ranked galaxies occupy in the FP different areas than standard objects, a segregation which is viewed essentially as zero-point offsets in the 2D correlations arising from standard projections of this plane. Our findings make a strong case for considering hierarchical dissipationless merging a viable route for the formation of the largest galaxies in the Universe.

  20. Nutritional properties of the largest bamboo fruit Melocanna baccifera and its ecological significance

    NASA Astrophysics Data System (ADS)

    Govindan, Balaji; Johnson, Anil John; Nair, Sadasivan Nair Ajikumaran; Gopakumar, Bhaskaran; Mallampalli, Karuna Sri Lakshmi; Venkataraman, Ramaswamy; Koshy, Konnath Chacko; Baby, Sabulal

    2016-05-01

    Melocanna baccifera is a unique bamboo which produces the largest fruits in the grass family. Its gregarious flowering once in 45–50 years in north east India and adjacent regions is a botanical enigma, resulting in a glut of fruits. Proper utilization of M. baccifera fruits is not extant, and huge quantities of fruits are left underexploited due to lack of scientific information on their chemical composition and nutritional potential. Here we report the nutritional properties of M. baccifera fruits, and the ecological significance of its fruiting. This pear-shaped, fleshy bamboo fruit is rich in amino acids (lysine, glutamic acid), sugars (sucrose, glucose, fructose) and phenolics (ferulic acid). Protein content (free, bound) in M. baccifera fruits is very low. Fruits are rich in saturated fatty acids (palmitic acid), minerals (potassium), and only B series vitamins (B3) are detected in them. Rat feeding experiments showed that M. baccifera fruit alone is not a complete food, but with other protein supplements, it is a valuable food additive. This study could lead to better utilization of M. baccifera fruits during future flowering/fruiting events. These results could also help in the successful management of rodent outbreaks and other ecological problems associated with M. baccifera fruiting.

  1. Characteristics and Trends in Hypnotics Consumption in the Largest Health Care System in Israel

    PubMed Central

    Rennert, G.; Stein, N.; Landsman, K.

    2016-01-01

    Objectives. To quantify and characterize hypnotics consumption habits among adult patients insured by Clalit Health Services (CHS), the largest health care provider in Israel, in 2000 and 2010. Methods. A retrospective analysis of CHS computerized pharmacy records. Data were collected for all patients over the age of 18 years who were prescribed hypnotics in 2000 and in 2010. Results. Sleep medications were consumed by 8.7% of the adult CHS population in 2000 and by 9.6% in 2010. About one-quarter of consumers were treated for more than 6 months in both years. Multiple sleeping drugs were consumed more often in 2010 (45.2%) than a decade before (22%). While in 2000 benzodiazepines accounted for 84.5% of hypnotics, in 2010 this was reduced to 73.7% (p < 0.05). Of all patients treated for longer than 6 months only 11% in 2000 and 9% in 2010 required a dose escalation suggesting the absence of tolerance. Conclusions. Nine percent of the Israeli population consumes hypnotics. There is a major increase in prescription of combination of medications between 2000 and 2010, with an increase in Z class medications use and reduction in benzodiazepines. Most patients chronically treated did not escalate dosage, suggesting the absence of tolerance. PMID:27660727

  2. Anatomizing one of the largest saltwater inflows into the Baltic Sea in December 2014

    NASA Astrophysics Data System (ADS)

    Gräwe, Ulf; Naumann, Michael; Mohrholz, Volker; Burchard, Hans

    2015-11-01

    In December 2014, an exceptional inflow event into the Baltic Sea was observed, a so-called Major Baltic Inflow (MBI). Such inflow events are important for the deep water ventilation in the Baltic Sea and typically occur every 3-10 years. Based on first observational data sets, this inflow had been ranked as the third largest since 100 years. With the help of a multinested modeling system, reaching from the North Atlantic (8 km resolution) to the Western Baltic Sea (600 m resolution, which is baroclinic eddy resolving), this event is reproduced in detail. The model gave a slightly lower salt transport of 3.8 Gt, compared to the observational estimate of four Gt. Moreover, by using passive tracers to mark the different inflowing water masses, including an age tracer, the inflowing water masses could be tracked and their paths and timing through the different basins could be reproduced and investigated. The analysis is supported by the recently developed Total Exchange Flow (TEF) to quantify the volume transport in different salinity classes. To account for uncertainties in the modeled velocity and tracer fields, a Monte Carlo Analysis (MCA) is applied to correct possible biases and errors. With the help of the MCA, 95% confidence intervals are computed for the transport estimates. Based on the MCA, the "best guess" of the volume transport is 291.0 ± 13.65 km3 and 3.89 ± 0.18 Gt for the total salt transport.

  3. Fire carbon emissions over maritime southeast Asia in 2015 largest since 1997

    NASA Astrophysics Data System (ADS)

    Huijnen, V.; Wooster, M. J.; Kaiser, J. W.; Gaveau, D. L. A.; Flemming, J.; Parrington, M.; Inness, A.; Murdiyarso, D.; Main, B.; van Weele, M.

    2016-05-01

    In September and October 2015 widespread forest and peatland fires burned over large parts of maritime southeast Asia, most notably Indonesia, releasing large amounts of terrestrially-stored carbon into the atmosphere, primarily in the form of CO2, CO and CH4. With a mean emission rate of 11.3 Tg CO2 per day during Sept-Oct 2015, emissions from these fires exceeded the fossil fuel CO2 release rate of the European Union (EU28) (8.9 Tg CO2 per day). Although seasonal fires are a frequent occurrence in the human modified landscapes found in Indonesia, the extent of the 2015 fires was greatly inflated by an extended drought period associated with a strong El Niño. We estimate carbon emissions from the 2015 fires to be the largest seen in maritime southeast Asia since those associated with the record breaking El Niño of 1997. Compared to that event, a much better constrained regional total carbon emission estimate can be made for the 2015 fires through the use of present-day satellite observations of the fire’s radiative power output and atmospheric CO concentrations, processed using the modelling and assimilation framework of the Copernicus Atmosphere Monitoring Service (CAMS) and combined with unique in situ smoke measurements made on Kalimantan.

  4. KIC-5473556: the largest and longest-period Kepler transiting circumbinary planet

    NASA Astrophysics Data System (ADS)

    Kostov, Veselin

    2015-12-01

    We report the discovery of a new Kepler transiting circumbinary planet (CBP). This latest addition to the still-small family of CBPs defies the current trend of short-period CBPs orbiting near the stability limit of binary stars. Unlike the previous discoveries, the planet in the KIC-5473556 system has a very long orbital period (~1100 days) and was at conjunction only twice during the Kepler mission -- making it the longest-period transiting CBP at the time of writing. With a radius of nearly 12 REarth, it is also the largest such planet to date. It produced three transits in the light curve of KIC 5473556, one of them during a syzygy. The planet revolves around an ~11-day Eclipsing Binary consisting of two Solar-mass stars on a slightly inclined to the line of sight, mildly eccentric (ebin = 0.16) orbit. The CBP measurably perturbs the times of the stellar eclipses, allowing us to constrain its mass well. Here we present our spectroscopic and photometric observations of the target, discuss our analysis of the system, and outline the theoretical implications of our discovery.

  5. Kepler-1647b: The Largest and Longest-period Kepler Transiting Circumbinary Planet

    NASA Astrophysics Data System (ADS)

    Kostov, Veselin B.; Orosz, Jerome A.; Welsh, William F.; Doyle, Laurance R.; Fabrycky, Daniel C.; Haghighipour, Nader; Quarles, Billy; Short, Donald R.; Cochran, William D.; Endl, Michael; Ford, Eric B.; Gregorio, Joao; Hinse, Tobias C.; Isaacson, Howard; Jenkins, Jon M.; Jensen, Eric L. N.; Kane, Stephen; Kull, Ilya; Latham, David W.; Lissauer, Jack J.; Marcy, Geoffrey W.; Mazeh, Tsevi; Müller, Tobias W. A.; Pepper, Joshua; Quinn, Samuel N.; Ragozzine, Darin; Shporer, Avi; Steffen, Jason H.; Torres, Guillermo; Windmiller, Gur; Borucki, William J.

    2016-08-01

    We report the discovery of a new Kepler transiting circumbinary planet (CBP). This latest addition to the still-small family of CBPs defies the current trend of known short-period planets orbiting near the stability limit of binary stars. Unlike the previous discoveries, the planet revolving around the eclipsing binary system Kepler-1647 has a very long orbital period (˜1100 days) and was at conjunction only twice during the Kepler mission lifetime. Due to the singular configuration of the system, Kepler-1647b is not only the longest-period transiting CBP at the time of writing, but also one of the longest-period transiting planets. With a radius of 1.06 ± 0.01 R Jup, it is also the largest CBP to date. The planet produced three transits in the light curve of Kepler-1647 (one of them during an eclipse, creating a syzygy) and measurably perturbed the times of the stellar eclipses, allowing us to measure its mass, 1.52 ± 0.65 M Jup. The planet revolves around an 11-day period eclipsing binary consisting of two solar-mass stars on a slightly inclined, mildly eccentric (e bin = 0.16), spin-synchronized orbit. Despite having an orbital period three times longer than Earth’s, Kepler-1647b is in the conservative habitable zone of the binary star throughout its orbit.

  6. Largest known Mesozoic multituberculate from Eurasia and implications for multituberculate evolution and biology.

    PubMed

    Xu, Li; Zhang, Xingliao; Pu, Hanyong; Jia, Songhai; Zhang, Jiming; Lü, Junchang; Meng, Jin

    2015-10-22

    A new multituberculate, Yubaartar zhongyuanensis gen. and sp. nov., is reported from the Upper Cretaceous of Luanchuan County, Henan Province, China. The holotype of the new taxon is a partial skeleton with nearly complete cranium and associated lower jaws with in situ dentitions. The new species is the southern-most record of a Late Cretaceous multituberculate from outside of the Mongolian Plateau in Asia and represents the largest known Mesozoic multituberculate from Eurasia. The new specimen displays some intriguing features previously unknown in multituberculates, such as the first evidence of replacement of the ultimate upper premolar and a unique paleopathological case in Mesozoic mammals in which the animal with a severely broken right tibia could heal and survive in natural condition. The phylogenetic analysis based on craniodental characters places Yubaartar as the immediate outgroup of Taeniolabidoidea, a group consisting of a North American clade and an Asian clade. This relationship indicates at least a faunal interchange of multituberculates before the K-Pg transition. The new evidence further supports the hypothesis that disparity in dental complexity, which relates to animal diets, increased with generic richness and disparity in body size, and that an adaptive shift towards increased herbivory across the K-Pg transitional interval.

  7. Monitoring coastal pollution associated with the largest oil refinery complex of Venezuela.

    PubMed

    Croquer, Aldo; Bone, David; Bastidas, Carolina; Ramos, Ruth; García, Elia

    2016-01-01

    This study evaluated pollution levels in water and sediments of Península de Paraguaná and related these levels with benthic macrofauna along a coastal area where the largest Venezuelan oil refineries have operated over the past 60 years. For this, the concentration of heavy metals, of hydrocarbon compounds and the community structure of the macrobenthos were examined at 20 sites distributed along 40 km of coastline for six consecutive years, which included windy and calm seasons. The spatial variability of organic and inorganic compounds showed considerably high coastal pollution along the study area, across both years and seasons. The southern sites, closest to the refineries, had consistently higher concentrations of heavy metals and organic compounds in water and sediments when compared to those in the north. The benthic community was dominated by polychaetes at all sites, seasons and years, and their abundance and distribution were significantly correlated with physical and chemical characteristics of the sediments. Sites close to the oil refineries were consistently dominated by families known to tolerate xenobiotics, such as Capitellidae and Spionidae. The results from this study highlight the importance of continuing long-term environmental monitoring programs to assess the impact of effluent discharge and spill events from the oil refineries that operate in the western coast of Paraguaná, Venezuela.

  8. Fire carbon emissions over maritime southeast Asia in 2015 largest since 1997.

    PubMed

    Huijnen, V; Wooster, M J; Kaiser, J W; Gaveau, D L A; Flemming, J; Parrington, M; Inness, A; Murdiyarso, D; Main, B; van Weele, M

    2016-05-31

    In September and October 2015 widespread forest and peatland fires burned over large parts of maritime southeast Asia, most notably Indonesia, releasing large amounts of terrestrially-stored carbon into the atmosphere, primarily in the form of CO2, CO and CH4. With a mean emission rate of 11.3 Tg CO2 per day during Sept-Oct 2015, emissions from these fires exceeded the fossil fuel CO2 release rate of the European Union (EU28) (8.9 Tg CO2 per day). Although seasonal fires are a frequent occurrence in the human modified landscapes found in Indonesia, the extent of the 2015 fires was greatly inflated by an extended drought period associated with a strong El Niño. We estimate carbon emissions from the 2015 fires to be the largest seen in maritime southeast Asia since those associated with the record breaking El Niño of 1997. Compared to that event, a much better constrained regional total carbon emission estimate can be made for the 2015 fires through the use of present-day satellite observations of the fire's radiative power output and atmospheric CO concentrations, processed using the modelling and assimilation framework of the Copernicus Atmosphere Monitoring Service (CAMS) and combined with unique in situ smoke measurements made on Kalimantan.

  9. In vivo degradation of RNA polymerase II largest subunit triggered by alpha-amanitin.

    PubMed Central

    Nguyen, V T; Giannoni, F; Dubois, M F; Seo, S J; Vigneron, M; Kédinger, C; Bensaude, O

    1996-01-01

    Alpha-Amanitin is a well-known specific inhibitor of RNA polymerase II (RNAPII) in vitro and in vivo. It is a cyclic octapeptide which binds with high affinity to the largest subunit of RNAPII, RPB1. We have found that in murine fibroblasts exposure to alpha-amanitin triggered degradation of the RPB1 subunit, while other RNAPII subunits, RPB5 and RPB8, remained almost unaffected. Transcriptional inhibition in alpha-amanitin-treated cells was slow and closely followed the disappearance of RPB1. The degradation rate of RPB1 was alpha-amanitin dose dependent and was not a consequence of transcriptional arrest. Alpha-Amanitin-promoted degradation of RPB1 was prevented in cells exposed to actinomycin D, another transcriptional inhibitor. Epitope-tagged recombinant human RPB1 subunits were expressed in mouse fibroblasts. In cells exposed to alpha-amanitin the wild-type recombinant subunit was degraded like the endogenous protein, but a mutated alpha-amanitin-resistant subunit remained unaffected. Hence, alpha-amanitin did not activate a proteolytic system, but instead its binding to mRPB1 likely represented a signal for degradation. Thus, in contrast to other inhibitors, such as actinomycin D or 5,6-dichloro-1-beta-D-ribofuranosyl-benzimidazole, which reversibly act on transcription, inhibition by alpha-amanitin cannot be but an irreversible process because of the destruction of RNAPII. PMID:8760875

  10. The Largest Multi-Planar Wire Arrays on Zebra with LCM and their Applications

    NASA Astrophysics Data System (ADS)

    Safronova, A. S.; Kantsyrev, V. L.; Weller, M. E.; Shlyaptseva, V. V.; Shrestha, I. K.; Lorance, M. Y.; Stafford, A.; Schultz, K. A.; Coverdale, C. A.; Chuvatin, A. S.

    2015-11-01

    Two new approaches of i) simultaneous study of implosion and radiative characteristics of different materials in wire array Z-pinch plasma in one shot [Safronova et al, PoP 21, 031205 (2014)] and ii) investigation of larger sized wire arrays (to enhance energy coupling to plasmas and provide better diagnostic access) were further developed in experiments with 1.7 MA Zebra with a Load Current Multiplier. In particular, the largest multi-Planar Wire Arrays with two outer planes from alloyed Al wires placed as far from each other as at 19 mm (compare with 6 and 9 mm studied before) and with a modified central plane from Ni-60 (mostly Cu), were investigated. Though K-shell Al and L-shell Cu plasmas have similar temperatures and densities, the ablation dynamics and radiation of Al and Cu planes is somewhat different, which was investigated in detail using the full set of diagnostics and modeling. Advantages of using such wire arrays at higher currents to study plasma flow and radiation from different materials and jets are highlighted. This work was supported by NNSA under DOE Cooperative Agreement DE-NA0001984 and in part by DE-NA0002075. SNL is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Company, for the U.S. DOE under Contract DE-AC04-94AL85000.

  11. Mapping the Cosmic Web with the largest all-sky surveys

    NASA Astrophysics Data System (ADS)

    Bilicki, Maciej; Peacock, John A.; Jarrett, Thomas H.; Cluver, Michelle E.; Steward, Louise

    2016-10-01

    Our view of the low-redshift Cosmic Web has been revolutionized by galaxy redshift surveys such as 6dFGS, SDSS and 2MRS. However, the trade-off between depth and angular coverage limits a systematic three-dimensional account of the entire sky beyond the Local Volume (z < 0.05). In order to reliably map the Universe to cosmologically significant depths over the full celestial sphere, one must draw on multiwavelength datasets and state-of-the-art photometric redshift techniques. We have undertaken a dedicated program of cross-matching the largest photometric all-sky surveys - 2MASS, WISE and SuperCOSMOS - to obtain accurate redshift estimates of millions of galaxies. The first outcome of these efforts - the 2MASS Photometric Redshift catalog (2MPZ, Bilicki et al. 2014a) - has been publicly released and includes almost 1 million galaxies with a mean redshift of z=0.08. Here we summarize how this catalog was constructed and how using the WISE mid-infrared sample together with SuperCOSMOS optical data allows us to push to redshift shells of z~ 0.2 -0.3 on unprecedented angular scales. Our catalogs, with ~ 20 million sources in total, provide access to cosmological volumes crucial for studies of local galaxy flows (clustering dipole, bulk flow) and cross-correlations with the cosmic microwave background such as the integrated Sachs-Wolfe effect or lensing studies.

  12. Monitoring carbon monoxide pollution over the largest ten cities in the US using satellite observations

    NASA Astrophysics Data System (ADS)

    Zheng, B.; de Beurs, K.; Owsley, B.; Krehbiel, C. P.; Henebry, G. M.

    2015-12-01

    Carbon monoxide (CO) is one of the several air pollutants that are largely produced by anthropogenic activities in urban areas as a result of incomplete combustion of carbon-containing fuels. Long-term satellite data can monitor spatial and temporal changes in CO globally. Here we investigated spatial, vertical, and temporal changes in CO concentrations over the largest ten US metropolitan statistical areas (MSAs) using Version 6 MOPITT TIR-only CO retrievals. The 15-year average of MOPITT Surface CO concentrations over urban areas were highest (388 ppbv) over New York City and lowest (151 ppbv) over Miami. The influence of cities on elevated CO levels extends well beyond the immediate urban area. The CO seasonal profiles above the surface show distinct seasonality with peaks March-April and troughs September-October. However, larger cities show a lack of CO seasonality near the surface. We applied the nonparametric Seasonal Kendall (SK) trend test to the CO time series. Results revealed significant decreasing trends in CO concentration, with stronger trends in the lower atmosphere (>700 hPa) than in the mid-troposphere (500-700 hPa). Our results demonstrate the strong influence of local urban emissions on (near-) surface CO concentrations. Decreasing urban CO over the past 15 years reflects improved urban metabolism through improved energy efficiency, and increasing use of alternative transportation and zero-emission vehicles.

  13. Nutritional properties of the largest bamboo fruit Melocanna baccifera and its ecological significance.

    PubMed

    Govindan, Balaji; Johnson, Anil John; Nair, Sadasivan Nair Ajikumaran; Gopakumar, Bhaskaran; Mallampalli, Karuna Sri Lakshmi; Venkataraman, Ramaswamy; Koshy, Konnath Chacko; Baby, Sabulal

    2016-01-01

    Melocanna baccifera is a unique bamboo which produces the largest fruits in the grass family. Its gregarious flowering once in 45-50 years in north east India and adjacent regions is a botanical enigma, resulting in a glut of fruits. Proper utilization of M. baccifera fruits is not extant, and huge quantities of fruits are left underexploited due to lack of scientific information on their chemical composition and nutritional potential. Here we report the nutritional properties of M. baccifera fruits, and the ecological significance of its fruiting. This pear-shaped, fleshy bamboo fruit is rich in amino acids (lysine, glutamic acid), sugars (sucrose, glucose, fructose) and phenolics (ferulic acid). Protein content (free, bound) in M. baccifera fruits is very low. Fruits are rich in saturated fatty acids (palmitic acid), minerals (potassium), and only B series vitamins (B3) are detected in them. Rat feeding experiments showed that M. baccifera fruit alone is not a complete food, but with other protein supplements, it is a valuable food additive. This study could lead to better utilization of M. baccifera fruits during future flowering/fruiting events. These results could also help in the successful management of rodent outbreaks and other ecological problems associated with M. baccifera fruiting. PMID:27194218

  14. Photographer: Voyager 1 Jupiter, its Great Red Spot and Three of its four largest satellites are

    NASA Technical Reports Server (NTRS)

    1979-01-01

    Photographer: Voyager 1 Jupiter, its Great Red Spot and Three of its four largest satellites are visible here. The spacecraft was 28.4 million kilometers (17.5 million miles) from the planet at this time. The inner-most large satellite, Io, can be seen against Jupiter's disk. Io is distinguished by its bright, brown-yellow surface. To the right of Jupiter is the satellite Europa, also very bright but with fainter surface markings. The darkest satellite, Callisto (still nearly twice as bright as Earth's Moon), is barely visible a the bottom left of the picture. Callisto shows a bright patch in its northern hemisphere. All three orbit Jupiter in the equatorial plane, and appear in their present position because Voyager is above the plane. All three satellites show the same face to Jupiter always -- just as Earth's Moon always shows us the same face. In this photo we see the sides of the satellites that always face away from the planet. Jupiters' colorfully banded atmosphere displays complex patterns highlighted by the Great Red Spot, a large, circulating atmospheric distrubance. This black-and-white photo was taken through a violet filter. (JPL ref: P-21083 1-22 B/W)

  15. Investigation of Science Faculty with Education Specialties within the Largest University System in the United States

    PubMed Central

    Bush, Seth D.; Pelaez, Nancy J.; Rudd, James A.; Stevens, Michael T.; Tanner, Kimberly D.; Williams, Kathy S.

    2011-01-01

    Efforts to improve science education include university science departments hiring Science Faculty with Education Specialties (SFES), scientists who take on specialized roles in science education within their discipline. Although these positions have existed for decades and may be growing more common, few reports have investigated the SFES approach to improving science education. We present comprehensive data on the SFES in the California State University (CSU) system, the largest university system in the United States. We found that CSU SFES were engaged in three key arenas including K–12 science education, undergraduate science education, and discipline-based science education research. As such, CSU SFES appeared to be well-positioned to have an impact on science education from within science departments. However, there appeared to be a lack of clarity and agreement about the purpose of these SFES positions. In addition, formal training in science education among CSU SFES was limited. Although over 75% of CSU SFES were fulfilled by their teaching, scholarship, and service, our results revealed that almost 40% of CSU SFES were seriously considering leaving their positions. Our data suggest that science departments would likely benefit from explicit discussions about the role of SFES and strategies for supporting their professional activities. PMID:21364098

  16. Monitoring coastal pollution associated with the largest oil refinery complex of Venezuela

    PubMed Central

    Bone, David; Bastidas, Carolina; Ramos, Ruth

    2016-01-01

    This study evaluated pollution levels in water and sediments of Península de Paraguaná and related these levels with benthic macrofauna along a coastal area where the largest Venezuelan oil refineries have operated over the past 60 years. For this, the concentration of heavy metals, of hydrocarbon compounds and the community structure of the macrobenthos were examined at 20 sites distributed along 40 km of coastline for six consecutive years, which included windy and calm seasons. The spatial variability of organic and inorganic compounds showed considerably high coastal pollution along the study area, across both years and seasons. The southern sites, closest to the refineries, had consistently higher concentrations of heavy metals and organic compounds in water and sediments when compared to those in the north. The benthic community was dominated by polychaetes at all sites, seasons and years, and their abundance and distribution were significantly correlated with physical and chemical characteristics of the sediments. Sites close to the oil refineries were consistently dominated by families known to tolerate xenobiotics, such as Capitellidae and Spionidae. The results from this study highlight the importance of continuing long-term environmental monitoring programs to assess the impact of effluent discharge and spill events from the oil refineries that operate in the western coast of Paraguaná, Venezuela. PMID:27375970

  17. Dramatic variations in emergent wetland area in China's largest freshwater lake, Poyang Lake

    NASA Astrophysics Data System (ADS)

    Mei, Xuefei; Dai, Zhijun; Fagherazzi, Sergio; Chen, Jiyu

    2016-10-01

    Freshwater wetlands are important ecosystems experiencing rapid degradation around the world. As much as 64% of world's wetland area has been lost since 1900; the situation is even more serious in Asia, where land reclamation and anthropogenic modifications of rivers are increasing the rate of wetland disappearance. In this study, we provide a first complete estimation of daily Emergent Wetland Area (EWA) in Poyang Lake, China's largest freshwater lake, from 1955 to 2012. A wavelet analysis indicates a strong periodicity in the monthly EWA time series with two oscillations having a period of 12 and 60-72 months, respectively. A dramatic increase in mean annual EWA is detected since 2003, when the Three Gorges Dam (TGD) was completed, mainly due to the seasonal drying of 1078 km2 of wetlands in October. It is found that the timing of wetland emergence during the dry season has been anticipated of one month, from November to October, since the establishment of TGD. It is argued that a significant increase in wetland exposure and an observable shift in the seasonal timing of flooding and drying will seriously degrade the wetland system and threaten the endangered migratory birds that inhabit it unless effective countermeasures are implemented.

  18. Predicting bite force and cranial biomechanics in the largest fossil rodent using finite element analysis.

    PubMed

    Cox, Philip G; Rinderknecht, Andrés; Blanco, R Ernesto

    2015-03-01

    Josephoartigasia monesi, from the Pliocene of Uruguay, is the largest known fossil rodent, with an estimated body mass of 1000 kg. In this study, finite element analysis was used to estimate the maximum bite force that J. monesi could generate at the incisors and the cheek teeth. Owing to uncertainty in the model inputs, a sensitivity study was conducted in which the muscle forces and orientations were sequentially altered. This enabled conclusions to be drawn on the function of some of the masticatory muscles. It was found that J. monesi had a bite of 1389 N at the incisors, rising to 4165 N at the third molar. Varying muscle forces by 20% and orientations by 10° around the medio-lateral aspect led to an error in bite force of under 35% at each tooth. Predicted stresses across the skull were only minimally affected by changes to muscle forces and orientations, but revealed a reasonable safety factor in the strength of the skull. These results, combined with previous work, lead us to speculate that J. monesi was behaving in an elephant-like manner, using its incisors like tusks, and processing tough vegetation with large bite forces at the cheek teeth.

  19. Human impact on the fish diversity in the four largest lakes of Sweden.

    PubMed

    Degerman, E; Hammar, J; Nyberg, P; Svärdson, G

    2001-12-01

    The four largest Swedish lakes, Vänern, Vättern, Mälaren, Hjälmaren, host important commercial fisheries for char, salmon, trout, whitefish, vendace (cisco), perch, pike-perch, pike and eel, i.e. highly diverse biological resources. Case studies illustrate physical, chemical and biological impacts on some of these commercial species caused by constructions of dams and ship canals, eutrophication, and overexploitation. Although some original species have been lost and a few new species have been added, the recent human interference has basically caused major shifts in dominance of the fish community structures because of eutrophication, alterations in the abundance of eel or crayfish, and due to overfishing. The latter is in some cases caused by the Great Lake Fishery Paradox--in an environment with several predators and competitors, but with ample food resources, especially salmonid fish but also species like pike-perch may adapt a life history favoring growth over sexual maturation. If harvested at a conventional size these populations will decline rapidly due to too small spawning stocks. PMID:11878026

  20. Sustained Presence of Cutaneous Leishmaniasis in Urban Manaus, the Largest Human Settlement in the Amazon.

    PubMed

    Benício, Ednelza; Cordeiro, Mayara; Monteiro, Hannah; Saboia Moura, Marco Antônio; Oliveira, Cintia; Nunes Gadelha, Ellen Pricilla; Chrusciak-Talhari, Anette; Talhari, Carolina; de Lima Ferreira, Luiz Carlos; Mira, Marcelo Távora; Lima Machado, Paulo Roberto; Talhari, Sinésio; Schriefer, Albert

    2015-12-01

    The Amazon is responsible for approximately 40% of the American tegumentary leishmaniasis (ATL) in Brazil. Herein the sustained presence of ATL in Manaus, the largest settlement in the Amazon, was investigated. Records of notification of historic cases, and data from cases prospectively enrolled in the Tropical Medicine Foundation of the Amazonas State were used. Geographic coordinates of prospective patients' living sites were used to detect inner-city clusters of ATL. Infecting Leishmania species was determined by polymerase chain reaction. Among prospectively enrolled subjects, 94.8% were infected with Leishmania (Viannia) guyanensis, 76.7% were male, 30.2% were 0-20 years old, and 69.8% had an urban residence. Historic cases showed a profile similar to that of prospectively enrolled subjects. Several clusters of ATL, widely distributed within the city of Manaus, could be detected. In conclusion, there was a high frequency of disease in young age groups and cases clustered in urban neighborhoods. It cannot be determined from these data whether transmission of these cases occurred within or outside the city of Manaus. PMID:26483119

  1. Mutations in the three largest subunits of yeast RNA polymerase II that affect enzyme assembly.

    PubMed Central

    Kolodziej, P A; Young, R A

    1991-01-01

    Mutations in the three largest subunits of yeast RNA polymerase II (RPB1, RPB2, and RPB3) were investigated for their effects on RNA polymerase II structure and assembly. Among 23 temperature-sensitive mutations, 6 mutations affected enzyme assembly, as assayed by immunoprecipitation of epitope-tagged subunits. In all six assembly mutants, RNA polymerase II subunits synthesized at the permissive temperature were incorporated into stably assembled, immunoprecipitable enzyme and remained stably associated when cells were shifted to the nonpermissive temperature, whereas subunits synthesized at the nonpermissive temperature were not incorporated into a completely assembled enzyme. The observation that subunit subcomplexes accumulated in assembly-mutant cells at the nonpermissive temperature led us to investigate whether these subcomplexes were assembly intermediates or merely byproducts of mutant enzyme instability. The time course of assembly of RPB1, RPB2, and RPB3 was investigated in wild-type cells and subsequently in mutant cells. Glycerol gradient fractionation of extracts of cells pulse-labeled for various times revealed that a subcomplex of RPB2 and RPB3 appears soon after subunit synthesis and can be chased into fully assembled enzyme. The RPB2-plus-RPB3 subcomplexes accumulated in all RPB1 assembly mutants at the nonpermissive temperature but not in an RPB2 or RPB3 assembly mutant. These data indicate that RPB2 and RPB3 form a complex that subsequently interacts with RPB1 during the assembly of RNA polymerase II. Images PMID:1715023

  2. Sixty years of environmental change in the world's largest freshwater lake – Lake Baikal, Siberia

    PubMed Central

    HAMPTON, STEPHANIE E; IZMEST'EVA, LYUBOV R; MOORE, MARIANNE V; KATZ, STEPHEN L; DENNIS, BRIAN; SILOW, EUGENE A

    2008-01-01

    High-resolution data collected over the past 60 years by a single family of Siberian scientists on Lake Baikal reveal significant warming of surface waters and long-term changes in the basal food web of the world's largest, most ancient lake. Attaining depths over 1.6 km, Lake Baikal is the deepest and most voluminous of the world's great lakes. Increases in average water temperature (1.21 °C since 1946), chlorophyll a (300% since 1979), and an influential group of zooplankton grazers (335% increase in cladocerans since 1946) may have important implications for nutrient cycling and food web dynamics. Results from multivariate autoregressive (MAR) modeling suggest that cladocerans increased strongly in response to temperature but not to algal biomass, and cladocerans depressed some algal resources without observable fertilization effects. Changes in Lake Baikal are particularly significant as an integrated signal of long-term regional warming, because this lake is expected to be among those most resistant to climate change due to its tremendous volume. These findings highlight the importance of accessible, long-term monitoring data for understanding ecosystem response to large-scale stressors such as climate change.

  3. High frequency of multiple paternity in the largest rookery of Mediterranean loggerhead sea turtles.

    PubMed

    Zbinden, Judith A; Largiadèr, Carlo R; Leippert, Fabio; Margaritoulis, Dimitris; Arlettaz, Raphaël

    2007-09-01

    Mating systems are a central component in the evolution of animal life histories and in conservation genetics. The patterns of male reproductive skew and of paternal shares in batches of offspring, for example, affect genetic effective population size. A prominent characteristic of mating systems of sea turtles seem to be a considerable intra- and interspecific variability in the degree of polyandry. Because of the difficulty of observing the mating behaviour of sea turtles directly in the open sea, genetic paternity analysis is particularly useful for gaining insights into this aspect of their reproductive behaviour. We investigated patterns of multiple paternity in clutches of loggerhead sea turtles in the largest Mediterranean rookery using four highly variable microsatellite loci. Furthermore, we tested for a relationship between the number of fathers detected in clutches and body size of females. More than one father was detected in the clutches of 14 out of 15 females, with two clutches revealing the contribution of at least five males. In more than half the cases, the contributions of different fathers to a clutch did not depart from equality. The number of detected fathers significantly increased with increasing female body size. This relationship indicates that males may prefer to mate with large, and therefore productive, females. Our results suggest that polyandry is likely to increase effective population size compared to a population in which females would mate with only one male; male reproductive contributions being equal.

  4. The nutrient economy of Lodoicea maldivica, a monodominant palm producing the world's largest seed.

    PubMed

    Edwards, Peter J; Fleischer-Dogley, Frauke; Kaiser-Bunbury, Christopher N

    2015-05-01

    The iconic Lodoicea maldivica palm appears to invest heavily in reproduction, with females bearing the world's largest seeds and males producing copious pollen. We asked how these palms, which grow in extremely poor soils, obtain sufficient nutrients to support such high levels of reproductive function. Our study site was the Vallée de Mai UNESCO Site on Praslin, Seychelles. We measured the trees' allocations of dry matter, nitrogen (N) and phosphorus (P) to aboveground growth and reproduction, quantified stemflow and throughfall, and measured availabilities of N and P in the soil. We show that the nutrient costs of reproduction are very high in male and female plants, and for P far exceed those of vegetative growth. We describe how the palm leaves form a huge funnel that intercepts particulate material, especially pollen, which is flushed to the base of the trunk when it rains. In this way, Lodoicea improves its nutrient supply and that of its dispersal-limited offspring. Lodoicea shares many functional characteristics with dominant trees of other monodominant forests in the humid tropics. It also exhibits unique features, including its huge seed, effective funnelling mechanism and diverse community of closely associated animals, suggesting a long evolutionary history under relatively stable conditions. PMID:25616088

  5. Emplacement and dewatering of the world's largest exposed sand injectite complex

    NASA Astrophysics Data System (ADS)

    Sherry, Timothy J.; Rowe, Christie D.; Kirkpatrick, James D.; Brodsky, Emily E.

    2012-08-01

    Sandstone injectites form by up or down-section flow of a mobilized sand slurry through fractures in overlying rock. They act as reservoirs and high-permeability conduits through lower permeability rock in hydrocarbon systems. The Yellow Bank Creek Complex, Santa Cruz County, California is the largest known exposure of a sandstone injectite in the world. The complex contains granular textures that record processes of sand slurry flow, multiple pore fluids, and dewatering after emplacement. The injection was initially mobilized from a source containing both water and hydrocarbons. The water-sand slurry reached emplacement depth first, due to lower fluid viscosity. As the sand slurry emplaced, the transition from slurry flow to pore water percolation occurred. This transition resulted in preferred flow channels ˜6 mm wide in which sand grains were weakly aligned (laminae). The hydrocarbon-sand slurry intruded the dewatering sands and locally deformed the laminae. Compaction of the injectite deposit and pore fluid escape caused spaced compaction bands and dewatering pipes which created convolutions of the laminae. The hydrocarbon-rich sand slurry is preserved today as dolomite-cemented sand with oil inclusions. The laminae in this injectite are easily detected due to preferential iron oxide-cementation of the well-aligned sand laminae, and lack of cement in the alternating laminae. Subtle textures like these may develop during sand flow and be present but difficult to detect in other settings. They may explain permeability anisotropy in other sand deposits.

  6. Landscapes of thermal inequity: disproportionate exposure to urban heat in the three largest US cities

    NASA Astrophysics Data System (ADS)

    Mitchell, Bruce C.; Chakraborty, Jayajit

    2015-11-01

    Heat waves are the most significant cause of mortality in the US compared to other natural hazards. Prior studies have found increased heat exposure for individuals of lower socioeconomic status in several US cities, but few comparative analyses of the social distribution of urban heat have been conducted. To address this gap, our paper examines and compares the environmental justice consequences of urban heat risk in the three largest US cities: New York City, Los Angeles, and Chicago. Risk to urban heat is estimated on the basis of three characteristics of the urban thermal landscape: land surface temperature, vegetation abundance, and structural density of the built urban environment. These variables are combined to develop an urban heat risk index, which is then statistically compared with social vulnerability indicators representing socioeconomic status, age, disability, race/ethnicity, and linguistic isolation. The results indicate a consistent and significant statistical association between lower socioeconomic and minority status and greater urban heat risk, in all three cities. Our findings support a growing body of environmental justice literature that indicates the presence of a landscape of thermal inequity in US cities and underscores the need to conduct comparative analyses of social inequities in exposure to urban heat.

  7. Carbon footprint of premium quality export bananas: case study in Ecuador, the world's largest exporter.

    PubMed

    Iriarte, Alfredo; Almeida, Maria Gabriela; Villalobos, Pablo

    2014-02-15

    Nowadays, the new international market demands challenge the food producing countries to include the measurement of the environmental impact generated along the production process for their products. In order to comply with the environmentally responsible market requests the measurement of the greenhouse gas emissions of Ecuadorian agricultural goods has been promoted employing the carbon footprint concept. Ecuador is the largest exporter of bananas in the world. Within this context, this study is a first assessment of the carbon footprint of the Ecuadorian premium export banana (Musa AAA) using a considerable amount of field data. The system boundaries considered from agricultural production to delivery in a European destination port. The data collected over three years permitted identifying the hot spot stages. For the calculation, the CCaLC V3.0 software developed by the University of Manchester is used. The carbon footprint of the Ecuadorian export banana ranged from 0.45 to 1.04 kg CO2-equivalent/kg banana depending on the international overseas transport employed. The principal contributors to the carbon footprint are the on farm production and overseas transport stages. Mitigation and reduction strategies were suggested for the main emission sources in order to achieve sustainable banana production. PMID:24361571

  8. Ticks associated with the three largest wild ruminant species in southern Africa.

    PubMed

    Horak, I G; Golezardy, H; Uys, A C

    2007-09-01

    The objective of this study was to assess the host status of the three largest southern African wild ruminants, namely giraffes, Giraffa camelopardalis, African buffaloes, Syncerus caffer, and eland, Taurotragus oryx for ixodid ticks. To this end recently acquired unpublished data are added here to already published findings on the tick burdens of these animals, and the total numbers and species of ticks recorded on 12 giraffes, 18 buffaloes and 36 eland are summarized and discussed. Twenty-eight ixodid tick species were recovered. All stages of development of ten species, namely Amblyomma hebraeum, Rhipicephalus (Boophilus) decoloratus, Haemaphysalis silacea, Ixodes pilosus group, Margaropus winthemi, Rhipicephalus appendiculatus, Rhipicephalus evertsi evertsi, Rhipicephalus glabroscutatum, Rhipicephalus maculatus and Rhipicephalus muehlensi were collected. The adults of 13 species, of which the immature stages use small mammals as hosts, namely Haemaphysalis aciculifer, Hyalomma glabrum, Hyalomma marginatum rufipes, Hyalomma truncatum, Ixodes rubicundus, Rhipicephalus capensis, Rhipicephalus exophthalmos, Rhipicephalus follis, Rhipicephalus gertrudae, Rhipicephalus lounsburyi, Rhipicephalus lunulatus, Rhipicephalus pravus group and Rhipicephalus simus, were also collected. PMID:17933365

  9. Evidence for protection of targeted reef fish on the largest marine reserve in the Caribbean.

    PubMed

    Pina-Amargós, Fabián; González-Sansón, Gaspar; Martín-Blanco, Félix; Valdivia, Abel

    2014-01-01

    Marine reserves can restore fish abundance and diversity in areas impacted by overfishing, but the effectiveness of reserves in developing countries where resources for enforcement are limited, have seldom been evaluated. Here we assess whether the establishment in 1996 of the largest marine reserve in the Caribbean, Gardens of the Queen in Cuba, has had a positive effect on the abundance of commercially valuable reef fish species in relation to neighboring unprotected areas. We surveyed 25 sites, including two reef habitats (reef crest and reef slope), inside and outside the marine reserve, on five different months, and over a one-and-a-half year period. Densities of the ten most frequent, highly targeted, and relatively large fish species showed a significant variability across the archipelago for both reef habitats that depended on the month of survey. These ten species showed a tendency towards higher abundance inside the reserve in both reef habitats for most months during the study. Average fish densities pooled by protection level, however, showed that five out of these ten species were at least two-fold significantly higher inside than outside the reserve at one or both reef habitats. Supporting evidence from previously published studies in the area indicates that habitat complexity and major benthic communities were similar inside and outside the reserve, while fishing pressure appeared to be homogeneous across the archipelago before reserve establishment. Although poaching may occur within the reserve, especially at the boundaries, effective protection from fishing was the most plausible explanation for the patterns observed.

  10. The Tissint Martian meteorite as evidence for the largest impact excavation.

    PubMed

    Baziotis, Ioannis P; Liu, Yang; DeCarli, Paul S; Melosh, H Jay; McSween, Harry Y; Bodnar, Robert J; Taylor, Lawrence A

    2013-01-01

    High-pressure minerals in meteorites provide clues for the impact processes that excavated, launched and delivered these samples to Earth. Most Martian meteorites are suggested to have been excavated from 3 to 7 km diameter impact craters. Here we show that the Tissint meteorite, a 2011 meteorite fall, contains virtually all the high-pressure phases (seven minerals and two mineral glasses) that have been reported in isolated occurrences in other Martian meteorites. Particularly, one ringwoodite (75 × 140 μm(2)) represents the largest grain observed in all Martian samples. Collectively, the ubiquitous high-pressure minerals of unusually large sizes in Tissint indicate that shock metamorphism was widely dispersed in this sample (~25 GPa and ~2,000 °C). Using the size and growth kinetics of the ringwoodite grains, we infer an initial impact crater with ~90 km diameter, with a factor of 2 uncertainty. These energetic conditions imply alteration of any possible low-T minerals in Tissint.

  11. Universal Scaling Law for the Largest Lyapunov Exponent in Coupled Map Lattices

    NASA Astrophysics Data System (ADS)

    Yang, Weiming; Ding, E.-Jiang; Ding, Mingzhou

    1996-03-01

    We consider coupled map lattices of the type xi\\(n+1\\) = \\(1-ɛ\\)f\\(xi\\(n\\)\\)+\\(ɛ/2\\) [ f\\(xi-1\\(n\\)\\)+f\\(xi+1\\(n\\)\\)], where for concreteness we take f\\(x\\) = 1-\\(μ/4\\) \\|1-2x\\|p, with p>1. We show that near ɛ = 0 (no coupling) and μ = 4 the envelope of the largest Lyapunov exponent of the full system obeys the scaling law Λ¯ = Λ0-[aɛ+b\\(4-μ\\)]1/p. We further argue that this law is universal in that it is independent of the details of f\\(x\\) insofar as f\\(x\\) has a single critical point xc in the interval [0,1] and its lowest order power expansion about xc has the form \\|x-xc\\|p. The dependence of Λ¯ on the size of the lattice as well as on the range of the coupling is also discussed.

  12. Tracking leatherback turtles from the world's largest rookery: assessing threats across the South Atlantic.

    PubMed

    Witt, Matthew J; Augowet Bonguno, Eric; Broderick, Annette C; Coyne, Michael S; Formia, Angela; Gibudi, Alain; Mounguengui Mounguengui, Gil Avery; Moussounda, Carine; NSafou, Monique; Nougessono, Solange; Parnell, Richard J; Sounguet, Guy-Philippe; Verhage, Sebastian; Godley, Brendan J

    2011-08-01

    Despite extensive work carried out on leatherback turtles (Dermochelys coriacea) in the North Atlantic and Indo-Pacific, very little is known of the at-sea distribution of this species in the South Atlantic, where the world's largest population nests in Gabon (central Africa). This paucity of data is of marked concern given the pace of industrialization in fisheries with demonstrable marine turtle bycatch in African/Latin American waters. We tracked the movements of 25 adult female leatherback turtles obtaining a range of fundamental and applied insights, including indications for methodological advancement. Individuals could be assigned to one of three dispersal strategies, moving to (i) habitats of the equatorial Atlantic, (ii) temperate habitats off South America or (iii) temperate habitats off southern Africa. While occupying regions with high surface chlorophyll concentrations, these strategies exposed turtles to some of the world's highest levels of longline fishing effort, in addition to areas with coastal gillnet fisheries. Satellite tracking highlighted that at least 11 nations should be involved in the conservation of this species in addition to those with distant fishing fleets. The majority of tracking days were, however, spent in the high seas, where effective implementation of conservation efforts is complex to achieve. PMID:21208949

  13. Percolation under noise: Detecting explosive percolation using the second-largest component

    NASA Astrophysics Data System (ADS)

    Viles, Wes; Ginestet, Cedric E.; Tang, Ariana; Kramer, Mark A.; Kolaczyk, Eric D.

    2016-05-01

    We consider the problem of distinguishing between different rates of percolation under noise. A statistical model of percolation is constructed allowing for the birth and death of edges as well as the presence of noise in the observations. This graph-valued stochastic process is composed of a latent and an observed nonstationary process, where the observed graph process is corrupted by type-I and type-II errors. This produces a hidden Markov graph model. We show that for certain choices of parameters controlling the noise, the classical (Erdős-Rényi) percolation is visually indistinguishable from a more rapid form of percolation. In this setting, we compare two different criteria for discriminating between these two percolation models, based on the interquartile range (IQR) of the first component's size, and on the maximal size of the second-largest component. We show through data simulations that this second criterion outperforms the IQR of the first component's size, in terms of discriminatory power. The maximal size of the second component therefore provides a useful statistic for distinguishing between different rates of percolation, under physically motivated conditions for the birth and death of edges, and under noise. The potential application of the proposed criteria for the detection of clinically relevant percolation in the context of applied neuroscience is also discussed.

  14. Bubble nucleation in simple and molecular liquids via the largest spherical cavity method

    SciTech Connect

    Gonzalez, Miguel A.; Abascal, José L. F.; Valeriani, Chantal; Bresme, Fernando

    2015-04-21

    In this work, we propose a methodology to compute bubble nucleation free energy barriers using trajectories generated via molecular dynamics simulations. We follow the bubble nucleation process by means of a local order parameter, defined by the volume of the largest spherical cavity (LSC) formed in the nucleating trajectories. This order parameter simplifies considerably the monitoring of the nucleation events, as compared with the previous approaches which require ad hoc criteria to classify the atoms and molecules as liquid or vapor. The combination of the LSC and the mean first passage time technique can then be used to obtain the free energy curves. Upon computation of the cavity distribution function the nucleation rate and free-energy barrier can then be computed. We test our method against recent computations of bubble nucleation in simple liquids and water at negative pressures. We obtain free-energy barriers in good agreement with the previous works. The LSC method provides a versatile and computationally efficient route to estimate the volume of critical bubbles the nucleation rate and to compute bubble nucleation free-energies in both simple and molecular liquids.

  15. Bubble nucleation in simple and molecular liquids via the largest spherical cavity method

    NASA Astrophysics Data System (ADS)

    Gonzalez, Miguel A.; Abascal, José L. F.; Valeriani, Chantal; Bresme, Fernando

    2015-04-01

    In this work, we propose a methodology to compute bubble nucleation free energy barriers using trajectories generated via molecular dynamics simulations. We follow the bubble nucleation process by means of a local order parameter, defined by the volume of the largest spherical cavity (LSC) formed in the nucleating trajectories. This order parameter simplifies considerably the monitoring of the nucleation events, as compared with the previous approaches which require ad hoc criteria to classify the atoms and molecules as liquid or vapor. The combination of the LSC and the mean first passage time technique can then be used to obtain the free energy curves. Upon computation of the cavity distribution function the nucleation rate and free-energy barrier can then be computed. We test our method against recent computations of bubble nucleation in simple liquids and water at negative pressures. We obtain free-energy barriers in good agreement with the previous works. The LSC method provides a versatile and computationally efficient route to estimate the volume of critical bubbles the nucleation rate and to compute bubble nucleation free-energies in both simple and molecular liquids.

  16. Storing and Accessing the Largest Astronomical Catalogs with the SAI CAS Project

    NASA Astrophysics Data System (ADS)

    Koposov, S.; Bartunov, O.; Belinskiy, A.; Karpov, S.

    2007-10-01

    We present a new project -- SAI CAS (Sternberg Astronomical Institute Catalog Access Services). The goal of this project is to provide the Russian and international community with online access to major large astronomical catalogs (USNO-A2.0/B1.0, SDSS, 2MASS, GSC I/II, DENIS, UCAC) and provide tools and services facilitating scientific research using these catalogs. Currently SAI CAS is the largest astronomical data center in Russia. It provides primary services such as cone search, cross match between catalogs inside a region on the sky, and between system and user catalogs, etc. Several science projects in Russia already use SAI CAS. The SAI CAS project is based on open source software and is an open source itself. The system uses relational database storage (PostgreSQL), where all data and metadata are stored. The spatial searches and cross matches are performed using the Q3C plugin for PostgreSQL. Our system can be accessed via web-services (SOAP and simple HTTP POST/GET) and web interfaces. The SAI CAS project is located at http://vo.astronet.ru.

  17. Hydroclimatological influences on recently increased droughts in China's largest freshwater lake

    NASA Astrophysics Data System (ADS)

    Liu, Y.; Wu, G.

    2016-01-01

    Lake droughts are the consequence of climatic, hydrologic and anthropogenic influences. Quantification of droughts and estimation of the contributions from the individual factors are essential for understanding drought features and their causation structure. This is also important for policymakers to make effective adaption decisions, especially under changing climate. This study examines Poyang Lake, China's largest freshwater lake, which has been undergoing drastic hydrological alternation in the past decade. Standardized lake stage is used to identify and quantify the lake droughts, and hydroclimatic contributions are determined with a water budget analysis, in which absolute deficiency is defined in reference to normal hydrologic conditions. Our analyses demonstrate that in the past decade the lake droughts worsened in terms of duration, frequency, intensity and severity. Hydroclimatic contributions to each individual drought varied between droughts, and the overall contribution to the lake droughts in the past decade came from decreased inflow, increased outflow, and reduced precipitation and increased evapotranspiration in the lake region. The decreased inflow resulted mainly from reduced precipitation and less from increased evapotranspiration over the Poyang Lake basin. The increased outflow was attributable to the weakened blocking effects of the Yangtze River, which the Three Gorges Dam (TGD) established upstream. The TGD impoundments were not responsible for the increased number of drought events, but they may have intensified the droughts and changed the frequency of classified droughts. However, the TGD contribution is limited in comparison with hydroclimatic influences. Hence, the recently increased droughts were due to hydroclimatic effects, with a less important contribution from anthropogenic influences.

  18. Monitoring coastal pollution associated with the largest oil refinery complex of Venezuela.

    PubMed

    Croquer, Aldo; Bone, David; Bastidas, Carolina; Ramos, Ruth; García, Elia

    2016-01-01

    This study evaluated pollution levels in water and sediments of Península de Paraguaná and related these levels with benthic macrofauna along a coastal area where the largest Venezuelan oil refineries have operated over the past 60 years. For this, the concentration of heavy metals, of hydrocarbon compounds and the community structure of the macrobenthos were examined at 20 sites distributed along 40 km of coastline for six consecutive years, which included windy and calm seasons. The spatial variability of organic and inorganic compounds showed considerably high coastal pollution along the study area, across both years and seasons. The southern sites, closest to the refineries, had consistently higher concentrations of heavy metals and organic compounds in water and sediments when compared to those in the north. The benthic community was dominated by polychaetes at all sites, seasons and years, and their abundance and distribution were significantly correlated with physical and chemical characteristics of the sediments. Sites close to the oil refineries were consistently dominated by families known to tolerate xenobiotics, such as Capitellidae and Spionidae. The results from this study highlight the importance of continuing long-term environmental monitoring programs to assess the impact of effluent discharge and spill events from the oil refineries that operate in the western coast of Paraguaná, Venezuela. PMID:27375970

  19. Eight years of operating experience of the world's largest coke oven battery at Krupp Mannesmann Steelworks

    SciTech Connect

    Beckmann, R.; Meyer, G.

    1993-01-01

    The world's largest coke oven battery at Huettenwerke Krupp Mannesmann has been in operation since December, 1984. The battery produces 1.1 million metric tons of coke per year and is comprised of 70 high capacity ovens with an effective volume of 70 m[sup 3]. Whereas the oven dimensions had nearly been built before, the chamber width of 550 mm was an innovative technological step. The CONTROLPRESS Bracing System was used to ensure the permanent stability of the refractory brickwork. All machines, including quenching car, are one-spot machines and are fully automatic. The rated capacity was reached after only eight weeks. In the following years, the average output was always between 99 and 104 % of rated capacity. Also with regard to meeting stringent environmental regulations, similar success was achieved. The good general condition of the battery and machines after eight years operating time at full capacity can largely be attributed to the high degree of preventive maintenance, the regular inspection of the bracing system by Krupp Koppers as well as the good qualification of the coking plant workforce by regular training. The widening of the oven chambers has proven to be the right decision. All difficulties that may result from the increase in oven length and height are compensated by the wider chamber. On the basis of the experience, the wider high capacity ovens can be expected to have the same service life as smaller ovens.

  20. The Tissint Martian meteorite as evidence for the largest impact excavation.

    PubMed

    Baziotis, Ioannis P; Liu, Yang; DeCarli, Paul S; Melosh, H Jay; McSween, Harry Y; Bodnar, Robert J; Taylor, Lawrence A

    2013-01-01

    High-pressure minerals in meteorites provide clues for the impact processes that excavated, launched and delivered these samples to Earth. Most Martian meteorites are suggested to have been excavated from 3 to 7 km diameter impact craters. Here we show that the Tissint meteorite, a 2011 meteorite fall, contains virtually all the high-pressure phases (seven minerals and two mineral glasses) that have been reported in isolated occurrences in other Martian meteorites. Particularly, one ringwoodite (75 × 140 μm(2)) represents the largest grain observed in all Martian samples. Collectively, the ubiquitous high-pressure minerals of unusually large sizes in Tissint indicate that shock metamorphism was widely dispersed in this sample (~25 GPa and ~2,000 °C). Using the size and growth kinetics of the ringwoodite grains, we infer an initial impact crater with ~90 km diameter, with a factor of 2 uncertainty. These energetic conditions imply alteration of any possible low-T minerals in Tissint. PMID:23360995

  1. Characteristics and Trends in Hypnotics Consumption in the Largest Health Care System in Israel

    PubMed Central

    Rennert, G.; Stein, N.; Landsman, K.

    2016-01-01

    Objectives. To quantify and characterize hypnotics consumption habits among adult patients insured by Clalit Health Services (CHS), the largest health care provider in Israel, in 2000 and 2010. Methods. A retrospective analysis of CHS computerized pharmacy records. Data were collected for all patients over the age of 18 years who were prescribed hypnotics in 2000 and in 2010. Results. Sleep medications were consumed by 8.7% of the adult CHS population in 2000 and by 9.6% in 2010. About one-quarter of consumers were treated for more than 6 months in both years. Multiple sleeping drugs were consumed more often in 2010 (45.2%) than a decade before (22%). While in 2000 benzodiazepines accounted for 84.5% of hypnotics, in 2010 this was reduced to 73.7% (p < 0.05). Of all patients treated for longer than 6 months only 11% in 2000 and 9% in 2010 required a dose escalation suggesting the absence of tolerance. Conclusions. Nine percent of the Israeli population consumes hypnotics. There is a major increase in prescription of combination of medications between 2000 and 2010, with an increase in Z class medications use and reduction in benzodiazepines. Most patients chronically treated did not escalate dosage, suggesting the absence of tolerance.

  2. Nutritional properties of the largest bamboo fruit Melocanna baccifera and its ecological significance

    PubMed Central

    Govindan, Balaji; Johnson, Anil John; Nair, Sadasivan Nair Ajikumaran; Gopakumar, Bhaskaran; Mallampalli, Karuna Sri Lakshmi; Venkataraman, Ramaswamy; Koshy, Konnath Chacko; Baby, Sabulal

    2016-01-01

    Melocanna baccifera is a unique bamboo which produces the largest fruits in the grass family. Its gregarious flowering once in 45–50 years in north east India and adjacent regions is a botanical enigma, resulting in a glut of fruits. Proper utilization of M. baccifera fruits is not extant, and huge quantities of fruits are left underexploited due to lack of scientific information on their chemical composition and nutritional potential. Here we report the nutritional properties of M. baccifera fruits, and the ecological significance of its fruiting. This pear-shaped, fleshy bamboo fruit is rich in amino acids (lysine, glutamic acid), sugars (sucrose, glucose, fructose) and phenolics (ferulic acid). Protein content (free, bound) in M. baccifera fruits is very low. Fruits are rich in saturated fatty acids (palmitic acid), minerals (potassium), and only B series vitamins (B3) are detected in them. Rat feeding experiments showed that M. baccifera fruit alone is not a complete food, but with other protein supplements, it is a valuable food additive. This study could lead to better utilization of M. baccifera fruits during future flowering/fruiting events. These results could also help in the successful management of rodent outbreaks and other ecological problems associated with M. baccifera fruiting. PMID:27194218

  3. Percolation under noise: Detecting explosive percolation using the second-largest component.

    PubMed

    Viles, Wes; Ginestet, Cedric E; Tang, Ariana; Kramer, Mark A; Kolaczyk, Eric D

    2016-05-01

    We consider the problem of distinguishing between different rates of percolation under noise. A statistical model of percolation is constructed allowing for the birth and death of edges as well as the presence of noise in the observations. This graph-valued stochastic process is composed of a latent and an observed nonstationary process, where the observed graph process is corrupted by type-I and type-II errors. This produces a hidden Markov graph model. We show that for certain choices of parameters controlling the noise, the classical (Erdős-Rényi) percolation is visually indistinguishable from a more rapid form of percolation. In this setting, we compare two different criteria for discriminating between these two percolation models, based on the interquartile range (IQR) of the first component's size, and on the maximal size of the second-largest component. We show through data simulations that this second criterion outperforms the IQR of the first component's size, in terms of discriminatory power. The maximal size of the second component therefore provides a useful statistic for distinguishing between different rates of percolation, under physically motivated conditions for the birth and death of edges, and under noise. The potential application of the proposed criteria for the detection of clinically relevant percolation in the context of applied neuroscience is also discussed. PMID:27300904

  4. Social and Spatial Clustering of People at Humanity’s Largest Gathering

    PubMed Central

    Barnett, Ian; Khanna, Tarun; Onnela, Jukka-Pekka

    2016-01-01

    Macroscopic behavior of scientific and societal systems results from the aggregation of microscopic behaviors of their constituent elements, but connecting the macroscopic with the microscopic in human behavior has traditionally been difficult. Manifestations of homophily, the notion that individuals tend to interact with others who resemble them, have been observed in many small and intermediate size settings. However, whether this behavior translates to truly macroscopic levels, and what its consequences may be, remains unknown. Here, we use call detail records (CDRs) to examine the population dynamics and manifestations of social and spatial homophily at a macroscopic level among the residents of 23 states of India at the Kumbh Mela, a 3-month-long Hindu festival. We estimate that the festival was attended by 61 million people, making it the largest gathering in the history of humanity. While we find strong overall evidence for both types of homophily for residents of different states, participants from low-representation states show considerably stronger propensity for both social and spatial homophily than those from high-representation states. These manifestations of homophily are amplified on crowded days, such as the peak day of the festival, which we estimate was attended by 25 million people. Our findings confirm that homophily, which here likely arises from social influence, permeates all scales of human behavior. PMID:27258037

  5. Carbon footprint of premium quality export bananas: case study in Ecuador, the world's largest exporter.

    PubMed

    Iriarte, Alfredo; Almeida, Maria Gabriela; Villalobos, Pablo

    2014-02-15

    Nowadays, the new international market demands challenge the food producing countries to include the measurement of the environmental impact generated along the production process for their products. In order to comply with the environmentally responsible market requests the measurement of the greenhouse gas emissions of Ecuadorian agricultural goods has been promoted employing the carbon footprint concept. Ecuador is the largest exporter of bananas in the world. Within this context, this study is a first assessment of the carbon footprint of the Ecuadorian premium export banana (Musa AAA) using a considerable amount of field data. The system boundaries considered from agricultural production to delivery in a European destination port. The data collected over three years permitted identifying the hot spot stages. For the calculation, the CCaLC V3.0 software developed by the University of Manchester is used. The carbon footprint of the Ecuadorian export banana ranged from 0.45 to 1.04 kg CO2-equivalent/kg banana depending on the international overseas transport employed. The principal contributors to the carbon footprint are the on farm production and overseas transport stages. Mitigation and reduction strategies were suggested for the main emission sources in order to achieve sustainable banana production.

  6. Human impact on the fish diversity in the four largest lakes of Sweden.

    PubMed

    Degerman, E; Hammar, J; Nyberg, P; Svärdson, G

    2001-12-01

    The four largest Swedish lakes, Vänern, Vättern, Mälaren, Hjälmaren, host important commercial fisheries for char, salmon, trout, whitefish, vendace (cisco), perch, pike-perch, pike and eel, i.e. highly diverse biological resources. Case studies illustrate physical, chemical and biological impacts on some of these commercial species caused by constructions of dams and ship canals, eutrophication, and overexploitation. Although some original species have been lost and a few new species have been added, the recent human interference has basically caused major shifts in dominance of the fish community structures because of eutrophication, alterations in the abundance of eel or crayfish, and due to overfishing. The latter is in some cases caused by the Great Lake Fishery Paradox--in an environment with several predators and competitors, but with ample food resources, especially salmonid fish but also species like pike-perch may adapt a life history favoring growth over sexual maturation. If harvested at a conventional size these populations will decline rapidly due to too small spawning stocks.

  7. TCM Database@Taiwan: the world's largest traditional Chinese medicine database for drug screening in silico.

    PubMed

    Chen, Calvin Yu-Chian

    2011-01-06

    Rapid advancing computational technologies have greatly speeded up the development of computer-aided drug design (CADD). Recently, pharmaceutical companies have increasingly shifted their attentions toward traditional Chinese medicine (TCM) for novel lead compounds. Despite the growing number of studies on TCM, there is no free 3D small molecular structure database of TCM available for virtual screening or molecular simulation. To address this shortcoming, we have constructed TCM Database@Taiwan (http://tcm.cmu.edu.tw/) based on information collected from Chinese medical texts and scientific publications. TCM Database@Taiwan is currently the world's largest non-commercial TCM database. This web-based database contains more than 20,000 pure compounds isolated from 453 TCM ingredients. Both cdx (2D) and Tripos mol2 (3D) formats of each pure compound in the database are available for download and virtual screening. The TCM database includes both simple and advanced web-based query options that can specify search clauses, such as molecular properties, substructures, TCM ingredients, and TCM classification, based on intended drug actions. The TCM database can be easily accessed by all researchers conducting CADD. Over the last eight years, numerous volunteers have devoted their time to analyze TCM ingredients from Chinese medical texts as well as to construct structure files for each isolated compound. We believe that TCM Database@Taiwan will be a milestone on the path towards modernizing traditional Chinese medicine.

  8. Largest known Mesozoic multituberculate from Eurasia and implications for multituberculate evolution and biology

    PubMed Central

    Xu, Li; Zhang, Xingliao; Pu, Hanyong; Jia, Songhai; Zhang, Jiming; Lü, Junchang; Meng, Jin

    2015-01-01

    A new multituberculate, Yubaartar zhongyuanensis gen. and sp. nov., is reported from the Upper Cretaceous of Luanchuan County, Henan Province, China. The holotype of the new taxon is a partial skeleton with nearly complete cranium and associated lower jaws with in situ dentitions. The new species is the southern-most record of a Late Cretaceous multituberculate from outside of the Mongolian Plateau in Asia and represents the largest known Mesozoic multituberculate from Eurasia. The new specimen displays some intriguing features previously unknown in multituberculates, such as the first evidence of replacement of the ultimate upper premolar and a unique paleopathological case in Mesozoic mammals in which the animal with a severely broken right tibia could heal and survive in natural condition. The phylogenetic analysis based on craniodental characters places Yubaartar as the immediate outgroup of Taeniolabidoidea, a group consisting of a North American clade and an Asian clade. This relationship indicates at least a faunal interchange of multituberculates before the K-Pg transition. The new evidence further supports the hypothesis that disparity in dental complexity, which relates to animal diets, increased with generic richness and disparity in body size, and that an adaptive shift towards increased herbivory across the K-Pg transitional interval. PMID:26492455

  9. Fire carbon emissions over maritime southeast Asia in 2015 largest since 1997

    PubMed Central

    Huijnen, V.; Wooster, M. J.; Kaiser, J. W.; Gaveau, D. L. A.; Flemming, J.; Parrington, M.; Inness, A.; Murdiyarso, D.; Main, B.; van Weele, M.

    2016-01-01

    In September and October 2015 widespread forest and peatland fires burned over large parts of maritime southeast Asia, most notably Indonesia, releasing large amounts of terrestrially-stored carbon into the atmosphere, primarily in the form of CO2, CO and CH4. With a mean emission rate of 11.3 Tg CO2 per day during Sept-Oct 2015, emissions from these fires exceeded the fossil fuel CO2 release rate of the European Union (EU28) (8.9 Tg CO2 per day). Although seasonal fires are a frequent occurrence in the human modified landscapes found in Indonesia, the extent of the 2015 fires was greatly inflated by an extended drought period associated with a strong El Niño. We estimate carbon emissions from the 2015 fires to be the largest seen in maritime southeast Asia since those associated with the record breaking El Niño of 1997. Compared to that event, a much better constrained regional total carbon emission estimate can be made for the 2015 fires through the use of present-day satellite observations of the fire’s radiative power output and atmospheric CO concentrations, processed using the modelling and assimilation framework of the Copernicus Atmosphere Monitoring Service (CAMS) and combined with unique in situ smoke measurements made on Kalimantan. PMID:27241616

  10. Scaling relationships among drivers of aquatic respiration from the smallest to the largest freshwater ecosystems

    USGS Publications Warehouse

    Hall, Ed K; Schoolmaster, Donald; Amado, A.M; Stets, Edward G.; Lennon, J.T.; Domaine, L.; Cotner, J.B.

    2016-01-01

    To address how various environmental parameters control or constrain planktonic respiration (PR), we used geometric scaling relationships and established biological scaling laws to derive quantitative predictions for the relationships among key drivers of PR. We then used empirical measurements of PR and environmental (soluble reactive phosphate [SRP], carbon [DOC], chlorophyll a [Chl-a)], and temperature) and landscape parameters (lake area [LA] and watershed area [WA]) from a set of 44 lakes that varied in size and trophic status to test our hypotheses. We found that landscape-level processes affected PR through direct effects on DOC and temperature and indirectly via SRP. In accordance with predictions made from known relationships and scaling laws, scale coefficients (the parameter that describes the shape of a relationship between 2 variables) were found to be negative and have an absolute value 1, others <1). We also found evidence of a significant relationship between temperature and SRP. Because our dataset included measurements of respiration from small pond catchments to the largest body of freshwater on the planet, Lake Superior, these findings should be applicable to controls of PR for the great majority of temperate aquatic ecosystems.

  11. Synchronized observations by using the STEREO and the largest ground-based decametre radio telescope

    NASA Astrophysics Data System (ADS)

    Konovalenko, A. A.; Stanislavsky, A. A.; Rucker, H. O.; Lecacheux, A.; Mann, G.; Bougeret, J.-L.; Kaiser, M. L.; Briand, C.; Zarka, P.; Abranin, E. P.; Dorovsky, V. V.; Koval, A. A.; Mel'nik, V. N.; Mukha, D. V.; Panchenko, M.

    2013-08-01

    We consider the approach to simultaneous (synchronous) solar observations of radio emission by using the STEREO-WAVES instruments (frequency range 0.125-16 MHz) and the largest ground-based low-frequency radio telescope. We illustrate it by the UTR-2 radio telescope implementation (10-30 MHz). The antenna system of the radio telescope is a T-shape-like array of broadband dipoles and is located near the village Grakovo in the Kharkiv region (Ukraine). The third observation point on the ground in addition to two space-based ones improves the space-mission performance capabilities for the determination of radio-emission source directivity. The observational results from the high sensitivity antenna UTR-2 are particularly useful for analysis of STEREO data in the condition of weak event appearances during solar activity minima. In order to improve the accuracy of flux density measurements, we also provide simultaneous observations with a large part of the UTR-2 radio telescope array and its single dipole close to the STEREO-WAVES antennas in sensitivity. This concept has been studied by comparing the STEREO data with ground-based records from 2007-2011 and shown to be effective. The capabilities will be useful in the implementation of new instruments (LOFAR, LWA, MWA, etc.) and during the future Solar Orbiter mission.

  12. The Transportation Energy and Carbon Footprints of the 100 Largest U.S. Metropolitan Areas

    SciTech Connect

    Southworth, Frank; Sonnenberg, Anthon; Brown, Marilyn A

    2008-01-01

    We present estimates of the automobile and truck travel based energy and carbon footprints of the largest 100 U.S. metropolitan areas. The footprints are based on the estimated vehicle miles traveled and the transportation fuels consumed. Results are presented on an annual basis and represent end use emissions only. Total carbon emissions, emissions per capita, and emissions per dollar of gross metropolitan product are reported. Two years of annual data were examined, 2000 and 2005, with most of the in-depth analysis focused on the 2005 results. In section 2 we provide background data on the national picture and derive some carbon and energy consumption figures for the nation as a whole. In section 3 of the paper we examine the metropolitan area-wide results based on the sums and averages across all 100 metro areas, and compare these with the national totals and averages. In section 4 we present metropolitan area specific footprints and examine the considerable variation that is found to exist across individual metro areas. In doing so we pay particular attention to the effects that urban form might have on these differences. Finally, section 5 provides a summary of major findings, and a list of caveats that need to be borne in mind when using the results due to known limitations in the data sources used.

  13. Characteristics and Trends in Hypnotics Consumption in the Largest Health Care System in Israel.

    PubMed

    Marom, O; Rennert, G; Stein, N; Landsman, K; Pillar, G

    2016-01-01

    Objectives. To quantify and characterize hypnotics consumption habits among adult patients insured by Clalit Health Services (CHS), the largest health care provider in Israel, in 2000 and 2010. Methods. A retrospective analysis of CHS computerized pharmacy records. Data were collected for all patients over the age of 18 years who were prescribed hypnotics in 2000 and in 2010. Results. Sleep medications were consumed by 8.7% of the adult CHS population in 2000 and by 9.6% in 2010. About one-quarter of consumers were treated for more than 6 months in both years. Multiple sleeping drugs were consumed more often in 2010 (45.2%) than a decade before (22%). While in 2000 benzodiazepines accounted for 84.5% of hypnotics, in 2010 this was reduced to 73.7% (p < 0.05). Of all patients treated for longer than 6 months only 11% in 2000 and 9% in 2010 required a dose escalation suggesting the absence of tolerance. Conclusions. Nine percent of the Israeli population consumes hypnotics. There is a major increase in prescription of combination of medications between 2000 and 2010, with an increase in Z class medications use and reduction in benzodiazepines. Most patients chronically treated did not escalate dosage, suggesting the absence of tolerance. PMID:27660727

  14. Identification of a nucleic acid-binding region within the largest subunit of Drosophila melanogaster RNA polymerase II.

    PubMed Central

    Kontermann, R. E.; Kobor, M.; Bautz, E. K.

    1993-01-01

    The largest and the second-largest subunit of the multisubunit eukaryotic RNA polymerases are involved in interaction with the DNA template and the nascent RNA chain. Using Southwestern DNA-binding techniques and nitrocellulose filter binding assays of bacterially expressed fusion proteins, we have identified a region of the largest, 215-kDa, subunit of Drosophila RNA polymerase II that has the potential to bind nucleic acids nonspecifically. This nucleic acid-binding region is located between amino acid residues 309-384 and is highly conserved within the largest subunits of eukaryotic and bacterial RNA polymerases. A homology to a region of the DNA-binding cleft of Escherichia coli DNA polymerase I involved in binding of the newly synthesized DNA duplex provides indirect evidence that the nucleic acid-binding region of the largest subunit participates in interaction with double-stranded nucleic acids during transcription. The nonspecific DNA-binding behavior of the region is similar to that observed for the native enzyme in nitrocellulose filter binding assays and that of the separated largest subunit in Southwestern assays. A high content of basic amino acid residues is consistent with the electrostatic nature of nonspecific DNA binding by RNA polymerases. PMID:8443600

  15. Astronomer's new guide to the galaxy: largest map of cold dust revealed

    NASA Astrophysics Data System (ADS)

    2009-07-01

    Astronomers have unveiled an unprecedented new atlas of the inner regions of the Milky Way, our home galaxy, peppered with thousands of previously undiscovered dense knots of cold cosmic dust -- the potential birthplaces of new stars. Made using observations from the APEX telescope in Chile, this survey is the largest map of cold dust so far, and will prove an invaluable map for observations made with the forthcoming ALMA telescope, as well as the recently launched ESA Herschel space telescope. ESO PR Photo 24a/09 View of the Galactic Plane from the ATLASGAL survey (annotated and in five sections) ESO PR Photo 24b/09 View of the Galactic Plane from the ATLASGAL survey (annotated) ESO PR Photo 24c/09 View of the Galactic Plane from the ATLASGAL survey (in five sections) ESO PR Photo 24d/09 View of the Galactic Plane from the ATLASGAL survey ESO PR Photo 24e/09 The Galactic Centre and Sagittarius B2 ESO PR Photo 24f/09 The NGC 6357 and NGC 6334 nebulae ESO PR Photo 24g/09 The RCW120 nebula ESO PR Video 24a/09 Annotated pan as seen by the ATLASGAL survey This new guide for astronomers, known as the APEX Telescope Large Area Survey of the Galaxy (ATLASGAL) shows the Milky Way in submillimetre-wavelength light (between infrared light and radio waves [1]). Images of the cosmos at these wavelengths are vital for studying the birthplaces of new stars and the structure of the crowded galactic core. "ATLASGAL gives us a new look at the Milky Way. Not only will it help us investigate how massive stars form, but it will also give us an overview of the larger-scale structure of our galaxy", said Frederic Schuller from the Max Planck Institute for Radio Astronomy, leader of the ATLASGAL team. The area of the new submillimetre map is approximately 95 square degrees, covering a very long and narrow strip along the galactic plane two degrees wide (four times the width of the full Moon) and over 40 degrees long. The 16 000 pixel-long map was made with the LABOCA submillimetre

  16. Heterogeneous Nuclear Ribonucleoprotein (HnRNP) K Genome-wide Binding Survey Reveals Its Role in Regulating 3′-End RNA Processing and Transcription Termination at the Early Growth Response 1 (EGR1) Gene through XRN2 Exonuclease*

    PubMed Central

    Mikula, Michal; Bomsztyk, Karol; Goryca, Krzysztof; Chojnowski, Krzysztof; Ostrowski, Jerzy

    2013-01-01

    The heterogeneous nuclear ribonucleoprotein K (hnRNPK) is a nucleic acid-binding protein that acts as a docking platform integrating signal transduction pathways to nucleic acid-related processes. Given that hnRNPK could be involved in other steps that compose gene expression the definition of its genome-wide occupancy is important to better understand its role in transcription and co-transcriptional processes. Here, we used chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) to analyze the genome-wide hnRNPK-DNA interaction in colon cancer cell line HCT116. 9.1/3.6 and 7.0/3.4 million tags were sequenced/mapped, then 1809 and 642 hnRNPK binding sites were detected in quiescent and 30-min serum-stimulated cells, respectively. The inspection of sequencing tracks revealed inducible hnRNPK recruitment along a number of immediate early gene loci, including EGR1 and ZFP36, with the highest densities present at the transcription termination sites. Strikingly, hnRNPK knockdown with siRNA resulted in increased pre-RNA levels transcribed downstream of the EGR1 polyadenylation (A) site suggesting altered 3′-end pre-RNA degradation. Further ChIP survey of hnRNPK knockdown uncovered decreased recruitment of the 5′-3′ exonuclease XRN2 along EGR1 and downstream of the poly(A) signal without altering RNA polymerase II density at these sites. Immunoprecipitation of hnRNPK and XRN2 from intact and RNase A-treated nuclear extracts followed by shotgun mass spectrometry revealed the presence of hnRNPK and XRN2 in the same complexes along with other spliceosome-related proteins. Our data suggest that hnRNPK may play a role in recruitment of XRN2 to gene loci thus regulating coupling 3′-end pre-mRNA processing to transcription termination. PMID:23857582

  17. Association of the 72/74-kDa proteins, members of the heterogeneous nuclear ribonucleoprotein M group, with the pre-mRNA at early stages of spliceosome assembly.

    PubMed Central

    Kafasla, Panayiota; Patrinou-Georgoula, Meropi; Lewis, Joe D; Guialis, Apostolia

    2002-01-01

    We have investigated the role played in precursor mRNA (pre-mRNA) splicing by the protein pair of molecular size 72/74 kDa, which are integral components of a discrete subset of heterogeneous nuclear (hn) ribonucleoproteins (RNPs) named large heterogeneous nuclear RNP (LH-nRNP). This 72/74 kDa pair of proteins has been shown to belong to the hnRNP M group, and are referred to as 72/74(M). By applying specific immunoprecipitation assays in a consecutive series of splicing reactions in vitro, the antigenic 72/74(M) protein species were found to associate with the pre-mRNA and not the intermediate or final products of splicing. Kinetic studies, combined with isolation of pre-spliceosomal and spliceosomal complexes from the splicing reaction, indicated a loose association of 72/74(M) with both the initially formed H assembly and the first splicing-committed E complex. Stable binding was seen at a later stage of the reaction, well in advance of the appearance of the first intermediate products of RNA splicing. Evidence is provided that supports the almost exclusive association of 72/74(M) with pre-mRNA within the pre-spliceosomal A complex. This dynamic binding appeared to involve pre-mRNA sites similar to those of spliceosomal U1 and U2 small nuclear RNP complexes. Moreover, a preferential binding to a truncated RNA containing the 5' exon-intron part, rather than the intron-3' exon part, of pre-mRNA was observed. PMID:11964181

  18. CERN and the Hunt for Elementary Particles and Forces

    NASA Astrophysics Data System (ADS)

    Tsesmelis, Emmanuel

    2008-04-01

    CERN is the European Laboratory for Particle Physics, the world's largest particle physics research centre. Founded in 1954, the Laboratory was one of Europe's first joint ventures and has become a premier example of international collaboration. CERN's subject of study is pure science and is concentrated on exploring the Universe's most fundamental questions, such as What is it made of? and How did it come to be the way it is? The Laboratory's tools, the particle accelerators and particle detectors, are amongst the world's largest and most complex scientific instruments. The Laboratory's primary aims will be presented and a look at past achievements and present endeavours, particularly the Large Hadron Collider (LHC), will be reviewed. A brief look into the future will also be given.

  19. Microfabricated particle focusing device

    DOEpatents

    Ravula, Surendra K.; Arrington, Christian L.; Sigman, Jennifer K.; Branch, Darren W.; Brener, Igal; Clem, Paul G.; James, Conrad D.; Hill, Martyn; Boltryk, Rosemary June

    2013-04-23

    A microfabricated particle focusing device comprises an acoustic portion to preconcentrate particles over large spatial dimensions into particle streams and a dielectrophoretic portion for finer particle focusing into single-file columns. The device can be used for high throughput assays for which it is necessary to isolate and investigate small bundles of particles and single particles.

  20. The Chaco Megafans: Hydrogeomorphology of the Largest Coalescing Megafans System in Earth

    NASA Astrophysics Data System (ADS)

    Latrubesse, E. M.; Cafaro, E. D.; Ramonell, C. G.

    2011-12-01

    Publications on megafans increased significantly providing information and opening debates on their global distribution and the importance of megafans across disciplines. With a few exceptions, however, little is known yet on the South American megafans evolution and on their present day morphodynamics. The Chaco plain, spreading 840,000 km2 to the east of the Andes mountain range along 1200 km from N to S, is the main area in the planet containing megafans. The main rivers drain the Andes and debouch on the Chaco plain, which acts as a sort of complex foreland-platform sedimentary basin. The Chaco rivers with headwaters in the Andes show, as a common geomorphological feature, alluvial fans ranging from typical piedmont alluvial fans to giant fluvial fans. The largest Chaco fans are generated by five major rivers (from north to south): Grande, Parapetí, Pilcomayo, Bermejo and Juramento rivers. We concentrated our analysis on an area of approximately 400,000 km2, 570 long (from 21°S to 27°S) and, 700 km wide from west to east, between the Subandean Ranges and the Paraguay and Paraná rivers where the Pilcomayo, Bermejo, Juramento, Itiyuro and del Valle megafans developed. The largest megafan is the Pilcomayo fan that stretches over an area of 220,000 km2, having a 610 km radius and a fan-front of 720 km. Systematic field work was developed in the area since 2005. Remote sensing products (Landsat 5, CBERS2, SRTM and MODIS) were processed in a GIS platform ENVI. Morphological parameters of alluvial fans and river channels such as planform areas, mean slopes, mean widths, thalweg sinuosity, among other morphometric parameters, were measured/estimated. Morpho-sedimentary units were identified in the field and the stratigraphic record ranges from the Late Pleistocene to present. Hydrological data were obtained from ten gauge stations. The main Chaco rivers built during the Late Pleistocene giant alluvial fans that were bigger than the present day fans. Water discharge

  1. Rewriting the Landform History of One of Africa's Three Largest Basins

    NASA Technical Reports Server (NTRS)

    Wilkinson, Justin

    2014-01-01

    The Kalahari Basin in southern Africa - one of the largest basins in Africa, along with the Congo and Chad basins - has attracted attention since David Livingstone traveled through the area in the 1840s. It is a semiarid desert with a large freshwater swampland known as the Okavango Swamp (150 km radius). This prominent megafan (a fan with radii >100 km), with its fingers of dark green forests projecting into the dun colors of the dunes of the Kalahari semi-desert, has been well photographed by astronauts over the years. The study area in the northern Kalahari basin is centered on the Okavango megafan of northwest Botswana, whose swampland has become well known as an African wildlife preserve of importance to biology and tourism alike. The Okavango River is unusual because it has deposited not one but two megafans along its course: the Okavango megafan and the Cubango megafan. The Okavango megafan is one of only three well-known megafans in Africa. Megafans on Earth were once thought to be rare, but recent research has documented 68 in Africa alone. Eleven megafans, plus three more candidates, have been documented in the area immediately surrounding the Okavango feature. These 11 megafans occupy the flattest and smoothest terrains adjacent to the neighboring upland and stand out as the darkest areas in the roughness map of the area. Megafan terrains occupy at least 200,000 sq km of the study area. The roughness map shown is based on an algorithm used first on Mars to quantify topographic roughness. Research of Earth's flattest terrains is just beginning with the aid of such maps, and it appears that these terrains are analogous to the flattest regions of Mars. Implications: 1. The variability in depositional style in each subbasin may apply Africa-wide: rift megafan length is dominated by rift width, whereas Owambo subbasin megafans are probably controlled by upland basin size; Zambezi subbasin megafans appear more like foreland basin types, with the position of

  2. Evidence for protection of targeted reef fish on the largest marine reserve in the Caribbean.

    PubMed

    Pina-Amargós, Fabián; González-Sansón, Gaspar; Martín-Blanco, Félix; Valdivia, Abel

    2014-01-01

    Marine reserves can restore fish abundance and diversity in areas impacted by overfishing, but the effectiveness of reserves in developing countries where resources for enforcement are limited, have seldom been evaluated. Here we assess whether the establishment in 1996 of the largest marine reserve in the Caribbean, Gardens of the Queen in Cuba, has had a positive effect on the abundance of commercially valuable reef fish species in relation to neighboring unprotected areas. We surveyed 25 sites, including two reef habitats (reef crest and reef slope), inside and outside the marine reserve, on five different months, and over a one-and-a-half year period. Densities of the ten most frequent, highly targeted, and relatively large fish species showed a significant variability across the archipelago for both reef habitats that depended on the month of survey. These ten species showed a tendency towards higher abundance inside the reserve in both reef habitats for most months during the study. Average fish densities pooled by protection level, however, showed that five out of these ten species were at least two-fold significantly higher inside than outside the reserve at one or both reef habitats. Supporting evidence from previously published studies in the area indicates that habitat complexity and major benthic communities were similar inside and outside the reserve, while fishing pressure appeared to be homogeneous across the archipelago before reserve establishment. Although poaching may occur within the reserve, especially at the boundaries, effective protection from fishing was the most plausible explanation for the patterns observed. PMID:24688853

  3. Using DNA to track the origin of the largest ivory seizure since the 1989 trade ban

    PubMed Central

    Wasser, Samuel K.; Mailand, Celia; Booth, Rebecca; Mutayoba, Benezeth; Kisamo, Emily; Clark, Bill; Stephens, Matthew

    2007-01-01

    The illegal ivory trade recently intensified to the highest levels ever reported. Policing this trafficking has been hampered by the inability to reliably determine geographic origin of contraband ivory. Ivory can be smuggled across multiple international borders and along numerous trade routes, making poaching hotspots and potential trade routes difficult to identify. This fluidity also makes it difficult to refute a country's denial of poaching problems. We extend an innovative DNA assignment method to determine the geographic origin(s) of large elephant ivory seizures. A Voronoi tessellation method is used that utilizes genetic similarities across tusks to simultaneously infer the origin of multiple samples that could have one or more common origin(s). We show that this joint analysis performs better than sample-by-sample methods in assigning sample clusters of known origin. The joint method is then used to infer the geographic origin of the largest ivory seizure since the 1989 ivory trade ban. Wildlife authorities initially suspected that this ivory came from multiple locations across forest and savanna Africa. However, we show that the ivory was entirely from savanna elephants, most probably originating from a narrow east-to-west band of southern Africa, centered on Zambia. These findings enabled law enforcement to focus their investigation to a smaller area and fewer trade routes and led to changes within the Zambian government to improve antipoaching efforts. Such outcomes demonstrate the potential of genetic analyses to help combat the expanding wildlife trade by identifying origin(s) of large seizures of contraband ivory. Broader applications to wildlife trade are discussed. PMID:17360505

  4. Forest biomonitoring of the largest Slovene thermal power plant with respect to reduction of air pollution.

    PubMed

    Al Sayegh Petkovšek, Samar

    2013-02-01

    The condition of the forest ecosystem in the vicinity of the largest Slovene power plant [the Šoštanj Thermal Power Plant (ŠTPP)] was monitored during the period 1991-2008 by determining the total concentration of sulphur, ascorbic acid and chlorophyll in Norway spruce needles. After 1995, the introduction of cleaning devices at the ŠTPP dramatically reduced the former extremely high SO(2) and dust emissions. The most significant findings of this comprehensive, long-duration survey are as follows: (1) the chosen parameters are suitable bioindicators of stress caused by air pollution in Norway spruce needles; they reflect both spatial and temporal variations in air pollution as well as the degree of efficiency of the cleaning devices; (2) observations show that the physiological condition of Norway spruce in northern Slovenia has significantly improved since 1995, when the first desulphurization device at ŠTPP was built, together with a reduction in the area influenced by pollution from ŠTPP; (3) metabolic processes in spruce needles react to air pollution according to the severity of the pollution and the length of exposure; exposure to high SO(2) ambient levels and/or spread over a long duration can damage the antioxidant defence mechanisms of spruce trees as well as diminishing the concentration of ascorbic acid; (4) a reduction in the exposure to air pollution improves the vitality of the trees (e.g. higher concentrations of total (a + b) chlorophyll), as well as restoring their defence capabilities as shown by higher concentrations of ascorbic acid; and (5) forest monitoring should be continued and focused on integrating the effects of multiple stressors, which can additionally affect a forest ecosystem.

  5. Flexible slip near the largest step-over along the North Anatolian fault system, Turkey

    NASA Astrophysics Data System (ADS)

    Kondo, H.; Kurcer, A.; Özalp, S.; Emre, O.

    2010-12-01

    Repeatability of surface slip distribution through earthquake cycles is basis to evaluate size and timing of future large earthquakes generated by active fault systems. In order to reveal surface slip history associated with paleoearthquakes on the North Anatolian fault system (NAFS), we have extensively performed 3D trenching survey on the 1942 Erbaa-Niksar earthquake (M 7.0) ruptures, to simultaneously reconstruct timing and surface slip associated with past large earthquakes. At Ayvaz site on the 1942 rupture, our 3D trench survey preliminary indicated that the penultimate earthquake, which can be correlated with the great Anatolian earthquake (M ~8.0) in 1668 AD, recorded larger surface slip of 6.0-8.0 m in comparison with the 1942 slip of 2.5 m. This result supports historical documents telling that the 1668 event ruptured for >600 km long on the central-eastern NAFS and it likely jumped across the 11-km-wide step-over that is the largest along the NAFS. In order to confirm this flexible slip history according to the magnitude of large earthquakes, we re-excavated 3D trenches to reconstruct longer slip history at the same site. The results are summarized as follows; 1) at the site, high-resolution alluvium exposed on the trench walls records six paleoearthquakes including the 1942 and 1668 events during the last ~2500 years, 2) we reconstructed five discrete slips during the individual events, 3) the amounts of paleo-slips are classified into two categories; the 1942-type smaller slips and the 1668-type larger slips. Thus, the repeatability of surface slip during large earthquakes is not constant like the assumption of the characteristic earthquake model, however, the amounts do not randomly vary from event to event on the assumption of the Gutenberg-Richter model.

  6. Effects of light on the largest extant benthic foraminifer, Cycloclypeus carpenteri

    NASA Astrophysics Data System (ADS)

    Fujita, Kazuhiko; Kanda, Yoji

    2015-04-01

    Cycloclypeus carpenteri is the largest extant benthic foraminifer. This species dwells in deep euphotic depths of warm oligotrophic waters, and is a host to diatom endosymbionts. Fossil Cycloclypeus has been found in tropical shelf carbonates since the Oligocene. Light is supposed to be the primary environmental factor controlling the depth distribution of this species. However, physiological responses of this foraminifer to light are not yet well understood. We investigated short-term and long-term effects of light on Cycloclypeus carpenteri collected from about 70 m depth, west of Okinawa Island (Japan). To determine short-term responses to light, net oxygen production was measured at different light levels and wavelengths using an oxygen microelectrode. Photosynthesis-irradiance curve of this species indicated that net oxygen production increased up to 50 µE m-2 s-1, was saturated until 100 µE m-2 s-1, then was photoinhibited over 100 µE m-2 s-1. Net production was higher when incubated on blue wavelength than on either red or green wavelengths. To determine long-term light effects, asexually reproduced clone individuals were incubated for about 4 months at different light levels ranging from 0 to 100 µE m-2 s-1. The long-term incubations indicated that growth rates measured by the surface area were optimal at light levels from 5 to 50 µE m-2 s-1, but were lowered at 0 and 100 µE m-2 s-1. These results suggest that Cycloclypeus carpenteri can be acclimatized at less than 100 µE m-2 s-1 of light by changing photopigment (chrolophyll) concentrations of algal symbionts, but this species cannot survive in dark and over 100 µE m-2 s-1 of light due to the breakdown of algal symbiosis.

  7. Preserving the world second largest hypersaline lake under future irrigation and climate change.

    PubMed

    Shadkam, Somayeh; Ludwig, Fulco; van Vliet, Michelle T H; Pastor, Amandine; Kabat, Pavel

    2016-07-15

    Iran Urmia Lake, the world second largest hypersaline lake, has been largely desiccated over the last two decades resulting in socio-environmental consequences similar or even larger than the Aral Sea disaster. To rescue the lake a new water management plan has been proposed, a rapid 40% decline in irrigation water use replacing a former plan which intended to develop reservoirs and irrigation. However, none of these water management plans, which have large socio-economic impacts, have been assessed under future changes in climate and water availability. By adapting a method of environmental flow requirements (EFRs) for hypersaline lakes, we estimated annually 3.7·10(9)m(3) water is needed to preserve Urmia Lake. Then, the Variable Infiltration Capacity (VIC) hydrological model was forced with bias-corrected climate model outputs for both the lowest (RCP2.6) and highest (RCP8.5) greenhouse-gas concentration scenarios to estimate future water availability and impacts of water management strategies. Results showed a 10% decline in future water availability in the basin under RCP2.6 and 27% under RCP8.5. Our results showed that if future climate change is highly limited (RCP2.6) inflow can be just enough to meet the EFRs by implementing the reduction irrigation plan. However, under more rapid climate change scenario (RCP8.5) reducing irrigation water use will not be enough to save the lake and more drastic measures are needed. Our results showed that future water management plans are not robust under climate change in this region. Therefore, an integrated approach of future land-water use planning and climate change adaptation is therefore needed to improve future water security and to reduce the desiccating of this hypersaline lake.

  8. The Quest for the Largest Depleted Galaxy Core: Supermassive Black Hole Binaries and Stalled Infalling Satellites

    NASA Astrophysics Data System (ADS)

    Bonfini, Paolo; Graham, Alister W.

    2016-10-01

    Partially depleted cores are practically ubiquitous in luminous early-type galaxies (M B ≲ -20.5 mag) and are typically smaller than 1 kpc. In one popular scenario, supermassive black hole (SMBH) binaries—established during dry (i.e., gas-poor) galaxy mergers—kick out the stars from a galaxy’s central region via three-body interactions. Here, this “binary black hole scouring scenario” is probed at its extremes by investigating the two galaxies reported to have the largest partially depleted cores found to date: 2MASX J09194427+5622012 and 2MASX J17222717+3207571 (the brightest galaxy in Abell 2261). We have fit these galaxy’s two-dimensional light distribution using the core-Sérsic model and found that the former galaxy has a core-Sérsic break radius {R}b,{cS}=0.55 {{kpc}}, which is three times smaller than the published value. We use this galaxy to caution that other reportedly large break radii may too have been overestimated if they were derived using the “sharp-transition” (inner core)-to-(outer Sérsic) model. In the case of 2MASX J17222717+3207571, we obtain R b,cS = 3.6 kpc. While we confirm that this is the biggest known partially depleted core of any galaxy, we stress that it is larger than expected from the evolution of SMBH binaries—unless one invokes substantial gravitational-wave-induced (black hole-)recoil events. Given the presence of multiple nuclei located (in projection) within the core radius of this galaxy, we explored and found support for the alternative “stalled infalling perturber” core-formation scenario, in which this galaxy’s core could have been excavated by the action of an infalling massive perturber.

  9. Dragon's Paradise Lost: Palaeobiogeography, Evolution and Extinction of the Largest-Ever Terrestrial Lizards (Varanidae)

    PubMed Central

    Hocknull, Scott A.; Piper, Philip J.; van den Bergh, Gert D.; Due, Rokus Awe; Morwood, Michael J.; Kurniawan, Iwan

    2009-01-01

    Background The largest living lizard species, Varanus komodoensis Ouwens 1912, is vulnerable to extinction, being restricted to a few isolated islands in eastern Indonesia, between Java and Australia, where it is the dominant terrestrial carnivore. Understanding how large-bodied varanids responded to past environmental change underpins long-term management of V. komodoensis populations. Methodology/Principal Findings We reconstruct the palaeobiogeography of Neogene giant varanids and identify a new (unnamed) species from the island of Timor. Our data reject the long-held perception that V. komodoensis became a giant because of insular evolution or as a specialist hunter of pygmy Stegodon. Phyletic giantism, coupled with a westward dispersal from mainland Australia, provides the most parsimonious explanation for the palaeodistribution of V. komodoensis and the newly identified species of giant varanid from Timor. Pliocene giant varanid fossils from Australia are morphologically referable to V. komodoensis suggesting an ultimate origin for V. komodoensis on mainland Australia (>3.8 million years ago). Varanus komodoensis body size has remained stable over the last 900,000 years (ka) on Flores, a time marked by major faunal turnovers, extinction of the island's megafauna, the arrival of early hominids by 880 ka, co-existence with Homo floresiensis, and the arrival of modern humans by 10 ka. Within the last 2000 years their populations have contracted severely. Conclusions/Significance Giant varanids were once a ubiquitous part of Subcontinental Eurasian and Australasian faunas during the Neogene. Extinction played a pivotal role in the reduction of their ranges and diversity throughout the late Quaternary, leaving only V. komodoensis as an isolated long-term survivor. The events over the last two millennia now threaten its future survival. PMID:19789642

  10. Using DNA to track the origin of the largest ivory seizure since the 1989 trade ban.

    PubMed

    Wasser, Samuel K; Mailand, Celia; Booth, Rebecca; Mutayoba, Benezeth; Kisamo, Emily; Clark, Bill; Stephens, Matthew

    2007-03-01

    The illegal ivory trade recently intensified to the highest levels ever reported. Policing this trafficking has been hampered by the inability to reliably determine geographic origin of contraband ivory. Ivory can be smuggled across multiple international borders and along numerous trade routes, making poaching hotspots and potential trade routes difficult to identify. This fluidity also makes it difficult to refute a country's denial of poaching problems. We extend an innovative DNA assignment method to determine the geographic origin(s) of large elephant ivory seizures. A Voronoi tessellation method is used that utilizes genetic similarities across tusks to simultaneously infer the origin of multiple samples that could have one or more common origin(s). We show that this joint analysis performs better than sample-by-sample methods in assigning sample clusters of known origin. The joint method is then used to infer the geographic origin of the largest ivory seizure since the 1989 ivory trade ban. Wildlife authorities initially suspected that this ivory came from multiple locations across forest and savanna Africa. However, we show that the ivory was entirely from savanna elephants, most probably originating from a narrow east-to-west band of southern Africa, centered on Zambia. These findings enabled law enforcement to focus their investigation to a smaller area and fewer trade routes and led to changes within the Zambian government to improve antipoaching efforts. Such outcomes demonstrate the potential of genetic analyses to help combat the expanding wildlife trade by identifying origin(s) of large seizures of contraband ivory. Broader applications to wildlife trade are discussed. PMID:17360505

  11. Solomon Islands largest hawksbill turtle rookery shows signs of recovery after 150 years of excessive exploitation.

    PubMed

    Hamilton, Richard J; Bird, Tomas; Gereniu, Collin; Pita, John; Ramohia, Peter C; Walter, Richard; Goerlich, Clara; Limpus, Colin

    2015-01-01

    The largest rookery for hawksbill turtles in the oceanic South Pacific is the Arnavon Islands, which are located in the Manning Strait between Isabel and Choiseul Province, Solomon Islands. The history of this rookery is one of overexploitation, conflict and violence. Throughout the 1800s Roviana headhunters from New Georgia repeatedly raided the Manning Strait to collect hawksbill shell which they traded with European whalers. By the 1970s the Arnavons hawksbill population was in severe decline and the national government intervened, declaring the Arnavons a sanctuary in 1976. But this government led initiative was short lived, with traditional owners burning down the government infrastructure and resuming intensive harvesting in 1982. In 1991 routine beach monitoring and turtle tagging commenced at the Arnavons along with extensive community consultations regarding the islands' future, and in 1995 the Arnavon Community Marine Conservation Area (ACMCA) was established. Around the same time national legislation banning the sale of all turtle products was passed. This paper represents the first analysis of data from 4536 beach surveys and 845 individual turtle tagging histories obtained from the Arnavons between 1991-2012. Our results and the results of others, reveal that many of the hawksbill turtles that nest at the ACMCA forage in distant Australian waters, and that nesting on the Arnavons occurs throughout the year with peak nesting activity coinciding with the austral winter. Our results also provide the first known evidence of recovery for a western pacific hawksbill rookery, with the number of nests laid at the ACMCA and the remigration rates of turtles doubling since the establishment of the ACMCA in 1995. The Arnavons case study provides an example of how changes in policy, inclusive community-based management and long term commitment can turn the tide for one of the most charismatic and endangered species on our planet.

  12. Nature appropriation and associations with population health in Canada's largest cities.

    PubMed

    Rainham, Daniel; Cantwell, Rory; Jason, Timothy

    2013-04-01

    Earth is a finite system with a limited supply of resources. As the human population grows, so does the appropriation of Earth's natural capital, thereby exacerbating environmental concerns such as biodiversity loss, increased pollution, deforestation and global warming. Such concerns will negatively impact human health although it is widely believed that improving socio-economic circumstances will help to ameliorate environmental impacts and improve health outcomes. However, this belief does not explicitly acknowledge the fact that improvements in socio-economic position are reliant on increased inputs from nature. Gains in population health, particularly through economic means, are disconnected from the appropriation of nature to create wealth so that health gains become unsustainable. The current study investigated the sustainability of human population health in Canada with regard to resource consumption or "ecological footprints" (i.e., the resources required to sustain a given population). Ecological footprints of the 20 largest Canadian cities, along with several important determinants of health such as income and education, were statistically compared with corresponding indicators of human population health outcomes. A significant positive relationship was found between ecological footprints and life expectancy, as well as a significant negative relationship between ecological footprints and the prevalence of high blood pressure. Results suggest that increased appropriation of nature is linked to improved health outcomes. To prevent environmental degradation from excessive appropriation of natural resources will require the development of health promotion strategies that are de-coupled from ever-increasing and unsustainable resource use. Efforts to promote population health should focus on health benefits achieved from a lifestyle based on significantly reduced consumption of natural resources.

  13. Using DNA to track the origin of the largest ivory seizure since the 1989 trade ban.

    PubMed

    Wasser, Samuel K; Mailand, Celia; Booth, Rebecca; Mutayoba, Benezeth; Kisamo, Emily; Clark, Bill; Stephens, Matthew

    2007-03-01

    The illegal ivory trade recently intensified to the highest levels ever reported. Policing this trafficking has been hampered by the inability to reliably determine geographic origin of contraband ivory. Ivory can be smuggled across multiple international borders and along numerous trade routes, making poaching hotspots and potential trade routes difficult to identify. This fluidity also makes it difficult to refute a country's denial of poaching problems. We extend an innovative DNA assignment method to determine the geographic origin(s) of large elephant ivory seizures. A Voronoi tessellation method is used that utilizes genetic similarities across tusks to simultaneously infer the origin of multiple samples that could have one or more common origin(s). We show that this joint analysis performs better than sample-by-sample methods in assigning sample clusters of known origin. The joint method is then used to infer the geographic origin of the largest ivory seizure since the 1989 ivory trade ban. Wildlife authorities initially suspected that this ivory came from multiple locations across forest and savanna Africa. However, we show that the ivory was entirely from savanna elephants, most probably originating from a narrow east-to-west band of southern Africa, centered on Zambia. These findings enabled law enforcement to focus their investigation to a smaller area and fewer trade routes and led to changes within the Zambian government to improve antipoaching efforts. Such outcomes demonstrate the potential of genetic analyses to help combat the expanding wildlife trade by identifying origin(s) of large seizures of contraband ivory. Broader applications to wildlife trade are discussed.

  14. The 100-C-7 Remediation Project. An Overview of One of DOE's Largest Remediation Projects - 13260

    SciTech Connect

    Post, Thomas C.; Strom, Dean; Beulow, Laura

    2013-07-01

    The U.S. Department of Energy Richland Operations Office (RL), U.S. Environmental Protection Agency (EPA) and Washington Closure Hanford LLC (WCH) completed remediation of one of the largest waste sites in the U.S. Department of Energy complex. The waste site, 100-C-7, covers approximately 15 football fields and was excavated to a depth of 85 feet (groundwater). The project team removed a total of 2.3 million tons of clean and contaminated soil, concrete debris, and scrap metal. 100-C-7 lies in Hanford's 100 B/C Area, home to historic B and C Reactors. The waste site was excavated in two parts as 100-C-7 and 100-C-7:1. The pair of excavations appear like pit mines. Mining engineers were hired to design their tiered sides, with safety benches every 17 feet and service ramps which allowed equipment access to the bottom of the excavations. The overall cleanup project was conducted over a span of almost 10 years. A variety of site characterization, excavation, load-out and sampling methodologies were employed at various stages of remediation. Alternative technologies were screened and evaluated during the project. A new method for cost effectively treating soils was implemented - resulting in significant cost savings. Additional opportunities for minimizing waste streams and recycling were identified and effectively implemented by the project team. During the final phase of cleanup the project team applied lessons learned throughout the entire project to address the final, remaining source of chromium contamination. The C-7 cleanup now serves as a model for remediating extensive deep zone contamination sites at Hanford. (authors)

  15. The world's largest macroalgal bloom in the Yellow Sea, China: Formation and implications

    NASA Astrophysics Data System (ADS)

    Liu, Dongyan; Keesing, John K.; He, Peimin; Wang, Zongling; Shi, Yajun; Wang, Yujue

    2013-09-01

    The world's largest trans-regional macroalgal blooms during 2008-2012 occurred in the Yellow Sea, China. This review addresses the causes, development and future challenges in this unique case. Satellite imagery and field observations showed that the macroalgal blooms in the Yellow Sea originated from the coast of Jiangsu province and that favorable geographic and oceanographic conditions brought the green macroalgae from the coast offshore. Optimal temperature, light, nutrients and wind contributed to the formation and transport of the massive bloom north into the Yellow Sea and its deposition onshore along the coast of Shandong province. Morphological and genetic evidence demonstrated that the species involved was Ulva prolifera, a fouling green commonly found growing on structures provided by facilities of Porphyra aquaculture. Large scale Porphyra aquaculture (covering >20,000 ha) along the Jiangsu coast thus hypothetically provided a nursery bed for the original biomass of U. prolifera. Porphyra growers remove U. prolifera from the mariculture rafts, and the cleaning releases about 5000 wet weight tonnes of green algae into the water column along the coast of Jiangsu province; the biomass then is dispersed by hydrographic forcing, and takes advantage of rather high nutrient supply and suitable temperatures to grow to impressive levels. Certain biological traits of U. prolifera —efficient photosynthesis, rapid growth rates, high capacity for nutrient uptake, and diverse reproductive systems— allowed growth of the original 5000 tonnes of U. prolifera biomass into more than one million tonnes of biomass in just two months. The proliferation of U. prolifera in the Yellow Sea resulted from a complex contingency of circumstances, including human activity (eutrophication by release of nutrients from wastewater, agriculture, and aquaculture), natural geographic and hydrodynamic conditions (current, wind) and the key organism's biological attributes. Better

  16. Solomon Islands largest hawksbill turtle rookery shows signs of recovery after 150 years of excessive exploitation.

    PubMed

    Hamilton, Richard J; Bird, Tomas; Gereniu, Collin; Pita, John; Ramohia, Peter C; Walter, Richard; Goerlich, Clara; Limpus, Colin

    2015-01-01

    The largest rookery for hawksbill turtles in the oceanic South Pacific is the Arnavon Islands, which are located in the Manning Strait between Isabel and Choiseul Province, Solomon Islands. The history of this rookery is one of overexploitation, conflict and violence. Throughout the 1800s Roviana headhunters from New Georgia repeatedly raided the Manning Strait to collect hawksbill shell which they traded with European whalers. By the 1970s the Arnavons hawksbill population was in severe decline and the national government intervened, declaring the Arnavons a sanctuary in 1976. But this government led initiative was short lived, with traditional owners burning down the government infrastructure and resuming intensive harvesting in 1982. In 1991 routine beach monitoring and turtle tagging commenced at the Arnavons along with extensive community consultations regarding the islands' future, and in 1995 the Arnavon Community Marine Conservation Area (ACMCA) was established. Around the same time national legislation banning the sale of all turtle products was passed. This paper represents the first analysis of data from 4536 beach surveys and 845 individual turtle tagging histories obtained from the Arnavons between 1991-2012. Our results and the results of others, reveal that many of the hawksbill turtles that nest at the ACMCA forage in distant Australian waters, and that nesting on the Arnavons occurs throughout the year with peak nesting activity coinciding with the austral winter. Our results also provide the first known evidence of recovery for a western pacific hawksbill rookery, with the number of nests laid at the ACMCA and the remigration rates of turtles doubling since the establishment of the ACMCA in 1995. The Arnavons case study provides an example of how changes in policy, inclusive community-based management and long term commitment can turn the tide for one of the most charismatic and endangered species on our planet. PMID:25853880

  17. Solomon Islands Largest Hawksbill Turtle Rookery Shows Signs of Recovery after 150 Years of Excessive Exploitation

    PubMed Central

    Hamilton, Richard J.; Bird, Tomas; Gereniu, Collin; Pita, John; Ramohia, Peter C.; Walter, Richard; Goerlich, Clara; Limpus, Colin

    2015-01-01

    The largest rookery for hawksbill turtles in the oceanic South Pacific is the Arnavon Islands, which are located in the Manning Strait between Isabel and Choiseul Province, Solomon Islands. The history of this rookery is one of overexploitation, conflict and violence. Throughout the 1800s Roviana headhunters from New Georgia repeatedly raided the Manning Strait to collect hawksbill shell which they traded with European whalers. By the 1970s the Arnavons hawksbill population was in severe decline and the national government intervened, declaring the Arnavons a sanctuary in 1976. But this government led initiative was short lived, with traditional owners burning down the government infrastructure and resuming intensive harvesting in 1982. In 1991 routine beach monitoring and turtle tagging commenced at the Arnavons along with extensive community consultations regarding the islands’ future, and in 1995 the Arnavon Community Marine Conservation Area (ACMCA) was established. Around the same time national legislation banning the sale of all turtle products was passed. This paper represents the first analysis of data from 4536 beach surveys and 845 individual turtle tagging histories obtained from the Arnavons between 1991-2012. Our results and the results of others, reveal that many of the hawksbill turtles that nest at the ACMCA forage in distant Australian waters, and that nesting on the Arnavons occurs throughout the year with peak nesting activity coinciding with the austral winter. Our results also provide the first known evidence of recovery for a western pacific hawksbill rookery, with the number of nests laid at the ACMCA and the remigration rates of turtles doubling since the establishment of the ACMCA in 1995. The Arnavons case study provides an example of how changes in policy, inclusive community-based management and long term commitment can turn the tide for one of the most charismatic and endangered species on our planet. PMID:25853880

  18. Gas migration and carbon capture in one of the World's largest pockmark fields, the Norwegian Sea

    NASA Astrophysics Data System (ADS)

    Mazzini, A.; Svensen, H.; Planke, S.; Hammer, O.; Linge, H. C.; Forsberg, C. F.; Tjelta, T.

    2013-12-01

    Acoustic imaging has revealed more than 7000 pockmarks above the Troll East gas field in the Norwegian Sea. The pockmarks range in size from 10 to 100 meters in diameter and are typically 6 meters deep. High-resolution bathymetric data shows that there is no evidence of structural control on the location of the pockmarks. This conclusion is in agreement with statistical analysis of the pockmark distribution which shows neighbor avoidance up to a scale of hundreds of meters and no indication of a fractal geometry. The pockmarks generally represent isolated structures and sometimes are identified in clusters with a central parent pockmark surrounded by smaller sized satellite pockmarks. Seafloor observations show that carbonate deposits are common within the pockmarks, providing shelter to the local fauna. Carbonate blocks collected from the pockmarks showed evidence for three distinct generations including micritic Mg-calcite/aragonite, micritic aragonite, and botryoidal aragonite. The carbon isotopic values of these phases are 13C depleted and 18O enriched, indicating a methanogenic origin and possibly a component sourced from dissociation of gas hydrates. Water geochemistry from shallow cores within and outside the pockmarks gave no indication of active seepage. This conclusion is further supported by no direct observations of fluid flow within the pockmarks, no bacterial mats nor obvious chemosymbiotic communities. In addition, oxidized carbonate surfaces indicate a gradual excavation and exposure at the sea floor. We conclude that one of the world's largest pockmark fields is currently inactive and that its formation is likely related to deglaciation processes about 11 ky ago.

  19. Lessons Learned in Deploying the World s Largest Scale Lustre File System

    SciTech Connect

    Dillow, David A; Fuller, Douglas; Wang, Feiyi; Oral, H Sarp; Zhang, Zhe; Hill, Jason J; Shipman, Galen M

    2010-01-01

    The Spider system at the Oak Ridge National Laboratory's Leadership Computing Facility (OLCF) is the world's largest scale Lustre parallel file system. Envisioned as a shared parallel file system capable of delivering both the bandwidth and capacity requirements of the OLCF's diverse computational environment, the project had a number of ambitious goals. To support the workloads of the OLCF's diverse computational platforms, the aggregate performance and storage capacity of Spider exceed that of our previously deployed systems by a factor of 6x - 240 GB/sec, and 17x - 10 Petabytes, respectively. Furthermore, Spider supports over 26,000 clients concurrently accessing the file system, which exceeds our previously deployed systems by nearly 4x. In addition to these scalability challenges, moving to a center-wide shared file system required dramatically improved resiliency and fault-tolerance mechanisms. This paper details our efforts in designing, deploying, and operating Spider. Through a phased approach of research and development, prototyping, deployment, and transition to operations, this work has resulted in a number of insights into large-scale parallel file system architectures, from both the design and the operational perspectives. We present in this paper our solutions to issues such as network congestion, performance baselining and evaluation, file system journaling overheads, and high availability in a system with tens of thousands of components. We also discuss areas of continued challenges, such as stressed metadata performance and the need for file system quality of service alongside with our efforts to address them. Finally, operational aspects of managing a system of this scale are discussed along with real-world data and observations.

  20. Grassland bird responses to land management in the largest remaining tallgrass prairie.

    PubMed

    Rahmig, Corina J; Jensen, William E; With, Kimberly A

    2009-04-01

    Extensive habitat loss and changing agricultural practices have caused widespread declines in grassland birds throughout North America. The Flint Hills of Kansas and Oklahoma--the largest remaining tallgrass prairie--is important for grassland bird conservation despite supporting a major cattle industry. In 2004 and 2005, we assessed the community, population, and demographic responses of grassland birds to the predominant management practices (grazing, burning, and haying) of the region, including grasslands restored under the Conservation Reserve Program (CRP). We targeted 3 species at the core of this avian community: the Dickcissel (Spiza americana), Grasshopper Sparrow (Ammodramus savannarum), and Eastern Meadowlark (Sturnella magna). Bird diversity was higher in native prairie hayfields and grazed pastures than CRP fields, which were dominated by Dickcissels. Although Dickcissel density was highest in CRP, their nest success was highest and nest parasitism by Brown-headed Cowbirds (Moluthrus ater) lowest in unburned hayfields (in 2004). Conversely, Grasshopper Sparrow density was highest in grazed pastures, but their nest success was lowest in these pastures and highest in burned hayfields, where cowbird parasitism was also lowest (in 2004). Management did not influence density and nest survival of Eastern Meadowlarks, which were uniformly low across the region. Nest success was extremely low (5-12%) for all 3 species in 2005, perhaps because of a record spring drought. Although the CRP has benefited grassland birds in agricultural landscapes, these areas may have lower habitat value in the context of native prairie. Hayfields may provide beneficial habitat for some grassland birds in the Flint Hills because they are mowed later in the breeding season than elsewhere in the Midwest. Widespread grazing and annual burning have homogenized habitat-and thus grassland-bird responses-across the Flint Hills. Diversification of management practices could increase

  1. Hydroclimatological influences at multi-spatial scales on recently increased droughts in China's largest freshwater lake

    NASA Astrophysics Data System (ADS)

    Liu, Y.; Wu, G.

    2014-05-01

    Lake droughts are the consequences of climatic, hydrologic and anthropogenic influences. It may produce substantial impacts on local water sources, inhabitants and economy, but few studies have determined the contributions from the individual influences, especially under the changing climate, which is of highly valuable for policymakers to make effective adaption. This study proposes to use a multi-scale hydroclimatic analysis for the determination, taking Poyang Lake as an example. It is the China's largest freshwater lake, which has been undergoing drastic hydrological alterations in recent decade. Our analysis demonstrates that in the recent decade the lake droughts worsened in terms of duration, frequency, magnitude and severity, and intensified in magnitude significantly. At the lake region, water deficiency severed as the hydroclimatic foundation for the worsening droughts. Overall contribution to the lake droughts included decreased inflow (45%), increased outflow (24%), reduced local precipitation (23%), and increased evapotranspiration (8%). At the basin scale, the decreased inflow was ascribed to reduced basin-scale precipitation (82%) and increased evapotranspiration (18%). The increased outflow was principally controlled by the weakened blocking effects of the Yangtze River, which serves as a boundary condition of Poyang Lake. Water impoundments of the Three Gorges Dam (TGD) established upstream should not be responsible for the increased drought occurrence, but they may have enhanced the drought magnitude with a limit contribution. The findings provide an example of intensified lake droughts, and offer an insightful view into lake droughts under the changing climate and anthropogenic influences. It should be valuable for improving our understanding and for promoting effective climate adaptation and water resources management practices.

  2. Evidence for protection of targeted reef fish on the largest marine reserve in the Caribbean

    PubMed Central

    Pina-Amargós, Fabián; González-Sansón, Gaspar; Martín-Blanco, Félix

    2014-01-01

    Marine reserves can restore fish abundance and diversity in areas impacted by overfishing, but the effectiveness of reserves in developing countries where resources for enforcement are limited, have seldom been evaluated. Here we assess whether the establishment in 1996 of the largest marine reserve in the Caribbean, Gardens of the Queen in Cuba, has had a positive effect on the abundance of commercially valuable reef fish species in relation to neighboring unprotected areas. We surveyed 25 sites, including two reef habitats (reef crest and reef slope), inside and outside the marine reserve, on five different months, and over a one-and-a-half year period. Densities of the ten most frequent, highly targeted, and relatively large fish species showed a significant variability across the archipelago for both reef habitats that depended on the month of survey. These ten species showed a tendency towards higher abundance inside the reserve in both reef habitats for most months during the study. Average fish densities pooled by protection level, however, showed that five out of these ten species were at least two-fold significantly higher inside than outside the reserve at one or both reef habitats. Supporting evidence from previously published studies in the area indicates that habitat complexity and major benthic communities were similar inside and outside the reserve, while fishing pressure appeared to be homogeneous across the archipelago before reserve establishment. Although poaching may occur within the reserve, especially at the boundaries, effective protection from fishing was the most plausible explanation for the patterns observed. PMID:24688853

  3. Climatic effects of urban expansion over the three largest urban agglomerations of China

    NASA Astrophysics Data System (ADS)

    Cao, Qian; Yu, Deyong; Georgescu, Matei; Wu, Jianguo

    2016-04-01

    Urbanization has long been known to affect local, regional, and global climate. China is urbanizing at an unprecedented rate, and modification of land surface to urban areas has raised climate concerns for its citizens. Using the Weather Research and Forecasting (WRF) model, we examine how urbanization under different intensities and climate regimes affects regional climate of the three largest urban agglomerations across China - the Beijing-Tianjin-Hebei (BTH), the Yangtze River Delta (YRD), and the Pearl River Delta (PRD). We simulated three urban expansion scenarios corresponding to 1988, 2000, and 2010 conditions into the WRF model, with each scenario simulated by three separate summers (i.e., 2001, 2003, and 2005). Urban extent of the three regions indicates stable growth during 1988 - 2000, followed by a phase of rapid expansion during 2000 - 2010. Our simulations show that urban environment-induced near-surface warming, mainly rising temperatures during nighttime, is greatest over the BTH with local maximum warming approaching 1.5 °C, followed by the YRD with peak warming reaching 1 °C and the PRD 0.8 °C. Due to the initial moisture conditions, the YRD and the PRD suffer more humidity deficit, particularly during daytime, with maximum reductions in water vapor mixing ratio reaching 0.8 g/kg. Our findings demonstrate that urban expansion has warmed and dried the urbanized regions in eastern China. The spatial pattern and magnitude of temperature and humidity differences quantified by our simulations provide useful information for understanding the impacts of urbanization on regional climate and for developing mitigation and adaptation strategies that can alleviate the deleterious impacts induced by urban expansion.

  4. Preserving the world second largest hypersaline lake under future irrigation and climate change.

    PubMed

    Shadkam, Somayeh; Ludwig, Fulco; van Vliet, Michelle T H; Pastor, Amandine; Kabat, Pavel

    2016-07-15

    Iran Urmia Lake, the world second largest hypersaline lake, has been largely desiccated over the last two decades resulting in socio-environmental consequences similar or even larger than the Aral Sea disaster. To rescue the lake a new water management plan has been proposed, a rapid 40% decline in irrigation water use replacing a former plan which intended to develop reservoirs and irrigation. However, none of these water management plans, which have large socio-economic impacts, have been assessed under future changes in climate and water availability. By adapting a method of environmental flow requirements (EFRs) for hypersaline lakes, we estimated annually 3.7·10(9)m(3) water is needed to preserve Urmia Lake. Then, the Variable Infiltration Capacity (VIC) hydrological model was forced with bias-corrected climate model outputs for both the lowest (RCP2.6) and highest (RCP8.5) greenhouse-gas concentration scenarios to estimate future water availability and impacts of water management strategies. Results showed a 10% decline in future water availability in the basin under RCP2.6 and 27% under RCP8.5. Our results showed that if future climate change is highly limited (RCP2.6) inflow can be just enough to meet the EFRs by implementing the reduction irrigation plan. However, under more rapid climate change scenario (RCP8.5) reducing irrigation water use will not be enough to save the lake and more drastic measures are needed. Our results showed that future water management plans are not robust under climate change in this region. Therefore, an integrated approach of future land-water use planning and climate change adaptation is therefore needed to improve future water security and to reduce the desiccating of this hypersaline lake. PMID:27070383

  5. Tobacco control challenges in East Asia: proposals for change in the world's largest epidemic region

    PubMed Central

    Katanoda, Kota; Jiang, Yuan; Park, Sohee; Lim, Min Kyung; Qiao, You-Lin; Inoue, Manami

    2014-01-01

    East Asia is one of the world's largest tobacco epidemic regions. Although several international studies have evaluated the status of tobacco control in this region, the findings have not been integrated with knowledge on domestic activities at the national and municipal levels. We analysed the current tobacco control situation in three East Asian countries, Japan, China and the Republic of Korea, using both international and domestic data sources. We collected data between 2008 and 2011 in each country according to the framework of WHO's MPOWER (Monitoring, Protect, Offer, Warn, Enforcement and Raise) approach for guiding implementation of the WHO Framework Convention on Tobacco Control. Analysis revealed that 37–53% of adult men were current smokers and that smoking prevalence among middle-aged men reached 63%. Less than 20% of male smokers plan to quit and the use of nicotine replacement drugs was 14% at maximum. Forty-six percent or more of men and 20% or more of women were exposed to passive smoking at workplaces and at home, respectively. Many tobacco industry activities remain unrestricted and prevalent. Our findings indicate an urgent need for the following set of policies: raise cigarette prices to increase the quit attempt rate, particularly among adult men; develop a multi-component quitting assistance system to provide adequate assistance for smoking cessation; implement effective smoke-free policies in workplaces and public places to reduce exposure to passive smoking; and rebuild the administrative structure to denormalise tobacco industry activities. The importance of these standard approaches should be reaffirmed by all tobacco control policymakers in East Asia. PMID:23596197

  6. NEGOTIATING PLACE AND GENDERED VIOLENCE IN CANADA’S LARGEST OPEN DRUG SCENE

    PubMed Central

    McNeil, Ryan; Shannon, Kate; Shaver, Laura; Kerr, Thomas; Small, Will

    2014-01-01

    Background Vancouver’s Downtown Eastside is home to Canada’s largest street-based drug scene and only supervised injection facility (Insite). High levels of violence among men and women have been documented in this neighbourhood. This study was undertaken to explore the role of violence in shaping the socio-spatial relations of women and ‘marginal men’ (i.e., those occupying subordinate positions within the drug scene) in the Downtown Eastside, including access to Insite. Methods Semi-structured qualitative interviews were conducted with 23 people who inject drugs (PWID) recruited through the Vancouver Area Network of Drug Users, a local drug user organization. Interviews included a mapping exercise. Interview transcripts and maps were analyzed thematically, with an emphasis on how gendered violence shaped participants’ spatial practices. Results Hegemonic forms of masculinity operating within the Downtown Eastside framed the everyday violence experienced by women and marginal men. This violence shaped the spatial practices of women and marginal men, in that they avoided drug scene milieus where they had experienced violence or that they perceived to be dangerous. Some men linked their spatial restrictions to the perceived 'dope quality' of neighbourhood drug dealers to maintain claims to dominant masculinities while enacting spatial strategies to promote safety. Environmental supports provided by health and social care agencies were critical in enabling women and marginal men to negotiate place and survival within the context of drug scene violence. Access to Insite did not motivate participants to enter into “dangerous” drug scene milieus but they did venture into these areas if necessary to obtain drugs or generate income. Conclusion Gendered violence is critical in restricting the geographies of men and marginal men within the street-based drug scene. There is a need to scale up existing environmental interventions, including supervised injection

  7. Assessing Climate Change Effect on the World's Largest Lakes Using Satellite Observation

    NASA Astrophysics Data System (ADS)

    Wang, C.; Gabriel, R.; Norouzi, H.

    2014-12-01

    The Landsat program offers the longest continuous global record of the Earth's surface using satellite imagery for over forty years (1972-2014). Millions of images and relevant data have since been acquired using the instrument on the Landsat satellite to monitor the Earth's interesting phenomena. There are Landsat receiving stations around the world including the United States that process and archive the images that are a unique resource for global change research and applications in agriculture, forestry, regional planning, geology, cartography and global warming. So far, National Oceanic Atmospheric and Administration (NOAA) and National Aeronautics and Space Administration (NASA), have launched a total of eight successfully orbiting satellites throughout its forty-two years of service. The main objective of this project aims to use Landsat images to monitor the changes of the world's largest lakes from 1972 to present. We focus on areas around the planet that are home to large scale lakes such as Lake Urmia, Lake Vanern, Lake Winnipegosis, Lake Albert and Lake Mweru. Then using U.S Geological Survey (USGS) database as a source for gathering cloud free images that are covering each lake, we were able to download and obtain necessary data. For larger lakes, images were mosaic to cover the entire area of the lake and using a Maximum Likelihood technique images were specifically classified into land and water content using ENVI software. The extent of the water content was quantified for each year and a temporal analysis of the area was performed. It is also found that the lakes which locates near the equator or at low latitude are seriously facing threats of becoming mostly dry. Future work is needed for establishing the dynamic characteristic of more lakes' water extent changes and also to compare them with other available information such as precipitation and soil moisture in each region. In lakes where high latitude, the change in extent of ice during winter

  8. Hydrological drivers of record-setting water level rise on Earth's largest lake system

    NASA Astrophysics Data System (ADS)

    Gronewold, A. D.; Bruxer, J.; Durnford, D.; Smith, J. P.; Clites, A. H.; Seglenieks, F.; Qian, S. S.; Hunter, T. S.; Fortin, V.

    2016-05-01

    Between January 2013 and December 2014, water levels on Lake Superior and Lake Michigan-Huron, the two largest lakes on Earth by surface area, rose at the highest rate ever recorded for a 2 year period beginning in January and ending in December of the following year. This historic event coincided with below-average air temperatures and extensive winter ice cover across the Great Lakes. It also brought an end to a 15 year period of persistently below-average water levels on Lakes Superior and Michigan-Huron that included several months of record-low water levels. To differentiate hydrological drivers behind the recent water level rise, we developed a Bayesian Markov chain Monte Carlo (MCMC) routine for inferring historical estimates of the major components of each lake's water budget. Our results indicate that, in 2013, the water level rise on Lake Superior was driven by increased spring runoff and over-lake precipitation. In 2014, reduced over-lake evaporation played a more significant role in Lake Superior's water level rise. The water level rise on Lake Michigan-Huron in 2013 was also due to above-average spring runoff and persistent over-lake precipitation, while in 2014, it was due to a rare combination of below-average evaporation, above-average runoff and precipitation, and very high inflow rates from Lake Superior through the St. Marys River. We expect, in future research, to apply our new framework across the other Laurentian Great Lakes, and to Earth's other large freshwater basins as well.

  9. Grassland bird responses to land management in the largest remaining tallgrass prairie.

    PubMed

    Rahmig, Corina J; Jensen, William E; With, Kimberly A

    2009-04-01

    Extensive habitat loss and changing agricultural practices have caused widespread declines in grassland birds throughout North America. The Flint Hills of Kansas and Oklahoma--the largest remaining tallgrass prairie--is important for grassland bird conservation despite supporting a major cattle industry. In 2004 and 2005, we assessed the community, population, and demographic responses of grassland birds to the predominant management practices (grazing, burning, and haying) of the region, including grasslands restored under the Conservation Reserve Program (CRP). We targeted 3 species at the core of this avian community: the Dickcissel (Spiza americana), Grasshopper Sparrow (Ammodramus savannarum), and Eastern Meadowlark (Sturnella magna). Bird diversity was higher in native prairie hayfields and grazed pastures than CRP fields, which were dominated by Dickcissels. Although Dickcissel density was highest in CRP, their nest success was highest and nest parasitism by Brown-headed Cowbirds (Moluthrus ater) lowest in unburned hayfields (in 2004). Conversely, Grasshopper Sparrow density was highest in grazed pastures, but their nest success was lowest in these pastures and highest in burned hayfields, where cowbird parasitism was also lowest (in 2004). Management did not influence density and nest survival of Eastern Meadowlarks, which were uniformly low across the region. Nest success was extremely low (5-12%) for all 3 species in 2005, perhaps because of a record spring drought. Although the CRP has benefited grassland birds in agricultural landscapes, these areas may have lower habitat value in the context of native prairie. Hayfields may provide beneficial habitat for some grassland birds in the Flint Hills because they are mowed later in the breeding season than elsewhere in the Midwest. Widespread grazing and annual burning have homogenized habitat-and thus grassland-bird responses-across the Flint Hills. Diversification of management practices could increase

  10. North American velvet ants form one of the world's largest known Müllerian mimicry complexes.

    PubMed

    Wilson, Joseph S; Jahner, Joshua P; Forister, Matthew L; Sheehan, Erica S; Williams, Kevin A; Pitts, James P

    2015-08-17

    Color mimicry is often celebrated as one of the most straightforward examples of evolution by natural selection, as striking morphological similarity between species evolves in response to a shared predation pressure. Recently, a large North American mimetic complex was described that included 65 species of Dasymutilla velvet ants (Hymenoptera: Mutillidae). Beyond those 65 species, little is known about how many species participate in this unique Müllerian complex, though several other arthropods are thought to be involved as Müllerian mimics (spider wasps) and Batesian mimics (beetles, antlions, and spiders; see references in). Müllerian mimicry is similarity in appearance or phenotype among harmful species, while Batesian mimicry is similarity in which not all species are harmful. Here, we investigate the extent of the velvet ant mimicry complex beyond Dasymutilla by examining distributional and color pattern similarities in all of the 21 North American diurnal velvet ant genera, including 302 of the 361 named species (nearly 84%), as well as 16 polymorphic color forms and an additional 33 undescribed species. Of the 351 species and color forms that were analyzed (including undescribed species), 336 exhibit some morphological similarities and we hypothesize that they form eight distinct mimicry rings (Figure 1A; Supplemental Information). Two of these eight mimicry rings, red-headed Timulla and black-headed Timulla, were not documented in earlier assessments of mimicry in velvet ants, and are newly described here. These findings identify one of the largest known Müllerian mimicry systems worldwide and provide a novel system to test hypotheses about aposematism and mimicry, especially those regarding the evolution of imperfect mimicry.

  11. THE CHANDRA VIEW OF THE LARGEST QUASAR LENS SDSS J1029+2623

    SciTech Connect

    Ota, Naomi; Oguri, Masamune; Dai, Xinyu; Kochanek, Christopher S.; Richards, Gordon T.; Ofek, Eran O.; Blandford, Roger D.; Schrabback, Tim; Inada, Naohisa

    2012-10-10

    We present results from Chandra observations of the cluster lens SDSS J1029+2623 at z{sub l} = 0.58, which is a gravitationally lensed quasar with the largest known image separation. We clearly detect X-ray emission both from the lensing cluster and the three lensed quasar images. The cluster has an X-ray temperature of kT = 8.1{sup +2.0}{sub -1.2} keV and bolometric luminosity of L{sub X} = 9.6 Multiplication-Sign 10{sup 44} erg s{sup -1}. Its surface brightness is centered near one of the brightest cluster galaxies, and it is elongated east-west. We identify a subpeak northwest of the main peak, which is suggestive of an ongoing merger. Even so, the X-ray mass inferred from the hydrostatic equilibrium assumption appears to be consistent with the lensing mass from the Einstein radius of the system. We find significant absorption in the soft X-ray spectrum of the faintest quasar image, which can be caused by an intervening material at either the lens or source redshift. The X-ray flux ratios between the quasar images (after correcting for absorption) are in reasonable agreement with those at optical and radio wavelengths, and all the flux ratios are inconsistent with those predicted by simple mass models. This implies that microlensing effect is not significant for this system and dark matter substructure is mainly responsible for the anomalous flux ratios.

  12. Circulating Hepatitis B Surface Antigen Particles Carry Hepatocellular microRNAs

    PubMed Central

    Novellino, Luisa; Rossi, Riccardo L.; Bonino, Ferruccio; Cavallone, Daniela; Abrignani, Sergio; Pagani, Massimiliano; Brunetto, Maurizia R.

    2012-01-01

    Hepatitis B virus (HBV) produces high quantities of subviral surface antigen particles (HBsAg) which circulate in the blood outnumbering virions of about 1\\103–6 times. In individuals coinfected with the defective hepatitis Delta virus (HDV) the small HDV-RNA-genome and Delta antigen circulate as ribonucleoprotein complexes within HBsAg subviral particles. We addressed the question whether subviral HBsAg particles may carry in the same way cellular microRNAs (miRNAs) which are released into the bloodstream within different subcellular forms such as exosomes and microvescicles. Circulating HBsAg particles were isolated from sera of 11 HBsAg carriers by selective immunoprecipitation with monoclonal anti-HBs-IgG, total RNA was extracted and human miRNAs were screened by TaqMan real-time quantitative PCR Arrays. Thirty-nine human miRNAs were found to be significantly associated with the immunoprecipitated HBsAg, as determined by both comparative DDCT analysis and non-parametric tests (Mann-Whitney, p<0.05) with respect to controls. Moreover immunoprecipitated HBsAg particles contained Ago2 protein that could be revealed in ELISA only after 0.5% NP40. HBsAg associated miRNAs were liver-specific (most frequent = miR-27a, miR-30b, miR-122, miR-126 and miR-145) as well as immune regulatory (most frequent = miR-106b and miR-223). Computationally predicted target genes of HBsAg-associated miRNAs highlighted molecular pathways dealing with host-pathogen The finding that HBsAg particles carry selective pools of hepatocellular miRNAs opens new avenues of research to disentangle the complex interactions between host and HBV and provides a non invasive tool to study the physiopathology of liver epigenetics. PMID:22470417

  13. Circulating hepatitis B surface antigen particles carry hepatocellular microRNAs.

    PubMed

    Novellino, Luisa; Rossi, Riccardo L; Bonino, Ferruccio; Cavallone, Daniela; Abrignani, Sergio; Pagani, Massimiliano; Brunetto, Maurizia R

    2012-01-01

    Hepatitis B virus (HBV) produces high quantities of subviral surface antigen particles (HBsAg) which circulate in the blood outnumbering virions of about 1\\10(3-6) times. In individuals coinfected with the defective hepatitis Delta virus (HDV) the small HDV-RNA-genome and Delta antigen circulate as ribonucleoprotein complexes within HBsAg subviral particles. We addressed the question whether subviral HBsAg particles may carry in the same way cellular microRNAs (miRNAs) which are released into the bloodstream within different subcellular forms such as exosomes and microvescicles. Circulating HBsAg particles were isolated from sera of 11 HBsAg carriers by selective immunoprecipitation with monoclonal anti-HBs-IgG, total RNA was extracted and human miRNAs were screened by TaqMan real-time quantitative PCR Arrays. Thirty-nine human miRNAs were found to be significantly associated with the immunoprecipitated HBsAg, as determined by both comparative DDCT analysis and non-parametric tests (Mann-Whitney, p<0.05) with respect to controls. Moreover immunoprecipitated HBsAg particles contained Ago2 protein that could be revealed in ELISA only after 0.5% NP40. HBsAg associated miRNAs were liver-specific (most frequent = miR-27a, miR-30b, miR-122, miR-126 and miR-145) as well as immune regulatory (most frequent = miR-106b and miR-223). Computationally predicted target genes of HBsAg-associated miRNAs highlighted molecular pathways dealing with host-pathogen. The finding that HBsAg particles carry selective pools of hepatocellular miRNAs opens new avenues of research to disentangle the complex interactions between host and HBV and provides a non invasive tool to study the physiopathology of liver epigenetics.

  14. Searching for Physics Beyond the Standard Model with the World's Largest Penning Trap

    NASA Astrophysics Data System (ADS)

    Roberts, B. Lee

    2015-05-01

    Measurements of the magnetic moments of the electron and muon were intertwined with the development of the modern physics of the 20th century, where μ --> = g(Qeℏ / 2 m) s --> with Q = +/- 1 and e > 0 . The g-value consists of a Dirac piece and the anomaly, g = 2(1 + a) or a =(g - 2) / 2 . For point-like particles, a arises from radiative corrections. The simplest correction, a = α / 2 π ~= 0 . 00116 ... , was first obtained by Schwinger. This result was also found to describe the muon's magnetic moment, indicating that the muon behaved like a heavy electron in a magnetic field. Loops containing all virtual particles that interact with the muon, including as yet undiscovered ones, can contribute to the muon anomaly. The relative contribution from heavier particles to the muon and electron anomalies scales as (mμ /me) 2 ~= 43 , 000 , giving the muon a distinct advantage in the search for effects from New Physics. E821 at the Brookhaven AGS obtained a relative precision of +/- 0 . 54 ppm, half the magnitude of the contributions from the Z and W gauge bosons. This result differs from the Standard-Model prediction by > 3 σ . To clarify whether this difference is a harbinger of New Physics beyond the Standard Model, E989 is being mounted at Fermilab with a design precision of 140 ppb. The 700 ton, 14 m diameter storage ring magnet will be shimmed to a point-to-point magnetic dipole field uniformity of +/- 25 ppm over the 1.137 m3 volume where the muon beam is stored, with the azimuthal averaged uniformity <= 1 ppm. Vertical focusing in the storage ring is provided by electrostatic quadrupoles placed with four-fold symmetry around the 44.7 m circumference of the storage ring. In this talk I will discuss the Standard-Model theory and the motivation for this new experiment, along with the experimental technique and outlook. This work supported in part by the US DOE and NSF.

  15. The Higgs Particle: A Useful Analogy for Physics Classrooms

    ERIC Educational Resources Information Center

    Cid, Xabier; Cid, Ramon

    2010-01-01

    In November 2009, the largest experiment in history was restarted. Its prime target is the Higgs particle--the last remaining undiscovered piece of our current theory of matter. We present a very simple way to introduce this topic to senior secondary school students, using a comparison with the refractive index of light.

  16. Cosmology with the largest galaxy cluster surveys: going beyond Fisher matrix forecasts

    SciTech Connect

    Khedekar, Satej; Majumdar, Subhabrata E-mail: subha@tifr.res.in

    2013-02-01

    We make the first detailed MCMC likelihood study of cosmological constraints that are expected from some of the largest, ongoing and proposed, cluster surveys in different wave-bands and compare the estimates to the prevalent Fisher matrix forecasts. Mock catalogs of cluster counts expected from the surveys — eROSITA, WFXT, RCS2, DES and Planck, along with a mock dataset of follow-up mass calibrations are analyzed for this purpose. A fair agreement between MCMC and Fisher results is found only in the case of minimal models. However, for many cases, the marginalized constraints obtained from Fisher and MCMC methods can differ by factors of 30-100%. The discrepancy can be alarmingly large for a time dependent dark energy equation of state, w(a); the Fisher methods are seen to under-estimate the constraints by as much as a factor of 4-5. Typically, Fisher estimates become more and more inappropriate as we move away from ΛCDM, to a constant-w dark energy to varying-w dark energy cosmologies. Fisher analysis, also, predicts incorrect parameter degeneracies. There are noticeable offsets in the likelihood contours obtained from Fisher methods that is caused due to an asymmetry in the posterior likelihood distribution as seen through a MCMC analysis. From the point of mass-calibration uncertainties, a high value of unknown scatter about the mean mass-observable relation, and its redshift dependence, is seen to have large degeneracies with the cosmological parameters σ{sub 8} and w(a) and can degrade the cosmological constraints considerably. We find that the addition of mass-calibrated cluster datasets can improve dark energy and σ{sub 8} constraints by factors of 2-3 from what can be obtained from CMB+SNe+BAO only . Finally, we show that a joint analysis of datasets of two (or more) different cluster surveys would significantly tighten cosmological constraints from using clusters only. Since, details of future cluster surveys are still being planned, we emphasize

  17. Evolution of Hang Son Doong, Vietnam: the largest cave passage in the world

    NASA Astrophysics Data System (ADS)

    Granger, D. E.

    2011-12-01

    Hang Son Doong (HSD), or Mountain River Cave, in the Quang Binh province of Vietnam, is considered to be the largest cave passage in the world. It has continuous widths near 100 m, and heights locally exceeding 200 m in a passage >6.5 km long. HSD is one of many extremely large caves in the tropical karst of the Ke Bang massif, a massively bedded limestone surrounded by metamorphic and clastic sedimentary rocks. Why are these caves so large? Is it because they are young and rapidly formed, or instead did they form slowly in exceptionally strong bedrock? To address these questions it is necessary to examine the style and timing of speleogenesis. Hang Son Doong was formed by an allogenic river sinking along a straight subvertical fault. The cave is formed largely within a brecciated fault zone that extends up to 100 m wide. A relict karst valley indicates that speleogenesis occurred due to wholesale capture of the surface river. The cave pattern is strongly fault-controlled with few branches, consistent with a primarily allogenic rather than distributed recharge. The cave is punctuated by two collapse dolines, one of which impedes discharge today. Massive slackwater deposits perhaps 100 m thick accumulated upstream of this doline collapse, and are overlain by corroded flowstone. To place some time constraints on speleogenesis, two samples were collected for cosmogenic nuclide burial dating with 26Al and 10Be in allogenic quartz. One was from the slackwater deposits, and another from a breccia-filled tributary passage at a fault junction. Both samples postdate cave formation, and can only be used to place minimum ages on the cave. Cosmogenic nuclide concentrations are very low, leading to large uncertainties in the ages. Nonetheless, the burial ages yield some important information. Initial results indicate that the slackwater deposits formed recently, during the past 300 ky. The filled passage, on the other hand, is much older and dates to the Pliocene. Re

  18. What happens after and during deglaciation? Some insight from observations at the largest glacier in Austria

    NASA Astrophysics Data System (ADS)

    Kellerer-Pirklbauer, Andreas; Avian, Michael; Lieb, Gerhard K.; Kaufmann, Viktor

    2014-05-01

    Pasterze Glacier is the largest glacier in Austria and the Eastern Alps. The glacier is located at the foot of Mt. Großglockner (3798 m a.s.l.), the highest peak in Austria, and is accessible rather easily by a high alpine road ending above the main glacier tongue. At present, the glacier covers an area of about 17 km2, has a length of 8.3 km, a maximum ice thickness of about 190 m and is characterized by two unequally sized glacier tongues. The main glacier tongue is c.4 km long and heavily covered by debris. Since the end of the Little Ice Age (LIA) at around AD 1850 this glacier receded by 2.1 km. During the last c.160 years the main glacier tongue lowered by some 250 m on average. The glacier surface flow velocity decreased substantially, i.e. for example by 32% between the time periods 2003-2006 and 2006-2009. Glacier recession revealed large areas of previously ice-buried bedrock as well as minerogenic and biogenic sediments. In this contribution we present a compendium of research results based on several projects related to pure proglacial but also paraglacial processes and landforms in the vicinity of the present glacier. We will discuss (a) rock slope adjustment processes and its causes influencing for instance the supraglacial debris cover of the main glacier tongue substantially, (b) landform dynamics in the outwash plain and adjacent slopes close to the present glacier terminus, (c) the role of dead-ice for the proglacial landsystem, (d) formation and rapid enlargement of rock outcrops within the ice-fall, and (e) related natural hazard aspects. A further aspect discussed here - which is rather particular for Pasterze Glacier - is the (e) biogenic material (peat lumps and wood fragments) which has been found in recently deglaciated terrain. This material provides valuable insight into past ecological, glaciological and climatological conditions. Further rapid back- and downwasting of this glacier is very likely due to lack of ice replenishment. The

  19. Net discharge anomalies drive uncertainty in catch in the world's largest inland fishery

    NASA Astrophysics Data System (ADS)

    Sabo, J. L.

    2013-12-01

    The Mekong River is one of the world's largest rivers at more than 4,600 km long and a watershed of nearly 800,000 km2. The Tonle Sap Lake (TSL) in Cambodia is believed to be one of the most productive inland fisheries in the world because of its unique hydrologic regime and large input of nutrient-rich sediment from the Mekong. The TSL is the cornerstone of food security in Cambodia yielding ~ 15% of the estimated 2.6M tonne catch in the Mekong basin and providing key nursery habitat for fishes that constitute the catch in other parts of the basin. The TSL fishery is driven by a flood pulse that occurs during and after the SE Asian Monsoon. The timing, duration and magnitude of the monsoon is thought to be a key driver of primary and secondary (fish) production in the system. All three-timing, duration and magnitude--are likely to be different under future climate and as a result of the proposed and recently constructed dams on tributaries in Vietnam and elsewhere. Here I use spectral methods to characterize the timing and magnitude of the flood pulse. Specifically, I use the Discrete Fast Fourier Transform (DFFT) to estimate the seasonal trend in daily discharge for the past 40 years at the Stung Treng gage. The whitened time series represent departures from the long term trend--anomalies--and hence implicitly capture the timing of unusual events. I hypothesize that 'timing is everything' and hence that anomalies will capture variation in the second moment of the fishery. Using a novel metric--the net annual discharge anomaly--I show that catch is significantly more variable in years with net negative flow anomalies; and quite predictable in years with net positive flow anomalies. These results suggest that changes in timing of monsoon flows alone--due to climate change or dams--can significantly increase the uncertainty in catch of a fishery that is vital for food security in the Mekong basin.

  20. Evaluation of world's largest social welfare scheme: An assessment using non-parametric approach.

    PubMed

    Singh, Sanjeet

    2016-08-01

    Mahatma Gandhi National Rural Employment Guarantee Act (MGNREGA) is the world's largest social welfare scheme in India for the poverty alleviation through rural employment generation. This paper aims to evaluate and rank the performance of the states in India under MGNREGA scheme. A non-parametric approach, Data Envelopment Analysis (DEA) is used to calculate the overall technical, pure technical, and scale efficiencies of states in India. The sample data is drawn from the annual official reports published by the Ministry of Rural Development, Government of India. Based on three selected input parameters (expenditure indicators) and five output parameters (employment generation indicators), I apply both input and output oriented DEA models to estimate how well the states utilize their resources and generate outputs during the financial year 2013-14. The relative performance evaluation has been made under the assumption of constant returns and also under variable returns to scale to assess the impact of scale on performance. The results indicate that the main source of inefficiency is both technical and managerial practices adopted. 11 states are overall technically efficient and operate at the optimum scale whereas 18 states are pure technical or managerially efficient. It has been found that for some states it necessary to alter scheme size to perform at par with the best performing states. For inefficient states optimal input and output targets along with the resource savings and output gains are calculated. Analysis shows that if all inefficient states operate at optimal input and output levels, on an average 17.89% of total expenditure and a total amount of $780million could have been saved in a single year. Most of the inefficient states perform poorly when it comes to the participation of women and disadvantaged sections (SC&ST) in the scheme. In order to catch up with the performance of best performing states, inefficient states on an average need to enhance

  1. What Caused the UK's Largest Common Dolphin (Delphinus delphis) Mass Stranding Event?

    PubMed Central

    Jepson, Paul D.; Deaville, Robert; Acevedo-Whitehouse, Karina; Barnett, James; Brownlow, Andrew; Brownell Jr., Robert L.; Clare, Frances C.; Davison, Nick; Law, Robin J.; Loveridge, Jan; Macgregor, Shaheed K.; Morris, Steven; Murphy, Sinéad; Penrose, Rod; Perkins, Matthew W.; Pinn, Eunice; Seibel, Henrike; Siebert, Ursula; Sierra, Eva; Simpson, Victor; Tasker, Mark L.; Tregenza, Nick; Cunningham, Andrew A.; Fernández, Antonio

    2013-01-01

    On 9 June 2008, the UK's largest mass stranding event (MSE) of short-beaked common dolphins (Delphinus delphis) occurred in Falmouth Bay, Cornwall. At least 26 dolphins died, and a similar number was refloated/herded back to sea. On necropsy, all dolphins were in good nutritive status with empty stomachs and no evidence of known infectious disease or acute physical injury. Auditory tissues were grossly normal (26/26) but had microscopic haemorrhages (5/5) and mild otitis media (1/5) in the freshest cases. Five lactating adult dolphins, one immature male, and one immature female tested were free of harmful algal toxins and had low chemical pollutant levels. Pathological evidence of mud/seawater inhalation (11/26), local tide cycle, and the relative lack of renal myoglobinuria (26/26) suggested MSE onset on a rising tide between 06∶30 and 08∶21 hrs (9 June). Potential causes excluded or considered highly unlikely included infectious disease, gas/fat embolism, boat strike, by-catch, predator attack, foraging unusually close to shore, chemical or algal toxin exposure, abnormal weather/climatic conditions, and high-intensity acoustic inputs from seismic airgun arrays or natural sources (e.g., earthquakes). International naval exercises did occur in close proximity to the MSE with the most intense part of the exercises (including mid-frequency sonars) occurring four days before the MSE and resuming with helicopter exercises on the morning of the MSE. The MSE may therefore have been a “two-stage process” where a group of normally pelagic dolphins entered Falmouth Bay and, after 3–4 days in/around the Bay, a second acoustic/disturbance event occurred causing them to strand en masse. This spatial and temporal association with the MSE, previous associations between naval activities and cetacean MSEs, and an absence of other identifiable factors known to cause cetacean MSEs, indicates naval activity to be the most probable cause of the Falmouth Bay MSE. PMID

  2. Macrobenthic invertebrate responses to prolonged drought in South Africa's largest estuarine lake complex

    NASA Astrophysics Data System (ADS)

    MacKay, F.; Cyrus, D.; Russell, K.-L.

    2010-03-01

    St Lucia, the largest estuarine lake complex of its type in Africa, is characterised by natural physico-chemical spatial and temporal fluctuations. This estuary functions as an important nursery area making use of a number of different habitat types and associated environmental conditions. The system has been subject to a number of natural episodic events such as cyclonic flooding and cyclical droughts, the most current has persisted since 2001, resulting in almost permanent mouth closure. Furthermore, high levels of evaporation have reduced lake levels and resulted in compartmentalisation of the system for up to several years at a time. St Lucia is sensitive to evaporation and therefore to vast salinity fluctuations and hypersaline conditions. The upper reaches in North Lake are particularly sensitive to drying out and extended hypersaline events. The macrobenthos has been well studied, but no studies have concentrated on the entire system for such an extent of time. Macrobenthic samples were initially collected in 2004, again in 2005 and biannually from 2006 to 2008. This study was part of a larger multidisciplinary programme aimed at determining the effects of long term drought conditions on the ecology of the St Lucia system, and increasing current understanding of the system response to future catastrophic climatic events. Three areas were sampled (North and South Lake and Estuary) at five sites per area, over five years. Data were analysed by representing communities through time series depictions and discriminating sites and sampling periods to test multidimensional relationships. Linkages between biological distribution and selected environmental forcing variables were investigated. The system was found to be highly variable and supporting a large number of different habitats and co-occurring environmental conditions. This variability makes it difficult to discern spatial or temporal patterns in environmental conditions and macrobenthic ecology. However

  3. Transcriptome Sequencing and Analysis for Culm Elongation of the World's Largest Bamboo (Dendrocalamus sinicus).

    PubMed

    Cui, Kai; Wang, Haiying; Liao, Shengxi; Tang, Qi; Li, Li; Cui, Yongzhong; He, Yuan

    2016-01-01

    Dendrocalamus sinicus is the world's largest bamboo species with strong woody culms, and known for its fast-growing culms. As an economic bamboo species, it was popularized for multi-functional applications including furniture, construction, and industrial paper pulp. To comprehensively elucidate the molecular processes involved in its culm elongation, Illumina paired-end sequencing was conducted. About 65.08 million high-quality reads were produced, and assembled into 81,744 unigenes with an average length of 723 bp. A total of 64,338 (79%) unigenes were annotated for their functions, of which, 56,587 were annotated in the NCBI non-redundant protein database and 35,262 were annotated in the Swiss-Prot database. Also, 42,508 and 21,009 annotated unigenes were allocated to gene ontology (GO) categories and clusters of orthologous groups (COG), respectively. By searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG), 33,920 unigenes were assigned to 128 KEGG pathways. Meanwhile, 8,553 simple sequence repeats (SSRs) and 81,534 single-nucleotide polymorphism (SNPs) were identified, respectively. Additionally, 388 transcripts encoding lignin biosynthesis were detected, among which, 27 transcripts encoding Shikimate O-hydroxycinnamoyltransferase (HCT) specifically expressed in D. sinicus when compared to other bamboo species and rice. The phylogenetic relationship between D. sinicus and other plants was analyzed, suggesting functional diversity of HCT unigenes in D. sinicus. We conjectured that HCT might lead to the high lignin content and giant culm. Given that the leaves are not yet formed and culm is covered with sheaths during culm elongation, the existence of photosynthesis of bamboo culm is usually neglected. Surprisedly, 109 transcripts encoding photosynthesis were identified, including photosystem I and II, cytochrome b6/f complex, photosynthetic electron transport and F-type ATPase, and 24 transcripts were characterized as antenna

  4. Drilling the Largest Oceanic Detachment in the World: the Godzilla Mullion in the Parece Vela Rift

    NASA Astrophysics Data System (ADS)

    Ohara, Y.; Okino, K.; Snow, J. E.; Salisbury, M.

    2003-12-01

    Recently discovered megamullions at slow-spreading ridges have been interpreted as exhumed footwalls of oceanic detachment faults in magma-starved ridge environments. These features are believed to result from extreme tectonic extension, and thus they are ideal to study processes of tectonic extension in oceanic lithosphere. In addition to tectonic issues, these features provide excellent tectonic windows to the lower crust and uppermost mantle. Drilling megamullion structures allows us to study tectonic processes, serpentinization and magnetization at shallow depth and mantle composition and fabrics at a deeper level. The largest megamullion structure in the world is the Godzilla Mullion in the extinct Parece Vela backarc basin, Philippine Sea. Recent reconnaissance studies by our group have revealed the following unique characteristics of this structure: (1) The Godzilla Mullion is huge, ˜ 10 times larger in area than megamullions identified so far on the Mid-Atlantic Ridge (MAR). (2) The latest KR03-01 cruise dredged mantle peridotites (see Snow et al., this session) from entire length of the Godzilla Mullion (over 125 km), suggesting that an ultramafic exposure of some ˜ 7000 km2. (3) The Godzilla Mullion develops along the full along-strike length of the spreading segment. In the MAR, the megamullions normally develop at inside corners of ridge-transform intersections. (4) Peridotites from the Parece Vela Basin include very fertile lherzolites with spinel Cr# [Cr/(Cr+Al)] = ˜ 0.17. (5) The Godzilla Mullion was formed in a relatively fast intermediate-spreading environment with 7.0 cm/y full-rate. We may expect a relatively high magmatic budget in the fast/intermediate-spreading Parece Vela Basin, since a high magmatic budget is generally expected for a fast-spreading ridge. However, the characteristics noted above instead indicate a small degree of mantle melting. We suggest that these features may result from the characteristic ridge-transform geometry of

  5. Sequencing of tsunami waves: why the first wave is not always the largest

    NASA Astrophysics Data System (ADS)

    Okal, Emile A.; Synolakis, Costas E.

    2016-02-01

    This paper examines the factors contributing to the `sequencing' of tsunami waves in the far field, that is, to the distribution of the maximum sea surface amplitude inside the dominant wave packet constituting the primary arrival at a distant harbour. Based on simple models of sources for which analytical solutions are available, we show that, as range is increased, the wave pattern evolves from a regime of maximum amplitude in the first oscillation to one of delayed maximum, where the largest amplitude takes place during a subsequent oscillation. In the case of the simple, instantaneous uplift of a circular disk at the surface of an ocean of constant depth, the critical distance for transition between those patterns scales as r_0^3 / h^2 where r0 is the radius of the disk and h the depth of the ocean. This behaviour is explained from simple arguments based on a model where sequencing results from frequency dispersion in the primary wave packet, as the width of its spectrum around its dominant period T0 becomes dispersed in time in an amount comparable to T0, the latter being controlled by a combination of source size and ocean depth. The general concepts in this model are confirmed in the case of more realistic sources for tsunami excitation by a finite-time deformation of the ocean floor, as well as in real-life simulations of tsunamis excited by large subduction events, for which we find that the influence of fault width on the distribution of sequencing is more important than that of fault length. Finally, simulation of the major events of Chile (2010) and Japan (2011) at large arrays of virtual gauges in the Pacific Basin correctly predicts the majority of the sequencing patterns observed on DART buoys during these events. By providing insight into the evolution with time of wave amplitudes inside primary wave packets for far field tsunamis generated by large earthquakes, our results stress the importance, for civil defense authorities, of issuing warning and

  6. Evaluation of world's largest social welfare scheme: An assessment using non-parametric approach.

    PubMed

    Singh, Sanjeet

    2016-08-01

    Mahatma Gandhi National Rural Employment Guarantee Act (MGNREGA) is the world's largest social welfare scheme in India for the poverty alleviation through rural employment generation. This paper aims to evaluate and rank the performance of the states in India under MGNREGA scheme. A non-parametric approach, Data Envelopment Analysis (DEA) is used to calculate the overall technical, pure technical, and scale efficiencies of states in India. The sample data is drawn from the annual official reports published by the Ministry of Rural Development, Government of India. Based on three selected input parameters (expenditure indicators) and five output parameters (employment generation indicators), I apply both input and output oriented DEA models to estimate how well the states utilize their resources and generate outputs during the financial year 2013-14. The relative performance evaluation has been made under the assumption of constant returns and also under variable returns to scale to assess the impact of scale on performance. The results indicate that the main source of inefficiency is both technical and managerial practices adopted. 11 states are overall technically efficient and operate at the optimum scale whereas 18 states are pure technical or managerially efficient. It has been found that for some states it necessary to alter scheme size to perform at par with the best performing states. For inefficient states optimal input and output targets along with the resource savings and output gains are calculated. Analysis shows that if all inefficient states operate at optimal input and output levels, on an average 17.89% of total expenditure and a total amount of $780million could have been saved in a single year. Most of the inefficient states perform poorly when it comes to the participation of women and disadvantaged sections (SC&ST) in the scheme. In order to catch up with the performance of best performing states, inefficient states on an average need to enhance

  7. Transcriptome Sequencing and Analysis for Culm Elongation of the World’s Largest Bamboo (Dendrocalamus sinicus)

    PubMed Central

    Cui, Kai; Wang, Haiying; Liao, Shengxi; Tang, Qi; Li, Li; Cui, Yongzhong; He, Yuan

    2016-01-01

    Dendrocalamus sinicus is the world’s largest bamboo species with strong woody culms, and known for its fast-growing culms. As an economic bamboo species, it was popularized for multi-functional applications including furniture, construction, and industrial paper pulp. To comprehensively elucidate the molecular processes involved in its culm elongation, Illumina paired-end sequencing was conducted. About 65.08 million high-quality reads were produced, and assembled into 81,744 unigenes with an average length of 723 bp. A total of 64,338 (79%) unigenes were annotated for their functions, of which, 56,587 were annotated in the NCBI non-redundant protein database and 35,262 were annotated in the Swiss-Prot database. Also, 42,508 and 21,009 annotated unigenes were allocated to gene ontology (GO) categories and clusters of orthologous groups (COG), respectively. By searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG), 33,920 unigenes were assigned to 128 KEGG pathways. Meanwhile, 8,553 simple sequence repeats (SSRs) and 81,534 single-nucleotide polymorphism (SNPs) were identified, respectively. Additionally, 388 transcripts encoding lignin biosynthesis were detected, among which, 27 transcripts encoding Shikimate O-hydroxycinnamoyltransferase (HCT) specifically expressed in D. sinicus when compared to other bamboo species and rice. The phylogenetic relationship between D. sinicus and other plants was analyzed, suggesting functional diversity of HCT unigenes in D. sinicus. We conjectured that HCT might lead to the high lignin content and giant culm. Given that the leaves are not yet formed and culm is covered with sheaths during culm elongation, the existence of photosynthesis of bamboo culm is usually neglected. Surprisedly, 109 transcripts encoding photosynthesis were identified, including photosystem I and II, cytochrome b6/f complex, photosynthetic electron transport and F-type ATPase, and 24 transcripts were characterized as antenna

  8. Distribution of icy particles across Enceladus' surface

    NASA Astrophysics Data System (ADS)

    Jaumann, R.; Stephan, K.; Wagner, R.; Hansen, G. B.; Brown, R. H.; Cassini Vims Science Team

    Compositionally, the surface of Enceladus is build up almost completely by water ice [1]. However, distinct variations in the size of water ice particles are apparent. The Visual and Infrared Mapping Spectrometer [2] observed Enceladus with high spatial resolution during two Cassini flybys in 2005 (orbit 4 and 11). A detailed analysis of the VIMS spectra in comparison to theoretically calculated water ice spectra supports the assumption that almost pure water ice characterizes the surface of Enceladus and that the particle size varies between 0.002 and 0.1mm. Three dis-tinct spectral units can be separated exhibiting different particle sizes which are strongly correlated to surface features. A comparison between the classifications of particle sizes and geological maps of the regions observed during the flybys 4 and 11 demonstrate this result. Our measurements show that the particle size of water ice increases toward younger regions with the largest ones in "fresh" surface material. The smallest particles were generally found in old more or less densely cratered plains and the larger ones in younger tectonically resurfaced areas [4]. The largest particles are concentrated in the so called "tiger stripes" of the south polar area [1,5]. Our findings support the results of [1,7] with amorphous water ice being concen-trated in older terrain due to the longterm exposure to incoming radiation, and crys-talline water ice in the vicinity of the younger resurfaced regions, esp. the South Pole. Amorphization usually goes along with the destruction of water ice particles, resulting in the decrease of mean particle size. Unlike the Galilean satellites, which undergo a daily thermal cycle resulting in the crystallization of ice particles, the surface stays cooler (70K) [6] on Enceladus and the water ice remains in an amor-phous state. In contrast the sulci esp. the "tiger stripes" close to the South Pole are characterized by higher temperature [1,5,6], which leads to the

  9. Cloning and sequence determination of the Schizosaccharomyces pombe rpb1 gene encoding the largest subunit of RNA polymerase II.

    PubMed Central

    Azuma, Y; Yamagishi, M; Ueshima, R; Ishihama, A

    1991-01-01

    The gene, rpb1, encoding the largest subunit of RNA polymerase II has been cloned from Schizosaccharomyces pombe using the corresponding gene, RPB1, of Saccharomyces cerevisiae as a cross-hybridization probe. We have determined the complete sequence of this gene, and parts of PCR-amplified rpb1 cDNA. The predicted coding sequence, interrupted by six introns, encodes a polypeptide of 1,752 amino acid residues in length with a molecular weight of 194 kilodaltons. This polypeptide contains eight conserved structural domains characteristic of the largest subunit of RNA polymerases from other eukaryotes and, in addition, 29 repetitions of the C-terminal heptapeptide found in all the eukaryotic RNA polymerase II largest subunits so far examined. Images PMID:2011520

  10. Class II ribonuclease H comigrates with, but is distinct from, the third largest subunit of calf thymus RNA polymerase I.

    PubMed

    Vonwirth, H; Frank, P; Kedinger, C; Büsen, W

    1990-09-10

    It has been reported (Iborra et al. (1979) J. Biol. Chem. 254, 10920-10924) that the third and the fifth largest subunit of yeast RNA polymerase I exhibit ribonuclease H activity. The authors suggested that the third largest subunit is identical with the chromatin-associated ribonuclease H49, the putative yeast equivalent of bovine ribonuclease H IIb. Although the third largest subunit of calf thymus RNA polymerase I and ribonuclease H IIb display nearly identical molecular masses under denaturing conditions, serological analysis reveals that, in contrast to their counterparts in yeast, these mammalian proteins are distinct entities. Interestingly, sera from some patients with mixed connective tissue disease which contain antibodies directed against RNA polymerase I, also react with ribonuclease H IIb epitopes. This observation suggests that a protein displaying ribonuclease H IIb antigenicity could be associated with RNA polymerase I. Additional indications supporting this conclusion are discussed.

  11. The largest chemical explosion on the Australian continent: The Ord River project

    SciTech Connect

    Oriard, L.L.

    1995-12-31

    The explosives were placed in specially designed tunnels under a quartzite mountain for the purpose of generating rock fill for the main dam on the project. This case offers some insight into several questions, including (1) blast design philosophy for large explosions, (2) the intensity and attenuation characteristics of the seismic waves generated by large energy sources, (3) potential fault movement generated by the detonation along a prominent regional fault, (4) potential effects on associated minor faults and steep foundation slopes, (5) potential shaking damage to freshly poured concrete in a tall intake structure being slipformed at the nearby construction site, (6) potential self-heating and accidental detonation of ANFO packed into open tunnels in an intensely hot climate (120 degrees Fahrenheit), and (7) the importance of the physical and geological properties of the rock mass in determining the fragmentation of the rock and the suitability of possible construction techniques. Because of its strength and abrasiveness, the quartzite rock proved very difficult to drill, blast and excavate, prompting the contractor to select coyote blasting techniques. However, an incomplete study of the rock jointing prompted an overly optimistic prediction of fragmentation and particle gradation after blasting. These results, and the geotechnical studies of the rock, may provide design and construction guidance for future projects.

  12. Crystal structure of a signal recognition particle Alu domain in the elongation arrest conformation.

    PubMed

    Bousset, Luc; Mary, Camille; Brooks, Mark A; Scherrer, Anne; Strub, Katharina; Cusack, Stephen

    2014-12-01

    The signal recognition particle (SRP) is a conserved ribonucleoprotein particle that targets membrane and secreted proteins to translocation channels in membranes. In eukaryotes, the Alu domain, which comprises the 5' and 3' extremities of the SRP RNA bound to the SRP9/14 heterodimer, is thought to interact with the ribosome to pause translation elongation during membrane docking. We present the 3.2 Å resolution crystal structure of a chimeric Alu domain, comprising Alu RNA from the archaeon Pyrococcus horikoshii bound to the human Alu binding proteins SRP9/14. The structure reveals how intricate tertiary interactions stabilize the RNA 5' domain structure and how an extra, archaeal-specific, terminal stem helps constrain the Alu RNA into the active closed conformation. In this conformation, highly conserved noncanonical base pairs allow unusually tight side-by-side packing of 5' and 3' RNA stems within the SRP9/14 RNA binding surface. The biological relevance of this structure is confirmed by showing that a reconstituted full-length chimeric archaeal-human SRP is competent to elicit elongation arrest in vitro. The structure will be useful in refining our understanding of how the SRP Alu domain interacts with the ribosome.

  13. Lessons from the Largest Epidemic of Avian Influenza Viruses in Taiwan, 2015.

    PubMed

    Chang, Ching-Fen; King, Chwan-Chuen; Wan, Cho-Hua; Chang, Yun-Cheng; Chan, Ta-Chien; David Lee, Chang-Chun; Chou, Po-Hao Borris; Li, Zheng-Rong Tiger; Li, Yao-Tsun; Tseng, Tzu-Jung; Lee, Pei-Fen; Chang, Chuan-Hsiung

    2016-05-01

    The largest epidemic of avian influenza (AI) in history attacked poultry and wild birds throughout Taiwan starting January 6, 2015. This study analyzed surveillance results, epidemiologic characteristics, and viral sequences by using government-released information, with the intention to provide recommendations to minimize future pandemic influenza. The H5 clade 2.3.4.4 highly pathogenic AI viruses (HPAIVs) had not been detected in Taiwan before 2015. During this epidemic, four types of etiologic agents were identified: the three novel subtypes H5N2, H5N8, and H5N3 clade 2.3.4.4 HPAIVs and one endemic chicken H5N2 subtype (Mexican-like lineage) of low pathogenic AI viruses. Cocirculation of mixed subtypes also occurred, with H5N2 clade 2.3.4.4 HPAIVs accompanied by the H5N8 and H5N3 subtypes or old H5N2 viruses in the same farm. More than 90% of domestic geese died from this AI epidemic; geese were affected the most at the early outbreaks. The epidemic peaked in mid-January for all three novel H5 subtypes. Spatial epidemiology found that most affected areas were located in southwestern coastal areas. In terrestrial poultry (mostly chickens), different geographic distributions of AI virus subtypes were detected, with hot spots of H5N2 clade 2.3.4.4 vs. past-endemic old H5N2 viruses in Changhwa (P = 0.03) and Yunlin (P = 0.007) counties, respectively, of central Taiwan. Phylogenetic and sequence analyses of all the early 10 Taiwan H5 clade 2.3.4.4 isolates covering the three subtypes showed that they were very different from the HA of the past local H5 viruses from domestic ducks (75%-80%) and chickens (70%-75%). However, they had the highest sequence identity percentages (99.53%-100%), with the HA of A/crane/Kagoshima/KU13/2014(H5N8) isolated on December 7, 2014, in Japan being higher than those of recent American and Korean H5 HPAIVs [A/Northern pintail/Washington/40964/2014 (H5N2) and A/gyrfalcon/Washington/41088-6/2014 (H5N8): 99.02%-99.54% and A/Baikal teal

  14. Lessons from the Largest Epidemic of Avian Influenza Viruses in Taiwan, 2015.

    PubMed

    Chang, Ching-Fen; King, Chwan-Chuen; Wan, Cho-Hua; Chang, Yun-Cheng; Chan, Ta-Chien; David Lee, Chang-Chun; Chou, Po-Hao Borris; Li, Zheng-Rong Tiger; Li, Yao-Tsun; Tseng, Tzu-Jung; Lee, Pei-Fen; Chang, Chuan-Hsiung

    2016-05-01

    The largest epidemic of avian influenza (AI) in history attacked poultry and wild birds throughout Taiwan starting January 6, 2015. This study analyzed surveillance results, epidemiologic characteristics, and viral sequences by using government-released information, with the intention to provide recommendations to minimize future pandemic influenza. The H5 clade 2.3.4.4 highly pathogenic AI viruses (HPAIVs) had not been detected in Taiwan before 2015. During this epidemic, four types of etiologic agents were identified: the three novel subtypes H5N2, H5N8, and H5N3 clade 2.3.4.4 HPAIVs and one endemic chicken H5N2 subtype (Mexican-like lineage) of low pathogenic AI viruses. Cocirculation of mixed subtypes also occurred, with H5N2 clade 2.3.4.4 HPAIVs accompanied by the H5N8 and H5N3 subtypes or old H5N2 viruses in the same farm. More than 90% of domestic geese died from this AI epidemic; geese were affected the most at the early outbreaks. The epidemic peaked in mid-January for all three novel H5 subtypes. Spatial epidemiology found that most affected areas were located in southwestern coastal areas. In terrestrial poultry (mostly chickens), different geographic distributions of AI virus subtypes were detected, with hot spots of H5N2 clade 2.3.4.4 vs. past-endemic old H5N2 viruses in Changhwa (P = 0.03) and Yunlin (P = 0.007) counties, respectively, of central Taiwan. Phylogenetic and sequence analyses of all the early 10 Taiwan H5 clade 2.3.4.4 isolates covering the three subtypes showed that they were very different from the HA of the past local H5 viruses from domestic ducks (75%-80%) and chickens (70%-75%). However, they had the highest sequence identity percentages (99.53%-100%), with the HA of A/crane/Kagoshima/KU13/2014(H5N8) isolated on December 7, 2014, in Japan being higher than those of recent American and Korean H5 HPAIVs [A/Northern pintail/Washington/40964/2014 (H5N2) and A/gyrfalcon/Washington/41088-6/2014 (H5N8): 99.02%-99.54% and A/Baikal teal

  15. The World's Largest Experiment Manipulating Solar Energy Input To Earth Resumed In 2003

    NASA Astrophysics Data System (ADS)

    Ward, P. L.

    2010-12-01

    -burning power plants in Asia. The 20th century rate of increase in tropospheric methane also approached zero by 1998 but began to increase in 2007 as explained by SO2 reducing the oxidizing capacity and thus the troposphere’s ability to remove methane. SO2 does not last long in the atmosphere, but a continual and increasing flux causes increased concentrations. SO2 from China is traceable across the Pacific Ocean even to eastern America, perhaps playing a major role in the unusually high air temperatures in 2010. Atmospheric circulation in the northern hemisphere moves SO2 towards the pole where it is the primary cause of Arctic Haze. In polar regions, solar radiation travels longer path lengths through the atmosphere during longer summer days than in equatorial regions, contributing to the well-documented excessive global warming in the Arctic. The resumed increase in SO2 emissions since 2003 provides the world’s largest geoengineering experiment and an excellent chance to measure, especially in China and India, the effects of SO2 and NO2 on global warming. Technology exists to reduce SO2 emissions economically. The time has come to control this large geoengineering experiment in the hopes that we can minimize continued global warming.

  16. Astronomers Break Ground on Atacama Large Millimeter Array (ALMA) - World's Largest Millimeter Wavelength Telescope

    NASA Astrophysics Data System (ADS)

    2003-11-01

    Scientists and dignitaries from Europe, North America and Chile are breaking ground today (Thursday, November 6, 2003) on what will be the world's largest, most sensitive radio telescope operating at millimeter wavelengths . ALMA - the "Atacama Large Millimeter Array" - will be a single instrument composed of 64 high-precision antennas located in the II Region of Chile, in the District of San Pedro de Atacama, at the Chajnantor altiplano, 5,000 metres above sea level. ALMA 's primary function will be to observe and image with unprecedented clarity the enigmatic cold regions of the Universe, which are optically dark, yet shine brightly in the millimetre portion of the electromagnetic spectrum. The Atacama Large Millimeter Array (ALMA) is an international astronomy facility. ALMA is an equal partnership between Europe and North America, in cooperation with the Republic of Chile, and is funded in North America by the U.S. National Science Foundation (NSF) in cooperation with the National Research Council of Canada (NRC), and in Europe by the European Southern Observatory (ESO) and Spain. ALMA construction and operations are led on behalf of North America by the National Radio Astronomy Observatory (NRAO), which is managed by Associated Universities, Inc. (AUI), and on behalf of Europe by ESO. " ALMA will be a giant leap forward for our studies of this relatively little explored spectral window towards the Universe" , said Dr. Catherine Cesarsky , Director General of ESO. "With ESO leading the European part of this ambitious and forward-looking project, the impact of ALMA will be felt in wide circles on our continent. Together with our partners in North America and Chile, we are all looking forward to the truly outstanding opportunities that will be offered by ALMA , also to young scientists and engineers" . " The U.S. National Science Foundation joins today with our North American partner, Canada, and with the European Southern Observatory, Spain, and Chile to prepare

  17. Healthy Cities, Healthy Suburbs: Progress in Meeting Healthy People Goals for the Nation's 100 Largest Cities & Their Suburbs.

    ERIC Educational Resources Information Center

    Andrulis, Dennis P.; Duchon, Lisa M.; Reid, Hailey Maier

    This review of seven Healthy People objectives for the nation's 100 largest cities and their surrounding areas documents considerable but inconsistent progress toward improving health in urban and suburban areas. It describes achievements in reaching Healthy People 2000/2010 goals, which were created by the Office of the Surgeon General of the…

  18. Current Offerings in Six Specified Subjects in Accredited (and the Largest Unaccredited ) Schools and Departments of Journalism.

    ERIC Educational Resources Information Center

    Collins, Erik L.; Rarick, Galen R.

    This survey was conducted to determen the extent of course offerings by the accredited and the largest unaccredited journalism programs in the areas of nonverbal communications, research methods for working journalists, media economics and management, major issues in contemporary society, the urban community, and new technology. Two mailings and…

  19. Lending a Hand: A Report on the Lobbying Expenditures and Political Contributions of the Five Largest Student Loan Corporations.

    ERIC Educational Resources Information Center

    United States Public Interest Research Group, Washington, DC.

    Using data from a variety of sources, including public records and the Web site of the Center for Responsive Politics, this study examined the political spending of the five largest holders of federally subsidized student loans: Sallie Mae, the Student Loan Corporation of Citibank, First Union National Bank, Wells Fargo Education Financial…

  20. German Migrant Teachers in Australia: Insights into the Largest Cohort of Non-English Speaking Background Teachers

    ERIC Educational Resources Information Center

    Bense, Katharina

    2015-01-01

    The research reported in this paper investigates the situation of German migrant teachers in Australia. Although German born teachers represent the largest group of non-English speaking background teachers in Australia, there is no study of the circumstances and experiences of these teachers in Australia. This study aims to fill this gap. It…