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Sample records for human spliceosomal u1

  1. Therapeutic activity of modified U1 core spliceosomal particles

    PubMed Central

    Rogalska, Malgorzata Ewa; Tajnik, Mojca; Licastro, Danilo; Bussani, Erica; Camparini, Luca; Mattioli, Chiara; Pagani, Franco

    2016-01-01

    Modified U1 snRNAs bound to intronic sequences downstream of the 5′ splice site correct exon skipping caused by different types of mutations. Here we evaluate the therapeutic activity and structural requirements of these exon-specific U1 snRNA (ExSpeU1) particles. In a severe spinal muscular atrophy, mouse model, ExSpeU1, introduced by germline transgenesis, increases SMN2 exon 7 inclusion, SMN protein production and extends life span. In vitro, RNA mutant analysis and silencing experiments show that while U1A protein is dispensable, the 70K and stem loop IV elements mediate most of the splicing rescue activity through improvement of exon and intron definition. Our findings indicate that precise engineering of the U1 core spliceosomal RNA particle has therapeutic potential in pathologies associated with exon-skipping mutations. PMID:27041075

  2. A 10S galectin-3–U1 snRNP complex assembles into active spliceosomes

    PubMed Central

    Haudek, Kevin C.; Voss, Patricia G.; Wang, John L.; Patterson, Ronald J.

    2016-01-01

    In previous studies, we reported that fractionation of HeLa cell nuclear extracts on glycerol gradients revealed an endogenous ∼10S particle that contained galectin-3 and U1 snRNP and this particle was sufficient to load the galectin polypeptide onto a pre-mRNA substrate. We now document that this interaction between the galectin-3–U1 snRNP particle and the pre-mRNA results in a productive spliceosomal complex, leading to intermediates and products of the splicing reaction. Nuclear extracts were depleted of U1 snRNP with a concomitant loss of splicing activity. Splicing activity in the U1-depleted extract can be reconstituted by the galectin-3–U1 snRNP particle, isolated by immunoprecipitation of the 10S region (fractions 3–5) of the glycerol gradient with anti-galectin-3 antibodies. In contrast, parallel anti-galectin-3 immunoprecipitation of free galectin-3 molecules not in a complex with U1 snRNP (fraction 1 of the same gradient), failed to restore splicing activity. These results indicate that the galectin-3–U1 snRNP-pre-mRNA ternary complex is a functional E complex and that U1 snRNP is required to assemble galectin-3 onto an active spliceosome. PMID:27105840

  3. Comprehensive proteomic analysis of the human spliceosome

    NASA Astrophysics Data System (ADS)

    Zhou, Zhaolan; Licklider, Lawrence J.; Gygi, Steven P.; Reed, Robin

    2002-09-01

    The precise excision of introns from pre-messenger RNA is performed by the spliceosome, a macromolecular machine containing five small nuclear RNAs and numerous proteins. Much has been learned about the protein components of the spliceosome from analysis of individual purified small nuclear ribonucleoproteins and salt-stable spliceosome `core' particles. However, the complete set of proteins that constitutes intact functional spliceosomes has yet to be identified. Here we use maltose-binding protein affinity chromatography to isolate spliceosomes in highly purified and functional form. Using nanoscale microcapillary liquid chromatography tandem mass spectrometry, we identify ~145 distinct spliceosomal proteins, making the spliceosome the most complex cellular machine so far characterized. Our spliceosomes comprise all previously known splicing factors and 58 newly identified components. The spliceosome contains at least 30 proteins with known or putative roles in gene expression steps other than splicing. This complexity may be required not only for splicing multi-intronic metazoan pre-messenger RNAs, but also for mediating the extensive coupling between splicing and other steps in gene expression.

  4. Large-Scale Proteomic Analysis of the Human Spliceosome

    PubMed Central

    Rappsilber, Juri; Ryder, Ursula; Lamond, Angus I.; Mann, Matthias

    2002-01-01

    In a previous proteomic study of the human spliceosome, we identified 42 spliceosome-associated factors, including 19 novel ones. Using enhanced mass spectrometric tools and improved databases, we now report identification of 311 proteins that copurify with splicing complexes assembled on two separate pre-mRNAs. All known essential human splicing factors were found, and 96 novel proteins were identified, of which 55 contain domains directly linking them to functions in splicing/RNA processing. We also detected 20 proteins related to transcription, which indicates a direct connection between this process and splicing. This investigation provides the most detailed inventory of human spliceosome-associated factors to date, and the data indicate a number of interesting links coordinating splicing with other steps in the gene expression pathway. PMID:12176931

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

    SciTech Connect

    Möhlmann, Sina; Mathew, Rebecca; Neumann, Piotr; Schmitt, Andreas; Lührmann, Reinhard; Ficner, Ralf

    2014-06-01

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

  6. Interaction between the RNA binding domains of Ser-Arg splicing factor 1 and U1-70K snRNP protein determines early spliceosome assembly.

    PubMed

    Cho, Suhyung; Hoang, Amy; Sinha, Rahul; Zhong, Xiang-Yang; Fu, Xiang-Dong; Krainer, Adrian R; Ghosh, Gourisankar

    2011-05-17

    It has been widely accepted that the early spliceosome assembly begins with U1 small nuclear ribonucleoprotein (U1 snRNP) binding to the 5' splice site (5'SS), which is assisted by the Ser/Arg (SR)-rich proteins in mammalian cells. In this process, the RS domain of SR proteins is thought to directly interact with the RS motif of U1-70K, which is subject to regulation by RS domain phosphorylation. Here we report that the early spliceosome assembly event is mediated by the RNA recognition domains (RRM) of serine/arginine-rich splicing factor 1 (SRSF1), which bridges the RRM of U1-70K to pre-mRNA by using the surface opposite to the RNA binding site. Specific mutation in the RRM of SRSF1 that disrupted the RRM-RRM interaction also inhibits the formation of spliceosomal E complex and splicing. We further demonstrate that the hypo-phosphorylated RS domain of SRSF1 interacts with its own RRM, thus competing with U1-70K binding, whereas the hyper-phosphorylated RS domain permits the formation of a ternary complex containing ESE, an SR protein, and U1 snRNP. Therefore, phosphorylation of the RS domain in SRSF1 appears to induce a key molecular switch from intra- to intermolecular interactions, suggesting a plausible mechanism for the documented requirement for the phosphorylation/dephosphorylation cycle during pre-mRNA splicing.

  7. Members of a family of proteins (the RD family) detected by a U1 70K monoclonal antibody are present in spliceosomal complexes.

    PubMed Central

    Staknis, D; Reed, R

    1995-01-01

    We have characterized a monoclonal antibody (mAb) to the U1 snRNP component U1 70K. We find that this antibody recognizes several proteins, in addition to U1 70K, in purified spliceosomal complexes and in total HeLa cell nuclear extract preparations. The novel mAb U1 70K antigens can also be specifically immunoprecipitated by the antibody. Similarly to U1 70K, many of the mAb U1 70K antigens can be phosphorylated by a co-purifying kinase activity. The epitope recognized by mAb U1 70K was previously shown to be a repeating arginine/aspartate (RD) dipeptide. Thus we have designated the novel mAb U1 70K antigens the RD family. Comparison of mAb U1 70K with a recently characterized antibody, mAb 16H3, whose epitope is a repeating R/D or R/E motif, showed that a large subset of the antigens are common. In contrast, most of the mAb U1 70K antigens are distinct from the proteins detected by mAb 104, an antibody to the SR family of splicing factors. Images PMID:7479068

  8. A fraction of the transcription factor TAF15 participates in interactions with a subset of the spliceosomal U1 snRNP complex.

    PubMed

    Leichter, Michael; Marko, Marija; Ganou, Vassiliki; Patrinou-Georgoula, Meropi; Tora, László; Guialis, Apostolia

    2011-12-01

    RNA/ssDNA-binding proteins comprise an emerging class of multifunctional proteins with an anticipated role in coupling transcription with RNA processing. We focused here on the highly related transcription factors of the TET sub-class: TLS/FUS, EWS and in particular the least studied member TAF15. An extensive array of immunoprecipitation studies on differentially extracted HeLa nuclei revealed the specific association of TAF15 with the spliceosomal U1 snRNP complex, as deduced by the co-precipitating U1 snRNA, U1-70K and Sm proteins. Additionally, application of anti-U1 RNP autoantibodies identified TAF15 in the immunoprecipitates. Minor fractions of nuclear TAF15 and U1 snRNP were involved in this association. Pull-down assays using recombinant TAF15 and U1 snRNP-specific proteins (U1-70K, U1A and U1C) provided in vitro evidence for a direct protein-protein interaction between TAF15 and U1C, which required the N-terminal domain of TAF15. The ability of TAF15 to directly contact RNA, most likely RNA pol II transcripts, was supported by in vivo UV cross-linking studies in the presence of α-amanitin. By all findings, the existence of a functionally discrete subset of U1 snRNP in association with TAF15 was suggested and provided further support for the involvement of U1 snRNP components in early steps of coordinated gene expression.

  9. Protein phosphatase 2A family members (PP2A and PP6) associate with U1 snRNP and the spliceosome during pre-mRNA splicing

    PubMed Central

    Kamoun, Malek; Filali, Mohammed; Murray, Michael V.; Awasthi, Sita; Wadzinski, Brian E.

    2013-01-01

    Protein phosphorylation and dephosphorylation are both important for multiple steps in the splicing pathway. Members of the PP1 and PP2A subfamilies of phospho-serine/threonine phosphatases play essential but redundant roles in the second step of the splicing reaction. PP6, a member of the PP2A subfamily, is the mammalian homologue of yeast Sit4p and ppe1, which are involved in cell cycle regulation; however, the involvement of PP6 in the splicing pathway remains unclear. Here we show that PP2A family members physically associate with the spliceosome throughout the splicing reaction. PP2A holoenzyme and PP6 were found stably associated with U1 snRNP. Together our findings indicate that these phosphatases regulate splicing catalysis involving U1 snRNP and suggest an important evolutionary conserved role of PP2A family phosphatases in pre-mRNA splicing. PMID:24064353

  10. A high throughput splicing assay identifies new classes of inhibitors of human and yeast spliceosomes

    PubMed Central

    Effenberger, Kerstin A.; Perriman, Rhonda J.; Bray, Walter M.; Lokey, R. Scott; Ares, Manuel; Jurica, Melissa S.

    2014-01-01

    The spliceosome is the macromolecular machine responsible for pre-mRNA splicing, an essential step in eukaryotic gene expression. During splicing a myriad of subunits join and leave the spliceosome as it works on the pre-mRNA substrate. Strikingly, there are very few small molecules known to interact with the spliceosome. Splicing inhibitors are needed to capture transient spliceosome conformations and probe important functional components. Such compounds may also have chemotherapeutic applications, as links between splicing and cancer are increasingly uncovered. To identify new splicing inhibitors, we developed a high throughput assay for in vitro splicing using an RT-qPCR readout. In a pilot screen of 3,080 compounds we identified three small molecules that inhibit splicing in HeLa extract by interfering with different stages of human spliceosome assembly. Two of the compounds similarly impact spliceosomes in yeast extracts, suggesting selective targeting of conserved components. By examining related molecules, we identified chemical features required for the activity of two of the splicing inhibitors. In addition to verifying our assay procedure and paving the way to larger screens, these studies establish new compounds as chemical probes for investigating the splicing machinery. PMID:23771823

  11. Major spliceosome defects cause male infertility and are associated with nonobstructive azoospermia in humans

    PubMed Central

    Wu, Hao; Sun, Liwei; Wen, Yang; Liu, Yujuan; Yu, Jun; Mao, Feiyu; Wang, Ya; Tong, Chao; Hu, Zhibin; Sha, Jiahao; Liu, Mingxi; Xia, Laixin

    2016-01-01

    Processing of pre-mRNA into mRNA is an important regulatory mechanism in eukaryotes that is mediated by the spliceosome, a huge and dynamic ribonucleoprotein complex. Splicing defects are implicated in a spectrum of human disease, but the underlying mechanistic links remain largely unresolved. Using a genome-wide association approach, we have recently identified single nucleotide polymorphisms in humans that associate with nonobstructive azoospermia (NOA), a common cause of male infertility. Here, using genetic manipulation of corresponding candidate loci in Drosophila, we show that the spliceosome component SNRPA1/U2A is essential for male fertility. Loss of U2A in germ cells of the Drosophila testis does not affect germline stem cells, but does result in the accumulation of mitotic spermatogonia that fail to differentiate into spermatocytes and mature sperm. Lack of U2A causes insufficient splicing of mRNAs required for the transition of germ cells from proliferation to differentiation. We show that germ cell-specific disruption of other components of the major spliceosome manifests with the same phenotype, demonstrating that mRNA processing is required for the differentiation of spermatogonia. This requirement is conserved, and expression of human SNRPA1 fully restores spermatogenesis in U2A mutant flies. We further report that several missense mutations in human SNRPA1 that inhibit the assembly of the major spliceosome dominantly disrupt spermatogonial differentiation in Drosophila. Collectively, our findings uncover a conserved and specific requirement for the major spliceosome during the transition from spermatogonial proliferation to differentiation in the male testis, suggesting that spliceosome defects affecting the differentiation of human spermatogonia contribute to NOA. PMID:27035939

  12. Biochemical and proteomic analysis of spliceosome factors interacting with intron-1 of human papillomavirus type-16.

    PubMed

    Martínez-Salazar, Martha; López-Urrutia, Eduardo; Arechaga-Ocampo, Elena; Bonilla-Moreno, Raul; Martínez-Castillo, Macario; Díaz-Hernández, Job; Del Moral-Hernández, Oscar; Cedillo-Barrón, Leticia; Martines-Juarez, Víctor; De Nova-Ocampo, Monica; Valdes, Jesús; Berumen, Jaime; Villegas-Sepúlveda, Nicolás

    2014-12-05

    The human papillomavirus type 16 (HPV-16) E6/E7 spliced transcripts are heterogeneously expressed in cervical carcinoma. The heterogeneity of the E6/E7 splicing profile might be in part due to the intrinsic variation of splicing factors in tumor cells. However, the splicing factors that bind the E6/E7 intron 1 (In-1) have not been defined. Therefore, we aimed to identify these factors; we used HeLa nuclear extracts (NE) for in vitro spliceosome assembly. The proteins were allowed to bind to an RNA/DNA hybrid formed by the In-1 transcript and a 5'-biotinylated DNA oligonucleotide complementary to the upstream exon sequence, which prevented interference in protein binding to the intron. The hybrid probes bound with the nuclear proteins were coupled to streptavidin magnetic beads for chromatography affinity purification. Proteins were eluted and identified by mass spectrometry (MS). Approximately 170 proteins were identified by MS, 80% of which were RNA binding proteins, including canonical spliceosome core components, helicases and regulatory splicing factors. The canonical factors were identified as components of the spliceosomal B-complex. Although 35-40 of the identified factors were cognate splicing factors or helicases, they have not been previously detected in spliceosome complexes that were assembled using in vivo or in vitro models.

  13. Cryo-EM structure of a human spliceosome activated for step 2 of splicing.

    PubMed

    Bertram, Karl; Agafonov, Dmitry E; Liu, Wen-Ti; Dybkov, Olexandr; Will, Cindy L; Hartmuth, Klaus; Urlaub, Henning; Kastner, Berthold; Stark, Holger; Lührmann, Reinhard

    2017-02-16

    Spliceosome rearrangements facilitated by RNA helicase PRP16 before catalytic step two of splicing are poorly understood. Here we report a 3D cryo-electron microscopy structure of the human spliceosomal C complex stalled directly after PRP16 action (C*). The architecture of the catalytic U2-U6 ribonucleoprotein (RNP) core of the human C* spliceosome is very similar to that of the yeast pre-Prp16 C complex. However, in C* the branched intron region is separated from the catalytic centre by approximately 20 Å, and its position close to the U6 small nuclear RNA ACAGA box is stabilized by interactions with the PRP8 RNase H-like and PRP17 WD40 domains. RNA helicase PRP22 is located about 100 Å from the catalytic centre, suggesting that it destabilizes the spliced mRNA after step two from a distance. Comparison of the structure of the yeast C and human C* complexes reveals numerous RNP rearrangements that are likely to be facilitated by PRP16, including a large-scale movement of the U2 small nuclear RNP.

  14. Modeling of the U1 snRNP assembly pathway in alternative splicing in human cells using Petri nets.

    PubMed

    Kielbassa, J; Bortfeldt, R; Schuster, S; Koch, I

    2009-02-01

    The investigation of spliceosomal processes is currently a topic of intense research in molecular biology. In the molecular mechanism of alternative splicing, a multi-protein-RNA complex - the spliceosome - plays a crucial role. To understand the biological processes of alternative splicing, it is essential to comprehend the biogenesis of the spliceosome. In this paper, we propose the first abstract model of the regulatory assembly pathway of the human spliceosomal subunit U1. Using Petri nets, we describe its highly ordered assembly that takes place in a stepwise manner. Petri net theory represents a mathematical formalism to model and analyze systems with concurrent processes at different abstraction levels with the possibility to combine them into a uniform description language. There exist many approaches to determine static and dynamic properties of Petri nets, which can be applied to analyze biochemical systems. In addition, Petri net tools usually provide intuitively understandable graphical network representations, which facilitate the dialog between experimentalists and theoreticians. Our Petri net model covers binding, transport, signaling, and covalent modification processes. Through the computation of structural and behavioral Petri net properties and their interpretation in biological terms, we validate our model and use it to get a better understanding of the complex processes of the assembly pathway. We can explain the basic network behavior, using minimal T-invariants which represent special pathways through the network. We find linear as well as cyclic pathways. We determine the P-invariants that represent conserved moieties in a network. The simulation of the net demonstrates the importance of the stability of complexes during the maturation pathway. We can show that complexes that dissociate too fast, hinder the formation of the complete U1 snRNP.

  15. The Natural Product N-Palmitoyl-l-leucine Selectively Inhibits Late Assembly of Human Spliceosomes*

    PubMed Central

    Effenberger, Kerstin A.; James, Robert C.; Urabe, Veronica K.; Dickey, Bailey J.; Linington, Roger G.; Jurica, Melissa S.

    2015-01-01

    The spliceosome is a dynamic complex of five structural RNAs and dozens of proteins, which assemble together to remove introns from nascent eukaryotic gene transcripts in a process called splicing. Small molecules that target different components of the spliceosome represent valuable research tools to investigate this complicated macromolecular machine. However, the current collection of spliceosome inhibitors is very limited. To expand the toolkit we used a high-throughput in vitro splicing assay to screen a collection of pre-fractions of natural compounds derived from marine bacteria for splicing inhibition. Further fractionation of initial hits generated individual peaks of splicing inhibitors that interfere with different stages of spliceosome assembly. With additional characterization of individual peaks, we identified N-palmitoyl-l-leucine as a new splicing inhibitor that blocks a late stage of spliceosome assembly. Structure-activity relationship analysis of the compound revealed that length of carbon chain is important for activity in splicing, as well as for effects on the cytological profile of cells in culture. Together these results demonstrate that our combination of in vitro splicing analysis with complex natural product libraries is a powerful strategy for identifying new small molecule tools with which to probe different aspects of spliceosome assembly and function. PMID:26408199

  16. The Natural Product N-Palmitoyl-l-leucine Selectively Inhibits Late Assembly of Human Spliceosomes.

    PubMed

    Effenberger, Kerstin A; James, Robert C; Urabe, Veronica K; Dickey, Bailey J; Linington, Roger G; Jurica, Melissa S

    2015-11-13

    The spliceosome is a dynamic complex of five structural RNAs and dozens of proteins, which assemble together to remove introns from nascent eukaryotic gene transcripts in a process called splicing. Small molecules that target different components of the spliceosome represent valuable research tools to investigate this complicated macromolecular machine. However, the current collection of spliceosome inhibitors is very limited. To expand the toolkit we used a high-throughput in vitro splicing assay to screen a collection of pre-fractions of natural compounds derived from marine bacteria for splicing inhibition. Further fractionation of initial hits generated individual peaks of splicing inhibitors that interfere with different stages of spliceosome assembly. With additional characterization of individual peaks, we identified N-palmitoyl-l-leucine as a new splicing inhibitor that blocks a late stage of spliceosome assembly. Structure-activity relationship analysis of the compound revealed that length of carbon chain is important for activity in splicing, as well as for effects on the cytological profile of cells in culture. Together these results demonstrate that our combination of in vitro splicing analysis with complex natural product libraries is a powerful strategy for identifying new small molecule tools with which to probe different aspects of spliceosome assembly and function.

  17. Spliceosomal intronogenesis

    PubMed Central

    Lee, Sujin; Stevens, Scott W.

    2016-01-01

    The presence of intervening sequences, termed introns, is a defining characteristic of eukaryotic nuclear genomes. Once transcribed into pre-mRNA, these introns must be removed within the spliceosome before export of the processed mRNA to the cytoplasm, where it is translated into protein. Although intron loss has been demonstrated experimentally, several mysteries remain regarding the origin and propagation of introns. Indeed, documented evidence of gain of an intron has only been suggested by phylogenetic analyses. We report the use of a strategy that detects selected intron gain and loss events. We have experimentally verified, to our knowledge, the first demonstrations of intron transposition in any organism. From our screen, we detected two separate intron gain events characterized by the perfect transposition of a reporter intron into the yeast genes RPL8B and ADH2, respectively. We show that the newly acquired introns are able to be removed from their respective pre-mRNAs by the spliceosome. Additionally, the novel allele, RPL8Bint, is functional when overexpressed within the genome in a strain lacking the Rpl8 paralogue RPL8A, demonstrating that the gene targeted for intronogenesis is functional. PMID:27217561

  18. Multiple protein–protein interactions converging on the Prp38 protein during activation of the human spliceosome

    PubMed Central

    Schütze, Tonio; Ulrich, Alexander K.C.; Apelt, Luise; Will, Cindy L.; Bartlick, Natascha; Seeger, Martin; Weber, Gert; Lührmann, Reinhard; Stelzl, Ulrich; Wahl, Markus C.

    2016-01-01

    Spliceosomal Prp38 proteins contain a conserved amino-terminal domain, but only higher eukaryotic orthologs also harbor a carboxy-terminal RS domain, a hallmark of splicing regulatory SR proteins. We show by crystal structure analysis that the amino-terminal domain of human Prp38 is organized around three pairs of antiparallel α-helices and lacks similarities to RNA-binding domains found in canonical SR proteins. Instead, yeast two-hybrid analyses suggest that the amino-terminal domain is a versatile protein–protein interaction hub that possibly binds 12 other spliceosomal proteins, most of which are recruited at the same stage as Prp38. By quantitative, alanine surface-scanning two-hybrid screens and biochemical analyses we delineated four distinct interfaces on the Prp38 amino-terminal domain. In vitro interaction assays using recombinant proteins showed that Prp38 can bind at least two proteins simultaneously via two different interfaces. Addition of excess Prp38 amino-terminal domain to in vitro splicing assays, but not of an interaction-deficient mutant, stalled splicing at a precatalytic stage. Our results show that human Prp38 is an unusual SR protein, whose amino-terminal domain is a multi-interface protein–protein interaction platform that might organize the relative positioning of other proteins during splicing. PMID:26673105

  19. Interactions between Giardia duodenalis Sm proteins and their association with spliceosomal snRNAs.

    PubMed

    Gómez, Vanessa; Wasserman, Moisés

    2017-02-01

    Giardia duodenalis is a parasite that colonises the intestines of humans and other vertebrates, causing diarrhoea and poor nutrient absorption. G. duodenalis is sometimes considered an early diverging eukaryote, and its genome exhibits simplified molecular machinery for many cellular processes, which makes it an interesting model to study. The spliceosome, one of the most complex molecular machines in the eukaryotic cell, is responsible for intron excision and exon splicing. Just over a decade ago, it was believed that the G. duodenalis genome did not contain introns or undergo splicing. Research now shows that this speculation was incorrect and that uncommon mechanisms, such as trans-splicing from different genes, occur. In silico studies of the parasite suggest the possibility of a simplified spliceosome and spliceosomal small nuclear RNA (snRNA) candidates; however, none of these components have been identified in vivo. Here, we developed a strategy to study the in vivo expression, interactions and localisation of these spliceosome components in G. duodenalis. Haemagglutinin (HA)-tagged SmB and SmD3 proteins, which form part of the spliceosome core, were overexpressed in the parasite. Immunoprecipitation with anti-HA revealed that the SmD3 protein is associated with the proteins SmB, SmD1, SmD2, SmE and SmF in vivo. In addition, the U1, U2 and U4 snRNA candidates reported previously were found in the protein complex, suggesting that these molecules are spliceosomal snRNAs of G. duodenalis and they contained a 2,2,7-trimethylguanosine modification at their 5' end. Our data indicate that the actively expressed spliceosome in G. duodenalis is similar to that of highly evolved protists and higher animals.

  20. Primary structure of a human arginine-rich nuclear protein that colocalizes with spliceosome components

    SciTech Connect

    Chaudhary, N.; McMahon, C.; Blobel, G. )

    1991-09-15

    The cDNA for a 54-kDa nuclear protein (p54) has been cloned from a human hepatoma expression library. Contained within p54 is an arginine/serine-rich region similar to segments of several proteins that participate in pre-mRNA splicing including the 70-kDa component of U1 small nuclear ribonucleoprotein particle (snRNP) and the Drosophila transformer and suppressor-of-white-apricot proteins. The arginine/serine-rich region is dominated by a series of 8-amino acid imperfect repetitive motifs (consensus sequence, Arg-Arg-Ser-Arg-Ser-Arg-Ser-Arg). Antibodies raised against synthetic peptides of p54 react with an {approximately}70-kDa protein on immunoblots of HeLa cell and rat liver nuclear proteins. This apparent discrepancy in mass is also observed when p54 mRNA is translated in vitro. Indirect immunofluorescence studies in HeLa cells show that p54 is distributed throughout the nucleus in a speckled pattern, with an additional diffuse labeling of the nucleus excluding the nucleoli. Double immunofluorescence experiments indicate that these punctate regions are coincident with the speckles seen in cells stained with antibodies against several constituents of the pre-mRNA splicing machinery. Sedimentation analysis of HeLa cell extracts on sucrose gradients showed that p54 migrates at 4-6 S, indicating that the protein is not a tightly associated component of snRNPs. Although the function of p54 is not yet known, the structure and immunolocalization data suggest that this protein may have a role in pre-mRNA processing.

  1. Novel regulatory principles of the spliceosomal Brr2 RNA helicase and links to retinal disease in humans.

    PubMed

    Mozaffari-Jovin, Sina; Wandersleben, Traudy; Santos, Karine F; Will, Cindy L; Lührmann, Reinhard; Wahl, Markus C

    2014-01-01

    For each round of pre-mRNA splicing, a spliceosome is assembled anew on its substrate. RNA-protein remodeling events required for spliceosome assembly, splicing catalysis, and spliceosome disassembly are driven and controlled by a conserved group of ATPases/RNA helicases. The activities of most of these enzymes are timed by their recruitment to the spliceosome. The Brr2 enzyme, however, which mediates spliceosome catalytic activation, is a stable subunit of the spliceosome, and thus, requires special regulation. Recent structural and functional studies have revealed diverse mechanisms whereby an RNaseH-like and a Jab1/MPN-like domain of the Prp8 protein regulate Brr2 activity during splicing both positively and negatively. Reversible Brr2 inhibition might in part be achieved via an intrinsically unstructured element of the Prp8 Jab1/MPN domain, a concept widespread in biological systems. Mutations leading to changes in the Prp8 Jab1/MPN domain, which are linked to a severe form of retinitis pigmentosa, disrupt Jab1/MPN-mediated regulation of Brr2.

  2. Physical and genetic interactions of yeast Cwc21p, an ortholog of human SRm300/SRRM2, suggest a role at the catalytic center of the spliceosome.

    PubMed

    Grainger, Richard J; Barrass, J David; Jacquier, Alain; Rain, Jean-Christophe; Beggs, Jean D

    2009-12-01

    In Saccharomyces cerevisiae, Cwc21p is a protein of unknown function that is associated with the NineTeen Complex (NTC), a group of proteins involved in activating the spliceosome to promote the pre-mRNA splicing reaction. Here, we show that Cwc21p binds directly to two key splicing factors-namely, Prp8p and Snu114p-and becomes the first NTC-related protein known to dock directly to U5 snRNP proteins. Using a combination of proteomic techniques we show that the N-terminus of Prp8p contains an intramolecular fold that is a Snu114p and Cwc21p interacting domain (SCwid). Cwc21p also binds directly to the C-terminus of Snu114p. Complementary chemical cross-linking experiments reveal reciprocal protein footprints between the interacting Prp8 and Cwc21 proteins, identifying the conserved cwf21 domain in Cwc21p as a Prp8p binding site. Genetic and functional interactions between Cwc21p and Isy1p indicate that they have related functions at or prior to the first catalytic step of splicing, and suggest that Cwc21p functions at the catalytic center of the spliceosome, possibly in response to environmental or metabolic changes. We demonstrate that SRm300, the only SR-related protein known to be at the core of human catalytic spliceosomes, is a functional ortholog of Cwc21p, also interacting directly with Prp8p and Snu114p. Thus, the function of Cwc21p is likely conserved from yeast to humans.

  3. RSR-2, the Caenorhabditis elegans Ortholog of Human Spliceosomal Component SRm300/SRRM2, Regulates Development by Influencing the Transcriptional Machinery

    PubMed Central

    Fontrodona, Laura; Porta-de-la-Riva, Montserrat; Morán, Tomás; Niu, Wei; Díaz, Mònica; Aristizábal-Corrales, David; Villanueva, Alberto; Schwartz, Simó; Reinke, Valerie; Cerón, Julián

    2013-01-01

    Protein components of the spliceosome are highly conserved in eukaryotes and can influence several steps of the gene expression process. RSR-2, the Caenorhabditis elegans ortholog of the human spliceosomal protein SRm300/SRRM2, is essential for viability, in contrast to the yeast ortholog Cwc21p. We took advantage of mutants and RNA interference (RNAi) to study rsr-2 functions in C. elegans, and through genetic epistasis analysis found that rsr-2 is within the germline sex determination pathway. Intriguingly, transcriptome analyses of rsr-2(RNAi) animals did not reveal appreciable splicing defects but instead a slight global decrease in transcript levels. We further investigated this effect in transcription and observed that RSR-2 colocalizes with DNA in germline nuclei and coprecipitates with chromatin, displaying a ChIP-Seq profile similar to that obtained for the RNA Polymerase II (RNAPII). Consistent with a novel transcription function we demonstrate that the recruitment of RSR-2 to chromatin is splicing-independent and that RSR-2 interacts with RNAPII and affects RNAPII phosphorylation states. Proteomic analyses identified proteins associated with RSR-2 that are involved in different gene expression steps, including RNA metabolism and transcription with PRP-8 and PRP-19 being the strongest interacting partners. PRP-8 is a core component of the spliceosome and PRP-19 is the core component of the PRP19 complex, which interacts with RNAPII and is necessary for full transcriptional activity. Taken together, our study proposes that RSR-2 is a multifunctional protein whose role in transcription influences C. elegans development. PMID:23754964

  4. RSR-2, the Caenorhabditis elegans ortholog of human spliceosomal component SRm300/SRRM2, regulates development by influencing the transcriptional machinery.

    PubMed

    Fontrodona, Laura; Porta-de-la-Riva, Montserrat; Morán, Tomás; Niu, Wei; Díaz, Mònica; Aristizábal-Corrales, David; Villanueva, Alberto; Schwartz, Simó; Reinke, Valerie; Cerón, Julián

    2013-06-01

    Protein components of the spliceosome are highly conserved in eukaryotes and can influence several steps of the gene expression process. RSR-2, the Caenorhabditis elegans ortholog of the human spliceosomal protein SRm300/SRRM2, is essential for viability, in contrast to the yeast ortholog Cwc21p. We took advantage of mutants and RNA interference (RNAi) to study rsr-2 functions in C. elegans, and through genetic epistasis analysis found that rsr-2 is within the germline sex determination pathway. Intriguingly, transcriptome analyses of rsr-2(RNAi) animals did not reveal appreciable splicing defects but instead a slight global decrease in transcript levels. We further investigated this effect in transcription and observed that RSR-2 colocalizes with DNA in germline nuclei and coprecipitates with chromatin, displaying a ChIP-Seq profile similar to that obtained for the RNA Polymerase II (RNAPII). Consistent with a novel transcription function we demonstrate that the recruitment of RSR-2 to chromatin is splicing-independent and that RSR-2 interacts with RNAPII and affects RNAPII phosphorylation states. Proteomic analyses identified proteins associated with RSR-2 that are involved in different gene expression steps, including RNA metabolism and transcription with PRP-8 and PRP-19 being the strongest interacting partners. PRP-8 is a core component of the spliceosome and PRP-19 is the core component of the PRP19 complex, which interacts with RNAPII and is necessary for full transcriptional activity. Taken together, our study proposes that RSR-2 is a multifunctional protein whose role in transcription influences C. elegans development.

  5. Variant U1 snRNAs are implicated in human pluripotent stem cell maintenance and neuromuscular disease

    PubMed Central

    Vazquez-Arango, Pilar; Vowles, Jane; Browne, Cathy; Hartfield, Elizabeth; Fernandes, Hugo J. R.; Mandefro, Berhan; Sareen, Dhruv; James, William; Wade-Martins, Richard; Cowley, Sally A.; Murphy, Shona; O'Reilly, Dawn

    2016-01-01

    The U1 small nuclear (sn)RNA (U1) is a multifunctional ncRNA, known for its pivotal role in pre-mRNA splicing and regulation of RNA 3′ end processing events. We recently demonstrated that a new class of human U1-like snRNAs, the variant (v)U1 snRNAs (vU1s), also participate in pre-mRNA processing events. In this study, we show that several human vU1 genes are specifically upregulated in stem cells and participate in the regulation of cell fate decisions. Significantly, ectopic expression of vU1 genes in human skin fibroblasts leads to increases in levels of key pluripotent stem cell mRNA markers, including NANOG and SOX2. These results reveal an important role for vU1s in the control of key regulatory networks orchestrating the transitions between stem cell maintenance and differentiation. Moreover, vU1 expression varies inversely with U1 expression during differentiation and cell re-programming and this pattern of expression is specifically de-regulated in iPSC-derived motor neurons from Spinal Muscular Atrophy (SMA) type 1 patient's. Accordingly, we suggest that an imbalance in the vU1/U1 ratio, rather than an overall reduction in Uridyl-rich (U)-snRNAs, may contribute to the specific neuromuscular disease phenotype associated with SMA. PMID:27536002

  6. 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

  7. Structural basis of the RNA-binding specificity of human U1A protein.

    PubMed Central

    Allain, F H; Howe, P W; Neuhaus, D; Varani, G

    1997-01-01

    The RNP domain is a very common eukaryotic protein domain involved in recognition of a wide range of RNA structures and sequences. Two structures of human U1A in complex with distinct RNA substrates have revealed important aspects of RNP-RNA recognition, but have also raised intriguing questions concerning the origin of binding specificity. The beta-sheet of the domain provides an extensive RNA-binding platform for packing aromatic RNA bases and hydrophobic protein side chains. However, many interactions between functional groups on the single-stranded nucleotides and residues on the beta-sheet surface are potentially common to RNP proteins with diverse specificity and therefore make only limited contribution to molecular discrimination. The refined structure of the U1A complex with the RNA polyadenylation inhibition element reported here clarifies the role of the RNP domain principal specificity determinants (the variable loops) in molecular recognition. The most variable region of RNP proteins, loop 3, plays a crucial role in defining the global geometry of the intermolecular interface. Electrostatic interactions with the RNA phosphodiester backbone involve protein side chains that are unique to U1A and are likely to be important for discrimination. This analysis provides a novel picture of RNA-protein recognition, much closer to our current understanding of protein-protein recognition than that of DNA-protein recognition. PMID:9312034

  8. M48U1 and Tenofovir combination synergistically inhibits HIV infection in activated PBMCs and human cervicovaginal histocultures

    PubMed Central

    Musumeci, Giuseppina; Bon, Isabella; Lembo, David; Cagno, Valeria; Re, Maria Carla; Signoretto, Caterina; Diani, Erica; Lopalco, Lucia; Pastori, Claudia; Martin, Loïc; Ponchel, Gilles; Gibellini, Davide; Bouchemal, Kawthar

    2017-01-01

    Microbicides are considered a promising strategy for preventing human immunodeficiency virus (HIV-1) transmission and disease. In this report, we first analyzed the antiviral activity of the miniCD4 M48U1 peptide formulated in hydroxyethylcellulose (HEC) hydrogel in activated peripheral blood mononuclear cells (PBMCs) infected with R5- and X4–tropic HIV-1 strains. The results demonstrate that M48U1 prevented infection by several HIV-1 strains including laboratory strains, and HIV-1 subtype B and C strains isolated from the activated PBMCs of patients. M48U1 also inhibited infection by two HIV-1 transmitted/founder infectious molecular clones (pREJO.c/2864 and pTHRO.c/2626). In addition, M48U1 was administered in association with tenofovir, and these two antiretroviral drugs synergistically inhibited HIV-1 infection. In the next series of experiments, we tested M48U1 alone or in combination with tenofovir in HEC hydrogel with an organ-like structure mimicking human cervicovaginal tissue. We demonstrated a strong antiviral effect in absence of significant tissue toxicity. Together, these results indicate that co-treatment with M48U1 plus tenofovir is an effective antiviral strategy that may be used as a new topical microbicide to prevent HIV-1 transmission. PMID:28145455

  9. Solution structure of human U1 snRNA. Derivation of a possible three-dimensional model.

    PubMed Central

    Krol, A; Westhof, E; Bach, M; Lührmann, R; Ebel, J P; Carbon, P

    1990-01-01

    The solution structure of human U1 snRNA was investigated by using base-specific chemical probes (dimethylsulfate, carbodiimide, diethylpyrocarbonate) and RNase V1. Chemical reagents were employed under various conditions of salt and temperature and allowed information at the Watson-Crick base-pairing positions to be obtained for 66% of the U1 snRNA bases. Double-stranded or stacked regions were examined with RNase V1. The dat gained from these experiments extend and support the previous 2D model for U1snRNA. However, to elucidate some aspects of the solution data that could not be accounted for by the secondary structure model, the information gathered from structure probing was used to provide the experimental basis required to construct and to test a tertiary structure model by computer graphics modeling. As a result, U1 snRNA is shown to adopt an asymmetrical X-shape that is formed by two helical domains, each one being generated by coaxial stacking of helices at the U1 snRNA cruciform. Chemical reactivities and model building show that a few nucleotides, previously proposed to be unpaired, can form A.G and U.U non Watson-Crick base-pairs, notably in stem-loop B. The structural model we propose for regions G12 to A124 integrates stereochemical constraints and is based both on solution structure data and sequence comparisons between U1 snRNAs. Images PMID:2374709

  10. Brr2 plays a role in spliceosomal activation in addition to U4/U6 unwinding.

    PubMed

    Zhang, Lingdi; Li, Xueni; Hill, Ryan C; Qiu, Yan; Zhang, Wenzheng; Hansen, Kirk C; Zhao, Rui

    2015-03-31

    Brr2 is a DExD/H-box RNA helicase that is responsible for U4/U6 unwinding, a critical step in spliceosomal activation. Brr2 is a large protein (∼250 kD) that consists of an N-terminal domain (∼500 residues) with unknown function and two Hel308-like modules that are responsible for RNA unwinding. Here we demonstrate that removal of the entire N-terminal domain is lethal to Saccharomyces cerevisiae and deletion of the N-terminal 120 residues leads to splicing defects and severely impaired growth. This N-terminal truncation does not significantly affect Brr2's helicase activity. Brr2-Δ120 can be successfully assembled into the tri-snRNP (albeit at a lower level than the WT Brr2) and the spliceosomal B complex. However, the truncation significantly impairs spliceosomal activation, leading to a dramatic reduction of U5, U6 snRNAs and accumulation of U1 snRNA in the B(act) complex. The N-terminal domain of Brr2 does not seem to be directly involved in regulating U1/5'ss unwinding. Instead, the N-terminal domain seems to be critical for retaining U5 and U6 snRNPs during/after spliceosomal activation through its interaction with snRNAs and possibly other spliceosomal proteins, revealing a new role of Brr2 in spliceosomal activation in addition to U4/U6 unwinding.

  11. Nuclear cyclophilins affect spliceosome assembly and function in vitro.

    PubMed

    Adams, B M; Coates, Miranda N; Jackson, S RaElle; Jurica, Melissa S; Davis, Tara L

    2015-07-15

    Cyclophilins are ubiquitously expressed proteins that bind to prolines and can catalyse cis/trans isomerization of proline residues. There are 17 annotated members of the cyclophilin family in humans, ubiquitously expressed and localized variously to the cytoplasm, nucleus or mitochondria. Surprisingly, all eight of the nuclear localized cyclophilins are found associated with spliceosomal complexes. However, their particular functions within this context are unknown. We have therefore adapted three established assays for in vitro pre-mRNA splicing to probe the functional roles of nuclear cyclophilins in the context of the human spliceosome. We find that four of the eight spliceosom-associated cyclophilins exert strong effects on splicing in vitro. These effects are dose-dependent and, remarkably, uniquely characteristic of each cyclophilin. Using both qualitative and quantitative means, we show that at least half of the nuclear cyclophilins can act as regulatory factors of spliceosome function in vitro. The present work provides the first quantifiable evidence that nuclear cyclophilins are splicing factors and provides a novel approach for future work into small molecule-based modulation of pre-mRNA splicing.

  12. Nuclear cyclophilins affect spliceosome assembly and function in vitro

    PubMed Central

    Adams, B.M.; Coates, Miranda N.; Jackson, S. RaElle; Jurica, Melissa S.; Davis, Tara L.

    2015-01-01

    Cyclophilins are ubiquitously expressed proteins that bind to prolines and can catalyse cis/trans isomerization of proline residues. There are 17 annotated members of the cyclophilin family in humans, ubiquitously expressed and localized variously to the cytoplasm, nucleus or mitochondria. Surprisingly, all eight of the nuclear localized cyclophilins are found associated with spliceosomal complexes. However, their particular functions within this context are unknown. We have therefore adapted three established assays for in vitro pre-mRNA splicing to probe the functional roles of nuclear cyclophilins in the context of the human spliceosome. We find that four of the eight spliceosom-associated cyclophilins exert strong effects on splicing in vitro. These effects are dose-dependent and, remarkably, uniquely characteristic of each cyclophilin. Using both qualitative and quantitative means, we show that at least half of the nuclear cyclophilins can act as regulatory factors of spliceosome function in vitro. The present work provides the first quantifiable evidence that nuclear cyclophilins are splicing factors and provides a novel approach for future work into small molecule-based modulation of pre-mRNA splicing. PMID:25967372

  13. Prp8 protein: At the heart of the spliceosome

    PubMed Central

    GRAINGER, RICHARD J.; BEGGS, JEAN D.

    2005-01-01

    Pre-messenger RNA (pre-mRNA) splicing is a central step in gene expression. Lying between transcription and protein synthesis, pre-mRNA splicing removes sequences (introns) that would otherwise disrupt the coding potential of intron-containing transcripts. This process takes place in the nucleus, catalyzed by a large RNA–protein complex called the spliceosome. Prp8p, one of the largest and most highly conserved of nuclear proteins, occupies a central position in the catalytic core of the spliceosome, and has been implicated in several crucial molecular rearrangements that occur there. Recently, Prp8p has also come under the spotlight for its role in the inherited human disease, Retinitis Pigmentosa. Prp8 is unique, having no obvious homology to other proteins; however, using bioinformatical analysis we reveal the presence of a conserved RNA recognition motif (RRM), an MPN/JAB domain and a putative nuclear localization signal (NLS). Here, we review biochemical and genetical data, mostly related to the human and yeast proteins, that describe Prp8’s central role within the spliceosome and its molecular interactions during spliceosome formation, as splicing proceeds, and in post-splicing complexes. PMID:15840809

  14. A review of craniofacial disorders caused by spliceosomal defects.

    PubMed

    Lehalle, D; Wieczorek, D; Zechi-Ceide, R M; Passos-Bueno, M R; Lyonnet, S; Amiel, J; Gordon, C T

    2015-11-01

    The spliceosome is a large ribonucleoprotein complex that removes introns from pre-mRNA transcripts. Mutations in EFTUD2, encoding a component of the major spliceosome, have recently been identified as the cause of mandibulofacial dysostosis, Guion-Almeida type (MFDGA), characterized by mandibulofacial dysostosis, microcephaly, external ear malformations and intellectual disability. Mutations in several other genes involved in spliceosomal function or linked aspects of mRNA processing have also recently been identified in human disorders with specific craniofacial malformations: SF3B4 in Nager syndrome, an acrofacial dysostosis (AFD); SNRPB in cerebrocostomandibular syndrome, characterized by Robin sequence and rib defects; EIF4A3 in the AFD Richieri-Costa-Pereira syndrome, characterized by Robin sequence, median mandibular cleft and limb defects; and TXNL4A in Burn-McKeown syndrome, involving specific craniofacial dysmorphisms. Here, we review phenotypic and molecular aspects of these syndromes. Given the apparent sensitivity of craniofacial development to defects in mRNA processing, it is possible that mutations in other proteins involved in spliceosomal function will emerge in the future as causative for related human disorders.

  15. Re-refinement of the spliceosomal U4 snRNP core-domain structure

    PubMed Central

    Li, Jade; Leung, Adelaine K.; Kondo, Yasushi; Oubridge, Chris; Nagai, Kiyoshi

    2016-01-01

    The core domain of small nuclear ribonucleoprotein (snRNP), comprised of a ring of seven paralogous proteins bound around a single-stranded RNA sequence, functions as the assembly nucleus in the maturation of U1, U2, U4 and U5 spliceosomal snRNPs. The structure of the human U4 snRNP core domain was initially solved at 3.6 Å resolution by experimental phasing using data with tetartohedral twinning. Molecular replacement from this model followed by density modification using untwinned data recently led to a structure of the minimal U1 snRNP at 3.3 Å resolution. With the latter structure providing a search model for molecular replacement, the U4 core-domain structure has now been re-refined. The U4 Sm site-sequence AAUUUUU has been shown to bind to the seven Sm proteins SmF–SmE–SmG–SmD3–SmB–SmD1–SmD2 in an identical manner as the U1 Sm-site sequence AAUUUGU, except in SmD1 where the bound U replaces G. The progression from the initial to the re-refined structure exemplifies a tortuous route to accuracy: where well diffracting crystals of complex assemblies are initially unavailable, the early model errors are rectified by exploiting preliminary interpretations in further experiments involving homologous structures. New insights are obtained from the more accurate model. PMID:26894541

  16. The spliceosome and its metal ions.

    PubMed

    Butcher, Samuel E

    2011-01-01

    The spliceosome is a massive complex of 5 RNAs and many proteins that associate to catalyze precursor messenger RNA splicing. The process of splicing involves two phosphoryl transfer reactions that result in intron excision and ligation of the flanking exons. Since it is required for normal protein production in eukaryotic cells, pre-mRNA splicing is an essential step in gene expression. Although high resolution structural views of the spliceosome do not yet exist, a growing body of evidence indicates that the spliceosome is a magnesium-dependent enzyme that utilizes catalytic metal ions to stabilize both transition states during the two phosphoryl transfer steps of splicing. A wealth of data also indicate that the core of the spliceosome is comprised of RNA, and suggest that the spliceosome may be a ribozyme. This chapter presents the evidence for metal ion catalysis by the spliceosome, draws comparisons to similar RNA enzymes, and discusses the future directions for research into the mechanism of pre-mRNA splicing.

  17. The spliceosome is a therapeutic vulnerability in MYC-driven cancer

    PubMed Central

    Hsu, Tiffany Y-T.; Simon, Lukas M.; Neill, Nicholas; Marcotte, Richard; Sayad, Azin; Bland, Christopher S.; Echeverria, Gloria V.; Sun, Tingting; Kurley, Sarah J.; Tyagi, Siddhartha; Karlin, Kristen L.; Dominguez-Vidaña, Rocio; Hartman, Jessica D.; Renwick, Alexander; Scorsone, Kathleen; Bernardi, Ronald J.; Skinner, Samuel O.; Jain, Antrix; Orellana, Mayra; Lagisetti, Chandraiah; Golding, Ido; Jung, Sung Y.; Neilson, Joel R.; Zhang, Xiang H.-F.; Cooper, Thomas A.; Webb, Thomas R.; Neel, Benjamin G.; Shaw, Chad A.; Westbrook, Thomas F.

    2016-01-01

    c-MYC (MYC) overexpression or hyperactivation is one of the most common drivers of human cancer. Despite intensive study, the MYC oncogene remains recalcitrant to therapeutic inhibition. MYC is a transcription factor, and many of its pro-tumorigenic functions have been attributed to its ability to regulate gene expression programs1–3. Notably, oncogenic MYC activation has also been shown to increase total RNA and protein production in many tissue and disease contexts4–7. While such increases in RNA and protein production may endow cancer cells with pro-tumor hallmarks, this elevation in synthesis may also generate new or heightened burden on MYC-driven cancer cells to properly process these macromolecules8. Herein, we discover the spliceosome as a new target of oncogenic stress in MYC-driven cancers. We identify BUD31 as a MYC-synthetic lethal gene, and demonstrate that BUD31 is a component of the core spliceosome required for its assembly and catalytic activity. Core spliceosomal factors (SF3B1, U2AF1, and others) associated with BUD31 are also required to tolerate oncogenic MYC. Notably, MYC hyperactivation induces an increase in total pre-mRNA synthesis, suggesting an increased burden on the core spliceosome to process pre-mRNA. In contrast to normal cells, partial inhibition of the spliceosome in MYC-hyperactivated cells leads to global intron retention, widespread defects in pre-mRNA maturation, and deregulation of many essential cell processes. Importantly, genetic or pharmacologic inhibition of the spliceosome in vivo impairs survival, tumorigenicity, and metastatic proclivity of MYC-dependent breast cancers. Collectively, these data suggest that oncogenic MYC confers a collateral stress on splicing and that components of the spliceosome may be therapeutic entry points for aggressive MYC-driven cancers. PMID:26331541

  18. Solution structure of the first RNA recognition motif domain of human spliceosomal protein SF3b49 and its mode of interaction with a SF3b145 fragment

    PubMed Central

    Nameki, Nobukazu; Tsuda, Kengo; Takahashi, Mari; Sato, Atsuko; Tochio, Naoya; Inoue, Makoto; Terada, Takaho; Kigawa, Takanori; Kobayashi, Naohiro; Shirouzu, Mikako; Ito, Takuhiro; Sakamoto, Taiichi; Wakamatsu, Kaori; Güntert, Peter; Takahashi, Seizo; Yokoyama, Shigeyuki

    2016-01-01

    Abstract The spliceosomal protein SF3b49, a component of the splicing factor 3b (SF3b) protein complex in the U2 small nuclear ribonucleoprotein, contains two RNA recognition motif (RRM) domains. In yeast, the first RRM domain (RRM1) of Hsh49 protein (yeast orthologue of human SF3b49) reportedly interacts with another component, Cus1 protein (orthologue of human SF3b145). Here, we solved the solution structure of the RRM1 of human SF3b49 and examined its mode of interaction with a fragment of human SF3b145 using NMR methods. Chemical shift mapping showed that the SF3b145 fragment spanning residues 598–631 interacts with SF3b49 RRM1, which adopts a canonical RRM fold with a topology of β1‐α1‐β2‐β3‐α2‐β4. Furthermore, a docking model based on NOESY measurements suggests that residues 607–616 of the SF3b145 fragment adopt a helical structure that binds to RRM1 predominantly via α1, consequently exhibiting a helix–helix interaction in almost antiparallel. This mode of interaction was confirmed by a mutational analysis using GST pull‐down assays. Comparison with structures of all RRM domains when complexed with a peptide found that this helix–helix interaction is unique to SF3b49 RRM1. Additionally, all amino acid residues involved in the interaction are well conserved among eukaryotes, suggesting evolutionary conservation of this interaction mode between SF3b49 RRM1 and SF3b145. PMID:27862552

  19. Solution structure of the first RNA recognition motif domain of human spliceosomal protein SF3b49 and its mode of interaction with a SF3b145 fragment.

    PubMed

    Kuwasako, Kanako; Nameki, Nobukazu; Tsuda, Kengo; Takahashi, Mari; Sato, Atsuko; Tochio, Naoya; Inoue, Makoto; Terada, Takaho; Kigawa, Takanori; Kobayashi, Naohiro; Shirouzu, Mikako; Ito, Takuhiro; Sakamoto, Taiichi; Wakamatsu, Kaori; Güntert, Peter; Takahashi, Seizo; Yokoyama, Shigeyuki; Muto, Yutaka

    2017-02-01

    The spliceosomal protein SF3b49, a component of the splicing factor 3b (SF3b) protein complex in the U2 small nuclear ribonucleoprotein, contains two RNA recognition motif (RRM) domains. In yeast, the first RRM domain (RRM1) of Hsh49 protein (yeast orthologue of human SF3b49) reportedly interacts with another component, Cus1 protein (orthologue of human SF3b145). Here, we solved the solution structure of the RRM1 of human SF3b49 and examined its mode of interaction with a fragment of human SF3b145 using NMR methods. Chemical shift mapping showed that the SF3b145 fragment spanning residues 598-631 interacts with SF3b49 RRM1, which adopts a canonical RRM fold with a topology of β1-α1-β2-β3-α2-β4. Furthermore, a docking model based on NOESY measurements suggests that residues 607-616 of the SF3b145 fragment adopt a helical structure that binds to RRM1 predominantly via α1, consequently exhibiting a helix-helix interaction in almost antiparallel. This mode of interaction was confirmed by a mutational analysis using GST pull-down assays. Comparison with structures of all RRM domains when complexed with a peptide found that this helix-helix interaction is unique to SF3b49 RRM1. Additionally, all amino acid residues involved in the interaction are well conserved among eukaryotes, suggesting evolutionary conservation of this interaction mode between SF3b49 RRM1 and SF3b145.

  20. Spliceosome twin introns in fungal nuclear transcripts.

    PubMed

    Flipphi, Michel; Fekete, Erzsébet; Ag, Norbert; Scazzocchio, Claudio; Karaffa, Levente

    2013-08-01

    The spliceosome is an RNA/protein complex, responsible for intron excision from eukaryotic nuclear transcripts. In bacteria, mitochondria and plastids, intron excision does not involve the spliceosome, but occurs through mechanisms dependent on intron RNA secondary and tertiary structure. For group II/III chloroplast introns, "twintrons" (introns within introns) have been described. The excision of the external intron, and thus proper RNA maturation, necessitates prior removal of the internal intron, which interrupts crucial sequences of the former. We have here predicted analogous instances of spliceosomal twintrons ("stwintrons") in filamentous fungi. In two specific cases, where the internal intron interrupts the donor of the external intron after the first or after the second nucleotide, respectively, we show that intermediates with the sequence predicted by the "stwintron" hypothesis, are produced in the splicing process. This implies that two successive rounds of RNA scanning by the spliceosome are necessary to produce the mature mRNA. The phylogenetic distributions of the stwintrons we have identified suggest that they derive from "late" events, subsequent to the appearance of the host intron. They may well not be limited to fungal nuclear transcripts, and their generation and eventual disappearance in the evolutionary process are relevant to hypotheses of intron origin and alternative splicing.

  1. An Exon-Specific U1snRNA Induces a Robust Factor IX Activity in Mice Expressing Multiple Human FIX Splicing Mutants

    PubMed Central

    Balestra, Dario; Scalet, Daniela; Pagani, Franco; Rogalska, Malgorzata Ewa; Mari, Rosella; Bernardi, Francesco; Pinotti, Mirko

    2016-01-01

    In cellular models we have demonstrated that a unique U1snRNA targeting an intronic region downstream of a defective exon (Exon-specific U1snRNA, ExSpeU1) can rescue multiple exon-skipping mutations, a relevant cause of genetic disease. Here, we explored in mice the ExSpeU1 U1fix9 toward two model Hemophilia B-causing mutations at the 5′ (c.519A > G) or 3′ (c.392-8T > G) splice sites of F9 exon 5. Hydrodynamic injection of wt-BALB/C mice with plasmids expressing the wt and mutant (hFIX-2G5′ss and hFIX-8G3′ss) splicing-competent human factor IX (hFIX) cassettes resulted in the expression of hFIX transcripts lacking exon 5 in liver, and in low plasma levels of inactive hFIX. Coinjection of U1fix9, but not of U1wt, restored exon inclusion of variants and in the intrinsically weak FIXwt context. This resulted in appreciable circulating hFIX levels (mean ± SD; hFIX-2G5′ss, 1.0 ± 0.5 µg/ml; hFIX-8G3′ss, 1.2 ± 0.3 µg/ml; and hFIXwt, 1.9 ± 0.6 µg/ml), leading to a striking shortening (from ~100 seconds of untreated mice to ~80 seconds) of FIX-dependent coagulation times, indicating a hFIX with normal specific activity. This is the first proof-of-concept in vivo that a unique ExSpeU1 can efficiently rescue gene expression impaired by distinct exon-skipping variants, which extends the applicability of ExSpeU1s to panels of mutations and thus cohort of patients. PMID:27701399

  2. The human U1-70K snRNP protein: cDNA cloning, chromosomal localization, expression, alternative splicing and RNA-binding.

    PubMed Central

    Spritz, R A; Strunk, K; Surowy, C S; Hoch, S O; Barton, D E; Francke, U

    1987-01-01

    We have isolated and sequenced cDNA clones encoding the human U1-70K snRNP protein, and have mapped this locus (U1AP1) to human chromosome 19. The gene produces two size classes of RNA, a major 1.7-kb RNA and a minor 3.9-kb RNA. The 1.7-kb species appears to be the functional mRNA; the role of the 3.9-kb RNA, which extends further in the 5' direction, is unclear. The actual size of the hU1-70K protein is probably 52 kd, rather than 70 kd. The protein contains three regions similar to known nucleic acid-binding proteins, and it binds RNA in an in vitro assay. Comparison of the cDNA sequences indicates that there are multiple subclasses of mRNA that arise by alternative pre-mRNA splicing of at least four alternative exon segments. This suggests that multiple forms of the hU1-70K protein may exist, possibly with different functions in vivo. Images PMID:2447561

  3. Spliceosomal small nuclear ribonucleoprotein particles repeatedly cycle through Cajal bodies.

    PubMed

    Stanek, David; Pridalová-Hnilicová, Jarmila; Novotný, Ivan; Huranová, Martina; Blazíková, Michaela; Wen, Xin; Sapra, Aparna K; Neugebauer, Karla M

    2008-06-01

    The Cajal body (CB) is a nuclear structure closely associated with import and biogenesis of small nuclear ribonucleoprotein particles (snRNPs). Here, we tested whether CBs also contain mature snRNPs and whether CB integrity depends on the ongoing snRNP splicing cycle. Sm proteins tagged with photoactivatable and color-maturing variants of fluorescent proteins were used to monitor snRNP behavior in living cells over time; mature snRNPs accumulated in CBs, traveled from one CB to another, and they were not preferentially replaced by newly imported snRNPs. To test whether CB integrity depends on the snRNP splicing cycle, two human orthologues of yeast proteins involved in distinct steps in spliceosome disassembly after splicing, hPrp22 and hNtr1, were depleted by small interfering RNA treatment. Surprisingly, depletion of either protein led to the accumulation of U4/U6 snRNPs in CBs, suggesting that reassembly of the U4/U6.U5 tri-snRNP was delayed. Accordingly, a relative decrease in U5 snRNPs compared with U4/U6 snRNPs was observed in CBs, as well as in nuclear extracts of treated cells. Together, the data show that particular phases of the spliceosome cycle are compartmentalized in living cells, with reassembly of the tri-snRNP occurring in CBs.

  4. Co-evolution of SNF spliceosomal proteins with their RNA targets in trans-splicing nematodes.

    PubMed

    Strange, Rex Meade; Russelburg, L Peyton; Delaney, Kimberly J

    2016-08-01

    Although the mechanism of pre-mRNA splicing has been well characterized, the evolution of spliceosomal proteins is poorly understood. The U1A/U2B″/SNF family (hereafter referred to as the SNF family) of RNA binding spliceosomal proteins participates in both the U1 and U2 small interacting nuclear ribonucleoproteins (snRNPs). The highly constrained nature of this system has inhibited an analysis of co-evolutionary trends between the proteins and their RNA binding targets. Here we report accelerated sequence evolution in the SNF protein family in Phylum Nematoda, which has allowed an analysis of protein:RNA co-evolution. In a comparison of SNF genes from ecdysozoan species, we found a correlation between trans-splicing species (nematodes) and increased phylogenetic branch lengths of the SNF protein family, with respect to their sister clade Arthropoda. In particular, we found that nematodes (~70-80 % of pre-mRNAs are trans-spliced) have experienced higher rates of SNF sequence evolution than arthropods (predominantly cis-spliced) at both the nucleotide and amino acid levels. Interestingly, this increased evolutionary rate correlates with the reliance on trans-splicing by nematodes, which would alter the role of the SNF family of spliceosomal proteins. We mapped amino acid substitutions to functionally important regions of the SNF protein, specifically to sites that are predicted to disrupt protein:RNA and protein:protein interactions. Finally, we investigated SNF's RNA targets: the U1 and U2 snRNAs. Both are more divergent in nematodes than arthropods, suggesting the RNAs have co-evolved with SNF in order to maintain the necessarily high affinity interaction that has been characterized in other species.

  5. A spliceosome intermediate with loosely associated tri-snRNP accumulates in the absence of Prp28 ATPase activity

    PubMed Central

    Boesler, Carsten; Rigo, Norbert; Anokhina, Maria M.; Tauchert, Marcel J.; Agafonov, Dmitry E.; Kastner, Berthold; Urlaub, Henning; Ficner, Ralf; Will, Cindy L.; Lührmann, Reinhard

    2016-01-01

    The precise role of the spliceosomal DEAD-box protein Prp28 in higher eukaryotes remains unclear. We show that stable tri-snRNP association during pre-catalytic spliceosomal B complex formation is blocked by a dominant-negative hPrp28 mutant lacking ATPase activity. Complexes formed in the presence of ATPase-deficient hPrp28 represent a novel assembly intermediate, the pre-B complex, that contains U1, U2 and loosely associated tri-snRNP and is stalled before disruption of the U1/5′ss base pairing interaction, consistent with a role for hPrp28 in the latter. Pre-B and B complexes differ structurally, indicating that stable tri-snRNP integration is accompanied by substantial rearrangements in the spliceosome. Disruption of the U1/5′ss interaction alone is not sufficient to bypass the block by ATPase-deficient hPrp28, suggesting hPrp28 has an additional function at this stage of splicing. Our data provide new insights into the function of Prp28 in higher eukaryotes, and the requirements for stable tri-snRNP binding during B complex formation. PMID:27377154

  6. Identification of a small molecule inhibitor that stalls splicing at an early step of spliceosome activation

    PubMed Central

    Sidarovich, Anzhalika; Will, Cindy L; Anokhina, Maria M; Ceballos, Javier; Sievers, Sonja; Agafonov, Dmitry E; Samatov, Timur; Bao, Penghui; Kastner, Berthold; Urlaub, Henning; Waldmann, Herbert; Lührmann, Reinhard

    2017-01-01

    Small molecule inhibitors of pre-mRNA splicing are important tools for identifying new spliceosome assembly intermediates, allowing a finer dissection of spliceosome dynamics and function. Here, we identified a small molecule that inhibits human pre-mRNA splicing at an intermediate stage during conversion of pre-catalytic spliceosomal B complexes into activated Bact complexes. Characterization of the stalled complexes (designated B028) revealed that U4/U6 snRNP proteins are released during activation before the U6 Lsm and B-specific proteins, and before recruitment and/or stable incorporation of Prp19/CDC5L complex and other Bact complex proteins. The U2/U6 RNA network in B028 complexes differs from that of the Bact complex, consistent with the idea that the catalytic RNA core forms stepwise during the B to Bact transition and is likely stabilized by the Prp19/CDC5L complex and related proteins. Taken together, our data provide new insights into the RNP rearrangements and extensive exchange of proteins that occurs during spliceosome activation. DOI: http://dx.doi.org/10.7554/eLife.23533.001 PMID:28300534

  7. Tumor suppressor microRNAs are downregulated in myelodysplastic syndrome with spliceosome mutations

    PubMed Central

    Aslan, Derya; Garde, Christian; Nygaard, Mette Katrine; Helbo, Alexandra Søgaard; Dimopoulos, Konstantinos; Hansen, Jakob Werner; Severinsen, Marianne Tang; Treppendahl, Marianne Bach; Sjø, Lene Dissing; Grønbæk, Kirsten; Kristensen, Lasse Sommer

    2016-01-01

    Spliceosome mutations are frequently observed in patients with myelodysplastic syndromes (MDS). However, it is largely unknown how these mutations contribute to the disease. MicroRNAs (miRNAs) are small noncoding RNAs, which have been implicated in most human cancers due to their role in post transcriptional gene regulation. The aim of this study was to analyze the impact of spliceosome mutations on the expression of miRNAs in a cohort of 34 MDS patients. In total, the expression of 76 miRNAs, including mirtrons and splice site overlapping miRNAs, was accurately quantified using reverse transcriptase quantitative PCR. The majority of the studied miRNAs have previously been implicated in MDS. Stably expressed miRNA genes for normalization of the data were identified using GeNorm and NormFinder algorithms. High-resolution melting assays covering all mutational hotspots within SF3B1, SRSF2, and U2AF1 (U2AF35) were developed, and all detected mutations were confirmed by Sanger sequencing. Overall, canonical miRNAs were downregulated in spliceosome mutated samples compared to wild-type (P = 0.002), and samples from spliceosome mutated patients clustered together in hierarchical cluster analyses. Among the most downregulated miRNAs were several tumor-suppressor miRNAs, including several let-7 family members, miR-423, and miR-103a. Finally, we observed that the predicted targets of the most downregulated miRNAs were involved in apoptosis, hematopoiesis, and acute myeloid leukemia among other cancer- and metabolic pathways. Our data indicate that spliceosome mutations may play an important role in MDS pathophysiology by affecting the expression of tumor suppressor miRNA genes involved in the development and progression of MDS. PMID:26848861

  8. U1A Complex

    SciTech Connect

    2014-10-28

    Some of the most sophisticated experiments in the stockpile stewardship program are conducted in an environmentally safe manner, nearly 1000 feet below the ground at the site. The U1a complex a sprawling underground laboratory and tunnel complex is home to a number of unique capabilities.

  9. U1A Complex

    ScienceCinema

    None

    2016-07-12

    Some of the most sophisticated experiments in the stockpile stewardship program are conducted in an environmentally safe manner, nearly 1000 feet below the ground at the site. The U1a complex a sprawling underground laboratory and tunnel complex is home to a number of unique capabilities.

  10. U1 snRNP-dependent function of TIAR in the regulation of alternative RNA processing of the human calcitonin/CGRP pre-mRNA.

    PubMed

    Zhu, Hui; Hasman, Robert A; Young, Katherine M; Kedersha, Nancy L; Lou, Hua

    2003-09-01

    Alternative RNA processing of human calcitonin/CGRP pre-mRNA is regulated by an intronic enhancer element. Previous studies have demonstrated that multiple sequence motifs within the enhancer and a number of trans-acting factors play critical roles in the regulation. Here, we report the identification of TIAR as a novel player in the regulation of human calcitonin/CGRP alternative RNA processing. TIAR binds to the U tract sequence motif downstream of a pseudo 5' splice site within the previously characterized intron enhancer element. Binding of TIAR promotes inclusion of the alternative 3'-terminal exon located more than 200 nucleotides upstream from the U tract. In cells that preferentially include this exon, overexpression of a mutant TIAR that lacks the RNA binding domains suppressed inclusion of this exon. In this report, we also demonstrate an unusual novel interaction between U6 snRNA and the pseudo 5' splice site, which was shown previously to bind U1 snRNA. Interestingly, TIAR binding to the U tract sequence depends on the interaction of not only U1 but also U6 snRNA with the pseudo 5' splice site. Conversely, TIAR binding promotes U6 snRNA binding to its target. The synergistic relationship between TIAR and U6 snRNA strongly suggests a novel role of U6 snRNP in regulated alternative RNA processing.

  11. Crystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5' splice site recognition.

    PubMed

    Kondo, Yasushi; Oubridge, Chris; van Roon, Anne-Marie M; Nagai, Kiyoshi

    2015-01-02

    U1 snRNP binds to the 5' exon-intron junction of pre-mRNA and thus plays a crucial role at an early stage of pre-mRNA splicing. We present two crystal structures of engineered U1 sub-structures, which together reveal at atomic resolution an almost complete network of protein-protein and RNA-protein interactions within U1 snRNP, and show how the 5' splice site of pre-mRNA is recognised by U1 snRNP. The zinc-finger of U1-C interacts with the duplex between pre-mRNA and the 5'-end of U1 snRNA. The binding of the RNA duplex is stabilized by hydrogen bonds and electrostatic interactions between U1-C and the RNA backbone around the splice junction but U1-C makes no base-specific contacts with pre-mRNA. The structure, together with RNA binding assays, shows that the selection of 5'-splice site nucleotides by U1 snRNP is achieved predominantly through basepairing with U1 snRNA whilst U1-C fine-tunes relative affinities of mismatched 5'-splice sites.

  12. Spliceosomal protein E regulates neoplastic cell growth by modulating expression of cyclin E/CDK2 and G2/M checkpoint proteins.

    PubMed

    Li, Z; Pützer, B M

    2008-12-01

    Small nuclear ribonucleoproteins are essential splicing factors. We previously identified the spliceosomal protein E (SmE) as a downstream effector of E2F1 in p53-deficient human carcinoma cells. Here, we investigated the biological relevance of SmE in determining the fate of cancer and non-tumourigenic cells. Adenovirus-mediated expression of SmE selectively reduces growth of cancerous cells due to decreased cell proliferation but not apoptosis. A similar growth inhibitory effect for SmD1 suggests that this is a general function of Sm-family members. Deletion of Sm-motifs reveals the importance of the Sm-1 domain for growth suppression. Consistently, SmE overexpression leads to inhibition of DNA synthesis and G2 arrest as shown by BrdU-incorporation and MPM2-staining. Real-time RT-PCR and immunoblotting showed that growth arrest by SmE directly correlates with the reduction of cyclin E, CDK2, CDC25C and CDC2 expression, and up-regulation of p27Kip. Importantly, SmE activity was not associated with enhanced expression of other spliceosome components such as U1 SnRNP70, suggesting that the growth inhibitory effect of SmE is distinct from its pre-mRNA splicing function. Furthermore, specific inactivation of SmE by shRNA significantly increased the percentage of cells in S phase, whereas the amount of G2/M arrested cells was reduced. Our data provide evidence that Sm proteins function as suppressors of tumour cell growth and may have major implications as cancer therapeutics.

  13. Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies.

    PubMed

    Xu, Mingchu; Xie, Yajing Angela; Abouzeid, Hana; Gordon, Christopher T; Fiorentino, Alessia; Sun, Zixi; Lehman, Anna; Osman, Ihab S; Dharmat, Rachayata; Riveiro-Alvarez, Rosa; Bapst-Wicht, Linda; Babino, Darwin; Arno, Gavin; Busetto, Virginia; Zhao, Li; Li, Hui; Lopez-Martinez, Miguel A; Azevedo, Liliana F; Hubert, Laurence; Pontikos, Nikolas; Eblimit, Aiden; Lorda-Sanchez, Isabel; Kheir, Valeria; Plagnol, Vincent; Oufadem, Myriam; Soens, Zachry T; Yang, Lizhu; Bole-Feysot, Christine; Pfundt, Rolph; Allaman-Pillet, Nathalie; Nitschké, Patrick; Cheetham, Michael E; Lyonnet, Stanislas; Agrawal, Smriti A; Li, Huajin; Pinton, Gaëtan; Michaelides, Michel; Besmond, Claude; Li, Yumei; Yuan, Zhisheng; von Lintig, Johannes; Webster, Andrew R; Le Hir, Hervé; Stoilov, Peter; Amiel, Jeanne; Hardcastle, Alison J; Ayuso, Carmen; Sui, Ruifang; Chen, Rui; Allikmets, Rando; Schorderet, Daniel F

    2017-04-06

    Pre-mRNA splicing factors play a fundamental role in regulating transcript diversity both temporally and spatially. Genetic defects in several spliceosome components have been linked to a set of non-overlapping spliceosomopathy phenotypes in humans, among which skeletal developmental defects and non-syndromic retinitis pigmentosa (RP) are frequent findings. Here we report that defects in spliceosome-associated protein CWC27 are associated with a spectrum of disease phenotypes ranging from isolated RP to severe syndromic forms. By whole-exome sequencing, recessive protein-truncating mutations in CWC27 were found in seven unrelated families that show a range of clinical phenotypes, including retinal degeneration, brachydactyly, craniofacial abnormalities, short stature, and neurological defects. Remarkably, variable expressivity of the human phenotype can be recapitulated in Cwc27 mutant mouse models, with significant embryonic lethality and severe phenotypes in the complete knockout mice while mice with a partial loss-of-function allele mimic the isolated retinal degeneration phenotype. Our study describes a retinal dystrophy-related phenotype spectrum as well as its genetic etiology and highlights the complexity of the spliceosomal gene network.

  14. Contribution of the tyrosines to the structure and function of the human U1A N-terminal RNA binding domain.

    PubMed Central

    Kranz, J. K.; Lu, J.; Hall, K. B.

    1996-01-01

    RNA binding domains (RBDs) are members of a large family of proteins that share minimal sequence conservation but adopt an alpha beta sandwich global fold. Defining the contributions of specific amino acids to RBD structure and RNA binding is critical to understanding the functions of these proteins. In these experiments with the human U1A N-terminal RNA binding domain (RBD1), the contributions from each of its four tyrosines to protein structure, stability, and RNA binding were measured. Each tyrosine was substituted with phenylalanine and one other selected residue, and the resulting proteins were characterized by chemical denaturation to measure their unfolding free energy, by binding free energies to the wild-type RNA hairpin, and by 19F NMR to probe for structural changes. Features of the protein identified in these experiments include a possible tyrosine/lysine contact in an alpha-helix, which may be an example of an energetically favorable aromatic/amino side chain interaction. One long loop of the protein, which shows unusual 15N backbone and tyrosine side-chain dynamics, is implicated in protein:protein association. The diverse interactions of the four tyrosine residues in the organization of RBD1 illustrate how each member of this family of proteins will have unique molecular details that contribute to function. PMID:8844847

  15. Use of the U1A protein to facilitate crystallization and structure determination of large RNAs

    PubMed Central

    Ferré-D’Amaré, Adrian R.

    2016-01-01

    Summary The preparation of well-ordered crystals of RNAs with complex three-dimensional architecture can be facilitated by engineering a binding site for the spliceosomal protein U1A into a functionally and structurally dispensable stem-loop of the RNA of interest. Once suitable crystals are obtained, the U1A protein, of known structure, can be employed to facilitate preparation of heavy atom or anomalously scattering atom derivatives, or as a source of partial model phases for the molecular replacement method. Here, we describe the methods for making U1A preparations suitable for cocrystallization with RNA. As an example, the cocrystallization of the tetracycline aptamer with U1A is also described. PMID:26227038

  16. U1h Superstructure

    SciTech Connect

    Glen Sykes

    2000-11-01

    The U1H Shaft Project is a design build subcontract to supply the U. S. Department of Energy (DOE) a 1,045 ft. deep, 20 ft. diameter, concrete lined shaft for unspecified purposes. The subcontract awarded to Atkinson Construction by Bechtel Nevada to design and construct the shaft for the DOE has been split into phases with portions of the work being released as dictated by available funding. The first portion released included the design for the shaft, permanent hoist, headframe, and collar arrangement. The second release consisted of constructing the shaft collar to a depth of 110 ft., the service entry, utility trenches, and installation of the temporary sinking plant. The temporary sinking plant included the installation of the sinking headframe, the sinking hoist, two deck winches, the shaft form, the sinking work deck, and temporary utilities required to sink the shaft. Both the design and collar construction were completed on schedule. The third release consisted of excavating and lining the shaft to the station depth of approximately 950 feet. Work is currently proceeding on this production sinking phase. At a depth of approximately 600 feet, Atkinson has surpassed production expectation and is more than 3 months ahead of schedule. Atkinson has employed the use of a Bobcat 331 excavator as the primary means of excavation. the shaft is being excavated entirely in an alluvial deposit with varying degrees of calcium carbonate cementation. Several more work packages are expected to be released in the near future. The remaining work packages include, construction of the shaft station a depth of 975 ft. and construction of the shaft sump to a depth of 1,045 ft., installation of the loading pocket and station steel and equipment, installation of the shaft steel and guides, installation of the shaft utilities, and installation of the permanent headframe, hoist, collar utilities, and facilities.

  17. Origin and evolution of spliceosomal introns

    PubMed Central

    2012-01-01

    Evolution of exon-intron structure of eukaryotic genes has been a matter of long-standing, intensive debate. The introns-early concept, later rebranded ‘introns first’ held that protein-coding genes were interrupted by numerous introns even at the earliest stages of life's evolution and that introns played a major role in the origin of proteins by facilitating recombination of sequences coding for small protein/peptide modules. The introns-late concept held that introns emerged only in eukaryotes and new introns have been accumulating continuously throughout eukaryotic evolution. Analysis of orthologous genes from completely sequenced eukaryotic genomes revealed numerous shared intron positions in orthologous genes from animals and plants and even between animals, plants and protists, suggesting that many ancestral introns have persisted since the last eukaryotic common ancestor (LECA). Reconstructions of intron gain and loss using the growing collection of genomes of diverse eukaryotes and increasingly advanced probabilistic models convincingly show that the LECA and the ancestors of each eukaryotic supergroup had intron-rich genes, with intron densities comparable to those in the most intron-rich modern genomes such as those of vertebrates. The subsequent evolution in most lineages of eukaryotes involved primarily loss of introns, with only a few episodes of substantial intron gain that might have accompanied major evolutionary innovations such as the origin of metazoa. The original invasion of self-splicing Group II introns, presumably originating from the mitochondrial endosymbiont, into the genome of the emerging eukaryote might have been a key factor of eukaryogenesis that in particular triggered the origin of endomembranes and the nucleus. Conversely, splicing errors gave rise to alternative splicing, a major contribution to the biological complexity of multicellular eukaryotes. There is no indication that any prokaryote has ever possessed a spliceosome

  18. Origin and evolution of spliceosomal introns.

    PubMed

    Rogozin, Igor B; Carmel, Liran; Csuros, Miklos; Koonin, Eugene V

    2012-04-16

    Evolution of exon-intron structure of eukaryotic genes has been a matter of long-standing, intensive debate. The introns-early concept, later rebranded 'introns first' held that protein-coding genes were interrupted by numerous introns even at the earliest stages of life's evolution and that introns played a major role in the origin of proteins by facilitating recombination of sequences coding for small protein/peptide modules. The introns-late concept held that introns emerged only in eukaryotes and new introns have been accumulating continuously throughout eukaryotic evolution. Analysis of orthologous genes from completely sequenced eukaryotic genomes revealed numerous shared intron positions in orthologous genes from animals and plants and even between animals, plants and protists, suggesting that many ancestral introns have persisted since the last eukaryotic common ancestor (LECA). Reconstructions of intron gain and loss using the growing collection of genomes of diverse eukaryotes and increasingly advanced probabilistic models convincingly show that the LECA and the ancestors of each eukaryotic supergroup had intron-rich genes, with intron densities comparable to those in the most intron-rich modern genomes such as those of vertebrates. The subsequent evolution in most lineages of eukaryotes involved primarily loss of introns, with only a few episodes of substantial intron gain that might have accompanied major evolutionary innovations such as the origin of metazoa. The original invasion of self-splicing Group II introns, presumably originating from the mitochondrial endosymbiont, into the genome of the emerging eukaryote might have been a key factor of eukaryogenesis that in particular triggered the origin of endomembranes and the nucleus. Conversely, splicing errors gave rise to alternative splicing, a major contribution to the biological complexity of multicellular eukaryotes. There is no indication that any prokaryote has ever possessed a spliceosome or

  19. Organellar maturases: A window into the evolution of the spliceosome.

    PubMed

    Schmitz-Linneweber, Christian; Lampe, Marie-Kristin; Sultan, Laure D; Ostersetzer-Biran, Oren

    2015-09-01

    During the evolution of eukaryotic genomes, many genes have been interrupted by intervening sequences (introns) that must be removed post-transcriptionally from RNA precursors to form mRNAs ready for translation. The origin of nuclear introns is still under debate, but one hypothesis is that the spliceosome and the intron-exon structure of genes have evolved from bacterial-type group II introns that invaded the eukaryotic genomes. The group II introns were most likely introduced into the eukaryotic genome from an α-proteobacterial predecessor of mitochondria early during the endosymbiosis event. These self-splicing and mobile introns spread through the eukaryotic genome and later degenerated. Pieces of introns became part of the general splicing machinery we know today as the spliceosome. In addition, group II introns likely brought intron maturases with them to the nucleus. Maturases are found in most bacterial introns, where they act as highly specific splicing factors for group II introns. In the spliceosome, the core protein Prp8 shows homology to group II intron-encoded maturases. While maturases are entirely intron specific, their descendant of the spliceosomal machinery, the Prp8 protein, is an extremely versatile splicing factor with multiple interacting proteins and RNAs. How could such a general player in spliceosomal splicing evolve from the monospecific bacterial maturases? Analysis of the organellar splicing machinery in plants may give clues on the evolution of nuclear splicing. Plants encode various proteins which are closely related to bacterial maturases. The organellar genomes contain one maturase each, named MatK in chloroplasts and MatR in mitochondria. In addition, several maturase genes have been found in the nucleus as well, which are acting on mitochondrial pre-RNAs. All plant maturases show sequence deviation from their progenitor bacterial maturases, and interestingly are all acting on multiple organellar group II intron targets. Moreover

  20. Saccharomyces cerevisiae U1 small nuclear RNA secondary structure contains both universal and yeast-specific domains.

    PubMed Central

    Kretzner, L; Krol, A; Rosbash, M

    1990-01-01

    The five small nuclear RNAs (snRNAs) involved in mammalian pre-mRNA splicing (U1, U2, U4, U5, and U6) are well conserved in length, sequence, and especially secondary structure. These five snRNAs from Saccharomyces cerevisiae show notable size and sequence differences from their metazoan counterparts. This is most striking for the large S. cerevisiae U1 and U2 snRNAs, for which no secondary structure models currently exist. Because of the importance of U1 snRNA in the early steps of "spliceosome" assembly, we wanted to compare the highly conserved secondary structure of metazoan U1 snRNA (approximately 165 nucleotides) with that of S. cerevisiae U1 snRNA (568 nucleotides). To this end, we have cloned and sequenced the U1 gene from two other yeast species possessing large U1 RNAs. Using computer-derived structure predictions, phylogenetic comparisons, and structure probing, we have arrived at a secondary structure model for S. cerevisiae U1 snRNA. The results show that most elements of higher eukaryotic U1 snRNA secondary structure are conserved in S. cerevisiae. The hundreds of "extra" nucleotides of yeast U1 RNA, also highly structured, suggest that large insertions and/or deletions have occurred during the evolution of the U1 gene. Images PMID:2405391

  1. Splicing Functions and Global Dependency on Fission Yeast Slu7 Reveal Diversity in Spliceosome Assembly

    PubMed Central

    Banerjee, Shataparna; Khandelia, Piyush; Melangath, Geetha; Bashir, Samirul; Nagampalli, Vijaykrishna

    2013-01-01

    The multiple short introns in Schizosaccharomyces pombe genes with degenerate cis sequences and atypically positioned polypyrimidine tracts make an interesting model to investigate canonical and alternative roles for conserved splicing factors. Here we report functions and interactions of the S. pombe slu7+ (spslu7+) gene product, known from Saccharomyces cerevisiae and human in vitro reactions to assemble into spliceosomes after the first catalytic reaction and to dictate 3′ splice site choice during the second reaction. By using a missense mutant of this essential S. pombe factor, we detected a range of global splicing derangements that were validated in assays for the splicing status of diverse candidate introns. We ascribe widespread, intron-specific SpSlu7 functions and have deduced several features, including the branch nucleotide-to-3′ splice site distance, intron length, and the impact of its A/U content at the 5′ end on the intron's dependence on SpSlu7. The data imply dynamic substrate-splicing factor relationships in multiintron transcripts. Interestingly, the unexpected early splicing arrest in spslu7-2 revealed a role before catalysis. We detected a salt-stable association with U5 snRNP and observed genetic interactions with spprp1+, a homolog of human U5-102k factor. These observations together point to an altered recruitment and dependence on SpSlu7, suggesting its role in facilitating transitions that promote catalysis, and highlight the diversity in spliceosome assembly. PMID:23754748

  2. Evolutionarily divergent spliceosomal snRNAs and a conserved non-coding RNA processing motif in Giardia lamblia.

    PubMed

    Hudson, Andrew J; Moore, Ashley N; Elniski, David; Joseph, Joella; Yee, Janet; Russell, Anthony G

    2012-11-01

    Non-coding RNAs (ncRNAs) have diverse essential biological functions in all organisms, and in eukaryotes, two such classes of ncRNAs are the small nucleolar (sno) and small nuclear (sn) RNAs. In this study, we have identified and characterized a collection of sno and snRNAs in Giardia lamblia, by exploiting our discovery of a conserved 12 nt RNA processing sequence motif found in the 3' end regions of a large number of G. lamblia ncRNA genes. RNA end mapping and other experiments indicate the motif serves to mediate ncRNA 3' end formation from mono- and di-cistronic RNA precursor transcripts. Remarkably, we find the motif is also utilized in the processing pathway of all four previously identified trans-spliced G. lamblia introns, revealing a common RNA processing pathway for ncRNAs and trans-spliced introns in this organism. Motif sequence conservation then allowed for the bioinformatic and experimental identification of additional G. lamblia ncRNAs, including new U1 and U6 spliceosomal snRNA candidates. The U6 snRNA candidate was then used as a tool to identity novel U2 and U4 snRNAs, based on predicted phylogenetically conserved snRNA-snRNA base-pairing interactions, from a set of previously identified G. lamblia ncRNAs without assigned function. The Giardia snRNAs retain the core features of spliceosomal snRNAs but are sufficiently evolutionarily divergent to explain the difficulties in their identification. Most intriguingly, all of these snRNAs show structural features diagnostic of U2-dependent/major and U12-dependent/minor spliceosomal snRNAs.

  3. Systematic genome-wide annotation of spliceosomal proteins reveals differential gene family expansion

    PubMed Central

    Barbosa-Morais, Nuno L.; Carmo-Fonseca, Maria; Aparício, Samuel

    2006-01-01

    Although more than 200 human spliceosomal and splicing-associated proteins are known, the evolution of the splicing machinery has not been studied extensively. The recent near-complete sequencing and annotation of distant vertebrate and chordate genomes provides the opportunity for an exhaustive comparative analysis of splicing factors across eukaryotes. We describe here our semiautomated computational pipeline to identify and annotate splicing factors in representative species of eukaryotes. We focused on protein families whose role in splicing is confirmed by experimental evidence. We visually inspected 1894 proteins and manually curated 224 of them. Our analysis shows a general conservation of the core spliceosomal proteins across the eukaryotic lineage, contrasting with selective expansions of protein families known to play a role in the regulation of splicing, most notably of SR proteins in metazoans and of heterogeneous nuclear ribonucleoproteins (hnRNP) in vertebrates. We also observed vertebrate-specific expansion of the CLK and SRPK kinases (which phosphorylate SR proteins), and the CUG-BP/CELF family of splicing regulators. Furthermore, we report several intronless genes amongst splicing proteins in mammals, suggesting that retrotransposition contributed to the complexity of the mammalian splicing apparatus. PMID:16344558

  4. Assembly of ribosomes and spliceosomes: complex ribonucleoprotein machines.

    PubMed

    Staley, Jonathan P; Woolford, John L

    2009-02-01

    Ribosomes and spliceosomes are ribonucleoprotein nanomachines that catalyze translation of mRNA to synthesize proteins and splicing of introns from pre-mRNAs, respectively. Assembly of ribosomes involves more than 300 proteins and RNAs, and that of spliceosomes over 100 proteins and RNAs. Construction of these enormous ribonucleoprotein particles (RNPs) is a dynamic process, in which the nascent RNPs undergo numerous ordered rearrangements of RNA-RNA, RNA-protein, and protein-protein interactions. Here we outline similar principles that have emerged from studies of ribosome and spliceosome assembly. Constituents of both RNPs form subassembly complexes, which can simplify the task of assembly and segregate functions of assembly factors. Reorganization of RNP topology, and proofreading of proper assembly, are catalyzed by protein- or RNA-dependent ATPases or GTPases. Dynamics of intermolecular interactions may be facilitated or regulated by cycles of post-translational modifications. Despite this repertoire of tools, mistakes occur in RNP assembly or in processing of RNA substrates. Quality control mechanisms recognize and turnover misassembled RNPs and reject improper substrates.

  5. Interleukin 1 induces expression of the human immunodeficiency virus alone and in synergy with interleukin 6 in chronically infected U1 cells: inhibition of inductive effects by the interleukin 1 receptor antagonist.

    PubMed Central

    Poli, G; Kinter, A L; Fauci, A S

    1994-01-01

    In the present study we have observed that interleukin (IL) 1 alpha or IL-1 beta directly induced expression of human immunodeficiency virus (HIV) in the latently infected human promonocytic cell line U1. In addition, IL-1 synergized with IL-6, but not with tumor necrosis factor, in the upregulation of virus expression in U1 cells as measured by accumulation of steady-state mRNAs and production of reverse transcriptase activity. The HIV inductive effect of IL-1 was blocked by transforming growth factor beta, anti-IL-1 antibodies, or monoclonal antibodies directed to the type 1, but not to the type 2, cell surface receptor for IL-1; the latter actually caused enhancement of the IL-1-mediated effect. Unlike tumor necrosis factor alpha, IL-1 either alone or in combination with IL-6 did not induce activation of the transcription activating factor NF-kappa B above the constitutive levels of unstimulated U1 cells. Finally, the IL-1 receptor antagonist effectively blocked IL-1-mediated direct and synergistic inductive effects on virus production. Thus, IL-1 may be an important mediator of HIV expression, and blocking of IL-1 expression and/or its effects may have a potential therapeutic role in the inhibition of HIV expression in infected individuals. Images Fig. 2 Fig. 3 PMID:7506410

  6. The G-patch protein Spp2 couples the spliceosome-stimulated ATPase activity of the DEAH-box protein Prp2 to catalytic activation of the spliceosome

    PubMed Central

    Warkocki, Zbigniew; Schneider, Cornelius; Mozaffari-Jovin, Sina; Schmitzová, Jana; Höbartner, Claudia

    2015-01-01

    Structural rearrangement of the activated spliceosome (Bact) to yield a catalytically active complex (B*) is mediated by the DEAH-box NTPase Prp2 in cooperation with the G-patch protein Spp2. However, how the energy of ATP hydrolysis by Prp2 is coupled to mechanical work and what role Spp2 plays in this process are unclear. Using a purified splicing system, we demonstrate that Spp2 is not required to recruit Prp2 to its bona fide binding site in the Bact spliceosome. In the absence of Spp2, the Bact spliceosome efficiently triggers Prp2’s NTPase activity, but NTP hydrolysis is not coupled to ribonucleoprotein (RNP) rearrangements leading to catalytic activation of the spliceosome. Transformation of the Bact to the B* spliceosome occurs only when Spp2 is present and is accompanied by dissociation of Prp2 and a reduction in its NTPase activity. In the absence of spliceosomes, Spp2 enhances Prp2’s RNA-dependent ATPase activity without affecting its RNA affinity. Our data suggest that Spp2 plays a major role in coupling Prp2’s ATPase activity to remodeling of the spliceosome into a catalytically active machine. PMID:25561498

  7. A U1 snRNP-Specific Assembly Pathway Reveals the SMN Complex as a Versatile RNP Exchange

    PubMed Central

    So, Byung Ran; Wan, Lili; Zhang, Zhenxi; Li, Pilong; Babiash, Eric; Duan, Jingqi; Younis, Ihab; Dreyfuss, Gideon

    2016-01-01

    Despite their equal stoichiometry in spliceosomes, U1 snRNP (U1) is typically the most abundant snRNP in vertebrates. What regulates U1 over-abundance and snRNP repertoire in general is unknown. Sm core assembly is a key step in snRNP biogenesis mediated by the SMN complex. All pre-snRNAs are delivered by the snRNA-specific RNA-binding protein (RBP) Gemin5 to join SMN-Gemin2-recruited Sm proteins. Here, we find that the U1-specific RBP U1-70K bridges pre-U1 to SMN-Gemin2-Sm, establishing an additional, Gemin5-independent Sm core assembly pathway. We show that U1-70K hijacks SMN-Gemin2-Sm, enhancing U1’s and inhibiting other snRNAs’ Sm core assembly, thereby promoting U1 over-abundance and regulating snRNP repertoire. Ubiquitous SMN-Gemin2’s surprising ability to facilitate transactions between different RBPs and RNAs explains its puzzling multi-RBP valency and myriad transcriptome perturbations associated with SMN’s deficiency in neurodegenerative spinal muscular atrophy. We propose that SMN-Gemin2 is a versatile RNP exchange that functions broadly in RNA metabolism. PMID:26828962

  8. A bipartite U1 site represses U1A expression by synergizing with PIE to inhibit nuclear polyadenylation.

    PubMed

    Guan, Fei; Caratozzolo, Rose M; Goraczniak, Rafal; Ho, Eric S; Gunderson, Samuel I

    2007-12-01

    U1A protein negatively autoregulates itself by polyadenylation inhibition of its own pre-mRNA by binding as two molecules to a 3'UTR-located Polyadenylation Inhibitory Element (PIE). The (U1A)2-PIE complex specifically blocks U1A mRNA biosynthesis by inhibiting polyA tail addition, leading to lower mRNA levels. U1 snRNP bound to a 5'ss-like sequence, which we call a U1 site, in the 3'UTRs of certain papillomaviruses leads to inhibition of viral late gene expression via a similar mechanism. Although such U1 sites can also be artificially used to potently silence reporter and endogenous genes, no naturally occurring U1 sites have been found in eukaryotic genes. Here we identify a conserved U1 site in the human U1A gene that is, unexpectedly, within a bipartite element where the other part represses the U1 site via a base-pairing mechanism. The bipartite element inhibits U1A expression via a synergistic action with the nearby PIE. Unexpectedly, synergy is not based on stabilizing binding of the inhibitory factors to the 3'UTR, but rather is a property of the larger ternary complex. Inhibition targets the biosynthetic step of polyA tail addition rather than altering mRNA stability. This is the first example of a functional U1 site in a cellular gene and of a single gene containing two dissimilar elements that inhibit nuclear polyadenylation. Parallels with other examples where U1 snRNP inhibits expression are discussed. We expect that other cellular genes will harbor functional U1 sites.

  9. U1 snDNA clusters in grasshoppers: chromosomal dynamics and genomic organization

    PubMed Central

    Anjos, A; Ruiz-Ruano, F J; Camacho, J P M; Loreto, V; Cabrero, J; de Souza, M J; Cabral-de-Mello, D C

    2015-01-01

    The spliceosome, constituted by a protein set associated with small nuclear RNA (snRNA), is responsible for mRNA maturation through intron removal. Among snRNA genes, U1 is generally a conserved repetitive sequence. To unveil the chromosomal/genomic dynamics of this multigene family in grasshoppers, we mapped U1 genes by fluorescence in situ hybridization in 70 species belonging to the families Proscopiidae, Pyrgomorphidae, Ommexechidae, Romaleidae and Acrididae. Evident clusters were observed in all species, indicating that, at least, some U1 repeats are tandemly arrayed. High conservation was observed in the first four families, with most species carrying a single U1 cluster, frequently located in the third or fourth longest autosome. By contrast, extensive variation was observed among Acrididae, from a single chromosome pair carrying U1 to all chromosome pairs carrying it, with occasional occurrence of two or more clusters in the same chromosome. DNA sequence analysis in Eyprepocnemis plorans (species carrying U1 clusters on seven different chromosome pairs) and Locusta migratoria (carrying U1 in a single chromosome pair) supported the coexistence of functional and pseudogenic lineages. One of these pseudogenic lineages was truncated in the same nucleotide position in both species, suggesting that it was present in a common ancestor to both species. At least in E. plorans, this U1 snDNA pseudogenic lineage was associated with 5S rDNA and short interspersed elements (SINE)-like mobile elements. Given that we conclude in grasshoppers that the U1 snDNA had evolved under the birth-and-death model and that its intragenomic spread might be related with mobile elements. PMID:25248465

  10. U1 snDNA clusters in grasshoppers: chromosomal dynamics and genomic organization.

    PubMed

    Anjos, A; Ruiz-Ruano, F J; Camacho, J P M; Loreto, V; Cabrero, J; de Souza, M J; Cabral-de-Mello, D C

    2015-02-01

    The spliceosome, constituted by a protein set associated with small nuclear RNA (snRNA), is responsible for mRNA maturation through intron removal. Among snRNA genes, U1 is generally a conserved repetitive sequence. To unveil the chromosomal/genomic dynamics of this multigene family in grasshoppers, we mapped U1 genes by fluorescence in situ hybridization in 70 species belonging to the families Proscopiidae, Pyrgomorphidae, Ommexechidae, Romaleidae and Acrididae. Evident clusters were observed in all species, indicating that, at least, some U1 repeats are tandemly arrayed. High conservation was observed in the first four families, with most species carrying a single U1 cluster, frequently located in the third or fourth longest autosome. By contrast, extensive variation was observed among Acrididae, from a single chromosome pair carrying U1 to all chromosome pairs carrying it, with occasional occurrence of two or more clusters in the same chromosome. DNA sequence analysis in Eyprepocnemis plorans (species carrying U1 clusters on seven different chromosome pairs) and Locusta migratoria (carrying U1 in a single chromosome pair) supported the coexistence of functional and pseudogenic lineages. One of these pseudogenic lineages was truncated in the same nucleotide position in both species, suggesting that it was present in a common ancestor to both species. At least in E. plorans, this U1 snDNA pseudogenic lineage was associated with 5S rDNA and short interspersed elements (SINE)-like mobile elements. Given that we conclude in grasshoppers that the U1 snDNA had evolved under the birth-and-death model and that its intragenomic spread might be related with mobile elements.

  11. The nuclear cap-binding complex interacts with the U4/U6·U5 tri-snRNP and promotes spliceosome assembly in mammalian cells.

    PubMed

    Pabis, Marta; Neufeld, Noa; Steiner, Michaela C; Bojic, Teodora; Shav-Tal, Yaron; Neugebauer, Karla M

    2013-08-01

    The nuclear cap-binding complex (CBC) binds to the 7-methyl guanosine cap present on every RNA polymerase II transcript. CBC has been implicated in many aspects of RNA biogenesis; in addition to roles in miRNA biogenesis, nonsense-mediated decay, 3'-end formation, and snRNA export from the nucleus, CBC promotes pre-mRNA splicing. An unresolved question is how CBC participates in splicing. To investigate CBC's role in splicing, we used mass spectrometry to identify proteins that copurify with mammalian CBC. Numerous components of spliceosomal snRNPs were specifically detected. Among these, three U4/U6·U5 snRNP proteins (hBrr2, hPrp4, and hPrp31) copurified with CBC in an RNA-independent fashion, suggesting that a significant fraction of CBC forms a complex with the U4/U6·U5 snRNP and that the activity of CBC might be associated with snRNP recruitment to pre-mRNA. To test this possibility, CBC was depleted from HeLa cells by RNAi. Chromatin immunoprecipitation and live-cell imaging assays revealed decreased cotranscriptional accumulation of U4/U6·U5 snRNPs on active transcription units, consistent with a requirement for CBC in cotranscriptional spliceosome assembly. Surprisingly, recruitment of U1 and U2 snRNPs was also affected, indicating that RNA-mediated interactions between CBC and snRNPs contribute to splicing. On the other hand, CBC depletion did not impair snRNP biogenesis, ruling out the possibility that decreased snRNP recruitment was due to changes in nuclear snRNP concentration. Taken together, the data support a model whereby CBC promotes pre-mRNA splicing through a network of interactions with and among spliceosomal snRNPs during cotranscriptional spliceosome assembly.

  12. Uranus moon - 1985U1

    NASA Technical Reports Server (NTRS)

    1986-01-01

    Several craters are seen on the surface of 1985U1, one of several small moons of Uranus discovered by Voyager 2. The spacecraft acquired this single image -- the only close-up it obtained of any of the new moons -- on Jan. 24, 1986. At the time, Voyager was at a distance of about 500,000 kilometers (300,000 miles) from 1985U1, yielding a resolution of about 10 km (6 mi) in this clear-filter, narrow-angle image. The moon was found Dec. 3O, 1985; it was the first and largest of nearly a dozen satellites discovered by the spacecraft cameras. This image shows 1985U1 to be a dark, nearly spherical object, with a diameter of about 150 km (90 mi); the dark surface reflects only 7 percent of the incident light. The picture was inserted into the Voyager encounter sequence late in its development. This image has had a complex history, having been recorded on the spacecraft tape recorder and first played back during the late afternoon of Jan. 24. An antenna-pointing problem at one of the Australian tracking stations led to loss of the data, so the image had to be transmitted a second time. It was successfully received shortly before 6 p.m. PST Jan. 26. The Voyager project is managed for NASA by the Jet Propulsion Laboratory.

  13. Plant-specific SR-related protein atSR45a interacts with spliceosomal proteins in plant nucleus.

    PubMed

    Tanabe, Noriaki; Kimura, Ayako; Yoshimura, Kazuya; Shigeoka, Shigeru

    2009-06-01

    Serine/arginine-rich (SR) protein and its homologues (SR-related proteins) are important regulators of constitutive and/or alternative splicing and other aspects of mRNA metabolism. To clarify the contribution of a plant-specific and stress-responsive SR-related protein, atSR45a, to splicing events, here we analyzed the interaction of atSR45a with the other splicing factors by conducting a yeast two-hybrid assay and a bimolecular fluorescence complementation analysis. The atSR45a-1a and -2 proteins, the presumed mature forms produced by alternative splicing of atSR45a, interacted with U1-70K and U2AF(35)b, splicing factors for the initial definition of 5' and 3' splice sites, respectively, in the early stage of spliceosome assembly. Both proteins also interacted with themselves, other SR proteins (atSR45 and atSCL28), and PRP38-like protein, a homologue of the splicing factor essential for cleavage of the 5' splice site. The mapping of deletion mutants of atSR45a proteins revealed that the C-terminal arginine/serine-rich (RS) domain of atSR45a proteins are required for the interaction with U1-70K, U2AF(35)b, atSR45, atSCL28, PRP38-like protein, and themselves, and the N-terminal RS domain enhances the interaction efficiency. Interestingly, the distinctive N-terminal extension in atSR45a-1a protein, but not atSR45a-2 protein, inhibited the interaction with these splicing factors. These findings suggest that the atSR45a proteins help to form the bridge between 5' and 3' splice sites in the spliceosome assembly and the efficiency of spliceosome formation is affected by the expression ratio of atSR45a-1a and atSR45a-2.

  14. Spliceosomal snRNAs: Mg(2+)-dependent chemistry at the catalytic core?

    PubMed

    Villa, Tommaso; Pleiss, Jeffrey A; Guthrie, Christine

    2002-04-19

    Since the discovery of self-splicing RNAs, it has been suspected that the snRNAs are the catalytic components of the spliceosome. Recent evidence supports both the catalytic potential of the spliceosomal snRNAs and their resemblance to elements of group II introns.

  15. Link of NTR-Mediated Spliceosome Disassembly with DEAH-Box ATPases Prp2, Prp16, and Prp22

    PubMed Central

    Chen, Hsin-Chou; Tseng, Chi-Kang; Tsai, Rong-Tzong; Chung, Che-Sheng

    2013-01-01

    The DEAH-box ATPase Prp43 is required for disassembly of the spliceosome after the completion of splicing or after the discard of the spliceosome due to a splicing defect. Prp43 associates with Ntr1 and Ntr2 to form the NTR complex and is recruited to the spliceosome via the interaction of Ntr2 and U5 component Brr2. Ntr2 alone can bind to U5 and to the spliceosome. To understand how NTR might mediate the disassembly of spliceosome intermediates, we arrested the spliceosome at various stages of the assembly pathway and assessed its susceptibility to disassembly. We found that NTR could catalyze the disassembly of affinity-purified spliceosomes arrested specifically after the ATP-dependent action of DEAH-box ATPase Prp2, Prp16, or Prp22 but not at steps before the action of these ATPases or upon their binding to the spliceosome. These results link spliceosome disassembly to the functioning of splicing ATPases. Analysis of the binding of Ntr2 to each splicing complex has revealed that the presence of Prp16 and Slu7, which also interact with Brr2, has a negative impact on Ntr2 binding. Our study provides insights into the mechanism by which NTR can be recruited to the spliceosome to mediate the disassembly of spliceosome intermediates when the spliceosome pathway is retarded, while disassembly is prevented in normal reactions. PMID:23166295

  16. The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA

    PubMed Central

    Law, Michael J.; Linde, Michael E.; Chambers, Eric J.; Oubridge, Chris; Katsamba, Phinikoula S.; Nilsson, Lennart; Haworth, Ian S.; Laird-Offringa, Ite A.

    2006-01-01

    Previous kinetic investigations of the N-terminal RNA recognition motif (RRM) domain of spliceosomal protein U1A, interacting with its RNA target U1 hairpin II, provided experimental evidence for a ‘lure and lock’ model of binding in which electrostatic interactions first guide the RNA to the protein, and close range interactions then lock the two molecules together. To further investigate the ‘lure’ step, here we examined the electrostatic roles of two sets of positively charged amino acids in U1A that do not make hydrogen bonds to the RNA: Lys20, Lys22 and Lys23 close to the RNA-binding site, and Arg7, Lys60 and Arg70, located on ‘top’ of the RRM domain, away from the RNA. Surface plasmon resonance-based kinetic studies, supplemented with salt dependence experiments and molecular dynamics simulation, indicate that Lys20 predominantly plays a role in association, while nearby residues Lys22 and Lys23 appear to be at least as important for complex stability. In contrast, kinetic analyses of residues away from the RNA indicate that they have a minimal effect on association and stability. Thus, well-positioned positively charged residues can be important for both initial complex formation and complex maintenance, illustrating the multiple roles of electrostatic interactions in protein–RNA complexes. PMID:16407334

  17. Molecular architecture of the Saccharomyces cerevisiae activated spliceosome.

    PubMed

    Rauhut, Reinhard; Fabrizio, Patrizia; Dybkov, Olexandr; Hartmuth, Klaus; Pena, Vladimir; Chari, Ashwin; Kumar, Vinay; Lee, Chung-Tien; Urlaub, Henning; Kastner, Berthold; Stark, Holger; Lührmann, Reinhard

    2016-09-23

    The activated spliceosome (B(act)) is in a catalytically inactive state and is remodeled into a catalytically active machine by the RNA helicase Prp2, but the mechanism is unclear. Here, we describe a 3D electron cryomicroscopy structure of the Saccharomyces cerevisiae B(act) complex at 5.8-angstrom resolution. Our model reveals that in B(act), the catalytic U2/U6 RNA-Prp8 ribonucleoprotein core is already established, and the 5' splice site (ss) is oriented for step 1 catalysis but occluded by protein. The first-step nucleophile-the branchsite adenosine-is sequestered within the Hsh155 HEAT domain and is held 50 angstroms away from the 5'ss. Our structure suggests that Prp2 adenosine triphosphatase-mediated remodeling leads to conformational changes in Hsh155's HEAT domain that liberate the first-step reactants for catalysis.

  18. Monoclonal antibody specific to a subclass of polyproline-Arg motif provides evidence for the presence of an snRNA-free spliceosomal Sm protein complex in vivo: implications for molecular interactions involving proline-rich sequences of Sm B/B' proteins.

    PubMed

    Filali, M; Qiu, J; Awasthi, S; Fischer, U; Monos, D; Kamoun, M

    1999-08-01

    The human spliceosomal Sm B/B' proteins are essential for the biogenesis of the snRNP particles. B/B' proteins contain several clusters of the PPPPGM/IR sequence, which occurs within the C-terminus of Sm B/B'. This sequence is very similar to the PPPPPGHR sequence of the cytoplasmic tail of the CD2 receptor and closely resembles the class II of SH3 ligands, suggesting a similarly important role. We report that a monoclonal antibody (3E10) against the PPPPPGHR sequence recognizes spliceosomal Sm B/B' proteins. Proteins that are specifically immunoprecipitated by 3E10 include Sm B, B', D1, D2, D3, E, F, and G. However, unlike Y12 and other anti-Sm immunoprecipitates, 3E10 immunoprecipitates appear to lack the U1 snRNP-specific proteins A and C and U snRNAs. These findings indicate that 3E10 recognizes a subset of Sm protein core and suggest the presence of snRNA-free Sm protein complex(es) in vivo. We propose that the epitope binding for 3E10 may become unaccessible upon interactions of Sm proteins and their subsequent incorporation into the core particles. The Sm proline-rich sequences may have an important role in mediating protein-protein interactions necessary for the proper snRNP core assembly or function, or both. To our knowledge, 3E10 is the first well characterized mAb specific for a subclass of polyproline-arg motif recognizing Sm B/B' and CD2 proteins. 3E10 antibody can be used to further characterize the nature of protein components in the snRNA-free Sm subcore protein complex(es) that are formed during the snRNP core assembly steps.

  19. Functional splicing network reveals extensive regulatory potential of the core spliceosomal machinery.

    PubMed

    Papasaikas, Panagiotis; Tejedor, J Ramón; Vigevani, Luisa; Valcárcel, Juan

    2015-01-08

    Pre-mRNA splicing relies on the poorly understood dynamic interplay between >150 protein components of the spliceosome. The steps at which splicing can be regulated remain largely unknown. We systematically analyzed the effect of knocking down the components of the splicing machinery on alternative splicing events relevant for cell proliferation and apoptosis and used this information to reconstruct a network of functional interactions. The network accurately captures known physical and functional associations and identifies new ones, revealing remarkable regulatory potential of core spliceosomal components, related to the order and duration of their recruitment during spliceosome assembly. In contrast with standard models of regulation at early steps of splice site recognition, factors involved in catalytic activation of the spliceosome display regulatory properties. The network also sheds light on the antagonism between hnRNP C and U2AF, and on targets of antitumor drugs, and can be widely used to identify mechanisms of splicing regulation.

  20. Modulation of splicing catalysis for therapeutic targeting of leukemias with spliceosomal mutations

    PubMed Central

    Lee, Stanley Chun-Wei; Dvinge, Heidi; Kim, Eunhee; Cho, Hana; Micol, Jean-Baptiste; Chung, Young Rock; Durham, Benjamin H.; Yoshimi, Akihide; Kim, Young Joon; Thomas, Michael; Lobry, Camille; Chen, Chun-Wei; Pastore, Alessandro; Taylor, Justin; Wang, Xujun; Krivtsov, Andrei; Armstrong, Scott A.; Palacino, James; Buonamici, Silvia; Smith, Peter G.; Bradley, Robert K.; Abdel-Wahab, Omar

    2016-01-01

    Mutations in spliceosomal genes are commonly found in patients with myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML)1–3. These mutations occur at highly recurrent amino acid residues and perturb normal splice site and exon recognition4–6. Spliceosomal mutations are always heterozygous and rarely co-occur with one another, suggesting that cells may only tolerate a partial deviation from normal splicing activity. To test this hypothesis, we engineered mice that express the SRSF2P95H mutation, which commonly occurs in MDS and AML, in an inducible hemizygous manner in hematopoietic cells. These mice developed lethal bone marrow failure, demonstrating that Srsf2-mutant cells depend on the wildtype Srsf2 allele for survival. In the context of leukemia, treatment with the spliceosome inhibitor E71077,8 resulted in significant reductions in leukemic burden specifically in isogenic mouse leukemias and patient-derived xenograft (PDX) AMLs carrying spliceosomal mutations. While in vivo E7107 exposure resulted in widespread intron retention and cassette exon skipping regardless of Srsf2 genotype, the magnitude of splicing inhibition following E7107 treatment was greater in Srsf2-mutant versus wildtype leukemias, consistent with its differential effect on survival in these two genotypes. Collectively, these data provide genetic and pharmacologic evidence that leukemias with spliceosomal mutations are preferentially susceptible to additional splicing perturbations in vivo compared with wildtype counterparts. Modulation of spliceosome function may provide a novel therapeutic avenue in genetically defined subsets of MDS and AML patients. PMID:27135740

  1. SKIP Is a Component of the Spliceosome Linking Alternative Splicing and the Circadian Clock in Arabidopsis[W

    PubMed Central

    Wang, Xiaoxue; Wu, Fangming; Xie, Qiguang; Wang, Huamei; Wang, Ying; Yue, Yanling; Gahura, Ondrej; Ma, Shuangshuang; Liu, Lei; Cao, Ying; Jiao, Yuling; Puta, Frantisek; McClung, C. Robertson; Xu, Xiaodong; Ma, Ligeng

    2012-01-01

    Circadian clocks generate endogenous rhythms in most organisms from cyanobacteria to humans and facilitate entrainment to environmental diurnal cycles, thus conferring a fitness advantage. Both transcriptional and posttranslational mechanisms are prominent in the basic network architecture of circadian systems. Posttranscriptional regulation, including mRNA processing, is emerging as a critical step for clock function. However, little is known about the molecular mechanisms linking RNA metabolism to the circadian clock network. Here, we report that a conserved SNW/Ski-interacting protein (SKIP) domain protein, SKIP, a splicing factor and component of the spliceosome, is involved in posttranscriptional regulation of circadian clock genes in Arabidopsis thaliana. Mutation in SKIP lengthens the circadian period in a temperature-sensitive manner and affects light input and the sensitivity of the clock to light resetting. SKIP physically interacts with the spliceosomal splicing factor Ser/Arg-rich protein45 and associates with the pre-mRNA of clock genes, such as PSEUDORESPONSE REGULATOR7 (PRR7) and PRR9, and is necessary for the regulation of their alternative splicing and mRNA maturation. Genome-wide investigations reveal that SKIP functions in regulating alternative splicing of many genes, presumably through modulating recognition or cleavage of 5′ and 3′ splice donor and acceptor sites. Our study addresses a fundamental question on how the mRNA splicing machinery contributes to circadian clock function at a posttranscriptional level. PMID:22942380

  2. PRP16, a DEAH-box RNA helicase, is recruited to the spliceosome primarily via its nonconserved N-terminal domain.

    PubMed Central

    Wang, Y; Guthrie, C

    1998-01-01

    Dynamic rearrangement of RNA structure is crucial for intron recognition and formation of the catalytic core during pre-mRNA splicing. Three of the splicing factors that contain sequence motifs characteristic of the DExD/DExH-box family of RNA-dependent ATPases (Prp16, Prp22, and the human homologue of Brr2) recently have been shown to unwind RNA duplexes in vitro, providing biochemical evidence that they may direct structural rearrangements on the spliceosome. Notably, however, the unwinding activity of these proteins is sequence nonspecific, raising the question of how their functional specificity is determined. Because the highly conserved DExD/DExH-box domain in these proteins is typically flanked by one or more nonconserved domains, we have tested the hypothesis that the nonconserved regions of Prp16 determine the functional specificity of the protein. We found that the nonconserved N-terminal domain of Prp16 is (1) essential for viability, (2) required for the nuclear localization of Prp16, and (3) capable of binding to the spliceosome specifically at the step of Prp16 function. Moreover, this domain can interact with the rest of the protein to allow trans-complementation. Based on these results, we propose that the spliceosomal target of the unwinding activity of Prp16, and possibly other DExD/DExH-box splicing factors as well, is defined by factors that specifically interact with the nonconserved domains of the protein. PMID:9769096

  3. CryoEM structure of the spliceosome immediately after branching

    PubMed Central

    Galej, Wojciech P.; Wilkinson, Max E.; Fica, Sebastian M.; Oubridge, Chris; Newman, Andrew J.; Nagai, Kiyoshi

    2016-01-01

    Pre-mRNA splicing proceeds by two consecutive trans-esterification reactions via a lariat-intron intermediate. We present the 3.8Å cryoEM structure of the spliceosome immediately after lariat formation. The 5’-splice site is cleaved but remains close to the catalytic Mg2+ site in the U2/U6 snRNA triplex, and the 5’-phosphate of the intron nucleotide G(+1) is linked to the branch adenosine 2’OH. The 5’-exon is held between the Prp8 N-terminal and Linker domains, and base-pairs with U5 snRNA loop 1. Non-Watson-Crick interactions between the branch helix and 5’-splice site dock the branch adenosine into the active site, while intron nucleotides +3 to +6 base-pair with the U6 snRNA ACAGAGA sequence. Isy1 and the step one factors Yju2 and Cwc25 stabilise docking of the branch helix. The intron downstream of the branch site emerges between the Prp8 RT and Linker domains and extends towards Prp16 helicase, suggesting a plausible mechanism of remodelling before exon ligation. PMID:27459055

  4. A high density of ancient spliceosomal introns in oxymonad excavates

    PubMed Central

    Slamovits, Claudio H; Keeling, Patrick J

    2006-01-01

    Background Certain eukaryotic genomes, such as those of the amitochondriate parasites Giardia and Trichomonas, have very low intron densities, so low that canonical spliceosomal introns have only recently been discovered through genome sequencing. These organisms were formerly thought to be ancient eukaryotes that diverged before introns originated, or at least became common. Now however, they are thought to be members of a supergroup known as excavates, whose members generally appear to have low densities of canonical introns. Here we have used environmental expressed sequence tag (EST) sequencing to identify 17 genes from the uncultivable oxymonad Streblomastix strix, to survey intron densities in this most poorly studied excavate group. Results We find that Streblomastix genes contain an unexpectedly high intron density of about 1.1 introns per gene. Moreover, over 50% of these are at positions shared between a broad spectrum of eukaryotes, suggesting theyare very ancient introns, potentially present in the last common ancestor of eukaryotes. Conclusion The Streblomastix data show that the genome of the ancestor of excavates likely contained many introns and the subsequent evolution of introns has proceeded very differently in different excavate lineages: in Streblomastix there has been much stasis while in Trichomonas and Giardia most introns have been lost. PMID:16638131

  5. Alternatively spliced, spliceosomal twin introns in Helminthosporium solani.

    PubMed

    Ág, Norbert; Flipphi, Michel; Karaffa, Levente; Scazzocchio, Claudio; Fekete, Erzsébet

    2015-12-01

    Spliceosomal twin introns, "stwintrons", have been defined as complex intervening sequences that carry a second intron ("internal intron") interrupting one of the conserved sequence domains necessary for their correct splicing via consecutive excision events. Previously, we have described and experimentally verified stwintrons in species of Sordariomycetes, where an "internal intron" interrupted the donor sequence of an "external intron". Here we describe and experimentally verify two novel stwintrons of the potato pathogen Helminthosporium solani. One instance involves alternative splicing of an internal intron interrupting the donor domain of an external intron and a second one interrupting the acceptor domain of an overlapping external intron, both events leading to identical mature mRNAs. In the second case, an internal intron interrupts the donor domain of the external intron, while an alternatively spliced intron leads to an mRNA carrying a premature chain termination codon. We thus extend the stwintron concept to the acceptor domain and establish a link of the occurrence of stwintrons with that of alternative splicing.

  6. Anomaly-free version of SU(2)U(1)U(1)/sup '/

    SciTech Connect

    Ponce, W.A.

    1987-08-01

    The most general anomaly-free version of the SU(2) x U(1) x U(1)' local gauge-invariant model is presented here, for two different Higgs structures (the minimal ones), as an extension of the SU(2) x U(1) Glashow-Weinberg-Salam model.

  7. Origin of a peculiar extra U(1)

    SciTech Connect

    Barr, S.M.; Dorsner, I.

    2005-07-01

    The origin of a family-independent ''extra U(1)'', discovered by Barr, Bednarz, and Benesh and independently by Ma, and whose phenomenology has recently been studied by Ma and Roy, is discussed. Even though it satisfies anomaly constraints in a highly economical way, with just a single extra triplet of leptons per family, this extra U(1) cannot come from four-dimensional grand unification. However, it is shown here that it can come from a Pati-Salam scheme with an extra U(1), which explains the otherwise surprising cancellation of anomalies.

  8. Spliceosomal gene mutations in myelodysplasia: molecular links to clonal abnormalities of hematopoiesis

    PubMed Central

    Inoue, Daichi; Bradley, Robert K.; Abdel-Wahab, Omar

    2016-01-01

    Genomic analyses of the myeloid malignancies and clonal disorders of hematopoiesis that may give rise to these disorders have identified that mutations in genes encoding core spliceosomal proteins and accessory regulatory splicing factors are among the most common targets of somatic mutations. These spliceosomal mutations often occur in a mutually exclusive manner with one another and, in aggregate, account for the most frequent class of mutations in patients with myelodysplastic syndromes (MDSs) in particular. Although substantial progress has been made in understanding the effects of several of these mutations on splicing and splice site recognition, functional connections linking the mechanistic changes in splicing induced by these mutations to the phenotypic consequences of clonal and aberrant hematopoiesis are not yet well defined. This review describes our current understanding of the mechanistic and biological effects of spliceosomal gene mutations in MDSs as well as the regulation of splicing throughout normal hematopoiesis. PMID:27151974

  9. Exhaustive analysis of the modular structure of the spliceosomal assembly network: a Petri net approach.

    PubMed

    Bortfeldt, Ralf H; Schuster, Stefan; Koch, Ina

    2010-01-01

    Spliceosomes are macro-complexes involving hundreds of proteins with many functional interactions. Spliceosome assembly belongs to the key processes that enable splicing of mRNA and modulate alternative splicing. A detailed list of factors involved in spliceosomal reactions has been assorted over the past decade, but, their functional interplay is often unknown and most of the present biological models cover only parts of the complete assembly process. It is a challenging task to build a computational model that integrates dispersed knowledge and combines a multitude of reaction schemes proposed earlier.Because for most reactions involved in spliceosome assembly kinetic parameters are not available, we propose a discrete modeling using Petri nets, through which we are enabled to get insights into the system's behavior via computation of structural and dynamic properties. In this paper, we compile and examine reactions from experimental reports that contribute to a functional spliceosome. All these reactions form a network, which describes the inventory and conditions necessary to perform the splicing process. The analysis is mainly based on system invariants. Transition invariants (T-invariants) can be interpreted as signaling routes through the network. Due to the huge number of T-invariants that arise with increasing network size and complexity, maximal common transition sets (MCTS) and T-clusters were used for further analysis. Additionally, we introduce a false color map representation, which allows a quick survey of network modules and the visual detection of single reactions or reaction sequences, which participate in more than one signaling route. We designed a structured model of spliceosome assembly, which combines the demands on a platform that i) can display involved factors and concurrent processes, ii) offers the possibility to run computational methods for knowledge extraction, and iii) is successively extendable as new insights into spliceosome

  10. Exhaustive analysis of the modular structure of the spliceosomal assembly network: a petri net approach.

    PubMed

    Bortfeldt, Ralf H; Schuster, Stefan; Koch, Ina

    2011-01-01

    Spliceosomes are macro-complexes involving hundreds of proteins with many functional interactions. Spliceosome assembly belongs to the key processes that enable splicing of mRNA and modulate alternative splicing. A detailed list of factors involved in spliceosomal reactions has been assorted over the past decade, but, their functional interplay is often unknown and most of the present biological models cover only parts of the complete assembly process. It is a challenging task to build a computational model that integrates dispersed knowledge and combines a multitude of reaction schemes proposed earlier. Because for most reactions involved in spliceosome assembly kinetic parameters are not available, we propose a discrete modeling using Petri nets, through which we are enabled to get insights into the system's behavior via computation of structural and dynamic properties. In this paper, we compile and examine reactions from experimental reports that contribute to a functional spliceosome. All these reactions form a network, which describes the inventory and conditions necessary to perform the splicing process. The analysis is mainly based on system invariants. Transition invariants (T-invariants) can be interpreted as signaling routes through the network. Due to the huge number of T-invariants that arise with increasing network size and complexity, maximal common transition sets (MCTS) and T-clusters were used for further analysis. Additionally, we introduce a false color map representation, which allows a quick survey of network modules and the visual detection of single reactions or reaction sequences, which participate in more than one signaling route. We designed a structured model of spliceosome assembly, which combines the demands on a platform that i) can display involved factors and concurrent processes, ii) offers the possibility to run computational methods for knowledge extraction, and iii) is successively extendable as new insights into spliceosome

  11. Mutations in U4atac snRNA, a Component of the Minor Spliceosome, in the Developmental Disorder MOPD I

    PubMed Central

    He, Huiling; Liyanarachchi, Sandya; Akagi, Keiko; Nagy, Rebecca; Li, Jingfeng; Dietrich, Rosemary C; Li, Wei; Sebastian, Nikhil; Wen, Bernard; Xin, Baozhong; Singh, Jarnail; Yan, Pearlly; Alder, Hansjuerg; Haan, Eric; Wieczorek, Dagmar; Albrecht, Beate; Puffenberger, Erik; Wang, Heng; Westman, Judith A.; Padgett, Richard A; Symer, David E; de la Chapelle, Albert

    2012-01-01

    Small nuclear RNAs (snRNAs) are essential factors in mRNA splicing. By homozygosity mapping and deep sequencing, we show that a gene encoding U4atac snRNA, a component of the minor U12-dependent spliceosome, is mutated in individuals with microcephalic osteodysplastic primordial dwarfism type I (MOPD I), a severe developmental disorder characterized by extreme intrauterine growth retardation and multiple organ abnormalities. Functional assays show that mutations (30G>A, 51G>A, 55G>A, and 111G>A) associated with MOPD I cause defective U12-dependent splicing. Endogenous U12-dependent but not U2-dependent introns are poorly spliced in MOPD I patient fibroblast cells while introduction of wild type U4atac snRNA into MOPD I cells enhances U12-dependent splicing. These results illustrate the critical role of minor intron splicing in human development. PMID:21474760

  12. Definition of a spliceosome interaction domain in yeast Prp2 ATPase.

    PubMed

    Edwalds-Gilbert, Gretchen; Kim, Dong-Ho; Silverman, Edward; Lin, Ren-Jang

    2004-02-01

    The Saccharomyces cerevisiae splicing factor Prp2 is an RNA-dependent ATPase required before the first transesterification reaction in pre-mRNA splicing. Prp2 binds to the spliceosome in the absence of ATP and is released following ATP hydrolysis. It contains three domains: a unique N-terminal domain, a helicase domain that is highly conserved in the DExD/H protein family, and a C-terminal domain that is conserved in spliceosomal DEAH proteins Prp2, Prp16, Prp22, and Prp43. We examined the role of each domain of Prp2 by deletion mutagenesis. Whereas deletions of either the helicase or C-terminal domain are lethal, deletions in the N-terminal domain have no detectable effect on Prp2 activity. Overexpression of the C-terminal domain of Prp2 exacerbates the temperature-sensitive phenotype of a prp2(Ts) strain, suggesting that the C-domain interferes with the activity of the Prp2(Ts) protein. A genetic approach was then taken to study interactions between Prp2 and the spliceosome. Previously, we isolated dominant negative mutants in the helicase domain of Prp2 that inhibit the activity of wild-type Prp2 when the mutant protein is overexpressed. We mutagenized one prp2 release mutant gene and screened for loss of dominant negative function. Several weak binding mutants were isolated and mapped to the C terminus of Prp2, further indicating the importance of the C terminus in spliceosome binding. This study is the first to indicate that amino acid substitutions outside the helicase domain can abolish spliceosome contact and splicing activity of a spliceosomal DEAH protein.

  13. TDRD6 mediates early steps of spliceosome maturation in primary spermatocytes

    PubMed Central

    Akpınar, Müge; Fanourgakis, Grigorios; Fu, Jun; Anasstasiadis, Konstantinos; Dahl, Andreas

    2017-01-01

    Tudor containing protein 6 (TDRD6) is a male germ line-specific protein essential for chromatoid body (ChB) structure, elongated spermatid development and male fertility. Here we show that in meiotic prophase I spermatocytes TDRD6 interacts with the key protein arginine methyl transferase PRMT5, which supports splicing. TDRD6 also associates with spliceosomal core protein SmB in the absence of RNA and in an arginine methylation dependent manner. In Tdrd6-/- diplotene spermatocytes PRMT5 association with SmB and arginine dimethylation of SmB are much reduced. TDRD6 deficiency impairs the assembly of spliceosomes, which feature 3.5-fold increased levels of U5 snRNPs. In the nucleus, these deficiencies in spliceosome maturation correlate with decreased numbers of SMN-positive bodies and Cajal bodies involved in nuclear snRNP maturation. Transcriptome analysis of TDRD6-deficient diplotene spermatocytes revealed high numbers of splicing defects such as aberrant usage of intron and exons as well as aberrant representation of splice junctions. Together, this study demonstrates a novel function of TDRD6 in spliceosome maturation and mRNA splicing in prophase I spermatocytes. PMID:28263986

  14. Recruitment of the NineTeen Complex to the activated spliceosome requires AtPRMT5

    PubMed Central

    Deng, Xian; Lu, Tiancong; Wang, Lulu; Gu, Lianfeng; Sun, Jing; Kong, Xiangfeng; Liu, Chunyan; Cao, Xiaofeng

    2016-01-01

    Protein arginine methylation, catalyzed by protein arginine methyltransferases (PRMTs), is involved in a multitude of biological processes in eukaryotes. Symmetric arginine dimethylation mediated by PRMT5 modulates constitutive and alternative pre-mRNA splicing of diverse genes to regulate normal growth and development in multiple species; however, the underlying molecular mechanism remains largely unknown. A genetic screen for suppressors of an Arabidopsis symmetric arginine dimethyltransferase mutant, atprmt5, identified two gain-of-function alleles of pre-mRNA processing factor 8 gene (prp8-8 and prp8-9), the highly conserved core component of the U5 small nuclear ribonucleoprotein (snRNP) and the spliceosome. These two atprmt5 prp8 double mutants showed suppression of the developmental and splicing alterations of atprmt5 mutants. In atprmt5 mutants, the NineTeen complex failed to be assembled into the U5 snRNP to form an activated spliceosome; this phenotype was restored in the atprmt5 prp8-8 double mutants. We also found that loss of symmetric arginine dimethylation of Sm proteins prevents recruitment of the NineTeen complex and initiation of spliceosome activation. Together, our findings demonstrate that symmetric arginine dimethylation has important functions in spliceosome assembly and activation, and uncover a key molecular mechanism for arginine methylation in pre-mRNA splicing that impacts diverse developmental processes. PMID:27114555

  15. Aberrant RNA splicing and mutations in spliceosome complex in acute myeloid leukemia

    PubMed Central

    2017-01-01

    The spliceosome, the cellular splicing machinery, regulates RNA splicing of messenger RNA precursors (pre-mRNAs) into maturation of protein coding RNAs. Recurrent mutations and copy number changes in genes encoding spliceosomal proteins and splicing regulatory factors have tumor promoting or suppressive functions in hematological malignancies, as well as some other cancers. Leukemia stem cell (LSC) populations, although rare, are essential contributors of treatment failure and relapse. Recent researches have provided the compelling evidence that link the erratic spicing activity to the LSC phenotype in acute myeloid leukemia (AML). In this article, we describe the diverse roles of aberrant splicing in hematological malignancies, particularly in AML and their contributions to the characteristics of LSC. We review these promising strategies to exploit the addiction of aberrant spliceosomal machinery for anti-leukemic therapy with aim to eradicate LSC. However, given the complexity and plasticity of spliceosome and not fully known functions of splicing in cancer, the challenges facing the development of the therapeutic strategies targeting RAN splicing are highlighted and future directions are discussed too. PMID:28217708

  16. Spliceosome discards intermediates via the DEAH box ATPase Prp43p.

    PubMed

    Mayas, Rabiah M; Maita, Hiroshi; Semlow, Daniel R; Staley, Jonathan P

    2010-06-01

    To promote fidelity in nuclear pre-mRNA splicing, the spliceosome rejects and discards suboptimal substrates that have engaged the spliceosome. Whereas DExD/H box ATPases have been implicated in rejecting suboptimal substrates, the mechanism for discarding suboptimal substrates has remained obscure. Corroborating evidence that suboptimal, mutated lariat intermediates can be exported to the cytoplasm for turnover, we have found that the ribosome can translate mutated lariat intermediates. By glycerol gradient analysis, we have found that the spliceosome can dissociate mutated lariat intermediates in vivo in a manner that requires the DEAH box ATPase Prp43p. Through an in vitro assay, we demonstrate that Prp43p promotes the discard of suboptimal and optimal 5' exon and lariat intermediates indiscriminately. Finally, we demonstrate a requirement for Prp43p in repressing splicing at a cryptic splice site. We propose a model for the fidelity of exon ligation in which the DEAH box ATPase Prp22p slows the flow of suboptimal intermediates through exon ligation and Prp43p generally promotes discard of intermediates, thereby establishing a pathway for turnover of stalled intermediates. Because Prp43p also promotes spliceosome disassembly after exon ligation, this work establishes a parallel between the discard of suboptimal intermediates and the dissociation of a genuine excised intron product.

  17. Aberrant RNA splicing and mutations in spliceosome complex in acute myeloid leukemia.

    PubMed

    Zhou, Jianbiao; Chng, Wee-Joo

    2017-01-01

    The spliceosome, the cellular splicing machinery, regulates RNA splicing of messenger RNA precursors (pre-mRNAs) into maturation of protein coding RNAs. Recurrent mutations and copy number changes in genes encoding spliceosomal proteins and splicing regulatory factors have tumor promoting or suppressive functions in hematological malignancies, as well as some other cancers. Leukemia stem cell (LSC) populations, although rare, are essential contributors of treatment failure and relapse. Recent researches have provided the compelling evidence that link the erratic spicing activity to the LSC phenotype in acute myeloid leukemia (AML). In this article, we describe the diverse roles of aberrant splicing in hematological malignancies, particularly in AML and their contributions to the characteristics of LSC. We review these promising strategies to exploit the addiction of aberrant spliceosomal machinery for anti-leukemic therapy with aim to eradicate LSC. However, given the complexity and plasticity of spliceosome and not fully known functions of splicing in cancer, the challenges facing the development of the therapeutic strategies targeting RAN splicing are highlighted and future directions are discussed too.

  18. Single molecule analysis reveals reversible and irreversible steps during spliceosome activation

    PubMed Central

    Hoskins, Aaron A; Rodgers, Margaret L; Friedman, Larry J; Gelles, Jeff; Moore, Melissa J

    2016-01-01

    The spliceosome is a complex machine composed of small nuclear ribonucleoproteins (snRNPs) and accessory proteins that excises introns from pre-mRNAs. After assembly the spliceosome is activated for catalysis by rearrangement of subunits to form an active site. How this rearrangement is coordinated is not well-understood. During activation, U4 must be released to allow U6 conformational change, while Prp19 complex (NTC) recruitment is essential for stabilizing the active site. We used multi-wavelength colocalization single molecule spectroscopy to directly observe the key events in Saccharomyces cerevisiae spliceosome activation. Following binding of the U4/U6.U5 tri-snRNP, the spliceosome either reverses assembly by discarding tri-snRNP or proceeds to activation by irreversible U4 loss. The major pathway for NTC recruitment occurs after U4 release. ATP stimulates both the competing U4 release and tri-snRNP discard processes. The data reveal the activation mechanism and show that overall splicing efficiency may be maintained through repeated rounds of disassembly and tri-snRNP reassociation. DOI: http://dx.doi.org/10.7554/eLife.14166.001 PMID:27244240

  19. Prevalent and distinct spliceosomal 3′-end processing mechanisms for fungal telomerase RNA

    PubMed Central

    Qi, Xiaodong; Rand, Dustin P.; Podlevsky, Joshua D.; Li, Yang; Mosig, Axel; Stadler, Peter F.; Chen, Julian J.-L.

    2015-01-01

    Telomerase RNA (TER) is an essential component of the telomerase ribonucleoprotein complex. The mechanism for TER 3′-end processing is highly divergent among different organisms. Here we report a unique spliceosome-mediated TER 3′-end cleavage mechanism in Neurospora crassa which is distinct from that found specifically in the fission yeast Schizosaccharomyces pombe. While the S. pombe TER intron contains the canonical 5′-splice site GUAUGU, the N. crassa TER intron contains a non-canonical 5′-splice site AUAAGU that alone prevents the second step of splicing and promotes spliceosomal cleavage. The unique N. crassa TER 5′-splice site sequence is evolutionarily conserved in TERs from Pezizomycotina and early branching Taphrinomycotina species. This suggests that the widespread and basal N. crassa-type spliceosomal cleavage mechanism is more ancestral than the S. pombe-type. The discovery of a prevalent, yet distinct, spliceosomal cleavage mechanism throughout diverse fungal clades furthers our understanding of TER evolution and non-coding RNA processing. PMID:25598218

  20. Vought O3U-1 Corsair

    NASA Technical Reports Server (NTRS)

    1931-01-01

    Vought O3U-1 Corsair: This aircraft, the Vought O3U-1 Corsair, was the first aircraft tested in the Full Scale Tunnel. It is shown here during preliminary tests in the FST before the balance was enclosed. NACA engineers checked the lift and drag characteristics of several aircraft with the results of earlier flight tests. Smith DeFrance concluded NACA TR No. 459, 'The agreement that has been obtained between the flight and full-scale tunnel results, together with the consistent manner in which measurements can be repeated when check tests are made, has demonstrated the accuracy and value of the equipment for aeronautical research.' (p. 298)

  1. Potential effect of spliceosome inhibition in small cell lung cancer irrespective of the MYC status

    PubMed Central

    Rozeboom, Leslie; Yu, Hui; Ellison, Kim; Rivard, Christopher J.; Mitsudomi, Tetsuya; Hirsch, Fred R.

    2017-01-01

    Small cell lung cancer (SCLC) is a highly aggressive malignancy with few therapeutic advances in the treatment in recent decades. Based on a recent study that identified the spliceosome as a therapeutic vulnerability in MYC-driven breast cancers, we evaluated the efficacy of a spliceosome inhibitor in SCLC cell lines and analyzed the correlation with MYC status. Among 23 SCLC cell lines examined, eight showed high MYC protein expression (> 80% positive cells) by immunohistochemistry (IHC), while 10 cell lines demonstrated no staining for MYC. The remaining five cell lines showed weak staining (< 40% positive cells). All four cell lines that were previously demonstrated to have MYC gene amplification were positive for MYC by IHC. Four cell lines with high MYC expression and four with low MYC expression were used in further analysis. A spliceosome inhibitor, pladienolide B, showed high efficacy (IC50 < 12nM) in all eight cell lines tested, irrespective of the MYC IHC or MYC gene amplification status. We observed that the four cell lines with higher sensitivity to the spliceosome inhibitor were established from patients with prior chemotherapy. Therefore we chronically treated H1048 cells, that were established from a treatment-naïve patient, with cisplatin for 4 weeks, and found that H1048-cisplatin treated cells became more sensitive to pladienolide B. In conclusion, our in vitro results indicate that spliceosome inhibitors would be promising molecular target drugs in SCLC irrespective of the MYC status, especially in the second-line settings after an effective front-line chemotherapy. PMID:28192473

  2. A novel intra-U1 snRNP cross-regulation mechanism: alternative splicing switch links U1C and U1-70K expression.

    PubMed

    Rösel-Hillgärtner, Tanja Dorothe; Hung, Lee-Hsueh; Khrameeva, Ekaterina; Le Querrec, Patrick; Gelfand, Mikhail S; Bindereif, Albrecht

    2013-01-01

    The U1 small nuclear ribonucleoprotein (snRNP)-specific U1C protein participates in 5' splice site recognition and regulation of pre-mRNA splicing. Based on an RNA-Seq analysis in HeLa cells after U1C knockdown, we found a conserved, intra-U1 snRNP cross-regulation that links U1C and U1-70K expression through alternative splicing and U1 snRNP assembly. To investigate the underlying regulatory mechanism, we combined mutational minigene analysis, in vivo splice-site blocking by antisense morpholinos, and in vitro binding experiments. Alternative splicing of U1-70K pre-mRNA creates the normal (exons 7-8) and a non-productive mRNA isoform, whose balance is determined by U1C protein levels. The non-productive isoform is generated through a U1C-dependent alternative 3' splice site, which requires an adjacent cluster of regulatory 5' splice sites and binding of intact U1 snRNPs. As a result of nonsense-mediated decay (NMD) of the non-productive isoform, U1-70K mRNA and protein levels are down-regulated, and U1C incorporation into the U1 snRNP is impaired. U1-70K/U1C-deficient particles are assembled, shifting the alternative splicing balance back towards productive U1-70K splicing, and restoring assembly of intact U1 snRNPs. Taken together, we established a novel feedback regulation that controls U1-70K/U1C homeostasis and ensures correct U1 snRNP assembly and function.

  3. Supergravity solutions without triholomorphic U(1) isometries

    SciTech Connect

    Ghezelbash, A. M.

    2008-12-15

    We investigate the construction of five-dimensional supergravity solutions that do not have any triholomorphic U(1) isometries. We construct a class of solutions that in various limits of parameters reduces to many of previously constructed five-dimensional supergravity solutions based on both hyper-Kaehler base spaces that can be put into a Gibbons-Hawking form and hyper-Kaehler base spaces that cannot be put into a Gibbons-Hawking form. We find a new solution which is over triaxial Bianchi type IX Einstein-hyper-Kaehler base space with no triholomorphic U(1) symmetry. One special case of this solution corresponds to a five-dimensional solution based on Eguchi-Hanson type II geometry.

  4. Phosphorylated SAP155, the spliceosomal component, is localized to chromatin in postnatal mouse testes

    SciTech Connect

    Eto, Ko; Sonoda, Yoshiyuki; Jin, Yuji; Abe, Shin-ichi

    2010-03-19

    SAP155 is an essential component of the spliceosome and its phosphorylation is required for splicing catalysis, but little is known concerning its expression and regulation during spermatogenesis in postnatal mouse testes. We report that SAP155 is ubiquitously expressed in nuclei of germ and Sertoli cells within the seminiferous tubules of 6- and 35-day postpartum (dpp) testes. Analyses by fractionation of testes revealed that (1) phosphorylated SAP155 was found in the fraction containing nuclear structures at 6 dpp in amounts much larger than that at other ages; (2) non-phosphorylated SAP155 was detected in the fraction containing nucleoplasm; and (3) phosphorylated SAP155 was preferentially associated with chromatin. Our findings suggest that the active spliceosome, containing phosphorylated SAP155, performs pre-mRNA splicing on chromatin concomitant with transcription during testicular development.

  5. Defective minor spliceosome mRNA processing results in isolated familial growth hormone deficiency

    PubMed Central

    Argente, Jesús; Flores, Raquel; Gutiérrez-Arumí, Armand; Verma, Bhupendra; Martos-Moreno, Gabriel Á; Cuscó, Ivon; Oghabian, Ali; Chowen, Julie A; Frilander, Mikko J; Pérez-Jurado, Luis A

    2014-01-01

    The molecular basis of a significant number of cases of isolated growth hormone deficiency remains unknown. We describe three sisters affected with severe isolated growth hormone deficiency and pituitary hypoplasia caused by biallelic mutations in the RNPC3 gene, which codes for a minor spliceosome protein required for U11/U12 small nuclear ribonucleoprotein (snRNP) formation and splicing of U12-type introns. We found anomalies in U11/U12 di-snRNP formation and in splicing of multiple U12-type introns in patient cells. Defective transcripts include preprohormone convertases SPCS2 and SPCS3 and actin-related ARPC5L genes, which are candidates for the somatotroph-restricted dysfunction. The reported novel mechanism for familial growth hormone deficiency demonstrates that general mRNA processing defects of the minor spliceosome can lead to very narrow tissue-specific consequences. Subject Categories Genetics, Gene Therapy ' Genetic Disease; Metabolism PMID:24480542

  6. Crystal structures of a group II intron maturase reveal a missing link in spliceosome evolution

    PubMed Central

    Zhao, Chen; Pyle, Anna Marie

    2016-01-01

    Group II introns are self-splicing ribozymes that are essential in many organisms, and they are hypothesized to share a common evolutionary ancestor with the spliceosome. While structural similarity of RNA components supports this connection, it is of interest to determine whether associated protein factors also share an evolutionary heritage. Here we present the crystal structures of reverse transcriptase (RT) domains from two group II intron encoded proteins (maturases) from Roseburia intestinalis and Eubacterium rectale, obtained at 1.2 Å and 2.1 Å respectively. Their architecture is more similar to the spliceosomal Prp8 RT-like domain than to any other RTs, and they share substantial similarity with flaviviral RNA polymerases. The RT domain itself is sufficient for binding intron RNA with high affinity and specificity, and it is contained within an active RT enzyme. These studies provide a foundation for understanding structure-function relationships within group II intron–maturase complexes. PMID:27136328

  7. Defective minor spliceosome mRNA processing results in isolated familial growth hormone deficiency.

    PubMed

    Argente, Jesús; Flores, Raquel; Gutiérrez-Arumí, Armand; Verma, Bhupendra; Martos-Moreno, Gabriel Á; Cuscó, Ivon; Oghabian, Ali; Chowen, Julie A; Frilander, Mikko J; Pérez-Jurado, Luis A

    2014-03-01

    The molecular basis of a significant number of cases of isolated growth hormone deficiency remains unknown. We describe three sisters affected with severe isolated growth hormone deficiency and pituitary hypoplasia caused by biallelic mutations in the RNPC3 gene, which codes for a minor spliceosome protein required for U11/U12 small nuclear ribonucleoprotein (snRNP) formation and splicing of U12-type introns. We found anomalies in U11/U12 di-snRNP formation and in splicing of multiple U12-type introns in patient cells. Defective transcripts include preprohormone convertases SPCS2 and SPCS3 and actin-related ARPC5L genes, which are candidates for the somatotroph-restricted dysfunction. The reported novel mechanism for familial growth hormone deficiency demonstrates that general mRNA processing defects of the minor spliceosome can lead to very narrow tissue-specific consequences.

  8. The canonical GU dinucleotide at the 5' splice site is recognized by p220 of the U5 snRNP within the spliceosome.

    PubMed Central

    Reyes, J L; Kois, P; Konforti, B B; Konarska, M M

    1996-01-01

    Specific recognition of the 5' splice site (5'SS) by the spliceosome components was studied using a simple in vitro system in which a short 5'SS RNA oligonucleotide specifically induces the assembly of snRNP particles into spliceosome-like complexes and actively participates in a trans-splicing reaction. Short-range cross-liking demonstrates that a U5 snRNP protein component, p220 (the human analogue of the yeast Prp8) specifically interacts with the invariant GU dinucleotide at the 5' end of the intron. The GU:p220 interaction can be detected in the functional splicing complex B. Although p220 has been known to contact several nucleotides around the 5' splice junction, the p220:GU dinucleotide interaction described here is remarkably specific. Consistent with the high conservation of the GU, even minor modifications of this element affect recognition of the 5'SS RNA by p220. Substitution of uridine at the GU with base analogues containing a large methyl or iodo group, but not a smaller flouro group at base position 5, interferes with association of 5'SS RNA with snRNP complexes and their functional participation in splicing. PMID:8608445

  9. Diabetic polyneuropathy, sensory neurons, nuclear structure and spliceosome alterations: a role for CWC22

    PubMed Central

    Kobayashi, Masaki; Chandrasekhar, Ambika; Cheng, Chu; Martinez, Jose A.; Ng, Hilarie; de la Hoz, Cristiane

    2017-01-01

    ABSTRACT Unique deficits in the function of adult sensory neurons as part of their early neurodegeneration might account for progressive polyneuropathy during chronic diabetes mellitus. Here, we provide structural and functional evidence for aberrant pre-mRNA splicing in a chronic type 1 model of experimental diabetic polyneuropathy (DPN). Cajal bodies (CBs), unique nuclear substructures involved in RNA splicing, increased in number in diabetic sensory neurons, but their expected colocalization with survival motor neuron (SMN) proteins was reduced – a mislocalization described in motor neurons of spinal muscular atrophy. Small nuclear ribonucleoprotein particles (snRNPs), also participants in the spliceosome, had abnormal multiple nuclear foci unassociated with CBs, and their associated snRNAs were reduced. CWC22, a key spliceosome protein, was aberrantly upregulated in diabetic dorsal root ganglia (DRG), and impaired neuronal function. CWC22 attenuated sensory neuron plasticity, with knockdown in vitro enhancing their neurite outgrowth. Further, axonal delivery of CWC22 siRNA unilaterally to locally knock down the aberrant protein in diabetic nerves improved aspects of sensory function in diabetic mice. Collectively, our findings identify subtle but significant alterations in spliceosome structure and function, including dysregulated CBs and CWC22 overexpression, in diabetic sensory neurons that offer new ideas regarding diabetic sensory neurodegeneration in polyneuropathy. PMID:28250049

  10. Mutant U2AF1-expressing cells are sensitive to pharmacological modulation of the spliceosome

    PubMed Central

    Shirai, Cara Lunn; White, Brian S.; Tripathi, Manorama; Tapia, Roberto; Ley, James N.; Ndonwi, Matthew; Kim, Sanghyun; Shao, Jin; Carver, Alexa; Saez, Borja; Fulton, Robert S.; Fronick, Catrina; O'Laughlin, Michelle; Lagisetti, Chandraiah; Webb, Thomas R.; Graubert, Timothy A.; Walter, Matthew J.

    2017-01-01

    Somatic mutations in spliceosome genes are detectable in ∼50% of patients with myelodysplastic syndromes (MDS). We hypothesize that cells harbouring spliceosome gene mutations have increased sensitivity to pharmacological perturbation of the spliceosome. We focus on mutant U2AF1 and utilize sudemycin compounds that modulate pre-mRNA splicing. We find that haematopoietic cells expressing mutant U2AF1(S34F), including primary patient cells, have an increased sensitivity to in vitro sudemycin treatment relative to controls. In vivo sudemycin treatment of U2AF1(S34F) transgenic mice alters splicing and reverts haematopoietic progenitor cell expansion induced by mutant U2AF1 expression. The splicing effects of sudemycin and U2AF1(S34F) can be cumulative in cells exposed to both perturbations—drug and mutation—compared with cells exposed to either alone. These cumulative effects may result in downstream phenotypic consequences in sudemycin-treated mutant cells. Taken together, these data suggest a potential for treating haematological cancers harbouring U2AF1 mutations with pre-mRNA splicing modulators like sudemycins. PMID:28067246

  11. Diabetic polyneuropathy, sensory neurons, nuclear structure and spliceosome alterations: a role for CWC22.

    PubMed

    Kobayashi, Masaki; Chandrasekhar, Ambika; Cheng, Chu; Martinez, Jose A; Ng, Hilarie; de la Hoz, Cristiane; Zochodne, Douglas W

    2017-03-01

    Unique deficits in the function of adult sensory neurons as part of their early neurodegeneration might account for progressive polyneuropathy during chronic diabetes mellitus. Here, we provide structural and functional evidence for aberrant pre-mRNA splicing in a chronic type 1 model of experimental diabetic polyneuropathy (DPN). Cajal bodies (CBs), unique nuclear substructures involved in RNA splicing, increased in number in diabetic sensory neurons, but their expected colocalization with survival motor neuron (SMN) proteins was reduced - a mislocalization described in motor neurons of spinal muscular atrophy. Small nuclear ribonucleoprotein particles (snRNPs), also participants in the spliceosome, had abnormal multiple nuclear foci unassociated with CBs, and their associated snRNAs were reduced. CWC22, a key spliceosome protein, was aberrantly upregulated in diabetic dorsal root ganglia (DRG), and impaired neuronal function. CWC22 attenuated sensory neuron plasticity, with knockdown in vitro enhancing their neurite outgrowth. Further, axonal delivery of CWC22 siRNA unilaterally to locally knock down the aberrant protein in diabetic nerves improved aspects of sensory function in diabetic mice. Collectively, our findings identify subtle but significant alterations in spliceosome structure and function, including dysregulated CBs and CWC22 overexpression, in diabetic sensory neurons that offer new ideas regarding diabetic sensory neurodegeneration in polyneuropathy.

  12. Structure of a yeast catalytic step I spliceosome at 3.4 Å resolution.

    PubMed

    Wan, Ruixue; Yan, Chuangye; Bai, Rui; Huang, Gaoxingyu; Shi, Yigong

    2016-08-26

    Each cycle of pre-messenger RNA splicing, carried out by the spliceosome, comprises two sequential transesterification reactions, which result in the removal of an intron and the joining of two exons. Here we report an atomic structure of a catalytic step I spliceosome (known as the C complex) from Saccharomyces cerevisiae, as determined by cryo-electron microscopy at an average resolution of 3.4 angstroms. In the structure, the 2'-OH of the invariant adenine nucleotide in the branch point sequence (BPS) is covalently joined to the phosphate at the 5' end of the 5' splice site (5'SS), forming an intron lariat. The freed 5' exon remains anchored to loop I of U5 small nuclear RNA (snRNA), and the 5'SS and BPS of the intron form duplexes with conserved U6 and U2 snRNA sequences, respectively. Specific placement of these RNA elements at the catalytic cavity of Prp8 is stabilized by 15 protein components, including Snu114 and the splicing factors Cwc21, Cwc22, Cwc25, and Yju2. These features, representing the conformation of the spliceosome after the first-step reaction, predict structural changes that are needed for the execution of the second-step transesterification reaction.

  13. Anomalous Flavor U(1)_X for Everything

    SciTech Connect

    Dreiner, Herbi K.; Murayama, Hitoshi; Thormeier, Marc

    2003-12-01

    We present an ambitious model of flavor, based on an anomalous U(1)_X gauge symmetry with one flavon, only two right-handed neutrinos and only two mass scales: M_{grav} and m_{3/2}. In particular, there are no new scales introduced for right-handed neutrino masses. The X-charges of the matter fields are such that R-parity is conserved exactly, higher-dimensional operators are sufficiently suppressed to guarantee a proton lifetime in agreement with experiment, and the phenomenology is viable for quarks, charged leptons, as well as neutrinos. In our model one of the three light neutrinos automatically is massless. The price we have to pay for this very successful model are highly fractional X-charges which can likely be improved with less restrictive phenomenological ansatze for mass matrices.

  14. Vought O3U-1 'Corsair'

    NASA Technical Reports Server (NTRS)

    1931-01-01

    Vought O3U-1 'Corsair' in Full-Scale Tunnel (FST). This photograph was taken in September 1931 after the balance had been enclosed. This aircraft was also used earlier during the summer for preliminary tests in the FST and as the subject of some of the first publicity photographs taken of FST operations. NACA engineers checked the lift and drag characteristics of several aircraft with the results of earlier flight tests. Smith DeFrance concluded NACA TR No. 459, 'The agreement that has been obtained between the flight and full-scale tunnel results, together with the consistent manner in which measurements can be repeated when check tests are made, has demonstrated the accuracy and value of the equipment for aeronautical research.' (p. 298)

  15. Tetramers reveal IL-17-secreting CD4+ T cells that are specific for U1-70 in lupus and mixed connective tissue disease.

    PubMed

    Kattah, Nicole H; Newell, Evan W; Jarrell, Justin Ansel; Chu, Alvina D; Xie, Jianming; Kattah, Michael G; Goldberger, Ofir; Ye, Jessica; Chakravarty, Eliza F; Davis, Mark M; Utz, Paul J

    2015-03-10

    Antigen-specific CD4(+) T cells are implicated in the autoimmune disease systemic lupus erythematosus (SLE), but little is known about the peptide antigens that they recognize and their precise function in disease. We generated a series of MHC class II tetramers of I-E(k)-containing peptides from the spliceosomal protein U1-70 that specifically stain distinct CD4(+) T-cell populations in MRL/lpr mice. The T-cell populations recognize an epitope differing only by the presence or absence of a single phosphate residue at position serine(140). The frequency of CD4(+) T cells specific for U1-70(131-150):I-E(k) (without phosphorylation) correlates with disease severity and anti-U1-70 autoantibody production. These T cells also express RORγt and produce IL-17A. Furthermore, the U1-70-specific CD4(+) T cells that produce IL-17A are detected in a subset of patients with SLE and are significantly increased in patients with mixed connective tissue disease. These studies provide tools for studying antigen-specific CD4(+) T cells in lupus, and demonstrate an antigen-specific source of IL-17A in autoimmune disease.

  16. The 35S U5 snRNP Is Generated from the Activated Spliceosome during In vitro Splicing

    PubMed Central

    2015-01-01

    Primary gene transcripts of eukaryotes contain introns, which are removed during processing by splicing machinery. Biochemical studies In vitro have identified a specific pathway in which introns are recognised and spliced out. This occurs by progressive formation of spliceosomal complexes designated as E, A, B, and C. The composition and structure of these spliceosomal conformations have been characterised in many detail. In contrast, transitions between the complexes and the intermediates of these reactions are currently less clear. We have previously isolated a novel 35S U5 snRNP from HeLa nuclear extracts. The protein composition of this particle differed from the canonical 20S U5 snRNPs but was remarkably similar to the activated B* spliceosomes. Based on this observation we have proposed a hypothesis that 35S U5 snRNPs represent a dissociation product of the spliceosome after both transesterification reactions are completed. Here we provide experimental evidence that 35S U5 snRNPs are generated from the activated B* spliceosomes during In vitro splicing. PMID:26020933

  17. LETTER TO THE EDITOR: U(1) × U(1) × U(1) symmetry of the Kimura 3ST model and phylogenetic branching processes

    NASA Astrophysics Data System (ADS)

    Bashford, J. D.; Jarvis, P. D.; Sumner, J. G.; Steel, M. A.

    2004-02-01

    An analysis of the Kimura 3ST model of DNA sequence evolution is given on the basis of its continuous Lie symmetries. The rate matrix commutes with a U(1) × U(1) × U(1) phase subgroup of the group GL(4) of 4 × 4 invertible complex matrices acting on a linear space spanned by the four nucleic acid base letters. The diagonal 'branching operator' representing speciation is defined, and shown to intertwine the U(1) × U(1) × U(1) action. Using the intertwining property, a general formula for the probability density on the leaves of a binary tree under the Kimura model is derived, which is shown to be equivalent to established phylogenetic spectral transform methods.

  18. Novel Introner-Like Elements in fungi Are Involved in Parallel Gains of Spliceosomal Introns

    PubMed Central

    Crous, Pedro W.; de Wit, Pierre J. G. M.; van der Burgt, Ate

    2015-01-01

    Spliceosomal introns are key components of the eukaryotic gene structure. Although they contributed to the emergence of eukaryotes, their origin remains elusive. In fungi, they might originate from the multiplication of invasive introns named Introner-Like Elements (ILEs). However, so far ILEs have been observed in six fungal species only, including Fulvia fulva and Dothistroma septosporum (Dothideomycetes), arguing against ILE insertion as a general mechanism for intron gain. Here, we identified novel ILEs in eight additional fungal species that are phylogenetically related to F. fulva and D. septosporum using PCR amplification with primers derived from previously identified ILEs. The ILE content appeared unique to each species, suggesting independent multiplication events. Interestingly, we identified four genes each containing two gained ILEs. By analysing intron positions in orthologues of these four genes in Ascomycota, we found that three ILEs had inserted within a 15 bp window that contains regular spliceosomal introns in other fungal species. These three positions are not the result of intron sliding because ILEs are newly gained introns. Furthermore, the alternative hypothesis of an inferred ancestral gain followed by independent losses contradicts the observed degeneration of ILEs. These observations clearly indicate three parallel intron gains in four genes that were randomly identified. Our findings suggest that parallel intron gain is a phenomenon that has been highly underestimated in ILE-containing fungi, and likely in the whole fungal kingdom. PMID:26046656

  19. A Shotgun Proteomics Approach Reveals a New Toxic Role for Alzheimer's Disease Aβ Peptide: Spliceosome Impairment.

    PubMed

    Nuzzo, Domenico; Inguglia, Luigi; Walters, Jessica; Picone, Pasquale; Di Carlo, Marta

    2017-03-06

    Proteomic changes have been described in many neurodegenerative diseases, including Alzheimer's disease (AD). However, the early events in the onset of the pathology are yet to be fully elucidated. A cell model system in which LAN5 neuroblastoma cells were incubated for a short time with a recombinant form of Aβ42 was utilized. Proteins extracted from these cells were subjected to shotgun proteomics analysis by LTQ-Orbitrap-MS followed by label-free quantitation. By bioinformatics tools we found that the most significant of those found to be up-regulated were related to cytoskeletal dynamics (Rho related) and membrane-related processes. The most significant of the down-regulated proteins were hnRNP-related. In particular, hnRNPs involved in ribosomal biogenesis and in splicing were down-regulated. The latter of these processes stood out as it was highlighted ubiquitously and with the highest significance in the results of every analysis. Furthermore, our findings revealed down-regulation at every stage of the splicing process through down-regulation of every subunit of the spliceosome. Dysregulation of the spliceosome was also confirmed using a Western blot. In conclusion, these data suggest dysregulation of the proteins and processes identified as early events in pathogenesis of AD following Aβ accumulation.

  20. Cross talk between spliceosome and microprocessor defines the fate of pre-mRNA.

    PubMed

    Mattioli, Chiara; Pianigiani, Giulia; Pagani, Franco

    2014-01-01

    The spliceosome and the microprocessor complex (MPC) are two important processing machineries that act on precursor (pre)-mRNA. Both cleave the pre-mRNA to generate spliced mature transcripts and microRNAs (miRNAs), respectively. While spliceosomes identify in a complex manner correct splice sites, MPCs typically target RNA hairpins (pri-miRNA hairpins). In addition, pre-mRNA transcripts can contain pri-miRNA-like hairpins that are cleaved by the MPC without generating miRNAs. Recent evidence indicates that the position of hairpins on pre-mRNA, their distance from splice sites, and the relative efficiency of cropping and splicing contribute to determine the fate of a pre-mRNA. Depending on these factors, a pre-mRNA can be preferentially used to generate a miRNA, a constitutively or even an alternative spliced transcript. For example, competition between splicing and cropping on splice-site-overlapping miRNAs (SO miRNAs) results in alternative spliced isoforms and influences miRNA biogenesis. In several cases, the outcome of a pre-mRNA transcript and its final handling as miRNA or mRNA substrate can be frequently closely connected to the functional relationships between diverse pre-mRNA processing events. These events are influenced by both gene context and physiopathological conditions.

  1. Spliceosome SNRNP200 Promotes Viral RNA Sensing and IRF3 Activation of Antiviral Response

    PubMed Central

    Tremblay, Nicolas; Baril, Martin; Chatel-Chaix, Laurent; Es-Saad, Salwa; Park, Alex Young; Koenekoop, Robert K.; Lamarre, Daniel

    2016-01-01

    Spliceosomal SNRNP200 is a Ski2-like RNA helicase that is associated with retinitis pigmentosa 33 (RP33). Here we found that SNRNP200 promotes viral RNA sensing and IRF3 activation through the ability of its amino-terminal Sec63 domain (Sec63-1) to bind RNA and to interact with TBK1. We show that SNRNP200 relocalizes into TBK1-containing cytoplasmic structures upon infection, in contrast to the RP33-associated S1087L mutant, which is also unable to rescue antiviral response of SNRNP200 knockdown cells. This functional rescue correlates with the Sec63-1-mediated binding of viral RNA. The hindered IFN-β production of knockdown cells was further confirmed in peripheral blood cells of RP33 patients bearing missense mutation in SNRNP200 upon infection with Sendai virus (SeV). This work identifies a novel immunoregulatory role of the spliceosomal SNRNP200 helicase as an RNA sensor and TBK1 adaptor for the activation of IRF3-mediated antiviral innate response. PMID:27454487

  2. The Dengue Virus NS5 Protein Intrudes in the Cellular Spliceosome and Modulates Splicing

    PubMed Central

    Shah, Priya; Pozzi, Berta; Gebhard, Leopoldo G.; Mammi, Pablo; Yanovsky, Marcelo J.; Andino, Raul; Krogan, Nevan; Srebrow, Anabella; Gamarnik, Andrea V.

    2016-01-01

    Dengue virus NS5 protein plays multiple functions in the cytoplasm of infected cells, enabling viral RNA replication and counteracting host antiviral responses. Here, we demonstrate a novel function of NS5 in the nucleus where it interferes with cellular splicing. Using global proteomic analysis of infected cells together with functional studies, we found that NS5 binds spliceosome complexes and modulates endogenous splicing as well as minigene-derived alternative splicing patterns. In particular, we show that NS5 alone, or in the context of viral infection, interacts with core components of the U5 snRNP particle, CD2BP2 and DDX23, alters the inclusion/exclusion ratio of alternative splicing events, and changes mRNA isoform abundance of known antiviral factors. Interestingly, a genome wide transcriptome analysis, using recently developed bioinformatics tools, revealed an increase of intron retention upon dengue virus infection, and viral replication was improved by silencing specific U5 components. Different mechanistic studies indicate that binding of NS5 to the spliceosome reduces the efficiency of pre-mRNA processing, independently of NS5 enzymatic activities. We propose that NS5 binding to U5 snRNP proteins hijacks the splicing machinery resulting in a less restrictive environment for viral replication. PMID:27575636

  3. Reprogramming the Dynamin 2 mRNA by Spliceosome-mediated RNA Trans-splicing

    PubMed Central

    Trochet, Delphine; Prudhon, Bernard; Jollet, Arnaud; Lorain, Stéphanie; Bitoun, Marc

    2016-01-01

    Dynamin 2 (DNM2) is a large GTPase, ubiquitously expressed, involved in membrane trafficking and regulation of actin and microtubule cytoskeletons. DNM2 mutations cause autosomal dominant centronuclear myopathy which is a rare congenital myopathy characterized by skeletal muscle weakness and histopathological features including nuclear centralization in absence of regeneration. No curative treatment is currently available for the DNM2-related autosomal dominant centronuclear myopathy. In order to develop therapeutic strategy, we evaluated here the potential of Spliceosome-Mediated RNA Trans-splicing technology to reprogram the Dnm2-mRNA in vitro and in vivo in mice. We show that classical 3′-trans-splicing strategy cannot be considered as accurate therapeutic strategy regarding toxicity of the pre-trans-splicing molecules leading to low rate of trans-splicing in vivo. Thus, we tested alternative strategies devoted to prevent this toxicity and enhance frequency of trans-splicing events. We succeeded to overcome the toxicity through a 5′-trans-splicing strategy which also allows detection of trans-splicing events at mRNA and protein levels in vitro and in vivo. These results suggest that the Spliceosome-Mediated RNA Trans-splicing strategy may be used to reprogram mutated Dnm2-mRNA but highlight the potential toxicity linked to the molecular tools which have to be carefully investigated during preclinical development. PMID:27623444

  4. Novel Introner-Like Elements in fungi Are Involved in Parallel Gains of Spliceosomal Introns.

    PubMed

    Collemare, Jérôme; Beenen, Henriek G; Crous, Pedro W; de Wit, Pierre J G M; van der Burgt, Ate

    2015-01-01

    Spliceosomal introns are key components of the eukaryotic gene structure. Although they contributed to the emergence of eukaryotes, their origin remains elusive. In fungi, they might originate from the multiplication of invasive introns named Introner-Like Elements (ILEs). However, so far ILEs have been observed in six fungal species only, including Fulvia fulva and Dothistroma septosporum (Dothideomycetes), arguing against ILE insertion as a general mechanism for intron gain. Here, we identified novel ILEs in eight additional fungal species that are phylogenetically related to F. fulva and D. septosporum using PCR amplification with primers derived from previously identified ILEs. The ILE content appeared unique to each species, suggesting independent multiplication events. Interestingly, we identified four genes each containing two gained ILEs. By analysing intron positions in orthologues of these four genes in Ascomycota, we found that three ILEs had inserted within a 15 bp window that contains regular spliceosomal introns in other fungal species. These three positions are not the result of intron sliding because ILEs are newly gained introns. Furthermore, the alternative hypothesis of an inferred ancestral gain followed by independent losses contradicts the observed degeneration of ILEs. These observations clearly indicate three parallel intron gains in four genes that were randomly identified. Our findings suggest that parallel intron gain is a phenomenon that has been highly underestimated in ILE-containing fungi, and likely in the whole fungal kingdom.

  5. The network organization of protein interactions in the spliceosome is reproduced by the simple rules of food-web models

    PubMed Central

    Pires, Mathias M.; Cantor, Maurício; Guimarães, Paulo R.; de Aguiar, Marcus A. M.; dos Reis, Sérgio F.; Coltri, Patricia P.

    2015-01-01

    The network structure of biological systems provides information on the underlying processes shaping their organization and dynamics. Here we examined the structure of the network depicting protein interactions within the spliceosome, the macromolecular complex responsible for splicing in eukaryotic cells. We show the interactions of less connected spliceosome proteins are nested subsets of the connections of the highly connected proteins. At the same time, the network has a modular structure with groups of proteins sharing similar interaction patterns. We then investigated the role of affinity and specificity in shaping the spliceosome network by adapting a probabilistic model originally designed to reproduce food webs. This food-web model was as successful in reproducing the structure of protein interactions as it is in reproducing interactions among species. The good performance of the model suggests affinity and specificity, partially determined by protein size and the timing of association to the complex, may be determining network structure. Moreover, because network models allow building ensembles of realistic networks while encompassing uncertainty they can be useful to examine the dynamics and vulnerability of intracelullar processes. Unraveling the mechanisms organizing the spliceosome interactions is important to characterize the role of individual proteins on splicing catalysis and regulation. PMID:26443080

  6. Disrupted auto-regulation of the spliceosomal gene SNRPB causes cerebro-costo-mandibular syndrome.

    PubMed

    Lynch, Danielle C; Revil, Timothée; Schwartzentruber, Jeremy; Bhoj, Elizabeth J; Innes, A Micheil; Lamont, Ryan E; Lemire, Edmond G; Chodirker, Bernard N; Taylor, Juliet P; Zackai, Elaine H; McLeod, D Ross; Kirk, Edwin P; Hoover-Fong, Julie; Fleming, Leah; Savarirayan, Ravi; Majewski, Jacek; Jerome-Majewska, Loydie A; Parboosingh, Jillian S; Bernier, Francois P

    2014-07-22

    Elucidating the function of highly conserved regulatory sequences is a significant challenge in genomics today. Certain intragenic highly conserved elements have been associated with regulating levels of core components of the spliceosome and alternative splicing of downstream genes. Here we identify mutations in one such element, a regulatory alternative exon of SNRPB as the cause of cerebro-costo-mandibular syndrome. This exon contains a premature termination codon that triggers nonsense-mediated mRNA decay when included in the transcript. These mutations cause increased inclusion of the alternative exon and decreased overall expression of SNRPB. We provide evidence for the functional importance of this conserved intragenic element in the regulation of alternative splicing and development, and suggest that the evolution of such a regulatory mechanism has contributed to the complexity of mammalian development.

  7. Assembly and disassembly of spliceosomes along a specific pre-messenger RNP fiber.

    PubMed

    Kiseleva, E; Wurtz, T; Visa, N; Daneholt, B

    1994-12-15

    Transcriptionally active Balbiani ring (BR) genes in the salivary glands of the dipteran Chironomus tentans were studied by immunoelectron microscopy to establish the distribution of spliceosome components along a specific pre-messenger ribonucleoprotein (pre-mRNP) fiber. The BR genes are 35-40 kb in size with three introns close to the 5' end and one close to the 3' end; a very large middle portion lacks introns. As a rule the 5' introns are spliced concomitant with transcription in the promoter proximal third of the gene, while the 3' intron is spliced post-transcriptionally. The BR genes with growing pre-mRNPs were visualized in situ, while completed and released pre-mRNPs were isolated from the nucleoplasm and studied unfolded on a grid surface. An anti-snRNP antibody (Y12) bound mainly to the promoter proximal third of the BR gene (86%) and only to a minor extent to the middle and distal thirds (7 and 7% respectively). An antibody to an hnRNP protein reacted with the proximal, middle and distal regions to an increasing extent (17, 38 and 45% respectively), reflecting the increase in size of the growing transcription product. In the nucleoplasmic pre-mRNP particle only one end of the RNP fiber was labeled by Y 12, presumably the 3' end; the anti-hnRNP antibody decorated the entire RNP fiber. Thus, the snRNPs do not associate along the whole pre-mRNP fiber but rather bind to the 5' and 3' ends, i.e. the regions containing the introns. The results also imply that the spliceosomes both assemble and disassemble rapidly on the pre-mRNP fiber.

  8. Mapping epitopes of U1-70K autoantibodies at single-amino acid resolution

    PubMed Central

    Haddon, David James; Jarrell, Justin Ansel; Diep, Vivian K.; Wand, Hannah E.; Price, Jordan V.; Tangsombatvisit, Stephanie; Credo, Grace M.; Mackey, Sally; Dekker, Cornelia L.; Baechler, Emily C.; Liu, Chih Long; Varma, Madoo; Utz, Paul J.

    2016-01-01

    The mechanisms underlying development of ribonucleoprotein (RNP) autoantibodies are unclear. The U1-70K protein is the predominant target of RNP autoantibodies, and the RNA binding domain has been shown to be the immunodominant autoantigenic region of U1-70K, although the specific epitopes are not known. To precisely map U1-70K epitopes, we developed silicon-based peptide microarrays with >5700 features, corresponding to 843 unique peptides derived from the U1-70K protein. The microarrays feature overlapping peptides, with single-amino acid resolution in length and location, spanning amino acids 110–170 within the U1-70K RNA binding domain. We evaluated the serum IgG of a cohort of patients with systemic lupus erythematosus (SLE; n = 26) using the microarrays, and identified multiple reactive epitopes, including peptides 116–121 and 143–148. Indirect peptide ELISA analysis of the sera of patients with SLE (n = 88) revealed that ~14% of patients had serum IgG reactivity to 116–121, while reactivity to 143–148 appeared to be limited to a single patient. SLE patients with serum reactivity to 116–121 had significantly lower SLE Disease Activity Index (SLEDAI) scores at the time of sampling, compared to non-reactive patients. Minimal reactivity to the peptides was observed in the sera of healthy controls (n = 92). Competitive ELISA showed antibodies to 116–121 bind a common epitope in U1-70K (68–72) and the matrix protein M1 of human influenza B viruses. Institutional Review Boards approved this study. Knowledge of the precise epitopes of U1-70K autoantibodies may provide insight into the mechanisms of development of anti-RNP, identify potential clinical biomarkers and inform ongoing clinical trails of peptide-based therapeutics. PMID:26333287

  9. The target of the DEAH-box NTP triphosphatase Prp43 in Saccharomyces cerevisiae spliceosomes is the U2 snRNP-intron interaction

    PubMed Central

    Fourmann, Jean-Baptiste; Dybkov, Olexandr; Agafonov, Dmitry E; Tauchert, Marcel J; Urlaub, Henning; Ficner, Ralf; Fabrizio, Patrizia; Lührmann, Reinhard

    2016-01-01

    The DEAH-box NTPase Prp43 and its cofactors Ntr1 and Ntr2 form the NTR complex and are required for disassembling intron-lariat spliceosomes (ILS) and defective earlier spliceosomes. However, the Prp43 binding site in the spliceosome and its target(s) are unknown. We show that Prp43 fused to Ntr1's G-patch motif (Prp43_Ntr1GP) is as efficient as the NTR in ILS disassembly, yielding identical dissociation products and recognizing its natural ILS target even in the absence of Ntr1’s C-terminal-domain (CTD) and Ntr2. Unlike the NTR, Prp43_Ntr1GP disassembles earlier spliceosomal complexes (A, B, Bact), indicating that Ntr2/Ntr1-CTD prevents NTR from disrupting properly assembled spliceosomes other than the ILS. The U2 snRNP-intron interaction is disrupted in all complexes by Prp43_Ntr1GP, and in the spliceosome contacts U2 proteins and the pre-mRNA, indicating that the U2 snRNP-intron interaction is Prp43’s major target. DOI: http://dx.doi.org/10.7554/eLife.15564.001 PMID:27115347

  10. Involvement of the spliceosomal U4 small nuclear RNA in heterochromatic gene silencing at fission yeast centromeres.

    PubMed

    Chinen, Madoka; Morita, Misato; Fukumura, Kazuhiro; Tani, Tokio

    2010-02-19

    prp13-1 is one of the mutants isolated in a screen for defective pre-mRNA splicing at a nonpermissive temperature in fission yeast Schizosaccharomyces pombe. We cloned the prp13(+) gene and found that it encodes U4 small nuclear RNA (snRNA) involved in the assembly of the spliceosome. The prp13-1 mutant produced elongated cells, a phenotype similar to cell division cycle mutants, and displays a high incidence of lagging chromosomes on anaphase spindles. The mutant is hypersensitive to the microtubule-destabilizing drug thiabendazole, supporting that prp13-1 has a defect in chromosomal segregation. We found that the prp13-1 mutation resulted in expression of the ura4(+) gene inserted in the pericentromeric heterochromatin region and reduced recruitment of the heterochromatin protein Swi6p to that region, indicating defects in the formation of pericentromeric heterochromatin, which is essential for the segregation of chromosomes, in prp13-1. The formation of centromeric heterochromatin is induced by the RNA interference (RNAi) system in S. pombe. In prp13-1, the processing of centromeric noncoding RNAs to siRNAs, which direct the heterochromatin formation, was impaired and unprocessed noncoding RNAs were accumulated. These results suggest that U4 snRNA is required for the RNAi-directed heterochromatic gene silencing at the centromeres. In relation to the linkage between the spliceosomal U4 snRNA and the RNAi-directed formation of heterochromatin, we identified a mRNA-type intron in the centromeric noncoding RNAs. We propose a model in which the assembly of the spliceosome or a sub-spliceosome complex on the intron-containing centromeric noncoding RNAs facilitates the RNAi-directed formation of heterochromatin at centromeres, through interaction with the RNA-directed RNA polymerase complex.

  11. Involvement of the Spliceosomal U4 Small Nuclear RNA in Heterochromatic Gene Silencing at Fission Yeast Centromeres*

    PubMed Central

    Chinen, Madoka; Morita, Misato; Fukumura, Kazuhiro; Tani, Tokio

    2010-01-01

    prp13-1 is one of the mutants isolated in a screen for defective pre-mRNA splicing at a nonpermissive temperature in fission yeast Schizosaccharomyces pombe. We cloned the prp13+ gene and found that it encodes U4 small nuclear RNA (snRNA) involved in the assembly of the spliceosome. The prp13-1 mutant produced elongated cells, a phenotype similar to cell division cycle mutants, and displays a high incidence of lagging chromosomes on anaphase spindles. The mutant is hypersensitive to the microtubule-destabilizing drug thiabendazole, supporting that prp13-1 has a defect in chromosomal segregation. We found that the prp13-1 mutation resulted in expression of the ura4+ gene inserted in the pericentromeric heterochromatin region and reduced recruitment of the heterochromatin protein Swi6p to that region, indicating defects in the formation of pericentromeric heterochromatin, which is essential for the segregation of chromosomes, in prp13-1. The formation of centromeric heterochromatin is induced by the RNA interference (RNAi) system in S. pombe. In prp13-1, the processing of centromeric noncoding RNAs to siRNAs, which direct the heterochromatin formation, was impaired and unprocessed noncoding RNAs were accumulated. These results suggest that U4 snRNA is required for the RNAi-directed heterochromatic gene silencing at the centromeres. In relation to the linkage between the spliceosomal U4 snRNA and the RNAi-directed formation of heterochromatin, we identified a mRNA-type intron in the centromeric noncoding RNAs. We propose a model in which the assembly of the spliceosome or a sub-spliceosome complex on the intron-containing centromeric noncoding RNAs facilitates the RNAi-directed formation of heterochromatin at centromeres, through interaction with the RNA-directed RNA polymerase complex. PMID:20018856

  12. Underground storage tank 291-D1U1: Closure plan

    SciTech Connect

    Mancieri, S.; Giuntoli, N.

    1993-09-01

    The 291-D1U1 tank system was installed in 1983 on the north side of Building 291. It supplies diesel fuel to the Building 291 emergency generator and air compressor. The emergency generator and air compressor are located southwest and southeast, respectively, of the tank (see Appendix B, Figure 2). The tank system consists of a single-walled, 2,000- gallon, fiberglass tank and a fuel pump system, fill pipe, vent pipe, electrical conduit, and fuel supply and return piping. The area to be excavated is paved with asphalt and concrete. It is not known whether a concrete anchor pad is associated with this tank. Additionally, this closure plan assumes that the diesel tank is below the fill pad. The emergency generator and air compressor for Building 291 and its associated UST, 291-D1U1, are currently in use. The generator and air compressor will be supplied by a temporary above-ground fuel tank prior to the removal of 291-D1U1. An above-ground fuel tank will be installed as a permanent replacement for 291-D1U1. The system was registered with the State Water Resources Control Board on June 27, 1984, as 291-41D and has subsequently been renamed 291-D1U1. Figure 1 (see Appendix B) shows the location of the 291-D1U1 tank system in relation to the Lawrence Livermore National Laboratory (LLNL). Figure 2 (see Appendix B) shows the 291-D1U1 tank system in relation to Building 291. Figure 3 (see Appendix B) shows a plan view of the 291-D1U1 tank system.

  13. U(1) axial charge in the chiral limit

    NASA Astrophysics Data System (ADS)

    Ji, Xiangdong

    1990-07-01

    The U(1) axial-vector form factor is studied using an unsubtracted dispersion relation. The associated axial charge is shown to be analytic in quark masses in the chiral limit although individual terms in the Cheng-Li separation exhibit large isospin and flavor-SU(3) symmetry breaking. A new separation of the U(1) axial charge is proposed, based on the wave functions of the physical states entering in the spectral density.

  14. Dirac-fermionic dark matter in U(1)X models

    NASA Astrophysics Data System (ADS)

    Alves, Alexandre; Berlin, Asher; Profumo, Stefano; Queiroz, Farinaldo S.

    2015-10-01

    We study a number of U(1)X models featuring a Dirac fermion dark matter particle. We perform a comprehensive analysis which includes the study of corrections to the muon magnetic moment, dilepton searches with LHC data, as well as direct and indirect dark matter detection constraints. We consider four different coupling structures, namely U(1) B-L , U(1) d-u , U(1)universal, and U{(1)}_{10+overline{5}} , all motivated by compelling extensions to the standard model. We outline the viable and excluded regions of parameter space using a large set of probes. Our key findings are that (i) the combination of direct detection and collider constraints rule out dark matter particle masses lighter than ˜ 1 TeV, unless rather suppressed Z '-fermion couplings exist, and that (ii) for several of the models under consideration, collider constraints rule out Z ' masses up to ˜ 3 TeV. Lastly, we show that we can accommodate the recent Diboson excess reported by ATLAS collaboration within the U(1) d- u model.

  15. 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.

  16. SART3-Dependent Accumulation of Incomplete Spliceosomal snRNPs in Cajal Bodies.

    PubMed

    Novotný, Ivan; Malinová, Anna; Stejskalová, Eva; Matějů, Daniel; Klimešová, Klára; Roithová, Adriana; Švéda, Martin; Knejzlík, Zdeněk; Staněk, David

    2015-01-13

    Cajal bodies (CBs) are evolutionarily conserved nuclear structures involved in the metabolism of spliceosomal small nuclear ribonucleoprotein particles (snRNPs). CBs are not present in all cell types, and the trigger for their formation is not yet known. Here, we depleted cells of factors required for the final steps of snRNP assembly and assayed for the presence of stalled intermediates in CBs. We show that depletion induces formation of CBs in cells that normally lack these nuclear compartments, suggesting that CB nucleation is triggered by an imbalance in snRNP assembly. Accumulation of stalled intermediates in CBs depends on the di-snRNP assembly factor SART3. SART3 is required for both the induction of CB formation as well as the tethering of incomplete snRNPs to coilin, the CB scaffolding protein. We propose a model wherein SART3 monitors tri-snRNP assembly and sequesters incomplete particles in CBs, thereby allowing cells to maintain a homeostatic balance of mature snRNPs in the nucleoplasm.

  17. Evidence for a group II intron-like catalytic triplex in the spliceosome

    PubMed Central

    Piccirilli, Joseph A.; Staley, Jonathan P.

    2014-01-01

    To catalyze pre-mRNA splicing, U6 snRNA positions two metals that interact directly with the scissile phosphates. The U6 metal ligands correspond stereospecifically to metal ligands within the catalytic domain V of a group II self-splicing intron. In domain V, the ligands are organized by base-triple interactions, which also juxtapose the 3′ splice site with the catalytic metals. However, in the spliceosome, the mechanism for organizing catalytic metals and recruiting the substrate has remained unclear. Here we show by genetics, crosslinking, and biochemistry in yeast that analogous triples form in U6 and promote catalytic metal binding and both chemical steps of splicing. Because the triples include an element that defines the 5′ splice site, the triples also provide a mechanism for juxtaposing the pre-mRNA substrate with the catalytic metals. Our data indicate that U6 adopts a group II intron-like tertiary conformation to catalyze splicing. PMID:24747940

  18. Tempo and mode of spliceosomal intron evolution in actin of foraminifera.

    PubMed

    Flakowski, Jérôme; Bolivar, Ignacio; Fahrni, José; Pawlowski, Jan

    2006-07-01

    Spliceosomal introns are present in almost all eukaryotic genes, yet little is known about their origin and turnover in the majority of eukaryotic phyla. There is no agreement whether most introns are ancestral and have been lost in some lineage or have been gained recently. We addressed this question by analyzing the spatial and temporal distribution of introns in actins of foraminifera, a group of testate protists whose exceptionally rich fossil record permits the calibration of molecular phylogenies to date intron origins. We identified 24 introns dispersed along the sequence of two foraminiferan actin paralogues and actin deviating proteins, an unconventional type of fast-evolving actin found in some foraminifera. Comparison of intron positions indicates that 20 of 24 introns are specific to foraminifera. Four introns shared between foraminifera and other eukaryotes were interpreted as parallel gains because they have been found only in single species belonging to phylogenetically distinctive lineages. Moreover, additional recent intron gain due to the transfer between the actin paralogues was observed in two cultured species. Based on a relaxed molecular clock timescale, we conclude that intron gains in actin took place throughout the evolution of foraminifera, with the oldest introns inserted between 550 and 500 million years ago and the youngest ones acquired less than 100 million years ago.

  19. Unique genome of dicyemid mesozoan: highly shortened spliceosomal introns in conservative exon/intron structure.

    PubMed

    Ogino, Kazutoyo; Tsuneki, Kazuhiko; Furuya, Hidetaka

    2010-01-01

    Dicyemids are enigmatic endoparasites, or endosymbionts, living in the renal sac of benthic cephalopod molluscs. The body of dicyemids consists of only 9-41 cells, with neither extracellular matrices nor differentiated tissues. Due to the unusually simple body organization, dicyemids have long been the subject of phylogenetic controversy. Molecular evidences suggest dicyemids are lophotrochozoans that have secondarily lost many morphological characters. We studied 40 genes of the dicyemid Dicyema japonicum and found that their spliceosomal introns are very short (mean length=26 bp). This size was shorter than that of introns of animals, such as Fugu rubripes and Oikopleura dioica which possess compact genome and introns. In the intron size, the dicyemid was nearly equal to the chlorarachniophyte Bigelowiella natans nucleomorph (18-21 bp) which has the shortest introns of any known eukaryote. Despite the short introns, the intron density (5.3 introns/gene) of the dicyemid is similar to that in model invertebrates. In addition, the exon/intron structure of the dicyemid is more similar to vertebrates than to the model invertebrates. These results suggest that the positions of the introns are possibly conserved under functional constraints.

  20. Endothelial cell-binding activity of anti-U1-ribonucleoprotein antibodies in patients with connective tissue diseases

    PubMed Central

    Okawa-Takatsuji, M; Aotsuka, S; Uwatoko, S; Takaono, M; Iwasaki, K; Kinoshita, M; Sumiya, M

    2001-01-01

    In order to elucidate the immunological properties of anti-U1-ribonucleoprotein (RNP) antibody, one of the autoantibodies detected in patients with connective tissue diseases (CTDs), we tested the endothelial cell-binding by anti-U1-RNP antibodies and epitopes on human pulmonary artery endothelial cells (HPAECs) to which the autoantibody bound. IgG fractions positive for anti-U1-RNP from patients with CTDs bound to the HPAECs. Furthermore, intact and F(ab′)2 IgG anti-U1-RNP purified by affinity chromatography also bound to endothelial cells. The binding activity of IgG fractions positive for anti-U1-RNP to the endothelial cells could be effectively absorbed by U1-RNP-Sepharose. An immunoblotting assay of purified IgG anti-U1-RNP antibodies showed that these antibodies could bind to various membrane proteins of NP40-treated HPAECs such as 68, 48, 43, 38, 33, 29, 28 and 24 kDa. Some bands, 68, 33, 28 and 24 kDa, seemed to correspond to components of U1-RNP, i.e. 68 kDa, A, B′ and C peptides, respectively. We confirmed that the anti-U1-RNP antibody from patients with CTDs can directly recognize a variety of antigens on the endothelial surface of the pulmonary artery, including the components of U1-RNP or other unknown polypeptides. These results suggest that binding to pulmonary artery endothelial cells of this autoantibody may be one of the triggers of endothelial cell inflammation in CTDs. PMID:11703381

  1. On the Partical Conservation of the U(1) Current

    NASA Astrophysics Data System (ADS)

    Kawarabayashi, K.; Ohta, N.

    1981-11-01

    Recently proposed partial conservation of the U(1) current(PCU1C) is applied to estimate the decay rates of various OZIforbidden processes. The results obtained are in good agreement withexperiments and thus indicate the important role played by the U(1)axial-vector anomaly in these decay processes. Octet Jp = (1/2)+ baryons are next introduced into this scheme and low energy theorems related to the θ dependence of the matrix elements are investigated. Physical consequences of non-zero θ (strong CP-violation) are also discussed with the help of the PCU1C. The results are used to give the bound on θ.

  2. In vitro synthesis of vertebrate U1 snRNA.

    PubMed Central

    Lund, E; Dahlberg, J E

    1989-01-01

    We have developed a DNA-dependent in vitro transcription system for vertebrate snRNA genes. By isolating the nuclei (germinal vesicles, GVs) of Xenopus laevis oocytes under oil to maintain the in vivo composition of their internal milieu, we are able to prepare nuclei that retain their ability to synthesize snRNAs efficiently. Homogenates of these GVs synthesize correctly initiated and terminated U1 snRNA using exogenous X.laevis U1 genes as templates. The templates may be either injected into the nucleus prior to its isolation or added to the nuclear homogenate. Images PMID:2714253

  3. The large N-terminal region of the Brr2 RNA helicase guides productive spliceosome activation

    PubMed Central

    Absmeier, Eva; Wollenhaupt, Jan; Mozaffari-Jovin, Sina; Becke, Christian; Lee, Chung-Tien; Preussner, Marco; Heyd, Florian; Urlaub, Henning; Lührmann, Reinhard; Santos, Karine F.; Wahl, Markus C.

    2015-01-01

    The Brr2 helicase provides the key remodeling activity for spliceosome catalytic activation, during which it disrupts the U4/U6 di-snRNP (small nuclear RNA protein), and its activity has to be tightly regulated. Brr2 exhibits an unusual architecture, including an ∼500-residue N-terminal region, whose functions and molecular mechanisms are presently unknown, followed by a tandem array of structurally similar helicase units (cassettes), only the first of which is catalytically active. Here, we show by crystal structure analysis of full-length Brr2 in complex with a regulatory Jab1/MPN domain of the Prp8 protein and by cross-linking/mass spectrometry of isolated Brr2 that the Brr2 N-terminal region encompasses two folded domains and adjacent linear elements that clamp and interconnect the helicase cassettes. Stepwise N-terminal truncations led to yeast growth and splicing defects, reduced Brr2 association with U4/U6•U5 tri-snRNPs, and increased ATP-dependent disruption of the tri-snRNP, yielding U4/U6 di-snRNP and U5 snRNP. Trends in the RNA-binding, ATPase, and helicase activities of the Brr2 truncation variants are fully rationalized by the crystal structure, demonstrating that the N-terminal region autoinhibits Brr2 via substrate competition and conformational clamping. Our results reveal molecular mechanisms that prevent premature and unproductive tri-snRNP disruption and suggest novel principles of Brr2-dependent splicing regulation. PMID:26637280

  4. The MUC1 Extracellular Domain Subunit Is Found in Nuclear Speckles and Associates with Spliceosomes

    PubMed Central

    Kumar, Priyadarsina; Ji, Jennifer W.; Martsching, Lindsay; Douglas, Gordon C.

    2012-01-01

    MUC1 is a large transmembrane glycoprotein and oncogene expressed by epithelial cells and overexpressed and underglycosylated in cancer cells. The MUC1 cytoplasmic subunit (MUC1-C) can translocate to the nucleus and regulate gene expression. It is frequently assumed that the MUC1 extracellular subunit (MUC1-N) does not enter the nucleus. Based on an unexpected observation that MUC1 extracellular domain antibody produced an apparently nucleus-associated staining pattern in trophoblasts, we have tested the hypothesis that MUC1-N is expressed inside the nucleus. Three different antibodies were used to identify MUC1-N in normal epithelial cells and tissues as well as in several cancer cell lines. The results of immunofluorescence and confocal microscopy analyses as well as subcellular fractionation, Western blotting, and siRNA/shRNA studies, confirm that MUC1-N is found within nuclei of all cell types examined. More detailed examination of its intranuclear distribution using a proximity ligation assay, subcellular fractionation, and immunoprecipitation suggests that MUC1-N is located in nuclear speckles (interchromatin granule clusters) and closely associates with the spliceosome protein U2AF65. Nuclear localization of MUC1-N was abolished when cells were treated with RNase A and nuclear localization was altered when cells were incubated with the transcription inhibitor 5,6-dichloro-1-b-d-ribofuranosylbenzimidazole (DRB). While MUC1-N predominantly associated with speckles, MUC1-C was present in the nuclear matrix, nucleoli, and the nuclear periphery. In some nuclei, confocal microscopic analysis suggest that MUC1-C staining is located close to, but only partially overlaps, MUC1-N in speckles. However, only MUC1-N was found in isolated speckles by Western blotting. Also, MUC1-C and MUC1-N distributed differently during mitosis. These results suggest that MUC1-N translocates to the nucleus where it is expressed in nuclear speckles and that MUC1-N and MUC1-C have

  5. Underground storage tank 511-D1U1 closure plan

    SciTech Connect

    Mancieri, S.; Giuntoli, N.

    1993-09-01

    This document contains the closure plan for diesel fuel underground storage tank 511-D1U1 and appendices containing supplemental information such as staff training certification and task summaries. Precision tank test data, a site health and safety plan, and material safety data sheets are also included.

  6. The final stages of spliceosome maturation require Spp2p that can interact with the DEAH box protein Prp2p and promote step 1 of splicing.

    PubMed Central

    Roy, J; Kim, K; Maddock, J R; Anthony, J G; Woolford, J L

    1995-01-01

    Pre-mRNA processing occurs by assembly of splicing factors on the substrate to form the spliceosome followed by two consecutive RNA cleavage-ligation reactions. The Prp2 protein hydrolyzes ATP and is required for the first reaction (Yean SL, Lin RJ, 1991, Mol Cell Biol 11:5571-5577; Kim SH, Smith J, Claude A, Lin RJ, 1992, EMBO J 11:2319-2326). The Saccharomyces cerevisiae SPP2 gene was previously identified as a high-copy suppressor of temperature-sensitive prp2 mutants (Last RL, Maddock JR, Woolford JL Jr, 1987, Genetics 117:619-631). We have characterized the function of Spp2p in vivo and in vitro. Spp2p is an essential protein required for the first RNA cleavage reaction in vivo. Depletion of Spp2p from yeast cells results in accumulation of unspliced pre-mRNAs. A temperature-sensitive spp2-1 mutant accumulates pre-mRNAs in vivo and is unable to undergo the first splicing reaction in vitro. However, spliceosomal complexes are assembled in extracts prepared from the mutant. We show that Spp2p function is required after spliceosome assembly but prior to the first reaction. Spp2p associates with the spliceosome before the first RNA cleavage reaction and is likely to be released from the spliceosome following ATP hydrolysis by Prp2p. The Prp2 and Spp2 proteins are capable of physically interacting with each other. These results suggest that Spp2p interacts with Prp2p in the spliceosome prior to the first cleavage-ligation reaction. Spp2p is the first protein that has been found to interact with a DEAD/H box splicing factor. Images FIGURE 1 FIGURE 2 FIGURE 3 FIGURE 4 FIGURE 5 FIGURE 6 FIGURE 7 FIGURE 8 FIGURE 9 PMID:7493316

  7. Genetic Interaction Mapping Reveals a Role for the SWI/SNF Nucleosome Remodeler in Spliceosome Activation in Fission Yeast

    PubMed Central

    Patrick, Kristin L.; Ryan, Colm J.; Xu, Jiewei; Lipp, Jesse J.; Nissen, Kelly E.; Roguev, Assen; Shales, Michael; Krogan, Nevan J.; Guthrie, Christine

    2015-01-01

    Although numerous regulatory connections between pre-mRNA splicing and chromatin have been demonstrated, the precise mechanisms by which chromatin factors influence spliceosome assembly and/or catalysis remain unclear. To probe the genetic network of pre-mRNA splicing in the fission yeast Schizosaccharomyces pombe, we constructed an epistatic mini-array profile (E-MAP) and discovered many new connections between chromatin and splicing. Notably, the nucleosome remodeler SWI/SNF had strong genetic interactions with components of the U2 snRNP SF3 complex. Overexpression of SF3 components in ΔSWI/SNF cells led to inefficient splicing of many fission yeast introns, predominantly those with non-consensus splice sites. Deletion of SWI/SNF decreased recruitment of the splicing ATPase Prp2, suggesting that SWI/SNF promotes co-transcriptional spliceosome assembly prior to first step catalysis. Importantly, defects in SWI/SNF as well as SF3 overexpression each altered nucleosome occupancy along intron-containing genes, illustrating that the chromatin landscape both affects—and is affected by—co-transcriptional splicing. PMID:25825871

  8. Genetic interaction mapping reveals a role for the SWI/SNF nucleosome remodeler in spliceosome activation in fission yeast.

    PubMed

    Patrick, Kristin L; Ryan, Colm J; Xu, Jiewei; Lipp, Jesse J; Nissen, Kelly E; Roguev, Assen; Shales, Michael; Krogan, Nevan J; Guthrie, Christine

    2015-03-01

    Although numerous regulatory connections between pre-mRNA splicing and chromatin have been demonstrated, the precise mechanisms by which chromatin factors influence spliceosome assembly and/or catalysis remain unclear. To probe the genetic network of pre-mRNA splicing in the fission yeast Schizosaccharomyces pombe, we constructed an epistatic mini-array profile (E-MAP) and discovered many new connections between chromatin and splicing. Notably, the nucleosome remodeler SWI/SNF had strong genetic interactions with components of the U2 snRNP SF3 complex. Overexpression of SF3 components in ΔSWI/SNF cells led to inefficient splicing of many fission yeast introns, predominantly those with non-consensus splice sites. Deletion of SWI/SNF decreased recruitment of the splicing ATPase Prp2, suggesting that SWI/SNF promotes co-transcriptional spliceosome assembly prior to first step catalysis. Importantly, defects in SWI/SNF as well as SF3 overexpression each altered nucleosome occupancy along intron-containing genes, illustrating that the chromatin landscape both affects--and is affected by--co-transcriptional splicing.

  9. Underground storage tank 431-D1U1, Closure Plan

    SciTech Connect

    Mancieri, S.

    1993-09-01

    This document contains information about the decommissioning of Tank 431-D1U1. This tank was installed in 1965 for diesel fuel storage. This tank will remain in active usage until closure procedures begin. Soils and ground water around the tank will be sampled to check for leakage. Appendices include; proof of proper training for workers, health and safety briefing record, task hazard analysis summary, and emergency plans.

  10. Transcription-dependent colocalization of the U1, U2, U4/U6, and U5 snRNPs in coiled bodies

    PubMed Central

    1992-01-01

    We have recently shown that discrete foci are present in the nuclei of mammalian cells in which each of the U1, U2, U4/U6, and U5 snRNPs involved in pre-mRNA splicing, and the non-snRNP-splicing factor U2AF, are concentrated (Carmo-Fonseca, M., D. Tollervey, R. Pepperkok, S. Barabino, A. Merdes, C. Brunner, P. D. Zamore, M. R. Green, E. Hurt, and A. I. Lamond. 1991. EMBO (Eur. Mol. Biol. Organ.) J. 10:195-206; Carmo-Fonseca, M., R. Pepperkok, B. S. Sproat, W. Ansorge, M. S. Swanson, and A. I. Lamond. 1991 EMBO (Eur. Mol. Biol. Organ.) J. 10:1863-1873). Here, we identify these snRNP-rich organelles as coiled bodies. snRNPs no longer concentrate in coiled bodies after cells are treated with the transcription inhibitors alpha-amanitin or actinomycin D. snRNP association with coiled bodies is also disrupted by heat shock. This indicates that the association of snRNPs with coiled bodies may be connected with the metabolism of nascent transcripts. A novel labeling method is described which shows both the RNA and protein components of individual snRNPs colocalizing in situ. Using this procedure all spliceosomal snRNPs are seen distributed in a nonhomogeneous pattern throughout the nucleoplasm, excluding nucleoli. They are most concentrated in coiled bodies, but in addition are present in "speckled" structures which are distinct from coiled bodies and which contain the non-snRNP splicing factor SC-35. U1 snRNP shows a more widespread nucleoplasmic staining, outside of coiled bodies and "speckled" structures, relative to the other snRNPs. The association of snRNPs with "speckles" is disrupted by heat shock but enhanced when cells are treated with alpha-amanitin. PMID:1532583

  11. The spliceosome U2 snRNP factors promote genome stability through distinct mechanisms; transcription of repair factors and R-loop processing

    PubMed Central

    Tanikawa, M; Sanjiv, K; Helleday, T; Herr, P; Mortusewicz, O

    2016-01-01

    Recent whole-exome sequencing of malignancies have detected recurrent somatic mutations in U2 small nuclear ribonucleoprotein complex (snRNP) components of the spliceosome. These factors have also been identified as novel players in the DNA-damage response (DDR) in several genome-wide screens and proteomic analysis. Although accumulating evidence implies that the spliceosome has an important role in genome stability and is an emerging hallmark of cancer, its precise role in DNA repair still remains elusive. Here we identify two distinct mechanisms of how spliceosome U2 snRNP factors contribute to genome stability. We show that the spliceosome maintains protein levels of essential repair factors, thus contributing to homologous recombination repair. In addition, real-time laser microirradiation analysis identified rapid recruitment of the U2 snRNP factor SNRPA1 to DNA-damage sites. Functional analysis of SNRPA1 revealed a more immediate and direct role in preventing R-loop-induced DNA damage. Our present study implies a complex interrelation between transcription, mRNA splicing and the DDR. Cells require rapid spatio-temporal coordination of these chromatin transactions to cope with various forms of genotoxic stress. PMID:27991914

  12. The DEAH-box protein PRP22 is an ATPase that mediates ATP-dependent mRNA release from the spliceosome and unwinds RNA duplexes.

    PubMed Central

    Wagner, J D; Jankowsky, E; Company, M; Pyle, A M; Abelson, J N

    1998-01-01

    Of the proteins required for pre-mRNA splicing, at least four, the DEAH-box proteins, are closely related due to the presence of a central 'RNA helicase-like' region, and extended homology through a large portion of the protein. A major unresolved question is the function of these proteins. Indirect evidence suggests that several of these proteins are catalysts for important structural rearrangements in the spliceosome. However, the mechanism for the proposed alterations is presently unknown. We present evidence that PRP22, a DEAH-box protein required for mRNA release from the spliceosome, unwinds RNA duplexes in a concentration- and ATP-dependent manner. This demonstrates that PRP22 can modify RNA structure directly. We also show that the PRP22-dependent release of mRNA from the spliceosome is an ATP-dependent process and that recombinant PRP22 is an ATPase. Non-hydrolyzable ATP analogs did not substitute for ATP in the RNA-unwinding reaction, suggesting that ATP hydrolysis is required for this reaction. Specific mutation of a putative ATP phosphate-binding motif in the recombinant protein eliminated the ATPase and RNA-unwinding capacity. Significantly, these data suggest that the DEAH-box proteins act directly on RNA substrates within the spliceosome. PMID:9582286

  13. Entanglement entropy of U (1) quantum spin liquids

    NASA Astrophysics Data System (ADS)

    Pretko, Michael; Senthil, T.

    2016-09-01

    We here investigate the entanglement structure of the ground state of a (3 +1 )-dimensional U (1 ) quantum spin liquid, which is described by the deconfined phase of a compact U (1 ) gauge theory. A gapless photon is the only low-energy excitation, with matter existing as deconfined but gapped excitations of the system. It is found that, for a given bipartition of the system, the elements of the entanglement spectrum can be grouped according to the electric flux between the two regions, leading to a useful interpretation of the entanglement spectrum in terms of electric charges living on the boundary. The entanglement spectrum is also given additional structure due to the presence of the gapless photon. Making use of the Bisognano-Wichmann theorem and a local thermal approximation, these two contributions to the entanglement (particle and photon) are recast in terms of boundary and bulk contributions, respectively. Both pieces of the entanglement structure give rise to universal subleading terms (relative to the area law) in the entanglement entropy, which are logarithmic in the system size (logL ), as opposed to the subleading constant term in gapped topologically ordered systems. The photon subleading logarithm arises from the low-energy conformal field theory and is essentially local in character. The particle subleading logarithm arises due to the constraint of closed electric loops in the wave function and is shown to be the natural generalization of topological entanglement entropy to the U (1 ) spin liquid. This contribution to the entanglement entropy can be isolated by means of the Grover-Turner-Vishwanath construction (which generalizes the Kitaev-Preskill scheme to three dimensions).

  14. Prp8, the pivotal protein of the spliceosomal catalytic center, evolved from a retroelement-encoded reverse transcriptase

    PubMed Central

    Dlakić, Mensur; Mushegian, Arcady

    2011-01-01

    Prp8 is the largest and most highly conserved protein of the spliceosome, encoded by all sequenced eukaryotic genomes but missing from prokaryotes and viruses. Despite all evidence that Prp8 is an integral part of the spliceosomal catalytic center, much remains to be learned about its molecular functions and evolutionary origin. By analyzing sequence and structure similarities between Prp8 and other protein domains, we show that its N-terminal region contains a putative bromodomain. The central conserved domain of Prp8 is related to the catalytic domain of reverse transcriptases (RTs) and is most similar to homologous enzymes encoded by prokaryotic retroelements. However, putative catalytic residues in this RT domain are only partially conserved and may not be sufficient for the nucleotidyltransferase activity. The RT domain is followed by an uncharacterized sequence region with relatives found in fungal RT-like proteins. This part of Prp8 is predicted to adopt an α-helical structure and may be functionally equivalent to diverse maturase/X domains of retroelements and to the thumb domain of retroviral RTs. Together with a previously identified C-terminal domain that has an RNaseH-like fold, our results suggest evolutionary connections between Prp8 and ancient mobile elements. Prp8 may have evolved by acquiring nucleic acid–binding domains from inactivated retroelements, and their present-day role may be in maintaining proper conformation of the bound RNA cofactors and substrates of the splicing reaction. This is only the second example—the other one being telomerase—of the RT recruitment from a genomic parasite to serve an essential cellular function. PMID:21441348

  15. Ribonucleoprotein assembly defects correlate with spinal muscular atrophy severity and preferentially affect a subset of spliceosomal snRNPs.

    PubMed

    Gabanella, Francesca; Butchbach, Matthew E R; Saieva, Luciano; Carissimi, Claudia; Burghes, Arthur H M; Pellizzoni, Livio

    2007-09-26

    Spinal muscular atrophy (SMA) is a motor neuron disease caused by reduced levels of the survival motor neuron (SMN) protein. SMN together with Gemins2-8 and unrip proteins form a macromolecular complex that functions in the assembly of small nuclear ribonucleoproteins (snRNPs) of both the major and the minor splicing pathways. It is not known whether the levels of spliceosomal snRNPs are decreased in SMA. Here we analyzed the consequence of SMN deficiency on snRNP metabolism in the spinal cord of mouse models of SMA with differing phenotypic severities. We demonstrate that the expression of a subset of Gemin proteins and snRNP assembly activity are dramatically reduced in the spinal cord of severe SMA mice. Comparative analysis of different tissues highlights a similar decrease in SMN levels and a strong impairment of snRNP assembly in tissues of severe SMA mice, although the defect appears smaller in kidney than in neural tissue. We further show that the extent of reduction in both Gemin proteins expression and snRNP assembly activity in the spinal cord of SMA mice correlates with disease severity. Remarkably, defective SMN complex function in snRNP assembly causes a significant decrease in the levels of a subset of snRNPs and preferentially affects the accumulation of U11 snRNP--a component of the minor spliceosome--in tissues of severe SMA mice. Thus, impairment of a ubiquitous function of SMN changes the snRNP profile of SMA tissues by unevenly altering the normal proportion of endogenous snRNPs. These findings are consistent with the hypothesis that SMN deficiency affects the splicing machinery and in particular the minor splicing pathway of a rare class of introns in SMA.

  16. Cooperative binding of TIA-1 and U1 snRNP in K-SAM exon splicing activation

    SciTech Connect

    Gesnel, Marie-Claude; Theoleyre, Sandrine; Del Gatto-Konczak, Fabienne; Breathnach, Richard . E-mail: breathna@nantes.inserm.fr

    2007-07-13

    In 293 cells, splicing of the human fibroblast growth factor receptor-2 K-SAM alternative exon is inefficient, but can be made efficient by provoking TIA-1 binding to the U-rich IAS1 sequence downstream from the exon's 5' splice site. We show here that TIA-1 domains known to interact with U1 snRNP and to recruit it to 5' splice sites in vitro are required for TIA-1 activation of K-SAM exon splicing in vivo. We further show that tethering downstream from the K-SAM exon a fusion between the U1 snRNP component U1C and the bacteriophage MS2 coat protein provokes IAS1-dependent exon splicing, and present evidence that the fusion functions after its incorporation into U1 snRNP. Our in vivo data, taken together with previous in vitro results, show that K-SAM splicing activation involves cooperative binding of TIA-1 and U1 snRNP to the exon's 5' splice site region.

  17. H2B Ubiquitylation Modulates Spliceosome Assembly and Function in Budding Yeast

    PubMed Central

    Hérissant, Lucas; Moehle, Erica A.; Bertaccini, Diego; Van Dorsselaer, Alain; Schaeffer-Reiss, Christine; Guthrie, Christine; Dargemont, Catherine

    2014-01-01

    Background information Commitment to splicing occurs co-transcriptionally, but a major unanswered question is the extent to which various modifications of chromatin, the template for transcription in vivo, contribute to the regulation of splicing. Results Here we perform genome-wide analyses showing that inhibition of specific marks – H2B ubiquitylation, H3K4 methylation, and H3K36 methylation – perturbs splicing in budding yeast, with each modification exerting gene-specific effects. Furthermore, semi-quantitative mass spectrometry on purified nuclear mRNPs and chromatin immunoprecipitation analysis on intron-containing genes indicated that H2B ubiquitylation, but not Set1-, Set2- or Dot1-dependent H3 methylation, stimulates recruitment of the early splicing factors, namely U1 and U2 snRNPs, onto nascent RNAs. Conclusions These results suggest that histone modifications impact splicing of distinct subsets of genes using distinct pathways. PMID:24476359

  18. Exactly solvable U (1) × U (1) boson models for integer and fractional quantum Hall insulators in two dimensions

    NASA Astrophysics Data System (ADS)

    Motrunich, Olexei; Geraedts, Scott

    2013-03-01

    We present a solvable boson model with U (1) × U (1) symmetry in (2+1) dimensions that realizes insulating phases with a quantized Hall conductivity σxy. The model is short-ranged, with no topological terms, and can be realized by a local Hamiltonian. For one set of parameters, the model has a non-fractionalized phase with σxy = 2 n in appropriate units, with n an integer. In this case, the physical origin is dynamical binding between n bosons of one species and a vortex of the other species and condensation of such composites. Other choices for the parameters of the model yield a phase with σxy = 2c/d , where c and d are mutually prime integers. In this phase, c bosons dynamically bind to d vortices and such objects condense. The are two species of excitations that are bosonic by themselves but carry fractional charge 1 / d and have mutual statistics 2 πb/d , where b is an integer such that ad - bc = 1 , and a is also an integer. The model can be studied using sign-free Monte Carlo. We have performed simulations which include a boundary between a quantum Hall insulator and a trivial insulator, and found gapless edge states on the boundary.

  19. Charge crossover at the U(1)-Higgs phase transition

    SciTech Connect

    Freire, Filipe; Litim, Daniel F.

    2001-08-15

    The type-I region of phase transitions at finite temperature of the U(1)-Higgs theory in 3+1 dimensions is investigated in detail using a Wilsonian renormalization group. We consider, in particular, the quantitative effects induced through the crossover of the scale-dependent Abelian charge from the Gaussian to a nontrivial Abelian fixed point. As a result, the strength of the first-order phase transition is weakened. Analytical solutions to approximate flow equations are obtained, and all characteristics of the phase transition are discussed and compared to the results obtained from perturbation theory. In addition, we present a detailed quantitative study regarding the dependence of the physical observables on the coarse-graining scheme. This results in error bars for the regularization scheme (RS) dependence. We find quantitative evidence for an intimate link between the RS dependence and truncations of flow equations.

  20. Subdimensional particle structure of higher rank U (1 ) spin liquids

    NASA Astrophysics Data System (ADS)

    Pretko, Michael

    2017-03-01

    Spin liquids are conventionally described by gauge theories with a vector gauge field. However, there exists a wider class of spin liquids with higher rank tensors as the gauge variable. In this work, we focus on (3+1)-dimensional spin liquids described by U (1 ) symmetric tensor gauge theories, which have recently been shown to be stable gapless spin liquids. We investigate the particle structure of these tensor gauge theories and find that they have deep connections with the "fracton" models recently discovered by Vijay, Haah, and Fu. Tensor gauge theories have more conservation laws than the simple charge conservation law of rank 1 theories. These conservation laws place severe restrictions on the motion of particles. Particles in some models are fully immobile (fractons), while other models have particles restricted to motion along lower-dimensional subspaces.

  1. U(1) prime dark matter and R-parity violation

    SciTech Connect

    Brahm, D.E.

    1990-04-01

    Attempts to understand physics beyond the Standard Model must face many phenomenological constraint, from recent Z{sup {degree}} data, neutral current measurements, cosmology and astrophysics, neutrino experiments, tests of lepton-and baryon-number conservation and CP violation, and many other ongoing experiments. The most interesting models are those which are allowed by current data, but offer predictions which can soon be experimentally confirmed or refuted. Two classes of such models are explored in this dissertation. The first, containing an extra U(1){prime} gauge group, has a dark matter candidate which could soon be detected. The second, incorporating supersymmetry with R-parity violation, predicts rare Z{sup {degree}} decays at LEP; some of these models can already be ruled out by LEP data and gluino searches at the Tevatron. 54 refs., 31 figs.

  2. SU(2) x U(1) vacuum and the Centauro events

    NASA Technical Reports Server (NTRS)

    Kazanas, D.; Balasubrahmanyan, V. K.; Streitmatter, R. E.

    1985-01-01

    It is proposed that the fireballs invoked to explain the Centauro events are bubbles of a metastable superdense state of nuclear matter, created in high energy (E approximately 10 to the 15th power eV) cosmic ray collisions at the top of the atmosphere. If these bubbles are created with a Lorentz factor gamma approximately equals 10 at their CM frame, the objections against the origin of these events in cosmic ray interactions are overcome. A relationship then between their lifetime, tau, and the threshold energy for bubble formation, E sub th, appears to be insensitive to the value of tau and always close to E sub th approximately 10 to 15th power eV. Finally it is speculated that these bubbles might be manifestations of the SU(2) x U(1) false vacuum excited in these collisions. The absence of in the Centauro events is then explained by the decay modes of these excitations.

  3. Drosophila melanogaster genes for U1 snRNA variants and their expression during development.

    PubMed Central

    Lo, P C; Mount, S M

    1990-01-01

    We have cloned and characterized a complete set of seven U1-related sequences from Drosophila melanogaster. These sequences are located at the three cytogenetic loci 21D, 82E, and 95C. Three of these sequences have been previously studied: one U1 gene at 21D which encodes the prototype U1 sequence (U1a), one U1 gene at 82E which encodes a U1 variant with a single nucleotide substitution (U1b), and a pseudogene at 82E. The four previously uncharacterized genes are another U1b gene at 82E, two additional U1a genes at 95C, and a U1 gene at 95C which encodes a new variant (U1c) with a distinct single nucleotide change relative to U1a. Three blocks of 5' flanking sequence similarity are common to all six full length genes. Using specific primer extension assays, we have observed that the U1b RNA is expressed in Drosophila Kc cells and is associated with snRNP proteins, suggesting that the U1b-containing snRNP particles are able to participate in the process of pre-mRNA splicing. We have also examined the expression throughout Drosophila development of the two U1 variants relative to the prototype sequence. The U1c variant is undetectable by our methods, while the U1b variant exhibits a primarily embryonic pattern reminiscent of the expression of certain U1 variants in sea urchin, Xenopus, and mouse. Images PMID:2124674

  4. Structure and expression of the Drosophila melanogaster gene for the U1 small nuclear ribonucleoprotein particle 70K protein.

    PubMed Central

    Mancebo, R; Lo, P C; Mount, S M

    1990-01-01

    A genomic clone encoding the Drosophila U1 small nuclear ribonucleoprotein particle 70K protein was isolated by hybridization with a human U1 small nuclear ribonucleoprotein particle 70K protein cDNA. Southern blot and in situ hybridizations showed that this U1 70K gene is unique in the Drosophila genome, residing at cytological position 27D1,2. Polyadenylated transcripts of 1.9 and 3.1 kilobases were observed. While the 1.9-kilobase mRNA is always more abundant, the ratio of these two transcripts is developmentally regulated. Analysis of cDNA and genomic sequences indicated that these two RNAs encode an identical protein with a predicted molecular weight of 52,879. Comparison of the U1 70K proteins predicted from Drosophila, human, and Xenopus cDNAs revealed 68% amino acid identity in the most amino-terminal 214 amino acids, which include a sequence motif common to many proteins which bind RNA. The carboxy-terminal half is less well conserved but is highly charged and contains distinctive arginine-rich regions in all three species. These arginine-rich regions contain stretches of arginine-serine dipeptides like those found in transformer, transformer-2, and suppressor-of-white-apricot proteins, all of which have been identified as regulators of mRNA splicing in Drosophila melanogaster. Images PMID:1692955

  5. Genetic suppression of intronic +1G mutations by compensatory U1 snRNA changes in Caenorhabditis elegans.

    PubMed Central

    Zahler, Alan M; Tuttle, John D; Chisholm, Andrew D

    2004-01-01

    Mutations to the canonical +1G of introns, which are commonly found in many human inherited disease alleles, invariably result in aberrant splicing. Here we report genetic findings in C. elegans that aberrant splicing due to +1G mutations can be suppressed by U1 snRNA mutations. An intronic +1G-to-U mutation, e936, in the C. elegans unc-73 gene causes aberrant splicing and loss of gene function. We previously showed that mutation of the sup-39 gene promotes splicing at the mutant splice donor in e936 mutants. We demonstrate here that sup-39 is a U1 snRNA gene; suppressor mutations in sup-39 are compensatory substitutions in the 5' end, which enhance recognition of the mutant splice donor. sup-6(st19) is an allele-specific suppressor of unc-13(e309), which contains an intronic +1G-to-A transition. The e309 mutation activates a cryptic splice site, and sup-6(st19) restores splicing to the mutant splice donor. sup-6 also encodes a U1 snRNA and the mutant contains a compensatory substitution at its 5' end. This is the first demonstration that U1 snRNAs can act to suppress the effects of mutations to the invariant +1G of introns. These findings are suggestive of a potential treatment of certain alleles of inherited human genetic diseases. PMID:15342508

  6. At the origin of spliceosomal introns: Is multiplication of introner-like elements the main mechanism of intron gain in fungi?

    PubMed

    Collemare, Jérôme; van der Burgt, Ate; de Wit, Pierre J G M

    2013-03-01

    The recent discovery of introner-like elements (ILEs) in six fungal species shed new light on the origin of regular spliceosomal introns (RSIs) and the mechanism of intron gains. These novel spliceosomal introns are found in hundreds of copies, are longer than RSIs and harbor stable predicted secondary structures. Yet, they are prone to degeneration in sequence and length to become undistinguishable from RSIs, suggesting that ILEs are predecessors of most RSIs. In most fungi, other near-identical introns were found duplicated in lower numbers in the same gene or in unrelated genes, indicating that intron duplication is a widespread phenomenon. However, ILEs are associated with the majority of intron gains, suggesting that the other types of duplication are of minor importance to the overall gains of introns. Our data support the hypothesis that ILEs' multiplication corresponds to the main mechanism of intron gain in fungi.

  7. Generating technique for U(1){sup 3} 5D supergravity

    SciTech Connect

    Gal'tsov, Dmitri V.; Scherbluk, Nikolai G.

    2008-09-15

    We develop a generating technique for solutions of U(1){sup 3} 5D supergravity via dimensional reduction to three dimensions. This theory, which recently attracted attention in connection with black rings, can be viewed as a consistent truncation of the T{sup 6} compactification of the 11-dimensional supergravity. Its further reduction to three dimensions accompanied by dualization of the vector fields leads to a 3D gravity coupled sigma model on the homogeneous space SO(4,4)/SO(4)xSO(4) or SO(4,4)/SO(2,2)xSO(2,2) depending on the signature of the three-space. We construct a 8x8 matrix representation of these cosets in terms of lower-dimensional blocks. Using it we express a solution generating transformations in terms of potentials and identify those preserving asymptotic conditions relevant to black holes and black rings. As an application we derive the doubly rotating black hole solution with three independent charges. A suitable contraction of the above cosets is used to construct a new representation of the coset G{sub 2(2)}/(SL(2,R)xSL(2,R)) relevant for minimal five-dimensional supergravity.

  8. SU(2) x U(1) vacuum and the Centauro events

    NASA Technical Reports Server (NTRS)

    Kazanas, D.; Balasubrahmanyan, V. K.; Streitmatter, R. E.

    1984-01-01

    It is proposed that the fireballs invoked to explain the Centauro events are bubbles of a metastable superdense state of nuclear matter, created in high energy (E is approximately 10 to the 15th power eV) cosmic ray collisions at the top of the atmosphere. If these bubbles are created with a Lorentz factor gamma approximately = 10 at their CM frame, the objections against the origin of these events in cosmic ray interactions are overcome. Assuming further, that the Centauro events are to the explosive decay of these metastable bubbles, a relationship between their lifetime, tau, and the threshold energy for bubble formation, E sub th, is derived. The minimum lifetime consistent with such an interpretation in tau is approximately 10 to the -8th power sec, while the E sub th appears to be insensitive to the value of tau and always close to E sub th is approximately 10 to the 15th power eV. Finally it is speculated that if the available CM energy is thermalized in such collisions, these bubbles might be manifestations of excitations of the SU(2) x U(1) false vacuum. The absence of neutral pions in the Centauro events is then explained by the decay of these excitations.

  9. Monopoles and Confinement in U(1) Lattice Gauge Theory

    NASA Astrophysics Data System (ADS)

    Copeland, Timothy John

    Available from UMI in association with The British Library. Requires signed TDF. Confinement in U(1) gauge theory is investigated, with particular emphasis on the role of monopoles. Starting from the work of Polyakov, the theoretical aspects are considered first, in some detail. This leads to the conclusion that the conventional techniques for analysing Monte Carlo data may not be adequate, and motivates the development of an alternative interpretation based on the theoretical insight gained. This takes more account of the expected physical properties of the theory, and does not assume beforehand that one type of behaviour (perturbative, or monopole driven) dominates. It is found that better fits to the Monte Carlo data can be achieved this way than by using the conventional methods, although different string tensions are found. The small distance behaviour is found to be best explained in terms of Coulomb effects, rather than the Luscher vibrating string picture sometimes used before. Perturbative calculations are made of Wilson loops on lattices of different shapes, and some comparisons with Monte Carlo data are made. Comments are made on the significance of these results for four dimensions, and for SU(2) and SU(3).

  10. A two-step approach for sequencing spliceosome-related genes as a complementary diagnostic assay in MDS patients with ringed sideroblasts.

    PubMed

    Janusz, Kamila; Del Rey, Mónica; Abáigar, María; Collado, Rosa; Ivars, David; Hernández-Sánchez, María; Valiente, Alberto; Robledo, Cristina; Benito, Rocío; Díez-Campelo, María; Ramos, Fernando; Kohlmann, Alexander; Cañizo, Consuelo Del; Hernández-Rivas, Jesús María

    2017-02-04

    Our study aimed to analyze the presence of mutations in SF3B1 and other spliceosome-related genes in myelodysplastic syndromes with ringed sideroblasts (MDS-RS) by combining conventional Sanger and next-generation sequencing (NGS) methods, and to determine the feasibility of this approach in a clinical setting. 122 bone marrow samples from MDS-RS patients were studied. Initially, exons 14 and 15 of the SF3B1 gene were analyzed by Sanger sequencing. Secondly, they were studied by NGS covering besides SF3B1, SRSF2, U2AF1 and ZRSR2 genes. An 86% of all patients showed mutations in the SF3B1 gene. Six of them, which were not identifiable by conventional sequencing in the first diagnostic step, were revealed by NGS. In addition, 19.5% of cases showed mutations in other splicing genes: SRSF2, U2AF1, and ZRSR2. Furthermore, 8.7% of patients had two mutations in SF3B1, SF3B1 and SRSF2, and SF3B1 and U2AF1, while 5.7% showed no mutations in the four spliceosome-related genes analyzed. The combined use of conventional Sanger and NGS allows the identification of mutations in spliceosome-related genes in almost all MDS patients with RS. This two-step approach is affordable and could be useful as a complementary technique in cases with an unclear diagnosis.

  11. Requirements for gene silencing mediated by U1 snRNA binding to a target sequence

    PubMed Central

    Abad, Xabi; Vera, Maria; Jung, Stephen P.; Oswald, Evelyn; Romero, Inés; Amin, Vaibhav; Fortes, Puri; Gunderson, Samuel I.

    2008-01-01

    U1 interference (U1i) is a novel method to block gene expression. U1i requires expression of a 5′-end-mutated U1 snRNA designed to base pair to the 3′-terminal exon of the target gene's pre-mRNA that leads to inhibition of polyadenylation. Here, we show U1i is robust (≥95%) and a 10-nt target length is sufficient for good silencing. Surprisingly, longer U1 snRNAs, which could increase annealing to the target, fail to improve silencing. Extensive mutagenesis of the 10-bp U1 snRNA:target duplex shows that any single mismatch different from GU at positions 3–8, destroys silencing. However, mismatches within the other positions give partial silencing, suggesting that off-target inhibition could occur. The specificity of U1i may be enhanced, however, by the fact that silencing is impaired by RNA secondary structure or by splicing factors binding nearby, the latter mediated by Arginine-Serine (RS) domains. U1i inhibition can be reconstituted in vivo by tethering of RS domains of U1-70K and U2AF65. These results help to: (i) define good target sites for U1i; (ii) identify and understand natural cellular examples of U1i; (iii) clarify the contribution of hydrogen bonding to U1i and to U1 snRNP binding to 5′ splice sites and (iv) understand the mechanism of U1i. PMID:18299285

  12. Restrained dark U (1 )d at low energies

    NASA Astrophysics Data System (ADS)

    Correia, Fagner C.; Fajfer, Svjetlana

    2016-12-01

    We investigate a spontaneously broken U (1 )d gauge symmetry with a muon-specific dark Higgs. Our first goal is to verify how the presence of a new dark Higgs, ϕ , and a dark gauge boson, V , can simultaneously face the anomalies from the muon magnetic moment and the proton charge radius. Second, by assuming that V must decay to an electron-positron pair, we explore the corresponding parameter space determined with the low-energy constraints coming from K →μ X , electron (g -2 )e, K →μ νμe+e-, K →μ νμμ+μ-, and τ →ντμ νμe+e-. We focus on the scenario where the V mass is below ˜2 mμ and the ϕ mass runs from few MeV to 250 MeV, with V -photon mixing of the order ˜O (10-3). Among weak process at low energies, we check the influence of the new light vector on kaon decays as well as on the scattering e+e-→μ+μ-e+e- and discuss the impact of the dark Higgs on e+e-→μ+μ-μ+μ-. Finally, we consider contributions of the V -photon mixing in the decays π0→γ e+e-, η →γ e+e-, ρ →π e+e-, K*→K e+e-, and ϕ (1020 )→η e+e-.

  13. A dominant negative mutation in the conserved RNA helicase motif 'SAT' causes splicing factor PRP2 to stall in spliceosomes.

    PubMed Central

    Plumpton, M; McGarvey, M; Beggs, J D

    1994-01-01

    To characterize sequences in the RNA helicase-like PRP2 protein of Saccharomyces cerevisiae that are essential for its function in pre-mRNA splicing, a pool of random PRP2 mutants was generated. A dominant negative allele was isolated which, when overexpressed in a wild-type yeast strain, inhibited cell growth by causing a defect in pre-mRNA splicing. This defect was partially alleviated by simultaneous co-overexpression of wild-type PRP2. The dominant negative PRP2 protein inhibited splicing in vitro and caused the accumulation of stalled splicing complexes. Immunoprecipitation with anti-PRP2 antibodies confirmed that dominant negative PRP2 protein competed with its wild-type counterpart for interaction with spliceosomes, with which the mutant protein remained associated. The PRP2-dn1 mutation led to a single amino acid change within the conserved SAT motif that in the prototype helicase eIF-4A is required for RNA unwinding. Purified dominant negative PRP2 protein had approximately 40% of the wild-type level of RNA-stimulated ATPase activity. As ATPase activity was reduced only slightly, but splicing activity was abolished, we propose that the dominant negative phenotype is due primarily to a defect in the putative RNA helicase activity of PRP2 protein. Images PMID:8112301

  14. Mechanistic insights into human pre-mRNA splicing of human ultra-short introns: potential unusual mechanism identifies G-rich introns.

    PubMed

    Sasaki-Haraguchi, Noriko; Shimada, Makoto K; Taniguchi, Ichiro; Ohno, Mutsuhito; Mayeda, Akila

    2012-06-29

    It is unknown how very short introns (<65 nt; termed 'ultra-short' introns) could be spliced in a massive spliceosome (>2.7 MDa) without steric hindrance. By screening an annotated human transcriptome database (H-InvDB), we identified three model ultra-short introns: the 56-nt intron in the HNRNPH1 (hnRNP H1) gene, the 49-nt intron in the NDOR1 (NADPH dependent diflavin oxidoreductase 1) gene, and the 43-nt intron in the ESRP2 (epithelial splicing regulatory protein 2) gene. We verified that these endogenous ultra-short introns are spliced, and also recapitulated this in cultured cells transfected with the corresponding mini-genes. The splicing of these ultra-short introns was repressed by a splicing inhibitor, spliceostatin A, suggesting that SF3b (a U2 snRNP component) is involved in their splicing processes. The 56-nt intron containing a pyrimidine-rich tract was spliced out in a lariat form, and this splicing was inhibited by the disruption of U1, U2, or U4 snRNA. In contrast, the 49- and 43-nt introns were purine-rich overall without any pyrimidine-rich tract, and these lariat RNAs were not detectable. Remarkably, shared G-rich intronic sequences in the 49- and 43-nt introns were required for their splicing, suggesting that these ultra-short introns may recruit a novel auxiliary splicing mechanism linked to G-rich intronic splicing enhancers.

  15. Single field inflation in supergravity with a U(1) gauge symmetry

    SciTech Connect

    Heurtier, L.; Khalil, S.; Moursy, A. E-mail: skhalil@zewailcity.edu.eg

    2015-10-01

    A single field inflation based on a supergravity model with a shift symmetry and U(1) extension of the MSSM is analyzed. We show that one of the real components of the two U(1) charged scalar fields plays the role of inflaton with an effective scalar potential similar to the ''new chaotic inflation'' scenario. Both non-anomalous and anomalous (with Fayet-Iliopoulos term) U(1) are studied. We show that the non-anomalous U(1) scenario is consistent with data of the cosmic microwave background and recent astrophysical measurements. A possible kinetic mixing between U(1) and U(1){sub B−L} is considered in order to allow for natural decay channels of the inflaton, leading to a reheating epoch. Upper limits on the reheating temperature thus turn out to favour an intermediate (∼ O(10{sup 13}) GeV) scale B−L symmetry breaking.

  16. Single field inflation in supergravity with a U(1) gauge symmetry

    SciTech Connect

    Heurtier, L.; Khalil, S.; Moursy, A.

    2015-10-19

    A single field inflation based on a supergravity model with a shift symmetry and U(1) extension of the MSSM is analyzed. We show that one of the real components of the two U(1) charged scalar fields plays the role of inflaton with an effective scalar potential similar to the “new chaotic inflation” scenario. Both non-anomalous and anomalous (with Fayet-Iliopoulos term) U(1) are studied. We show that the non-anomalous U(1) scenario is consistent with data of the cosmic microwave background and recent astrophysical measurements. A possible kinetic mixing between U(1) and U(1){sub B−L} is considered in order to allow for natural decay channels of the inflaton, leading to a reheating epoch. Upper limits on the reheating temperature thus turn out to favour an intermediate (∼O(10{sup 13}) GeV) scale B−L symmetry breaking.

  17. Symmetry enriched U(1) topological orders for dipole-octupole doublets on a pyrochlore lattice

    NASA Astrophysics Data System (ADS)

    Li, Yao-Dong; Chen, Gang

    2017-01-01

    Symmetry plays a fundamental role in our understanding of both conventional symmetry breaking phases and the more exotic quantum and topological phases of matter. We explore the experimental signatures of symmetry enriched U(1) quantum spin liquids (QSLs) on the pyrochlore lattice. We point out that the Ce local moment of the newly discovered pyrochlore QSL candidate Ce2Sn2O7 , is a dipole-octupole doublet. The generic model for these unusual doublets supports two distinct symmetry enriched U(1) QSL ground states in the corresponding quantum spin ice regimes. These two U(1) QSLs are dubbed dipolar U(1) QSL and octupolar U(1) QSL. While the dipolar U(1) QSL has been discussed in many contexts, the octupolar U(1) QSL is rather unique. Based on the symmetry properties of the dipole-octupole doublets, we predict the peculiar physical properties of the octupolar U(1) QSL, elucidating the unique spectroscopic properties in the external magnetic fields. We further predict the Anderson-Higgs transition from the octupolar U(1) QSL driven by the external magnetic fields. We identify the experimental relevance with the candidate material Ce2Sn2O7 and other dipole-octupole doublet systems.

  18. Multivalent binding of formin-binding protein 21 (FBP21)-tandem-WW domains fosters protein recognition in the pre-spliceosome.

    PubMed

    Klippel, Stefan; Wieczorek, Marek; Schümann, Michael; Krause, Eberhard; Marg, Berenice; Seidel, Thorsten; Meyer, Tim; Knapp, Ernst-Walter; Freund, Christian

    2011-11-04

    The high abundance of repetitive but nonidentical proline-rich sequences in spliceosomal proteins raises the question of how these known interaction motifs recruit their interacting protein domains. Whereas complex formation of these adaptors with individual motifs has been studied in great detail, little is known about the binding mode of domains arranged in tandem repeats and long proline-rich sequences including multiple motifs. Here we studied the interaction of the two adjacent WW domains of spliceosomal protein FBP21 with several ligands of different lengths and composition to elucidate the hallmarks of multivalent binding for this class of recognition domains. First, we show that many of the proteins that define the cellular proteome interacting with FBP21-WW1-WW2 contain multiple proline-rich motifs. Among these is the newly identified binding partner SF3B4. Fluorescence resonance energy transfer (FRET) analysis reveals the tandem-WW domains of FBP21 to interact with splicing factor 3B4 (SF3B4) in nuclear speckles where splicing takes place. Isothermal titration calorimetry and NMR shows that the tandem arrangement of WW domains and the multivalency of the proline-rich ligands both contribute to affinity enhancement. However, ligand exchange remains fast compared with the NMR time scale. Surprisingly, a N-terminal spin label attached to a bivalent ligand induces NMR line broadening of signals corresponding to both WW domains of the FBP21-WW1-WW2 protein. This suggests that distinct orientations of the ligand contribute to a delocalized and semispecific binding mode that should facilitate search processes within the spliceosome.

  19. 46 CFR 54.01-10 - Steam-generating pressure vessels (modifies U-1(g)).

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 2 2010-10-01 2010-10-01 false Steam-generating pressure vessels (modifies U-1(g)). 54... ENGINEERING PRESSURE VESSELS General Requirements § 54.01-10 Steam-generating pressure vessels (modifies U-1(g)). (a) Pressure vessels in which steam is generated are classed as “Unfired Steam Boilers” except...

  20. 46 CFR 54.01-10 - Steam-generating pressure vessels (modifies U-1(g)).

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 46 Shipping 2 2013-10-01 2013-10-01 false Steam-generating pressure vessels (modifies U-1(g)). 54... ENGINEERING PRESSURE VESSELS General Requirements § 54.01-10 Steam-generating pressure vessels (modifies U-1(g)). (a) Pressure vessels in which steam is generated are classed as “Unfired Steam Boilers” except...

  1. 46 CFR 54.01-10 - Steam-generating pressure vessels (modifies U-1(g)).

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 46 Shipping 2 2012-10-01 2012-10-01 false Steam-generating pressure vessels (modifies U-1(g)). 54... ENGINEERING PRESSURE VESSELS General Requirements § 54.01-10 Steam-generating pressure vessels (modifies U-1(g)). (a) Pressure vessels in which steam is generated are classed as “Unfired Steam Boilers” except...

  2. 46 CFR 54.01-10 - Steam-generating pressure vessels (modifies U-1(g)).

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 46 Shipping 2 2011-10-01 2011-10-01 false Steam-generating pressure vessels (modifies U-1(g)). 54... ENGINEERING PRESSURE VESSELS General Requirements § 54.01-10 Steam-generating pressure vessels (modifies U-1(g)). (a) Pressure vessels in which steam is generated are classed as “Unfired Steam Boilers” except...

  3. 46 CFR 54.01-10 - Steam-generating pressure vessels (modifies U-1(g)).

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 46 Shipping 2 2014-10-01 2014-10-01 false Steam-generating pressure vessels (modifies U-1(g)). 54... ENGINEERING PRESSURE VESSELS General Requirements § 54.01-10 Steam-generating pressure vessels (modifies U-1(g)). (a) Pressure vessels in which steam is generated are classed as “Unfired Steam Boilers” except...

  4. Phenomenological study on the wino radiative decay in anomalous U(1){sup '} models

    SciTech Connect

    Fucito, Francesco; Lionetto, Andrea; Pacifici, Daniel Ricci; Racioppi, Antonio

    2010-12-01

    An extension of the standard model by at least one extra U(1) gauge symmetry has been investigated by many authors. In this paper we explore the possibility that this extra U(1) is anomalous. One possible signature of this model could be given by the photons produced in the decays of the next to lightest supersymmetric particle into the lightest supersymmetric particle.

  5. Closure report for underground storage tank 141-R3U1 and its associated underground piping

    SciTech Connect

    Mallon, B.J.; Blake, R.G.

    1994-03-01

    Underground storage tank UST 141-R3U1 at Lawrence Livermore National Laboratory (LLNL), was registered with the State Water Resources Control Board on June 27, 1984. This tank system consisted of a concrete tank, lined with polyvinyl chloride, and approximately 100 feet of PVC underground piping. UST 141-R3U1 had a capacity of 450 gallons. The underground piping connected three floor drains and one sink inside Building 141 to UST 141-R3U1. The wastewater collected in UST 141-R3U1 contained organic solvents, metals, and inorganic acids. On November 30, 1987, the 141-R3U1 tank system failed a precision tank test. The 141-R3U1 tank system was subsequently emptied and removed from service pending further precision tests to determine the location of the leak within the tank system. A precision tank test on February 5, 1988, was performed to confirm the November 30, 1987 test. Four additional precision tests were performed on this tank system between February 25, 1988, and March 6, 1988. The leak was located where the inlet piping from Building 141 penetrates the concrete side of UST 141-R3U1. The volume of wastewater that entered the backfill and soil around and/or beneath UST 141-R3U1 is unknown. On December 13, 1989, the LLNL Environmental Restoration Division submitted a plan to close UST 141-R3U1 and its associated piping to the Alameda County Department of Environmental Health. UST 141-R3U1 was closed as an UST, and shall be used instead as additional secondary containment for two aboveground storage tanks.

  6. Reduction of Target Gene Expression by a Modified U1 snRNA

    PubMed Central

    Beckley, S. A.; Liu, P.; Stover, M. L.; Gunderson, S. I.; Lichtler, A. C.; Rowe, D. W.

    2001-01-01

    Although the primary function of U1 snRNA is to define the 5′ donor site of an intron, it can also block the accumulation of a specific RNA transcript when it binds to a donor sequence within its terminal exon. This work was initiated to investigate if this property of U1 snRNA could be exploited as an effective method for inactivating any target gene. The initial 10-bp segment of U1 snRNA, which is complementary to the 5′ donor sequence, was modified to recognize various target mRNAs (chloramphenicol acetyltransferase [CAT], β-galactosidase, or green fluorescent protein [GFP]). Transient cotransfection of reporter genes and appropriate U1 antitarget vectors resulted in >90% reduction of transgene expression. Numerous sites within the CAT transcript were suitable for targeting. The inhibitory effect of the U1 antitarget vector is directly related to the hybrid formed between the U1 vector and target transcripts and is dependent on an intact 70,000-molecular-weight binding domain within the U1 gene. The effect is long lasting when the target (CAT or GFP) and U1 antitarget construct are inserted into fibroblasts by stable transfection. Clonal cell lines derived from stable transfection with a pOB4GFP target construct and subsequently stably transfected with the U1 anti-GFP construct were selected. The degree to which GFP fluorescence was inhibited by U1 anti-GFP in the various clonal cell lines was assessed by fluorescence-activated cell sorter analysis. RNA analysis demonstrated reduction of the GFP mRNA in the nuclear and cytoplasmic compartment and proper 3′ cleavage of the GFP residual transcript. An RNase protection strategy demonstrated that the transfected U1 antitarget RNA level varied between 1 to 8% of the endogenous U1 snRNA level. U1 antitarget vectors were demonstrated to have potential as effective inhibitors of gene expression in intact cells. PMID:11283260

  7. Identification of a novel nuclear localization signal and speckle-targeting sequence of tuftelin-interacting protein 11, a splicing factor involved in spliceosome disassembly

    SciTech Connect

    Tannukit, Sissada; Crabb, Tara L.; Hertel, Klemens J.; Wen, Xin; Jans, David A.; Paine, Michael L.

    2009-12-18

    Tuftelin-interacting protein 11 (TFIP11) is a protein component of the spliceosome complex that promotes the release of the lariat-intron during late-stage splicing through a direct recruitment and interaction with DHX15/PRP43. Expression of TFIP11 is essential for cell and organismal survival. TFIP11 contains a G-patch domain, a signature motif of RNA-processing proteins that is responsible for TFIP11-DHX15 interactions. No other functional domains within TFIP11 have been described. TFIP11 is localized to distinct speckled regions within the cell nucleus, although excluded from the nucleolus. In this study sequential C-terminal deletions and mutational analyses have identified two novel protein elements in mouse TFIP11. The first domain covers amino acids 701-706 (VKDKFN) and is an atypical nuclear localization signal (NLS). The second domain is contained within amino acids 711-735 and defines TFIP11's distinct speckled nuclear localization. The identification of a novel TFIP11 nuclear speckle-targeting sequence (TFIP11-STS) suggests that this domain directly interacts with additional spliceosomal components. These data help define the mechanism of nuclear/nuclear speckle localization of the splicing factor TFIP11, with implications for it's function.

  8. Proteins cross-linked to U1 RNA by ultraviolet irradiation

    SciTech Connect

    Marti, A.; Jimenez, R.; Matos, J.

    1987-05-01

    Proteins associated to U1 RNA react with antinuclear antibodies obtained from sera of patients with autoimmune diseases. K.B. cells were labeled with /sup 3/H-amino acids of /sup 3/H-uridine. The U1 RNA particles were immunoprecipitated. Protein and RNA analysis was by electrophoresis and fluorography. The ratio of material at the top of the RNA gel to the U1 RNA band was 0.79. After exposure of the cells to UV irradiation, the ratio was 5.04. A substantial amount of U1 RNA was cross-linked to proteins or other nuclear components. Protein patterns obtained from U1 RNP particles subjected to UV irradiation revealed a change in electrophoretic mobility by four proteins in the molecular range of 14,000 to 28,000 daltons. The 33,000 dalton protein was reduced by 50% but its electrophoretic mobility was unchanged. The protein band at 68,000 daltons was unchanged in amount or mobility by UV irradiation. It is concluded that the low molecular weight proteins (14,000 - 28,000) and the protein of 33,000 daltons are in close proximity to U1 RNA and possibly play a role in the molecular function(s) attributed to U1 RNA.

  9. Functional analysis of U1-70K interacting SR proteins in pre-mRNA splicing in Arabidopsis

    SciTech Connect

    A.S.N. Reddy

    2008-11-25

    Proteins of a serine/arginine-rich (SR) family are part of the spliceosome and are implicated in both constitutive and alternative splicing of pre-mRNAs. With the funding from DOE we have been studying alternative of splicing of genes encoding serine/arginine-rich (SR) proteins and the roles of SR proteins that interact with U1-70K in regulating basic and alternative splicing. Alternative splicing of pre-mRNAs of Arabidopsis serine/arginine-rich proteins and its regulation by hormones and stresses: We analyzed the splicing of all 19 Arabidopsis genes in different tissues, during different seedling stages and in response to various hormonal and stress treatments. Remarkably, about 90 different transcripts are produced from 15 SR genes, thereby increasing the transcriptome complexity of SR genes by about five fold. Using the RNA isolated from polysomes we have shown that most of the splice variants are recruited for translation. Alternative splicing of some SR genes is controlled in a developmental and tissue-specific manner (Palusa et al., 2007). Interestingly, among the various hormones and abiotic stresses tested, temperature stress (cold and heat) and ultraviolet light dramatically altered alternative splicing of pre-mRNAs of several SR genes whereas hormones altered the splicing of only two SR genes (Palusa et al., 2007). Localization and dynamics of a novel serine/arginine-rich protein that interacts with U1-70K: We analyzed the intranuclear movement of SR45 fused to GFP by fluorescence recovery after photobleaching (FRAP) and fluorescence loss in photobleaching (FLIP). We demonstrate that the movement of GFP-SR45 is ATP-dependent. Interestingly, inhibition of transcription or phosphorylation slowed the mobility of GFP-SR45 (Ali et al., 2006). Our studies have revealed that the nuclear localization signals are located in arg/ser-rich domains (RS) 1 and 2, whereas the speckle targeting signals are exclusively present in RS2 (Ali et al., 2006). The regulation of

  10. 40 CFR Table U-1 to Subpart U of... - CO2 Emission Factors for Common Carbonates

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 21 2014-07-01 2014-07-01 false CO2 Emission Factors for Common.... 98, Subpt. U, Table U-1 Table U-1 to Subpart U of Part 98—CO2 Emission Factors for Common Carbonates Mineral name—carbonate CO2 emission factor(tons CO2/ton carbonate) Limestone—CaCO3 0.43971...

  11. 40 CFR Table U-1 to Subpart U of... - CO2 Emission Factors for Common Carbonates

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 22 2013-07-01 2013-07-01 false CO2 Emission Factors for Common.... 98, Subpt. U, Table U-1 Table U-1 to Subpart U of Part 98—CO2 Emission Factors for Common Carbonates Mineral name—carbonate CO2 emission factor(tons CO2/ton carbonate) Limestone—CaCO3 0.43971...

  12. 40 CFR Table U-1 to Subpart U of... - CO2 Emission Factors for Common Carbonates

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 22 2012-07-01 2012-07-01 false CO2 Emission Factors for Common.... 98, Subpt. U, Table U-1 Table U-1 to Subpart U of Part 98—CO2 Emission Factors for Common Carbonates Mineral name—carbonate CO2 emission factor(tons CO2/ton carbonate) Limestone—CaCO3 0.43971...

  13. Structural requirements for the functional activity of a U1 snRNA gene enhancer.

    PubMed Central

    Cheung, C H; Fan, Q N; Stumph, W E

    1993-01-01

    The transcriptional enhancer of a chicken U1 small nuclear RNA (snRNA) gene contains a GC-box, an octamer motif, and an SPH motif that are recognized by the transcription factors Sp1, Oct-1, and SBF respectively. Previous work indicated that the octamer and the SPH motifs were both required for U1 gene enhancer activity in frog oocytes when the U1 gene was coinjected with a competing snRNA gene template. Here we show that neither two copies of the octamer motif, nor two copies of the SPH motif, can effectively substitute for the natural combination of octamer and SPH. Furthermore, neither the octamer nor the SPH motif (in the absence of the other) functioned efficiently in combination with a GC-box. Alteration of the spacing between the octamer and SPH motifs also reduced U1 template activity. Several potential cis-acting elements other than the SPH motif, with one possible exception among those tested, were unable to cooperate with the octamer motif to effectively enhance U1 gene expression. These results indicate that rather stringent structural requirements exist with respect to the essential cis-acting motifs present in the U1 enhancer, possibly reflecting the unique properties of the transcription complexes assembled on snRNA gene promoters. Images PMID:8441636

  14. Closure report for underground storage tank 161-R1U1 and its associated underground piping

    SciTech Connect

    Mallon, B.J.; Blake, R.G.

    1994-05-01

    Underground storage tank (UST) 161-31 R at the Lawrence Livermore National Laboratory (LLNL) was registered with the State Water Resources Control Board on June 27, 1984. UST 161-31R was subsequently renamed UST 161-R1U1 (Fig. A-1, Appendix A). UST 161-R1U1 was installed in 1976, and had a capacity of 383 gallons. This tank system consisted of a fiberglass reinforced plastic tank, approximately 320 feet of polyvinyl chloride (PVC) underground piping from Building 161, and approximately 40 feet of PVC underground piping from Building 160. The underground piping connected laboratory drains and sinks inside Buildings 160 and 161 to UST 161-R1U1. The wastewater collected in UST 161-R1U1, contained organic solvents, metals, inorganic acids, and radionuclides, most of which was produced within Building 161. On June 28, 1989, the UST 161-R1U1 piping system.around the perimeter of Building 161 failed a precision test performed by Gary Peters Enterprises (Appendix B). The 161-R1U1 tank system was removed from service after the precision test. In July 1989, additional hydrostatic tests and helium leak detection tests were performed (Appendix B) to determine the locations of the piping failures in the Building 161 piping system. The locations of the piping system failures are shown in Figure A-2 (Appendix A). On July 11, 1989, LLNL submitted an Unauthorized Release Report to Alameda County Department of Environmental Health (ACDEH), Appendix C.

  15. A diversity of U1 small nuclear RNAs in the silk moth Bombyx mori.

    PubMed

    Sierra-Montes, J M; Pereira-Simon, S; Freund, A V; Ruiz, L M; Szmulewicz, M N; Herrera, R J

    2003-01-01

    Variants of U1 small nuclear RNAs (snRNAs) have been previously detected in a permanent cell line (BmN) of the silk moth Bombyx mori. In this study, the existence of U1 snRNA isoforms in the silk gland (SG) of the organism is investigated. The polyploidy (approximately 200,000X the 2N somatic value) state of the B. mori silk gland cells represents a unique system to explore the potential presence and differential expression of multiple U1 variants in a normal tissue. B. mori U1-specific RT-PCR libraries from the silk gland were generated and five U1 isoforms were isolated and characterized. Nucleotide differences, structural alterations, as well as protein and RNA interaction sites were examined in these variants and compared to the previously reported isoforms from the transformed BmN cell line. In all these SG U1 variants, variant sites and inter-species differences are located in moderately conserved regions. Substitutional or compensatory changes were found in the double stranded areas and clustered in moderately conserved regions. Some of the changes generate stronger base pairing. Calculated free energy (DeltaG) values for the entire U1 snRNA secondary structures and for the individual stem/loops (I, II, III and IV) domains of the isoforms were generated and compared to determine their structural stability. Using phylogenetic analysis, an evolutionary parallelism is observed between the polymorphic sites in B. mori and variant locations found among animal and plant species.

  16. An siRNA Screen Identifies the U2 snRNP Spliceosome as a Host Restriction Factor for Recombinant Adeno-associated Viruses

    PubMed Central

    Schreiber, Claire A.; Sakuma, Toshie; Izumiya, Yoshihiro; Holditch, Sara J.; Hickey, Raymond D.; Bressin, Robert K.; Basu, Upamanyu; Koide, Kazunori; Asokan, Aravind; Ikeda, Yasuhiro

    2015-01-01

    Adeno-associated viruses (AAV) have evolved to exploit the dynamic reorganization of host cell machinery during co-infection by adenoviruses and other helper viruses. In the absence of helper viruses, host factors such as the proteasome and DNA damage response machinery have been shown to effectively inhibit AAV transduction by restricting processes ranging from nuclear entry to second-strand DNA synthesis. To identify host factors that might affect other key steps in AAV infection, we screened an siRNA library that revealed several candidate genes including the PHD finger-like domain protein 5A (PHF5A), a U2 snRNP-associated protein. Disruption of PHF5A expression selectively enhanced transgene expression from AAV by increasing transcript levels and appears to influence a step after second-strand synthesis in a serotype and cell type-independent manner. Genetic disruption of U2 snRNP and associated proteins, such as SF3B1 and U2AF1, also increased expression from AAV vector, suggesting the critical role of U2 snRNP spliceosome complex in this host-mediated restriction. Notably, adenoviral co-infection and U2 snRNP inhibition appeared to target a common pathway in increasing expression from AAV vectors. Moreover, pharmacological inhibition of U2 snRNP by meayamycin B, a potent SF3B1 inhibitor, substantially enhanced AAV vector transduction of clinically relevant cell types. Further analysis suggested that U2 snRNP proteins suppress AAV vector transgene expression through direct recognition of intact AAV capsids. In summary, we identify U2 snRNP and associated splicing factors, which are known to be affected during adenoviral infection, as novel host restriction factors that effectively limit AAV transgene expression. Concurrently, we postulate that pharmacological/genetic manipulation of components of the spliceosomal machinery might enable more effective gene transfer modalities with recombinant AAV vectors. PMID:26244496

  17. A U1-U2 snRNP interaction network during intron definition.

    PubMed

    Shao, Wei; Kim, Hyun-Soo; Cao, Yang; Xu, Yong-Zhen; Query, Charles C

    2012-01-01

    The assembly of prespliceosomes is responsible for selection of intron sites for splicing. U1 and U2 snRNPs recognize 5' splice sites and branch sites, respectively; although there is information regarding the composition of these complexes, little is known about interaction among the components or between the two snRNPs. Here we describe the protein network of interactions linking U1 and U2 snRNPs with the ATPase Prp5, important for branch site recognition and fidelity during the first steps of the reaction, using fission yeast Schizosaccharomyces pombe. The U1 snRNP core protein U1A binds to a novel SR-like protein, Rsd1, which has homologs implicated in transcription. Rsd1 also contacts S. pombe Prp5 (SpPrp5), mediated by SR-like domains in both proteins. SpPrp5 then contacts U2 snRNP through SF3b, mediated by a conserved DPLD motif in Prp5. We show that mutations in this motif have consequences not only in vitro (defects in prespliceosome formation) but also in vivo, yielding intron retention and exon skipping defects in fission yeast and altered intron recognition in budding yeast Saccharomyces cerevisiae, indicating that the U1-U2 network provides critical, evolutionarily conserved contacts during intron definition.

  18. Cytochrome P450 107U1 is required for sporulation and antibiotic production in Streptomyces coelicolor

    PubMed Central

    Tian, Zhenghua; Cheng, Qian; Yoshimoto, Francis K.; Lei, Li; Lamb, David C.; Guengerich, F. Peter

    2013-01-01

    The filamentous bacterium Streptomyces coelicolor has a complex life cycle involving the formation of hair-like aerial mycelia on the colony surface, which differentiate into chains of spores. Genes required for the initiation of aerial mycelium formation have been termed ‘bld’ (bald), describing the smooth, undifferentiated colonies of mutant strains. We report the identification of a new bld gene designated as sco3099 and biochemical analysis of its encoded enzyme, cytochrome P450 (P450, or CYP) 107U1. Deletion of sco3099 resulted in a mutant defective in aerial hyphae sporulation and sensitive to heat shock, indicating that P450 107U1 plays a key role in growth and development of S. coelicolor. This is the first P450 reported to participate in a sporulation process in Streptomycetes. The substrate and catalytic properties of P450 107U1 were further investigated in mass spectrometry-based metabolomic studies. Glycocholic acid (from the medium) was identified as a substrate of P450 107U1 and was oxidized to glyco-7-oxo-deoxycholic acid. Although this reaction is apparently not relevant to the observed sporulation deficiency, it suggests that P450 107U1 might exert its physiological function by oxidizing other steroid-like molecules. PMID:23357279

  19. Phenomenology of dark matter in chiral U(1 ) X dark sector

    NASA Astrophysics Data System (ADS)

    Ko, P.; Nomura, Takaaki

    2016-12-01

    We consider dark matter physics in a model for the dark sector with extra dark U(1 ) X gauge symmetry. The dark sector is composed of exotic fermions that are charged under both dark U(1 ) X and the standard model SU(3 ) C×U (1 )Y gauge groups, as well as standard model singlet complex scalars Φ and X with nonzero U(1 ) X charge. In this model, there are two dark matter candidates—a scalar and a fermion—both of which are stabilized by accidental Z2 symmetry. Their thermal relic density, and direct and indirect detection constraints are discussed in detail and we search for the parameter space of the model accommodating dark matter observations. We also discuss constraints from diphoton resonance searches associated with the scalar field which breaks the dark U(1 ) X , in a way consistent with dark matter physics. In addition, implications for collider physics are discussed, focusing on the production cross section of the scalar boson.

  20. SIMP from a strong U(1) gauge theory with a monopole condensation

    NASA Astrophysics Data System (ADS)

    Kamada, Ayuki; Yamada, Masaki; Yanagida, Tsutomu T.; Yonekura, Kazuya

    2016-09-01

    We provide a variant model of a strongly interacting massive particle (SIMP), where composite dark matter (DM) comes from a strongly interacting U(1) theory. We first explain a non-Abelian version of the model with an additional singlet field, which is mixed with the Higgs field to maintain kinetic equilibrium between the hidden and Standard Model (SM) sectors. The mixing leads to signals that would be detected by future collider experiments, direct DM detection experiments, and beam-dump experiments. Then we investigate a U(1) theory with a scalar monopole, where U(1) charged particles are confined by a monopole condensation. In this model, the radial component of the monopole can mix with the Higgs field, so that we do not need to introduce the additional singlet field.

  1. Modular invariant gaugino condensation in the presence of ananomalous U(1)*

    SciTech Connect

    Gaillard, Mary K.; Giedt, Joel; Mints, Aleksey L.

    2003-12-10

    Starting from the previously constructed effective supergravity theory below the scale of U(1) breaking in orbifold compactifications of the weakly coupled heterotic string, we study the effective theory below the scale of supersymmetry breaking by gaugino and matter condensation in a hidden sector. Questions we address include vacuum stability and the masses of the various moduli fields, including those associated with flat directions at the U(1) breaking scale, and of their fermionic superpartners. The issue of soft supersymmetry-breaking masses in the observable sector presents a particularly serious challenge for this class of models.

  2. Dilatometric study of U1-xAmxO2±δ and U1-xCexO2±δ reactive sintering

    NASA Astrophysics Data System (ADS)

    Horlait, Denis; Feledziak, Alex; Lebreton, Florent; Clavier, Nicolas; Prieur, Damien; Dacheux, Nicolas; Delahaye, Thibaud

    2013-10-01

    In order to reduce the radiotoxicity of nuclear fuel waste, the transmutation of americium in U1-xAmxO2±δ dedicated fuels is considered. A convenient route to produce such fuels is reactive sintering from a UO2+δ/AmO2-δ green pellet, i.e., a single heat treatment during which both the densification and the formation of the U1-xAmxO2±δ solid solution occur. The mechanisms of such sintering are however barely known and require experimental data. In this aim, the densification through reactive sintering of a UO2+δ/AmO2-δ sample was monitored by dilatometry. The obtained results were compared to those reported for the formation of the U1-xAmxO2±δ solid solution monitored by in situ high-temperature X-ray diffraction. To assess the use of Ce as a substitute of Am, similar dilatometric studies were also carried out on UO2+δ/CeO2 pellets. Obtained results show that the use of a reactive sintering causes a delay in the densification process associated to the competition between solid solution formation and densification, which yields limitations in pellet final densities. The importance of redox behavior of Am (or Ce) on the achievement of solid solution formation and densification are also discussed, especially based on discrepancies in densification behavior between UO2+δ/AmO2-δ and UO2+δ/CeO2.

  3. 13. DETAIL, U1 JOINT, FROM BELOW AND SOUTH, SHOWING RIVETED ...

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

    13. DETAIL, U1 JOINT, FROM BELOW AND SOUTH, SHOWING RIVETED CONNECTION, AND INTERSECTION OF END POST, VERTICAL, DIAGONAL AND UPPER CHORD MEMBERS AND LATERAL BRACING - Glendale Road Bridge, Spanning Deep Creek Lake on Glendale Road, McHenry, Garrett County, MD

  4. Draft Genome Sequence of Erythromycin- and Oxytetracycline-Sensitive Nocardia seriolae Strain U-1 (NBRC 110359)

    PubMed Central

    Sukeda, Masaki; Shimizu, Masato; Yamane, Jin; Ohnishi, Kouhei; Oshima, Syun-ichirou

    2016-01-01

    In Japan, the emergence of macrolide- and oxytetracycline-resistant strains of Nocardia seriolae has previously been reported. Here, we describe the draft genome sequence of N. seriolae strain U-1, isolated in 2011 from a diseased yellowtail in Kagoshima Prefecture. The draft genome does not have any genes responsible for macrolide and tetracycline resistance. PMID:26798107

  5. Cluster algorithm for two-dimensional U(1) lattice gauge theory

    NASA Astrophysics Data System (ADS)

    Sinclair, R.

    1992-03-01

    We use gauge fixing to rewrite the two-dimensional U(1) pure gauge model with Wilson action and periodic boundary conditions as a nonfrustrated XY model on a closed chain. The Wolff single-cluster algorithm is then applied, eliminating critical slowing down of topological modes and Polyakov loops.

  6. Classically conformal U(1 ) ' extended standard model, electroweak vacuum stability, and LHC Run-2 bounds

    NASA Astrophysics Data System (ADS)

    Das, Arindam; Oda, Satsuki; Okada, Nobuchika; Takahashi, Dai-suke

    2016-06-01

    We consider the minimal U(1 ) ' extension of the standard model (SM) with the classically conformal invariance, where an anomaly-free U(1 ) ' gauge symmetry is introduced along with three generations of right-handed neutrinos and a U(1 ) ' Higgs field. Since the classically conformal symmetry forbids all dimensional parameters in the model, the U(1 ) ' gauge symmetry is broken by the Coleman-Weinberg mechanism, generating the mass terms of the U(1 ) ' gauge boson (Z' boson) and the right-handed neutrinos. Through a mixing quartic coupling between the U(1 ) ' Higgs field and the SM Higgs doublet field, the radiative U(1 ) ' gauge symmetry breaking also triggers the breaking of the electroweak symmetry. In this model context, we first investigate the electroweak vacuum instability problem in the SM. Employing the renormalization group equations at the two-loop level and the central values for the world average masses of the top quark (mt=173.34 GeV ) and the Higgs boson (mh=125.09 GeV ), we perform parameter scans to identify the parameter region for resolving the electroweak vacuum instability problem. Next we interpret the recent ATLAS and CMS search limits at the LHC Run-2 for the sequential Z' boson to constrain the parameter region in our model. Combining the constraints from the electroweak vacuum stability and the LHC Run-2 results, we find a bound on the Z' boson mass as mZ'≳3.5 TeV . We also calculate self-energy corrections to the SM Higgs doublet field through the heavy states, the right-handed neutrinos and the Z' boson, and find the naturalness bound as mZ'≲7 TeV , in order to reproduce the right electroweak scale for the fine-tuning level better than 10%. The resultant mass range of 3.5 TeV ≲mZ'≲7 TeV will be explored at the LHC Run-2 in the near future.

  7. Dynamic Contacts of U2, RES, Cwc25, Prp8 and Prp45 Proteins with the Pre-mRNA Branch-Site and 3' Splice Site during Catalytic Activation and Step 1 Catalysis in Yeast Spliceosomes

    PubMed Central

    Schneider, Cornelius; Agafonov, Dmitry E.; Schmitzová, Jana; Hartmuth, Klaus; Fabrizio, Patrizia; Lührmann, Reinhard

    2015-01-01

    Little is known about contacts in the spliceosome between proteins and intron nucleotides surrounding the pre-mRNA branch-site and their dynamics during splicing. We investigated protein-pre-mRNA interactions by UV-induced crosslinking of purified yeast Bact spliceosomes formed on site-specifically labeled pre-mRNA, and analyzed their changes after conversion to catalytically-activated B* and step 1 C complexes, using a purified splicing system. Contacts between nucleotides upstream and downstream of the branch-site and the U2 SF3a/b proteins Prp9, Prp11, Hsh49, Cus1 and Hsh155 were detected, demonstrating that these interactions are evolutionarily conserved. The RES proteins Pml1 and Bud13 were shown to contact the intron downstream of the branch-site. A comparison of the Bact crosslinking pattern versus that of B* and C complexes revealed that U2 and RES protein interactions with the intron are dynamic. Upon step 1 catalysis, Cwc25 contacts with the branch-site region, and enhanced crosslinks of Prp8 and Prp45 with nucleotides surrounding the branch-site were observed. Cwc25’s step 1 promoting activity was not dependent on its interaction with pre-mRNA, indicating it acts via protein-protein interactions. These studies provide important insights into the spliceosome's protein-pre-mRNA network and reveal novel RNP remodeling events during the catalytic activation of the spliceosome and step 1 of splicing. PMID:26393790

  8. The Arabidopsis U11/U12-65K is an indispensible component of minor spliceosome and plays a crucial role in U12 intron splicing and plant development.

    PubMed

    Jung, Hyun Ju; Kang, Hunseung

    2014-06-01

    The U12-dependent introns have been identified in a wide range of eukaryotes and are removed from precursor-mRNAs by U12 intron-specific minor spliceosome. Although several proteins unique to minor spliceosome have been identified, the nature of their effect on U12 intron splicing as well as plant growth and development remain largely unknown. Here, we characterized the functional role of an U12-type spliceosomal protein, U11/U12-65K in Arabidopsis thaliana. The transgenic knockdown plants generated by artificial miRNA-mediated silencing strategy exhibited severe defect in growth and development, such as severely arrested primary inflorescence stems, serrated leaves, and the formation of many rosette leaves after bolting. RNA sequencing and reverse transcription polymerase chain reaction (RT-PCR) analyses revealed that splicing of 198 out of the 234 previously predicted U12 intron-containing genes and 32 previously unidentified U12 introns was impaired in u11/u12-65k mutant. Moreover, the U11/U12-65K mutation affected alternative splicing, as well as U12 intron splicing, of many introns. Microarray analysis revealed that the genes involved in cell wall biogenesis and function, plant development, and metabolic processes are differentially expressed in the mutant plants. U11/U12-65K protein bound specifically to U12 small nuclear RNA (snRNA), which is necessary for branch-point site recognition. Taken together, these results provide clear evidence that U11/U12-65K is an indispensible component of minor spliceosome and involved in U12 intron splicing and alternative splicing of many introns, which is crucial for plant development.

  9. Preparation and identification of anti-transforming growth factor β1 U1 small nuclear RNA chimeric ribozyme in vitro

    PubMed Central

    Lin, Ju-Sheng; Song, Yu-Hu; Kong, Xin-Juan; Li, Bin; Liu, Nan-Zhi; Wu, Xiao-Li; Jin, You-Xin

    2003-01-01

    AIM: To study the preparation and cleavage activity of anti-transforming growth factor (TGF)β1 U1 small nuclear (sn) RNA chimeric hammerhead ribozymes in vitro. METHODS: TGFβ1 partial gene fragment was cloned into T-vector at the downstream of T7 promoter. 32p-labeled TGFβ1 partial transcripts as target RNA were transcribed in vitro and purified by denaturing polyacrylamide gel electrophoresis (PAGE). Anti-TGFβ1 ribozymes were designed by computer, then synthetic ribozyme fragments were cloned into the U1 ribozyme vector pZeoU1EcoSpe containing U1 snRNA promoter/enhancer and terminator. 32p-labeled U1 snRNA chimeric ribozyme transcripts were gel-purified, incubated with target-RNAs at different conditions and autoradiographed after running denaturing PAGE. RESULTS: Active U1snRNA chimeric ribozyme (U1Rz803) had the best cleavage activity at 50 °C; at 37 °C, it was active, Km = 34.48 nmol/L, Kcat = 0.14 min-1; while the point mutant ribozyme U1Rz803m had no cleavage activity, so these indicated the design of U1Rz803 was correct. CONCLUSION: U1Rz803 prepared in this study possessed the perfect specific catalytic cleavage activity. These results indicate U1 snRNA chimeric ribozyme U1Rz803 may suppress the expression of TGFβ1 in vivo, therefore it may provide a new avenue for the treatment of liver fibrosis in the future. PMID:12632521

  10. Dirac dark matter and b →s ℓ+ℓ- with U(1) gauge symmetry

    NASA Astrophysics Data System (ADS)

    Celis, Alejandro; Feng, Wan-Zhe; Vollmann, Martin

    2017-02-01

    We revisit the possibility of a Dirac fermion dark matter candidate in the light of current b →s ℓ+ℓ- anomalies by investigating a minimal extension of the Standard Model with a horizontal U(1 ) ' local symmetry. Dark matter stability is protected by a remnant Z2 symmetry arising after spontaneous symmetry breaking of U(1 ) '. The associated Z' gauge boson can accommodate current hints of new physics in b →s ℓ+ℓ- decays, and acts as a vector portal between dark matter and the visible sector. We find that the model is severely constrained by a combination of precision measurements at flavor factories, LHC searches for dilepton resonances, as well as direct and indirect dark matter searches. Despite this, viable regions of the parameter space accommodating the observed dark matter relic abundance and the b →s ℓ+ℓ-anomalies still persist for dark matter and Z ' masses in the TeV range.

  11. Yukawa couplings in SU(3)×SU(2)×U(1) Y orbifold models

    NASA Astrophysics Data System (ADS)

    Casas, J. A.; Muñoz, C.

    1988-09-01

    We analyze the Yukawa couplings of the first SU(3)×SU(2)×U(1) Y orbifold models recently obtained. In these models the rank is naturally lowered due to the presence of a Fayet-Iliopoulos term associated with an “anomalous” U(1) in the four-dimensional theory. It is shown that the phenomenological viability of the models selects a favoured class of vacua. In particular, for the specific examples considered, some twisted fields with one moded oscillator acting, must acquire non-vanishing VEVs. However other possibilities may exist. We also find that all the baryon and lepton violating operators can be, in general, avoided in a completely natural way.

  12. Program package for multicanonical simulations of U(1) lattice gauge theory-Second version

    NASA Astrophysics Data System (ADS)

    Bazavov, Alexei; Berg, Bernd A.

    2013-03-01

    A new version STMCMUCA_V1_1 of our program package is available. It eliminates compatibility problems of our Fortran 77 code, originally developed for the g77 compiler, with Fortran 90 and 95 compilers. New version program summaryProgram title: STMC_U1MUCA_v1_1 Catalogue identifier: AEET_v1_1 Licensing provisions: Standard CPC license, http://cpc.cs.qub.ac.uk/licence/licence.html Programming language: Fortran 77 compatible with Fortran 90 and 95 Computers: Any capable of compiling and executing Fortran code Operating systems: Any capable of compiling and executing Fortran code RAM: 10 MB and up depending on lattice size used No. of lines in distributed program, including test data, etc.: 15059 No. of bytes in distributed program, including test data, etc.: 215733 Keywords: Markov chain Monte Carlo, multicanonical, Wang-Landau recursion, Fortran, lattice gauge theory, U(1) gauge group, phase transitions of continuous systems Classification: 11.5 Catalogue identifier of previous version: AEET_v1_0 Journal Reference of previous version: Computer Physics Communications 180 (2009) 2339-2347 Does the new version supersede the previous version?: Yes Nature of problem: Efficient Markov chain Monte Carlo simulation of U(1) lattice gauge theory (or other continuous systems) close to its phase transition. Measurements and analysis of the action per plaquette, the specific heat, Polyakov loops and their structure factors. Solution method: Multicanonical simulations with an initial Wang-Landau recursion to determine suitable weight factors. Reweighting to physical values using logarithmic coding and calculating jackknife error bars. Reasons for the new version: The previous version was developed for the g77 compiler Fortran 77 version. Compiler errors were encountered with Fortran 90 and Fortran 95 compilers (specified below). Summary of revisions: epsilon=one/10**10 is replaced by epsilon/10.0D10 in the parameter statements of the subroutines u1_bmha.f, u1_mucabmha.f, u1wl

  13. Role of the U(1) ghost beyond leading order in a large-Nc expansion

    SciTech Connect

    Hrayr Matevosyan; Anthony Thomas

    2008-09-01

    The 1/Nc expansion is one of the very few methods we have for generating a systematic expansion of QCD at the energy scale relevant to hadron structure. The present formulation of this theory relies on 't Hooft's double-line notation for calculating the leading order of a diagram in the 1/Nc expansion, where the local SU(Nc) gauge symmetry is substituted by a U(Nc) symmetry and the associated U(1) ghost field is ignored. In the current work we demonstrate the insufficiency of this formulation for describing certain non-planar diagrams. We derive a more complete set of Feynman rules that include the U(1) ghost field and provide a useful tool for calculating both color factors and 1/Nc orders of given color-singlet diagrams.

  14. Kagome Chiral Spin Liquid as a Gauged U(1) Symmetry Protected Topological Phase.

    PubMed

    He, Yin-Chen; Bhattacharjee, Subhro; Pollmann, Frank; Moessner, R

    2015-12-31

    While the existence of a chiral spin liquid (CSL) on a class of spin-1/2 kagome antiferromagnets is by now well established numerically, a controlled theoretical path from the lattice model leading to a low-energy topological field theory is still lacking. This we provide via an explicit construction starting from reformulating a microscopic model for a CSL as a lattice gauge theory and deriving the low-energy form of its continuum limit. A crucial ingredient is the realization that the bosonic spinons of the gauge theory exhibit a U(1) symmetry protected topological (SPT) phase, which upon promoting its U(1) global symmetry to a local gauge structure ("gauging"), yields the CSL. We suggest that such an explicit lattice-based construction involving gauging of a SPT phase can be applied more generally to understand topological spin liquids.

  15. Shaft Sinking at the Nevada Test Site, U1h Shaft Project

    SciTech Connect

    B. Briggs; R. Musick

    2001-03-01

    The U1h Shaft Project is a design/build subcontract to construct one 6.1 meter (m) (20 feet (ft)) finished diameter shaft to a depth of 321.6 m (1,055 ft.) at the Nevada Test Site. Atkinson Construction was subcontracted by Bechtel Nevada to construct the U1h Shaft for the U.S. Department of Energy. The project consists of furnishing and installing the sinking plant, construction of the 321.6 m (1,055 ft.) of concrete lined shaft, development of a shaft station at a depth of 297.5 m (976 ft.), and construction of a loading pocket at the station. The outfitting of the shaft and installation of a new hoist may be incorporated into the project at a later date. This paper will describe the design phase, the excavation and lining operation, shaft station construction and the contractual challenges encountered on this project.

  16. Low energy dynamics of U(1) vortices in systems with cholesteric vacuum structure

    NASA Astrophysics Data System (ADS)

    Peterson, Adam J.; Shifman, Mikhail; Tallarita, Gianni

    2015-02-01

    We discuss flux tubes in systems with U(1) gauge, and spin-orbit locked SO(3) S + L symmetry. The spin-orbit locking is achieved explicitly in the Lagrangian by introducing a parity violating twist term which causes the spontaneous breaking of SO(3) S + L → SO(2) . Additionally, this term causes a spontaneous breaking of the translational symmetry along a particular direction. Thus, the system appears with a cholesteric vacuum under certain conditions of the parameter space. With this term, the system admits U(1) topologically stable vortices with additional structure in the vortex cores. This added structure leads to additional moduli appearing in the low energy dynamics. We determine these solutions and their low energy theory.

  17. D-branes and extended characters in SL(2,R)/U(1)

    NASA Astrophysics Data System (ADS)

    Fotopoulos, Angelos; Niarchos, Vasilis; Prezas, Nikolaos

    2005-03-01

    We present a detailed study of D-branes in the axially gauged SL(2/U(1) coset conformal field theory for integer level k. Our analysis is based on the modular bootstrap approach and utilizes the extended SL(2,R)/U(1) characters and the embedding of the parafermionic coset algebra in the N=2 superconformal algebra. We propose three basic classes of boundary states corresponding to D0-, D1- and D2-branes. We verify that these boundary states satisfy the Cardy consistency conditions and discuss their physical properties. The D0- and D1-branes agree with those found in earlier work by Ribault and Schomerus using different methods (descent from the Euclidean AdS model). The D2-branes are new. They are not, in general, space-filling but extend from the asymptotic circle at infinity up to a minimum distance ρ⩾0 from the tip of the cigar.

  18. The 5'-terminal sequence of U1 RNA complementary to the consensus 5' splice site of hnRNA is single-stranded in intact U1 snRNP particles.

    PubMed Central

    Rinke, J; Appel, B; Blöcker, H; Frank, R; Lührmann, R

    1984-01-01

    The 5'-terminal region of U1 snRNA is highly complementary to the consensus exon-intron regions of hnRNA and it has been suggested that U1 snRNP might play a role in the splicing of the pre-mRNA by intermolecular base-pairing between these regions. Here the secondary structure of the 5' terminus of U1 RNA in the isolated native U1 snRNP particle has been investigated by site-directed enzymatic cleavage of the RNA. Individual oligodeoxynucleotides complementary to various sequences within the first 15 nucleotides of the 5' terminus of U1 RNA have been tested for their ability to form stable DNA X RNA hybrids, with subsequent cleavage of the U1 RNA by RNase H. Our results show unequivocally that the 9 nucleotides at the 5' terminus which are complementary to a consensus 5' splice site are indeed single-stranded in the intact U1 snRNP particle, and are not protected by snRNP proteins. However, they also indicate that the U1 sequence complementary to an intron's consensus 3' end is not readily available for intermolecular base-pairing, either in the intact U1 snRNP particle or in the deproteinized U1 RNA molecule. Therefore our data favour the possibility that U1 snRNP plays a role only in the recognition of a 5' splice site of hnRNA, rather than being involved in the alignment of both ends of an intron for splicing. Images PMID:6203096

  19. Slavnov and Gaudin-Korepin Formulas for Models without U(1) Symmetry: the Twisted XXX Chain

    NASA Astrophysics Data System (ADS)

    Belliard, Samuel; Pimenta, Rodrigo A.

    2015-12-01

    We consider the XXX spin-1/2 Heisenberg chain on the circle with an arbitrary twist. We characterize its spectral problem using the modified algebraic Bethe anstaz and study the scalar product between the Bethe vector and its dual. We obtain modified Slavnov and Gaudin-Korepin formulas for the model. Thus we provide a first example of such formulas for quantum integrable models without U(1) symmetry characterized by an inhomogenous Baxter T-Q equation.

  20. A local formulation of lattice Wess-Zumino model with exact U(1)R symmetry

    NASA Astrophysics Data System (ADS)

    Kikukawa, Yoshio; Suzuki, Hiroshi

    2005-02-01

    A lattice Wess-Zumino model is formulated on the basis of Ginsparg-Wilson fermions. In perturbation theory, our formulation is equivalent to the formulation by Fujikawa and Ishibashi and by Fujikawa. Our formulation is, however, free from a singular nature of the latter formulation due to an additional auxiliary chiral supermultiplet on a lattice. The model posssesses an exact U(1)R symmetry as a supersymmetric counterpart of the Lüscher lattice chiral U(1) symmetry. A restration of the supersymmetric Ward-Takahashi identity in the continuum limit is analyzed in renormalized perturbation theory. In the one-loop level, a supersymmetric continuum limit is ensured by suitably adjusting a coefficient of a single local term tilde F*tilde F. The non-renormalization theorem holds to this order of perturbation theory. In higher orders, on the other hand, coefficents of local terms with dimension <= 4 that are consistent with the U(1)R symmetry have to be adjusted for a supersymmetric continuum limit. The origin of this complexicity in higher-order loops is clarified on the basis of the Reisz power counting theorem. Therefore, from a view point of supersymmetry, the present formulation is not quite better than a lattice Wess-Zumino model formulated by using Wilson fermions, although a number of coefficients which require adjustment is much less due to the exact U(1)R symmetry. We also comment on an exact non-linear fermionic symmetry which corresponds to the one studied by Bonini and Feo; an existence of this exact symmetry itself does not imply a restoration of supersymmetry in the continuum limit without any adjustment of parameters.

  1. A conserved intronic U1 snRNP-binding sequence promotes trans-splicing in Drosophila.

    PubMed

    Gao, Jun-Li; Fan, Yu-Jie; Wang, Xiu-Ye; Zhang, Yu; Pu, Jia; Li, Liang; Shao, Wei; Zhan, Shuai; Hao, Jianjiang; Xu, Yong-Zhen

    2015-04-01

    Unlike typical cis-splicing, trans-splicing joins exons from two separate transcripts to produce chimeric mRNA and has been detected in most eukaryotes. Trans-splicing in trypanosomes and nematodes has been characterized as a spliced leader RNA-facilitated reaction; in contrast, its mechanism in higher eukaryotes remains unclear. Here we investigate mod(mdg4), a classic trans-spliced gene in Drosophila, and report that two critical RNA sequences in the middle of the last 5' intron, TSA and TSB, promote trans-splicing of mod(mdg4). In TSA, a 13-nucleotide (nt) core motif is conserved across Drosophila species and is essential and sufficient for trans-splicing, which binds U1 small nuclear RNP (snRNP) through strong base-pairing with U1 snRNA. In TSB, a conserved secondary structure acts as an enhancer. Deletions of TSA and TSB using the CRISPR/Cas9 system result in developmental defects in flies. Although it is not clear how the 5' intron finds the 3' introns, compensatory changes in U1 snRNA rescue trans-splicing of TSA mutants, demonstrating that U1 recruitment is critical to promote trans-splicing in vivo. Furthermore, TSA core-like motifs are found in many other trans-spliced Drosophila genes, including lola. These findings represent a novel mechanism of trans-splicing, in which RNA motifs in the 5' intron are sufficient to bring separate transcripts into close proximity to promote trans-splicing.

  2. Dark Matter in Supersymmetric U(1){sub B-L} Model

    SciTech Connect

    Khalil, S.; Okada, H.

    2009-04-17

    We analyze the dark matter problem in the context of supersymmetric, U(1){sub B-L} model. In this model, the lightest neutalino can be B-L gaugino Z-tilde{sub B-L} or Higgsinos {chi}-tilde{sub 1,2} dominated. We examine the thermal relic abundance of these particles and discuss the prospects for their direct detection if they form part of our galactic halo.

  3. Minimal flavor violation in the minimal U(1)B-L model and resonant leptogenesis

    NASA Astrophysics Data System (ADS)

    Okada, Nobuchika; Orikasa, Yuta; Yamada, Toshifumi

    2012-10-01

    We investigate the resonant leptogenesis scenario in the minimally U(1)B-L extended standard model with minimal flavor violation. In our model, the U(1)B-L gauge symmetry is broken at the TeV scale and standard model singlet neutrinos gain Majorana masses of order TeV. In addition, we introduce a flavor symmetry on the singlet neutrinos at a scale higher than TeV. The flavor symmetry is explicitly broken by the neutrino Dirac Yukawa coupling, which induces splittings in the singlet neutrino Majorana masses at lower scales through renormalization group evolutions. We call this setup minimal flavor violation. The mass splittings are proportional to the tiny Dirac Yukawa coupling, and hence they automatically enhance the CP asymmetry parameter necessary for the resonant leptogenesis mechanism. In this paper, we calculate the baryon number yield by solving the Boltzmann equations, including the effects of U(1)B-L gauge boson that also has TeV scale mass and causes washing-out of the singlet neutrinos in the course of thermal leptogenesis. The Dirac Yukawa coupling for neutrinos is fixed in terms of neutrino oscillation data and an arbitrary 3×3 complex-valued orthogonal matrix. We show that the right amount of baryon number asymmetry can be achieved through thermal leptogenesis in the context of the minimal flavor violation with singlet neutrinos and U(1)B-L gauge boson at the TeV scale. These particles can be discovered at the LHC in the near future.

  4. Structural basis for the recognition of spliceosomal SmN/B/B’ proteins by the RBM5 OCRE domain in splicing regulation

    PubMed Central

    Mourão, André; Bonnal, Sophie; Soni, Komal; Warner, Lisa; Bordonné, Rémy; Valcárcel, Juan; Sattler, Michael

    2016-01-01

    The multi-domain splicing factor RBM5 regulates the balance between antagonistic isoforms of the apoptosis-control genes FAS/CD95, Caspase-2 and AID. An OCRE (OCtamer REpeat of aromatic residues) domain found in RBM5 is important for alternative splicing regulation and mediates interactions with components of the U4/U6.U5 tri-snRNP. We show that the RBM5 OCRE domain adopts a unique β–sheet fold. NMR and biochemical experiments demonstrate that the OCRE domain directly binds to the proline-rich C-terminal tail of the essential snRNP core proteins SmN/B/B’. The NMR structure of an OCRE-SmN peptide complex reveals a specific recognition of poly-proline helical motifs in SmN/B/B’. Mutation of conserved aromatic residues impairs binding to the Sm proteins in vitro and compromises RBM5-mediated alternative splicing regulation of FAS/CD95. Thus, RBM5 OCRE represents a poly-proline recognition domain that mediates critical interactions with the C-terminal tail of the spliceosomal SmN/B/B’ proteins in FAS/CD95 alternative splicing regulation. DOI: http://dx.doi.org/10.7554/eLife.14707.001 PMID:27894420

  5. CTNNBL1 facilitates the association of CWC15 with CDC5L and is required to maintain the abundance of the Prp19 spliceosomal complex

    PubMed Central

    van Maldegem, Febe; Maslen, Sarah; Johnson, Christopher M.; Chandra, Anita; Ganesh, Karuna; Skehel, Mark; Rada, Cristina

    2015-01-01

    In order to catalyse the splicing of messenger RNA, multiple proteins and RNA components associate and dissociate in a dynamic highly choreographed process. The Prp19 complex is a conserved essential part of the splicing machinery thought to facilitate the conformational changes the spliceosome undergoes during catalysis. Dynamic protein interactions often involve highly disordered regions that are difficult to study by structural methods. Using amine crosslinking and hydrogen–deuterium exchange coupled to mass spectrometry, we describe the architecture of the Prp19 sub-complex that contains CTNNBL1. Deficiency in CTNNBL1 leads to delayed initiation of cell division and embryonic lethality. Here we show that in vitro CTNNBL1 enhances the association of CWC15 and CDC5L, both core Prp19 complex proteins and identify an overlap in the region of CDC5L that binds either CTNNBL1 or CWC15 suggesting the two proteins might exchange places in the complex. Furthermore, in vivo, CTNNBL1 is required to maintain normal levels of the Prp19 complex and to facilitate the interaction of CWC15 with CDC5L. Our results identify a chaperone function for CTNNBL1 within the essential Prp19 complex, a function required to maintain the integrity of the complex and to support efficient splicing. PMID:26130721

  6. FIMP and muon ( g - 2) in a U(1) Lμ- Lτ model

    NASA Astrophysics Data System (ADS)

    Biswas, Anirban; Choubey, Sandhya; Khan, Sarif

    2017-02-01

    The tightening of the constraints on the standard thermal WIMP scenario has forced physicists to propose alternative dark matter (DM) models. One of the most popular alternate explanations of the origin of DM is the non-thermal production of DM via freeze-in. In this scenario the DM never attains thermal equilibrium with the thermal soup because of its feeble coupling strength (˜10-12) with the other particles in the thermal bath and is generally called the Feebly Interacting Massive Particle (FIMP). In this work, we present a gauged U(1) Lμ- Lτ extension of the Standard Model (SM) which has a scalar FIMP DM candidate and can consistently explain the DM relic density bound. In addition, the spontaneous breaking of the U(1) Lμ- Lτ gauge symmetry gives an extra massive neutral gauge boson Z μτ which can explain the muon ( g - 2) data through its additional one-loop contribution to the process. Lastly, presence of three right-handed neutrinos enable the model to successfully explain the small neutrino masses via the Type-I seesaw mechanism. The presence of the spontaneously broken U(1) Lμ- Lτ gives a particular structure to the light neutrino mass matrix which can explain the peculiar mixing pattern of the light neutrinos.

  7. Engineering assessment and certification of integrity of the 325-I1U1 tank system

    SciTech Connect

    Schwartz, W W; Graser, D A

    1991-12-01

    This Engineering Assessment and Certification of Integrity of retention tank 325-I1U1 of Lawrence Livermore Laboratory has been prepared in response to 40 CFR 265.191 for an existing tank system that stores hazardous waste and does not have secondary containment. This technical assessment has been reviewed by an independent, qualified, California-registered professional engineer, who has certified the tank system to be adequately designed and compatible with the stored waste so that it will not collapse, rupture, or fail. Certification of the 325-I1U1 tank system is qualified by the fact that 40 CFR 265-193 requires that a system be upgraded to include secondary containment when it reaches 15 years of age or within two years after January 12, 1987, whichever comes later. Tank 325-I1U1 was built in 1968 and required upgrading to secondary containment by January 12, 1989. This Engineering Assessment has been prepared as Best Management practice since this tank system was in service after January 12, 1989, but is not in use at this time. This document will be kept on file at the facility. Certification and documentation of the onground retention tank 325-I1O1, which is part of the 325-I1 retention tank system, is not included in this assessment. A discussion of tank 325-I1O1, however, is included in this report to provide a complete description of the 325-I1 retention tank system.

  8. Mixed-state form factors of U(1) twist fields in the Dirac theory

    NASA Astrophysics Data System (ADS)

    Chen, Yixiong

    2016-08-01

    Using the ‘Liouville space’ (the space of operators) of the massive Dirac theory, we define mixed-state form factors of U(1) twist fields. We consider mixed states with density matrices diagonal in the asymptotic particle basis. This includes the thermal Gibbs state as well as all generalized Gibbs ensembles of the Dirac theory. When the mixed state is specialized to a thermal Gibbs state, using a Riemann-Hilbert problem and low-temperature expansion, we obtain finite-temperature form factors of U(1) twist fields. We then propose the expression for form factors of U(1) twist fields in general diagonal mixed states. We verify that these form factors satisfy a system of nonlinear functional differential equations, which is derived from the trace definition of mixed-state form factors. At last, under weak analytic conditions on the eigenvalues of the density matrix, we write down the large distance form factor expansions of two-point correlation functions of these twist fields. Using the relation between the Dirac and Ising models, this provides the large-distance expansion of the Rényi entropy (for integer Rényi parameter) in the Ising model in diagonal mixed states.

  9. Cation and Vacancy Disorder in U1-yNdyO2.00-X Alloys

    DOE PAGES

    Barabash, Rozaliya I.; Voit, Stewart L.; Aidhy, Dilpuneet S.; ...

    2015-09-14

    In this study, the intermixing and clustering of U/Nd, O, and vacancies were studied by both laboratory and synchrotron-based x-ray diffraction in U1-yNdyO2-X alloys. It was found that an increased holding time at the high experimental temperature during initial alloy preparation results in a lower disorder of the Nd distribution in the alloys. Adjustment of the oxygen concentration in the U1-yNdyO2-X alloys with different Nd concentrations was accompanied by the formation of vacancies on the oxygen sublattice and a nanocrystalline component. The lattice parameters in the U1-yNdyO2-X alloys were also found to deviate significantly from Vegard's law when the Ndmore » concentration was high (53%) and decreased with increasing oxygen concentration. Such changes indicate the formation of large vacancy concentrations during oxygen adjustment at these high temperatures. Finally, the change in the vacancy concentration after the oxygen adjustment was estimated relative to Nd concentration and oxygen stoichiometry.« less

  10. Geology of the U-1a. 01 horizontal drift complex, southwestern Yucca Flat, Nevada Test Site

    SciTech Connect

    Drellack, S.L. Jr.; Thompson, P.H.; Rayburn, C.J.

    1989-03-01

    The U-1a.01 complex, site of a Los Alamos National Laboratory-sponsored experiment, is located in southwestern Yucca Flat on the Nevada Test Site. The complex is comprised of the vertical U-1a shaft, two large-diameter cable access holes, and approximately 229 m (750') of horizontal drift mined within alluvium 292.6 m (960') below the surface. Geologic mapping and related work at U-1a.01 afforded a unique opportunity to observe and evaluate the characteristics of alluvium in the subsurface of Yucca Flat, and to compare the results with surface and drill hole alluvium data. The Los Alamos Support Group of the Fenix and Scisson, Inc. Geology and Hydrology Division carried out a program of mapping, sampling and photography while mining was in progress, with the dual purpose of characterizing the geology of the site and documenting the mining operation. This report details the products and the results of that effort. 12 refs., 8 figs., 25 tabs.

  11. The PSI–U1 snRNP interaction regulates male mating behavior in Drosophila

    PubMed Central

    Wang, Qingqing; Taliaferro, J. Matthew; Klibaite, Ugne; Hilgers, Valérie; Shaevitz, Joshua W.; Rio, Donald C.

    2016-01-01

    Alternative pre-mRNA splicing (AS) is a critical regulatory mechanism that operates extensively in the nervous system to produce diverse protein isoforms. Fruitless AS isoforms have been shown to influence male courtship behavior, but the underlying mechanisms are unknown. Using genome-wide approaches and quantitative behavioral assays, we show that the P-element somatic inhibitor (PSI) and its interaction with the U1 small nuclear ribonucleoprotein complex (snRNP) control male courtship behavior. PSI mutants lacking the U1 snRNP-interacting domain (PSIΔAB mutant) exhibit extended but futile mating attempts. The PSIΔAB mutant results in significant changes in the AS patterns of ∼1,200 genes in the Drosophila brain, many of which have been implicated in the regulation of male courtship behavior. PSI directly regulates the AS of at least one-third of these transcripts, suggesting that PSI–U1 snRNP interactions coordinate the behavioral network underlying courtship behavior. Importantly, one of these direct targets is fruitless, the master regulator of courtship. Thus, PSI imposes a specific mode of regulatory control within the neuronal circuit controlling courtship, even though it is broadly expressed in the fly nervous system. This study reinforces the importance of AS in the control of gene activity in neurons and integrated neuronal circuits, and provides a surprising link between a pleiotropic pre-mRNA splicing pathway and the precise control of successful male mating behavior. PMID:27114556

  12. U1-RNP and TLR receptors in the pathogenesis of mixed connective tissue diseasePart I. The U1-RNP complex and its biological significance in the pathogenesis of mixed connective tissue disease.

    PubMed

    Paradowska-Gorycka, Agnieszka

    2015-01-01

    Mixed connective tissue disease (MCTD) is a rare autoimmune syndrome, signified by complex interactions between disease-related phenomena, including inflammation, proliferative vascular arteriopathy, thrombotic events and humoral autoimmune processes. It is still controversial whether MCTD is a distinct clinical entity among systemic connective tissue diseases, although several authors consider that it is distinct and underline characteristic, distinct clinical, serological and immunogenetic features. The putative target of autoimmunity in MCTD is U1-RNP, which is a complex of U1-RNA and small nuclear RNP. Both the U1-RNA component and the specific proteins, particularly U1-70K, engage immune cells and their receptors in a complex network of interactions that ultimately lead to autoimmunity, inflammation, and tissue injury. U1-RNA is capable of inducing manifestations consistent with TLR activation. Stimulation of innate immunity by native RNA molecules with a double-stranded secondary structure may help explain the high prevalence of autoimmunity to RNA binding proteins.

  13. Peccei-Quinn invariant singlet extended SUSY with anomalous U(1) gauge symmetry

    NASA Astrophysics Data System (ADS)

    Im, Sang Hui; Seo, Min-Seok

    2015-05-01

    Recent discovery of the SM-like Higgs boson with m h ≃ 125 GeV motivates an extension of the minimal supersymmetric standard model (MSSM), which involves a singlet Higgs superfield with a sizable Yukawa coupling to the doublet Higgs superfields. We examine such singlet-extended SUSY models with a Peccei-Quinn (PQ) symmetry that originates from an anomalous U(1) A gauge symmetry. We focus on the specific scheme that the PQ symmetry is spontaneously broken at an intermediate scale v PQ ˜ m SUSY M Pl by an interplay between Planck scale suppressed operators and tachyonic soft scalar mass induced dominantly by the U(1) A D-term D A . This scheme also results in spontaneous SUSY breaking in the PQ sector, generating the gaugino masses when it is transmitted to the MSSM sector by the conventional gauge mediation mechanism. As a result, the MSSM soft parameters in this scheme are induced mostly by the U(1) A D-term and the gauge mediated SUSY breaking from the PQ sector, so that the sparticle masses can be near the present experimental bounds without causing the SUSY flavor problem. The scheme is severely constrained by the condition that a phenomenologically viable form of the low energy operators of the singlet and doublet Higgs superfields is generated by the PQ breaking sector in a way similar to the Kim-Nilles solution of the μ problem, and the resulting Higgs mass parameters allow the electroweak symmetry breaking with small tan β. We find two minimal models with two singlet Higgs superfields, satisfying this condition with a relatively simple form of the PQ breaking sector, and briefly discuss some phenomenological aspects of the model.

  14. Atomic quantum simulation of a three-dimensional U(1) gauge-Higgs model

    NASA Astrophysics Data System (ADS)

    Kuno, Yoshihito; Sakane, Shinya; Kasamatsu, Kenichi; Ichinose, Ikuo; Matsui, Tetsuo

    2016-12-01

    In this paper, we study theoretically atomic quantum simulations of a U(1) gauge-Higgs model on a three-dimensional (3D) spatial lattice by using an extended Bose-Hubbard model with intersite repulsions on a 3D optical lattice. Here, the phase and density fluctuations of the boson variable on each site of the optical lattice describe the vector potential and the electric field on each link of the gauge-model lattice, respectively. The target gauge model is different from the standard Wilson-type U(1) gauge-Higgs model because it has plaquette and Higgs interactions with asymmetric couplings in the space-time directions. Nevertheless, the corresponding quantum simulation is still important as it provides us with a platform to study unexplored time-dependent phenomena characteristic of each phase in the general gauge-Higgs models. To determine the phase diagram of the gauge-Higgs model at zero temperature, we perform Monte Carlo simulations of the corresponding 3+1-dimensional U(1) gauge-Higgs model, and obtain the confinement and Higgs phases. To investigate the dynamical properties of the gauge-Higgs model, we apply the Gross-Pitaevskii equations to the extended Bose-Hubbard model. We simulate the time evolution of an electric flux that initially is put on a straight line connecting two external point charges. We also calculate the potential energy between this pair of charges and obtain the string tension in the confinement phase. Finally, we propose a feasible experimental setup for the atomic simulations of this quantum gauge-Higgs model on the 3D optical lattice. These results may serve as theoretical guides for future experiments.

  15. Systematic U(1 ) B - L extensions of loop-induced neutrino mass models with dark matter

    NASA Astrophysics Data System (ADS)

    Ho, Shu-Yu; Toma, Takashi; Tsumura, Koji

    2016-08-01

    We study the gauged U(1 ) B - L extensions of the models for neutrino masses and dark matter. In this class of models, tiny neutrino masses are radiatively induced through the loop diagrams, while the origin of the dark matter stability is guaranteed by the remnant of the gauge symmetry. Depending on how the lepton number conservation is violated, these models are systematically classified. We present complete lists for the one-loop Z2 and the two-loop Z3 radiative seesaw models as examples of the classification. The anomaly cancellation conditions in these models are also discussed.

  16. Decaying neutralino dark matter in anomalous U(1){sub H} models

    SciTech Connect

    Sierra, D. Aristizabal; Restrepo, D.; Zapata, Oscar

    2009-09-01

    In supersymmetric models extended with an anomalous U(1){sub H} different R-parity violating couplings can yield an unstable neutralino. We show that in this context astrophysical and cosmological constraints on neutralino decaying dark matter forbid bilinear R-parity breaking neutralino decays and lead to a class of purely trilinear R-parity violating scenarios in which the neutralino is stable on cosmological scales. We have found that among the resulting models some of them become suitable to explain the observed anomalies in cosmic-ray electron/positron fluxes.

  17. U(1)-invariant membranes: The geometric formulation, Abel, and pendulum differential equations

    SciTech Connect

    Zheltukhin, A. A.; Trzetrzelewski, M.

    2010-06-15

    The geometric approach to study the dynamics of U(1)-invariant membranes is developed. The approach reveals an important role of the Abel nonlinear differential equation of the first type with variable coefficients depending on time and one of the membrane extendedness parameters. The general solution of the Abel equation is constructed. Exact solutions of the whole system of membrane equations in the D=5 Minkowski space-time are found and classified. It is shown that if the radial component of the membrane world vector is only time dependent, then the dynamics is described by the pendulum equation.

  18. Vibrationally resolved 2a 2u-1 photoionization of C 6F 6

    NASA Astrophysics Data System (ADS)

    Wu, Chuanyong; Poliakoff, E. D.

    1998-07-01

    We report vibrationally resolved results on 2a 2u-1 photoionization of C 6F 6. Vibrational branching ratios are determined for the ring breathing mode by measuring dispersed fluorescence spectra of the C 6F 6+ ( B˜ 2A2 u→ X˜ 2E1 g) transition. Data are presented in the excitation energy range from 20 to 35 eV, and the vibrational branching ratios show a striking departure from Franck-Condon behavior from 20 to 25 eV. This deviation is attributed to a shape resonance.

  19. Fermion masses and mixing in SU(5)×D4 × U(1) model

    NASA Astrophysics Data System (ADS)

    Ahl Laamara, R.; Loualidi, M. A.; Miskaoui, M.; Saidi, E. H.

    2017-03-01

    We propose a supersymmetric SU (5) ×Gf GUT model with flavor symmetry Gf =D4 × U (1) providing a good description of fermion masses and mixing. The model has twenty eight free parameters, eighteen are fixed to produce approximative experimental values of the physical parameters in the quark and charged lepton sectors. In the neutrino sector, the TBM matrix is generated at leading order through type I seesaw mechanism, and the deviation from TBM studied to reconcile with the phenomenological values of the mixing angles. Other features in the charged sector such as Georgi-Jarlskog relations and CKM mixing matrix are also studied.

  20. Renormalization of Tensorial Group Field Theories: Abelian U(1) Models in Four Dimensions

    NASA Astrophysics Data System (ADS)

    Carrozza, Sylvain; Oriti, Daniele; Rivasseau, Vincent

    2014-04-01

    We tackle the issue of renormalizability for Tensorial Group Field Theories (TGFT) including gauge invariance conditions, with the rigorous tool of multi-scale analysis, to prepare the ground for applications to quantum gravity models. In the process, we define the appropriate generalization of some key QFT notions, including connectedness, locality and contraction of (high) subgraphs. We also define a new notion of Wick ordering, corresponding to the subtraction of (maximal) melonic tadpoles. We then consider the simplest examples of dynamical 4-dimensional TGFT with gauge invariance conditions for the Abelian U(1) case. We prove that they are super-renormalizable for any polynomial interaction.

  1. Gaussian effective potential for the standard model SU(2)xU(1) electroweak theory

    SciTech Connect

    Siringo, Fabio; Marotta, Luca

    2008-07-01

    The Gaussian effective potential is derived for the non-Abelian SU(2)xU(1) gauge theory of electroweak interactions. At variance with naive derivations, the Gaussian effective potential is proven to be a genuine variational tool in any gauge. The role of ghosts is discussed and the unitarity gauge is shown to be the only choice which allows calculability without insertion of further approximations. The full non-Abelian calculation confirms the existence of a light Higgs boson in the nonperturbative strong coupling regime of the Higgs sector.

  2. U(1){sub R} mediation from the flux compactification in six dimensions

    SciTech Connect

    Lee, Hyun Min

    2008-11-23

    We consider a supersymmetric completion of codimension-two branes with nonzero tension in a 6D gauged supergravity. As a consequence, we obtain the football solution with 4D Minkowski space as a new supersymmetric background that preserves 4D N = 1 SUSY. In the presence of brane multiplets, we derive the 4D effective supergravity action for the football background and show that the remaining modulus can be stabilized by a bulk non-perturbative correction with brane uplifting potentials at a zero vacuum energy. We find that the U(1){sub R} mediation can be a dominant source of SUSY breaking for a brane scalar with nonzero R charge.

  3. Deconfinement Phase Transition in a 3D Nonlocal U(1) Lattice Gauge Theory

    SciTech Connect

    Arakawa, Gaku; Ichinose, Ikuo; Matsui, Tetsuo; Sakakibara, Kazuhiko

    2005-06-03

    We introduce a 3D compact U(1) lattice gauge theory having nonlocal interactions in the temporal direction, and study its phase structure. The model is relevant for the compact QED{sub 3} and strongly correlated electron systems like the t-J model of cuprates. For a power-law decaying long-range interaction, which simulates the effect of gapless matter fields, a second-order phase transition takes place separating the confinement and deconfinement phases. For an exponentially decaying interaction simulating matter fields with gaps, the system exhibits no signals of a second-order transition.

  4. Analysis of the CD2 and spliceosomal Sm B/B' polyproline-arginine motifs defined by a monoclonal antibody using a phage-displayed random peptide library.

    PubMed

    Monos, Dimitri; Heliopoulos, John; Argyris, Elias; Cordopatis, Paul; Zompra, Aikaterini; Kamoun, Malek

    2006-01-01

    The cytoplasmic region of the CD2 receptor of lymphocytes contains proline-rich motifs, which are involved in T cell activation and interleukin-2 production. An intracellular CD2 binding protein, CD2BP2, interacts with two tandem PPPPGHR segments of the CD2 tail. CD2BP2 contains a GYF (glycine-tyrosine-phenylalanine) domain that confers binding to these proline-rich sequences. Monoclonal antibody 3E10 that was previously raised against a peptide containing the CD2 PPPPGHR segment reacts with the native CD2 molecule and spliceosomal Sm B/B' proteins. To identify the exact epitope on the CD2 peptide recognized by 3E10, a phage-displayed combinatorial peptide library was used. Analysis of the selected clones revealed that the mAb 3E10 binds preferentially to the motif PxxPPGxR. Experiments using amino acid substitutions with synthetic peptides confirmed the reactivity of mAb 3E10 with this motif. In addition, we show that several similarities exist between this motif and the CD2BP2-GFY recognition motif PPGxR/K. Binding of antibody 3E10 indicates some degree of degeneracy, which is consistent with its ability to recognize structurally related polyproline-arginine motifs found in intracellular proteins including Sm B/B' proteins and other RNA binding proteins. Thus, mAb 3E10 can be used to specifically identify a sub-class of proline-rich motifs, and as such can be used to study the potential role of these proline-rich sequences in mediating protein-protein interactions.

  5. Defective control of pre–messenger RNA splicing in human disease

    PubMed Central

    Shkreta, Lulzim

    2016-01-01

    Examples of associations between human disease and defects in pre–messenger RNA splicing/alternative splicing are accumulating. Although many alterations are caused by mutations in splicing signals or regulatory sequence elements, recent studies have noted the disruptive impact of mutated generic spliceosome components and splicing regulatory proteins. This review highlights recent progress in our understanding of how the altered splicing function of RNA-binding proteins contributes to myelodysplastic syndromes, cancer, and neuropathologies. PMID:26728853

  6. Defective control of pre-messenger RNA splicing in human disease.

    PubMed

    Chabot, Benoit; Shkreta, Lulzim

    2016-01-04

    Examples of associations between human disease and defects in pre-messenger RNA splicing/alternative splicing are accumulating. Although many alterations are caused by mutations in splicing signals or regulatory sequence elements, recent studies have noted the disruptive impact of mutated generic spliceosome components and splicing regulatory proteins. This review highlights recent progress in our understanding of how the altered splicing function of RNA-binding proteins contributes to myelodysplastic syndromes, cancer, and neuropathologies.

  7. The neutralino sector in the U(1)-extended supersymmetric Standard Model

    NASA Astrophysics Data System (ADS)

    Choi, S. Y.; Haber, H. E.; Kalinowski, J.; Zerwas, P. M.

    2007-08-01

    Motivated by grand unified theories and string theories we analyze the general structure of the neutralino sector in the USSM, an extension of the minimal supersymmetric Standard Model that involves a broken extra U(1) gauge symmetry. This supersymmetric U(1)-extended model includes an Abelian gauge superfield and a Higgs singlet superfield in addition to the standard gauge and Higgs superfields of the MSSM. The interactions between the MSSM fields and the new fields are in general weak and the mixing is small, so that the coupling of the two subsystems can be treated perturbatively. As a result, the mass spectrum and mixing matrix in the neutralino sector can be analyzed analytically and the structure of this 6-state system is under good theoretical control. We describe the decay modes of the new states and the impact of this extension on decays of the original MSSM neutralinos, including radiative transitions in cross-over zones. Production channels in cascade decays at the LHC and pair production at ee colliders are also discussed.

  8. Fermion mass hierarchy and nonhierarchical mass ratios in SU(5)xU(1){sub F}

    SciTech Connect

    Duque, Luis F.; Gutierrez, Diego A.; Nardi, Enrico; Norena, Jorge

    2008-08-01

    We consider a SU(5)xU(1){sub F} grand unified theory (GUT)-flavor model in which the number of effects that determine the charged fermions Yukawa matrices is much larger than the number of observables, resulting in a hierarchical fermion spectrum with no particular regularities. The GUT-flavor symmetry is broken by flavons in the adjoint of SU(5), realizing a variant of the Froggatt-Nielsen mechanism that gives rise to a large number of effective operators. By assuming a common mass for the heavy fields and universality of the fundamental Yukawa couplings, we reduce the number of free parameters to one. The observed fermion mass spectrum is reproduced thanks to selection rules that discriminate among various contributions. Bottom-tau Yukawa unification is preserved at leading order, but there is no unification for the first two families. Interestingly, U(1){sub F} charges alone do not determine the hierarchy, and can only give upper bounds on the parametric suppression of the Yukawa operators.

  9. Z ', Higgses and heavy neutrinos in U(1)' models: from the LHC to the GUT scale

    NASA Astrophysics Data System (ADS)

    Accomando, Elena; Corianò, Claudio; Rose, Luigi Delle; Fiaschi, Juri; Marzo, Carlo; Moretti, Stefano

    2016-07-01

    We study a class of non-exotic minimal U(1)' extensions of the Standard Model, which includes all scenarios that are anomaly-free with the ordinary fermion content augmented by one Right-Handed neutrino per generation, wherein the new Abelian gauge group is spontaneously broken by the non-zero Vacuum Expectation Value of an additional Higgs singlet field, in turn providing mass to a Z ' state. By adopting the B - L example, whose results can be recast into those pertaining to the whole aforementioned class, and allowing for both scalar and gauge mixing, we first extract the surviving parameter space in presence of up-to-date theoretical and experimental constraints. Over the corresponding parameter configurations, we then delineate the high energy behaviour of such constructs in terms of their stability and perturbativity. Finally, we highlight key production and decay channels of the new states entering the spectra of this class of models, i.e., heavy neutrinos, a second Higgs state and the Z ', which are amenable to experimental investigation at the Large Hadron Collider. We therefore set the stage to establish a direct link between measurements obtainable at the Electro-Weak scale and the dynamics of the underlying model up to those where a Grand Unification Theory embedding a U(1)' can be realised.

  10. Z'-portal right-handed neutrino dark matter in the minimal U(1 ) X extended Standard Model

    NASA Astrophysics Data System (ADS)

    Okada, Nobuchika; Okada, Satomi

    2017-02-01

    We consider a concise dark matter (DM) scenario in the context of a nonexotic U(1) extension of the Standard Model (SM), where a new U(1 ) X gauge symmetry is introduced along with three generations of right-handed neutrinos (RHNs) and a SM gauge singlet Higgs field. The model is a generalization of the minimal gauged U (1 )B -L (baryon number minus lepton number) extension of the SM, in which the extra U(1 ) X gauge symmetry is expressed as a linear combination of the SM U(1 ) Y and U (1 )B -L gauge symmetries. We introduce a Z2-parity and assign an odd-parity only for one RHN among all particles, so that this Z2-odd RHN plays the role of DM. The so-called minimal seesaw mechanism is implemented in this model with only two Z2-even RHNs. In this context, we investigate the physics of RHN DM, focusing on the case where this DM particle communicates with the SM particles through the U(1 ) X gauge boson (Z' boson). This "Z'-portal RHN DM" scenario is controlled by only three free parameters: the U(1 ) X gauge coupling (αX), the Z' boson mass (mZ'), and the U(1 ) X charge of the SM Higgs doublet (xH). We consider various phenomenological constraints to identify a phenomenologically viable parameter space. The most important constraints are the observed DM relic abundance and the latest LHC Run-2 results on the search for a narrow resonance with the dilepton final state. We find that these are complementary with each other and narrow the allowed parameter region, leading to the lower mass bound of mZ'≳2.7 TeV .

  11. TG-43 U1 based dosimetric characterization of model 67-6520 Cs-137 brachytherapy source

    SciTech Connect

    Meigooni, Ali S.; Wright, Clarissa; Koona, Rafiq A.; Awan, Shahid B.; Granero, Domingo; Perez-Calatayud, Jose; Ballester, Facundo

    2009-10-15

    Purpose: Brachytherapy treatment has been a cornerstone for management of various cancer sites, particularly for the treatment of gynecological malignancies. In low dose rate brachytherapy treatments, {sup 137}Cs sources have been used for several decades. A new {sup 137}Cs source design has been introduced (model 67-6520, source B3-561) by Isotope Products Laboratories (IPL) for clinical application. The goal of the present work is to implement the TG-43 U1 protocol in the characterization of the aforementioned {sup 137}Cs source. Methods: The dosimetric characteristics of the IPL {sup 137}Cs source are measured using LiF thermoluminescent dosimeters in a Solid Water phantom material and calculated using Monte Carlo simulations with the GEANT4 code in Solid Water and liquid water. The dose rate constant, radial dose function, and two-dimensional anisotropy function of this source model were obtained following the TG-43 U1 recommendations. In addition, the primary and scatter dose separation (PSS) formalism that could be used in convolution/superposition methods to calculate dose distributions around brachytherapy sources in heterogeneous media was studied. Results: The measured and calculated dose rate constants of the IPL {sup 137}Cs source in Solid Water were found to be 0.930({+-}7.3%) and 0.928({+-}2.6%) cGy h{sup -1} U{sup -1}, respectively. The agreement between these two methods was within our experimental uncertainties. The Monte Carlo calculated value in liquid water of the dose rate constant was {Lambda}=0.948({+-}2.6%) cGy h{sup -1} U{sup -1}. Similarly, the agreement between measured and calculated radial dose functions and the anisotropy functions was found to be within {+-}5%. In addition, the tabulated data that are required to characterize the source using the PSS formalism were derived. Conclusions: In this article the complete dosimetry of the newly designed {sup 137}Cs IPL source following the AAPM TG-43 U1 dosimetric protocol and the PSS

  12. Black rings in U(1)3 supergravity and their dual 2d CFT

    NASA Astrophysics Data System (ADS)

    Sadeghian, S.; Yavartanoo, H.

    2016-05-01

    We study the near-horizon geometry of black ring solutions in five-dimensional U(1)3 supergravity with three electric dipole charges and one angular momentum. We consider the extremal vanishing horizon (EVH) limit of these solutions and show that the near-horizon geometries develop AdS3 throats locally. At the near-EVH near horizon limit, the AdS3 factor turns into a BTZ black hole. By analysing the first law of thermodynamics for black rings we show that at the EVH limit, they reduce to the first law of thermodynamics for BTZ black holes. Using the AdS3/CFT2 duality, we propose a dual CFT to describe the near-horizon low energy dynamics of near-EVH black rings. We also discuss the connection between our CFT proposal and the Kerr/CFT correspondence in the cases where these two overlap.

  13. Functional renormalization group for the U (1 )-T56 tensorial group field theory with closure constraint

    NASA Astrophysics Data System (ADS)

    Lahoche, Vincent; Ousmane Samary, Dine

    2017-02-01

    This paper is focused on the functional renormalization group applied to the T56 tensor model on the Abelian group U (1 ) with closure constraint. For the first time, we derive the flow equations for the couplings and mass parameters in a suitable truncation around the marginal interactions with respect to the perturbative power counting. For the second time, we study the behavior around the Gaussian fixed point, and show that the theory is nonasymptotically free. Finally, we discuss the UV completion of the theory. We show the existence of several nontrivial fixed points, study the behavior of the renormalization group flow around them, and point out evidence in favor of an asymptotically safe theory.

  14. Family nonuniversal U(1){sup '} gauge symmetries and b{yields}s transitions

    SciTech Connect

    Barger, Vernon; Everett, Lisa; Jiang Jing; Langacker, Paul; Liu Tao; Wagner, Carlos E. M.

    2009-09-01

    We present a correlated analysis for the {delta}B=1, 2 processes which occur via b{yields}s transitions within models with a family nonuniversal U(1){sup '}. We take a model-independent approach and only require family universal charges for the first and second generations and small fermion mixing angles. The results of our analysis show that within this class of models, the anomalies in B{sub s}-B{sub s} mixing and the time-dependent CP asymmetries of the penguin-dominated B{sub d}{yields}({pi},{phi},{eta}{sup '},{rho},{omega},f{sub 0})K{sub S} decays can be accommodated.

  15. b {r-arrow} s transitions in family-dependent U(1)' models.

    SciTech Connect

    Barger, V.; Everett, L.; Jiang, J.; Langacker, P.; Liu, T.; Wagner, C. E. M.; High Energy Physics; Univ. of Chicago; Univ. of Wisconsin; Inst. for Advanced Study

    2009-01-01

    We analyze flavor-changing-neutral-current (FCNC) effects in the b {yields} s transitions that are induced by family non-universal U(1){prime} gauge symmetries. After systematically developing the necessary formalism, we present a correlated analysis for the {Delta}B = 1,2 processes. We adopt a model-independent approach in which we only require family-universal charges for the first and second generations and small fermion mixing angles. We analyze the constraints on the resulting parameter space from B{sub s}-{bar B} mixing and the time-dependent CP asymmetries of the penguin-dominated B{sub d} {yields} ({pi},{phi}, {eta}{prime}, {rho},{omega},f0)K{sub S} decays. Our results indicate that the currently observed discrepancies in some of these modes with respect to the Standard Model predictions can be consistently accommodated within this general class of models.

  16. Family non-universal U(1)' gauge symmetries and b {r_arrow} s transitions.

    SciTech Connect

    Barger, V.; Everett, L.; Jiang, J.; Langacker, P.; Liu, T.; Wagner, C .E. M.; High Energy Physics; Univ. of Chicago; Univ. of Wisconsin at Madison; Inst. for Advanced Study

    2009-01-01

    We present a correlated analysis for the {Delta}B = 1, 2 processes which occur via b {yields} s transitions within models with a family nonuniversal U(1){prime}. We take a model-independent approach and only require family universal charges for the first and second generations and small fermion mixing angles. The results of our analysis show that within this class of models, the anomalies in B{sub s}-B{sub s}{sup -} mixing and the time-dependent CP asymmetries of the penguin-dominated B{sub d} {yields} ({pi},{psi},{eta}{prime},{rho},{omega},f{sub 0})K{sub S} decays can be accommodated.

  17. Canonical quantization of four- and five-dimensional U(1) gauge theories

    NASA Astrophysics Data System (ADS)

    Shnerb, N.; Horwitz, L. P.

    1993-12-01

    We discuss the canonical quantization of an interacting massless U(1) gauge field using a bosonic gauge-fixing method. We present a way to make the transformation between the Lorentz and the Coulomb gauge of such theories, without using an explicit representation of the fields in terms of creation-annihilation operators. We demonstrate this method in the case of Maxwell photons interacting with Schrödinger electrons and then we treat, with the same methods, a system of higher-dimensional equations appearing in the framework of a manifestly covariant relativistic quantum theory. The nonrelativistic limit of the Coulomb term for such a theory is discussed and compared to the Fokker action appearing in the Wheeler-Feynman action-at-a-distance theory for electromagnetic interactions.

  18. Engineering assessment and certification of integrity of the 141-R1U1 tank system

    SciTech Connect

    Graser, D.A. )

    1990-09-01

    This Engineering Assessment and Certification of Integrity of retention tank 141-R1U1 is in response to the requirements of 40 CFR 265.191 for an existing tank system that stores hazardous waste and does not have secondary containment. This technical assessment has been reviewed by an independent, qualified, California registered professional engineer, who has certified the tank system to be adequately designed and compatible with the stored waste so that it will not collapse rupture, or fail. This document will be kept on file at the facility. Onground retention tanks 141-R1O1 and 141-R1O2, which are also part of the 141-R1 retention tank system, do not have secondary containment; consequently, certification documentation for these tanks is not included in this assessment. A discussion of the onground tanks, however, is included in this report to provide a complete description of the 141-R1 retention tank system. 8 refs., 7 figs.

  19. Integrable spin chain for the SL(2,R)/U(1) black hole sigma model.

    PubMed

    Ikhlef, Yacine; Jacobsen, Jesper Lykke; Saleur, Hubert

    2012-02-24

    We introduce a spin chain based on finite-dimensional spin-1/2 SU(2) representations but with a non-Hermitian "Hamiltonian" and show, using mostly analytical techniques, that it is described at low energies by the SL(2,R)/U(1) Euclidian black hole conformal field theory. This identification goes beyond the appearance of a noncompact spectrum; we are also able to determine the density of states, and show that it agrees with the formulas in [J. Maldacena, H. Ooguri, and J. Son, J. Math. Phys. (N.Y.) 42, 2961 (2001)] and [A. Hanany, N. Prezas, and J. Troost, J. High Energy Phys. 04 (2002) 014], hence providing a direct "physical measurement" of the associated reflection amplitude.

  20. Diphoton decay for a 750 GeV scalar boson in a U(1)X model

    NASA Astrophysics Data System (ADS)

    Martinez, R.; Ochoa, F.; Sierra, C. F.

    2016-12-01

    In the context of a nonuniversal and anomaly free U(1)X extension of the standard model, we examine the decay of a 750 GeV scalar singlet state, ξχ, as a possible explanation of the observed diphoton excess announced by the ATLAS and CMS collaborations at CERN-LHC collider. The one-loop decay to photons is allowed through three heavy singlet quarks and one charged Higgs boson into the loop. We obtain, for different width approximations and for masses of the exotic singlet quarks in the region [ 900 , 3000 ] GeV, a production cross section σ (pp →ξχ → γγ) compatible with ATLAS and CMS collaborations data. We also include another scalar singlet, σ, as a dark matter candidate that may couple with the 750 GeV scalar at tree level with production cross sections in agreement with ATLAS and CMS.

  1. A guide to flat direction analysis in anomalous U(1) models

    SciTech Connect

    Irges, N.; Lavignac, S. |

    1997-12-01

    The authors suggest a systematic procedure to study D- and F-flat directions in a large class of models with an anomalous U(1). This class of models is characterized by the existence of a vacuum that breaks all Abelian gauge symmetries connecting the observable sector to the hidden sector. They show that, under some conditions, there is no other stable vacuum that breaks these symmetries. As a consequence, the model yields definite (order of magnitude) predictions for low-energy mass hierarchies. Then they study generic flat directions and identify the ones that may lead to undesirable vacua. They give necessary conditions for those to be lifted, and show that supersymmetry breaking only slightly affects the conclusions from the flat direction analysis.

  2. Sterile neutrino portal to Dark Matter I: the U(1) B- L case

    NASA Astrophysics Data System (ADS)

    Escudero, Miguel; Rius, Nuria; Sanz, Verónica

    2017-02-01

    In this paper we explore the possibility that the sterile neutrino and Dark Matter sectors in the Universe have a common origin. We study the consequences of this assumption in the simple case of coupling the dark sector to the Standard Model via a global U(1) B-L , broken down spontaneously by a dark scalar. This dark scalar provides masses to the dark fermions and communicates with the Higgs via a Higgs portal coupling. We find an interesting interplay between Dark Matter annihilation to dark scalars — the CP-even that mixes with the Higgs and the CP-odd which becomes a Goldstone boson, the Majoron — and heavy neutrinos, as well as collider probes via the coupling to the Higgs. Moreover, Dark Matter annihilation into sterile neutrinos and its subsequent decay to gauge bosons and quarks, charged leptons or neutrinos lead to indirect detection signatures which are close to current bounds on the gamma ray flux from the galactic center and dwarf galaxies.

  3. Boundary conditions, gauge fixing ambiguities and exact expectation values in U(1) lattice gauge theory

    NASA Astrophysics Data System (ADS)

    Pinto, Carlos

    2016-03-01

    We analyze the interplay between gauge fixing and boundary conditions in two-dimensional U(1) lattice gauge theory. We show on the basis of a general argument that periodic boundary conditions result in an ill-defined weak coupling approximation but that the approximation can be made well-defined if the boundaries are fixed to zero. We confirm this result in the particular case of the Feynman gauge. We show that the zero momentum mode divergence in the propagator that appears in the Feynman gauge vanishes when the weak coupling approximation is well-defined. In addition we obtain exact results (for arbitrary coupling), including finite size corrections, for the partition function and for general one-point and two-point functions in the axial gauge under both periodic and zero boundary conditions and confirm these results numerically. The dependence of these objects on both lattice size and coupling constant is investigated using specific examples. These exact results may provide insight into similar gauge fixing issues in more complex models.

  4. Entanglement entropy in (3 + 1)-d free U(1) gauge theory

    NASA Astrophysics Data System (ADS)

    Soni, Ronak M.; Trivedi, Sandip P.

    2017-02-01

    We consider the entanglement entropy for a free U(1) theory in 3+1 dimensions in the extended Hilbert space definition. By taking the continuum limit carefully we obtain a replica trick path integral which calculates this entanglement entropy. The path integral is gauge invariant, with a gauge fixing delta function accompanied by a Faddeev -Popov determinant. For a spherical region it follows that the result for the logarithmic term in the entanglement, which is universal, is given by the a anomaly coefficient. We also consider the extractable part of the entanglement, which corresponds to the number of Bell pairs which can be obtained from entanglement distillation or dilution. For a spherical region we show that the coefficient of the logarithmic term for the extractable part is different from the extended Hilbert space result. We argue that the two results will differ in general, and this difference is accounted for by a massless scalar living on the boundary of the region of interest.

  5. All supersymmetric solutions of 3D U(1)3 gauged supergravity.

    NASA Astrophysics Data System (ADS)

    Colgáin, Eoin Ó.

    2015-11-01

    D3-branes wrapping constant curvature Riemann surfaces give rise to 2D N=(0,2) SCFTs, where the superconformal fixed-points are mapped to vacua of 3D N=2 U(1)3 gauged supergravity. In this work we determine the fermionic supersymmetry variations of the theory and present all supersymmetric solutions. For spacetimes with a timelike Killing vector, we identify new timelike warped AdS3 (Gödel) and timelike warped dS3 fixed-points. We outline the construction of numerical solutions interpolating between fixed-points, demonstrate that these flows are driven by an irrelevant scalar operator in the SCFT and identify the inverse of the superpotential as a candidate c-function. We further classify all spacetimes with a null Killing vector, in the process producing loci in parameter space where null-warped AdS3 vacua with Schrödinger z = 2 symmetry exist. We construct non-supersymmetric spacelike warped AdS3 geometries based on D3-branes.

  6. Implications of SU(2)_L x U(1) Symmetry for SIM(2) Invariant Neutrino Masses

    SciTech Connect

    Alan Dunn; Thomas Mehen

    2006-10-16

    We consider SU(2){sub L} x U(1) gauge invariant generalizations of a nonlocal, Lorentz violating mass term for neutrinos that preserves a SIM(2) subgroup. This induces Lorentz violating effects in QED as well as tree-level lepton family number violating interactions. Measurements of g{sub e} - 2 with trapped electrons severely constrain possible SIM(2) mass terms for electrons which violate C invariance. We study Lorentz violating effects in a C invariant and SIM(2) invariant extension of QED. We examine the Lorentz violating interactions of nonrelativistic electrons with electromagnetic fields to determine their impact on the spectroscopy of hydrogen-like atoms and g{sub e} - 2 measurements with trapped electrons. Generically, Lorentz violating corrections are suppressed by m{sub v}{sup 2}/m{sub e}{sup 2} and are within experimental limits. We study one-loop corrections to electron and photon self-energies and point out the need for a prescription to handle IR divergences induced by the nonlocality of the theory. We also calculate the tree level contribution to {mu} {yields} e + {gamma} from SIM(2) invariant mass terms.

  7. Alterations in cellular pharmacokinetics and pharmacodynamics of elvitegravir in response to ethanol exposure in HIV-1 infected monocytic (U1) cells

    PubMed Central

    Midde, Narasimha M.; Sinha, Namita; Lukka, Pradeep B.; Meibohm, Bernd

    2017-01-01

    Ethanol consumption is negatively associated with antiretroviral therapy (ART) adherence and general health in HIV positive individuals. Previously, we demonstrated ethanol-mediated alterations to metabolism of elvitegravir (EVG) in human liver microsomes. In the current study, we investigated ethanol influence on the pharmacokinetic and pharmacodynamic interactions of EVG in HIV infected monocytic (U1) cells. U1 cells were treated with 5 μM EVG, 2 μM Cobicistat (COBI), a booster drug, and 20 mM ethanol for up to 24 hours. EVG, HIV p24 levels, alterations in cytochrome P450 (CYP) 3A4, MRP1, and MDR1 protein expressions were measured. Presence of ethanol demonstrated a significant effect on the total exposures of both EVG and EVG in combination with COBI. Ethanol also increased the HIV replication despite the presence of drugs and this elevated HIV replication was reduced in the presence of MRP1 and MDR1 inhibitors. Consequently, a slight increase in EVG concentration was observed in the presence of MRP1 inhibitor but not with MDR1 inhibitor. Furthermore, CYP3A4, MRP1 and MDR1 protein levels were significantly induced in treatment groups which included ethanol compared to those with no treatment. In summary, these findings suggest that Ethanol reduces intra cellular EVG exposure by modifying drug metabolism and transporter protein expression. This study provides valuable evidence for further investigation of ethanol effects on the intracellular concentration of EVG in ex vivo or in vivo studies. PMID:28231276

  8. Numerical solutions of Einstein's equations for cosmological spacetimes with spatial topology S3 and symmetry group U(1)

    NASA Astrophysics Data System (ADS)

    Beyer, F.; Escobar, L.; Frauendiener, J.

    2016-02-01

    In this paper we consider the single patch pseudospectral scheme for tensorial and spinorial evolution problems on the 2-sphere presented by Beyer et al. [Classical Quantum Gravity 32, 175013 (2015); Classical Quantum Gravity31, 075019 (2014)], which is based on the spin-weighted spherical harmonics transform. We apply and extend this method to Einstein's equations and certain classes of spherical cosmological spacetimes. More specifically, we use the hyperbolic reductions of Einstein's equations obtained in the generalized wave map gauge formalism combined with Geroch's symmetry reduction, and focus on cosmological spacetimes with spatial S3 -topologies and symmetry groups U(1) or U (1U (1 ) . We discuss analytical and numerical issues related to our implementation. We test our code by reproducing the exact inhomogeneous cosmological solutions of the vacuum Einstein field equations obtained by Beyer and Hennig [Classical Quantum Gravity 31, 095010 (2014)].

  9. Chiral U(1) flavor models and flavored Higgs doublets: the top FB asymmetry and the W jj

    SciTech Connect

    Ko, P.; Omura, Yuji; Yu, Chaehyun

    2012-01-01

    We present U(1) flavor models for leptophobic Z' with flavor dependent couplings to the right-handed up-type quarks in the Standard Model (SM), which can accommodate the recent data on the top forward-backward (FB) asymmetry and the dijet resonance associated with a W boson reported by CDF Collaboration. Such flavor-dependent leptophobic charge assignments generally require extra chiral fermions for anomaly cancellation. Also the chiral nature of U(1)' flavor symmetry calls for new U(1)'-charged Higgs doublets in order for the SM fermions to have realistic renormalizable Yukawa couplings. The stringent constraints from the top FB asymmetry at the Tevatron and the same sign top pair production at the LHC can be evaded due to contributions of the extra Higgs doublets. We also show that the extension could realize cold dark matter candidates.

  10. Collider signatures of the SO(5)xU(1) gauge-Higgs unification

    SciTech Connect

    Hosotani, Yutaka; Tanaka, Minoru; Uekusa, Nobuhiro

    2011-10-01

    Collider signatures of the SO(5)xU(1) gauge-Higgs unification model in the Randall-Sundrum warped space are explored. Gauge couplings of quarks and leptons receive small corrections from the fifth dimension whose effects are tested by the precision data. It is found that the forward-backward asymmetries in e{sup +}e{sup -} collisions on the Z pole are well explained in a wide range of the warp factor z{sub L}, but the model is consistent with the branching fractions of Z decay only for large z{sub L} > or approx. 10{sup 15}. Kaluza-Klein (KK) spectra of gauge bosons, quarks, and leptons as well as gauge and Higgs couplings of low-lying KK excited states are determined. Right-handed quarks and leptons have larger couplings to the KK gauge bosons than left-handed ones. Production rates of Higgs bosons and KK states at the Tevatron, LHC, and International Linear Collider are evaluated. The first KK Z has a mass 1130 GeV with a width 422 GeV for z{sub L}=10{sup 15}. The current limit on the Z' production at the Tevatron and LHC indicates z{sub L}>10{sup 15}. A large effect of parity violation appears in the difference between the rapidity distributions of e{sup +} and e{sup -} in the decay of the first KK Z. The first KK gauge bosons decay into light and heavy quarks evenly.

  11. Quasi-Yukawa unification and fine-tuning in U(1) extended SSM

    NASA Astrophysics Data System (ADS)

    Hiçyılmaz, Yaşar; Ceylan, Meltem; Altaş, Aslı; Solmaz, Levent; Ün, Cem Salih

    2016-11-01

    We consider the low scale implications in the U(1 ) ' extended minimal supersymmetric Standard Model (UMSSM). We restrict the parameter space such that the lightest supersymmetric particle (LSP) is always the lightest neutralino. In addition, we impose quasi-Yukawa unification (QYU) at the grand unification scale (MGUT). QYU strictly requires the ratios among the Yukawa couplings as yt/yb˜1.2 , yτ/yb˜1.4 , and yt/yτ˜0.8 . We find that the need for fine-tuning over the fundamental parameter space of QYU is in the acceptable range (ΔEW≤1 03), even if the universal boundary conditions are imposed at MGUT, in contrast to CMSSM and nonuniversal Higgs masses. The UMSSM with universal boundary conditions yields heavy stops (mt ˜≳2.5 TeV ), gluinos (mg ˜≳2 TeV ), and squarks from the first two families (mq ˜≳4 TeV ). Similarly, the stau mass is bounded from below at about 1.5 TeV. Despite this heavy spectrum, we find ΔEW≳300 , which is much lower than that needed for the minimal supersymmetric models. In addition, the UMSSM yields a relatively small μ term, and the LSP neutralino is mostly formed by the Higgsinos of mass ≳700 GeV . We also obtain bino-like dark matter of mass about 400 GeV. The wino is usually found to be heavier than Higgsinos and binos, but there is a small region where μ ˜M1˜M2˜1 TeV . We also identify a chargino-neutralino coannihilation channel and A -resonance solutions which reduce the relic abundance of LSP neutralinos down to the ranges compatible with the current WMAP and Planck measurements.

  12. Electroweak theory based on S U (4 )L⊗U (1 )X gauge group

    NASA Astrophysics Data System (ADS)

    Long, H. N.; Hue, L. T.; Loi, D. V.

    2016-07-01

    This paper includes two main parts. In the first part, we present generalized gauge models based on the S U (3 )C⊗S U (4 )L⊗U (1 )X (3-4-1) gauge group with arbitrary electric charges of exotic leptons. The mixing matrix of neutral gauge bosons is analyzed, and the eigenmasses and eigenstates are obtained. The anomaly-free as well as matching conditions are discussed precisely. In the second part, we present a new development of the original 3-4-1 model [R. Foot, H. N. Long, and T. A. Tran, Phys. Rev. D 50, R34 (1994), F. Pisano and V. Pleitez, Phys. Rev. D 51, 3865 (1995).]. Different from previous works, in this paper the neutrinos, with the help of the scalar decuplet H , get the Dirac masses at the tree level. The vacuum expectation value (VEV) of the Higgs boson field in the decuplet H acquiring the VEV responsible for neutrino Dirac mass leads to mixing in separated pairs of singly charged gauge bosons, namely the Standard Model (SM) W boson and K , the new gauge boson acting in the right-handed lepton sector, as well as the singly charged bileptons X and Y . Due to the mixing, there occurs a right-handed current carried by the W boson. From the expression of the electromagnetic coupling constant, ones get the limit of the sine-squared of the Weinberg angle, sin2θW<0.25 , and a constraint on electric charges of extra leptons. In the limit of lepton number conservation, the Higgs sector contains all massless Goldstone bosons for massive gauge bosons and the SM-like Higgs boson. Some phenomenology is discussed.

  13. RBFOX2 Promotes Protein 4.1R Exon 16 Selection via U1 snRNP Recruitment

    PubMed Central

    Ou, Alexander C.; Park, Jennie; Yu, Faye; Yu, Brian; Lee, Angela; Yang, Guang; Zhou, Anyu; Benz, Edward J.

    2012-01-01

    The erythroid differentiation-specific splicing switch of protein 4.1R exon 16, which encodes a spectrin/actin-binding peptide critical for erythrocyte membrane stability, is modulated by the differentiation-induced splicing factor RBFOX2. We have now characterized the mechanism by which RBFOX2 regulates exon 16 splicing through the downstream intronic element UGCAUG. Exon 16 possesses a weak 5′ splice site (GAG/GTTTGT), which when strengthened to a consensus sequence (GAG/GTAAGT) leads to near-total exon 16 inclusion. Impaired RBFOX2 binding reduces exon 16 inclusion in the context of the native weak 5′ splice site, but not the engineered strong 5′ splice site, implying that RBFOX2 achieves its effect by promoting utilization of the weak 5′ splice site. We further demonstrate that RBFOX2 increases U1 snRNP recruitment to the weak 5′ splice site through direct interaction between its C-terminal domain (CTD) and the zinc finger region of U1C and that the CTD is required for the effect of RBFOX2 on exon 16 splicing. Our data suggest a novel mechanism for exon 16 5′ splice site activation in which the binding of RBFOX2 to downstream intronic splicing enhancers stabilizes the pre-mRNA–U1 snRNP complex through interactions with U1C. PMID:22083953

  14. Multi-Higgs doublet models with local U(1){sub H} gauge symmetry and neutrino physics therein

    SciTech Connect

    Ko, P.; Yu, Chaehyun; Omura, Yuji

    2014-01-01

    Multi-Higgs doublet models appear in many interesting extensions of the standard model (SM). But they suffer from Higgs-mediated flavor changing neutral current (FCNC) problem which is very generic. In this talk, I describe that this problem can be resolved or mitigated if we introduce local U(1){sub H} Higgs flavor gauge symmetry. As examples, I describe chiral U(1){sub H} models where the right-handed up-type quarks also carry U(1){sub H} charges and discuss the top forward-backward asymmetry (FBA) and B → D{sup (*)}τν puzzle. Next I describe the two-Higgs doublet models where the usual Z₂ symmetry is implemented to U(1){sub H} and show how the Type-I and Type-II models are extended. One possible extension of Type-II has the same fermion contents with the leptophobic E₆Z´ model by Rosner, and I discuss the neutrino sector in this model briefly.

  15. About a peculiar extra U(1): Z{sup '} discovery limit, muon anomalous magnetic moment, and electron electric dipole moment

    SciTech Connect

    Heo, Jae Ho

    2009-08-01

    The model (Lagrangian) with a peculiar extra U(1)[S. M. Barr and I. Dorsner, Phys. Rev. D 72, 015011 (2005); S. M. Barr and A. Khan, Phys. Rev. D 74, 085023 (2006)] is clearly presented. The assigned extra U(1) gauge charges give a strong constraint to build Lagrangians. The Z{sup '} discovery limits are estimated and predicted at the Tevatron and the LHC. The new contributions of the muon anomalous magnetic moment are investigated at one and two loops, and we predict that the deviation from the standard model may be explained. The electron electric dipole moment could also be generated because of the explicit CP-violation effect in the Higgs sector, and a sizable contribution is expected for a moderately sized CP phase [argument of the CP-odd Higgs], 0.1{<=}sin{delta}{<=}1[6 deg. {<=}arg(A){<=}90 deg.].

  16. Experimentally verifiable Yang-Mills spin 2 gauge theory of gravity with group U(1) x SU(2)

    NASA Astrophysics Data System (ADS)

    Peng, Huei

    1988-06-01

    A Yang-Mills spin 2 gauge theory of gravity is proposed. Based on both the verification of the helicity 2 property of the SU(2) gauge bosons of the theory and the agreement of the theory with most observational and experimental evidence, it is argued that the theory is truly a gravitational theory. Generation by the 4-momentum P sup mu of a fermion of U(1) x SU(2) internal symmetry group for gravity, but not the transformation group T sup 4 is demonstrated. It is shown that the U(1) x SU(2) group represents the time displacement and rotation in ordinary space. Thereby internal space associated with gravity is identical with Minkowski spacetime, so a gauge potential of gravity carries two spacetime indices. Then it is verified that the SU(2) gravitational boson has helicity 2. This theory predicts experimentally verifiable gravitomagnetic fields 4 times smaller than that of general relativity.

  17. U(1) gauge field localization on a Bloch brane with Chumbes-Holf da Silva-Hott mechanism

    NASA Astrophysics Data System (ADS)

    Zhao, Zhen-Hua; Liu, Yu-Xiao; Zhong, Yuan

    2014-08-01

    We follow the Chumbes-Holf da Silva-Hott mechanism to study the (quasi)localization of the U(1) gauge field on the Bloch brane. The localization and resonances of the U(1) gauge field are discussed for four kinds of Bloch brane solutions: the original and generalized Bloch brane solutions, as well as the degenerate Bloch brane solutions I and II. With the Chumbes-Holf da Silva-Hott mechanism, we find that the mass spectrum of the gauge field Kaluza-Klein modes is continuous and there is no tachyonic mode. The zero mode is localized on all the branes and there are resonant Kaluza-Klein modes on the degenerate Bloch branes.

  18. A Nonminimal SO(10) x U(1)-F SUSY GUT model obtained from a bottom up approach

    SciTech Connect

    Albright, Carl H.

    1996-08-01

    Many of the ingredients are explored which are needed to develop a super- symmetric SO(10) x U(1)_F grand unified model based on the Yukawa structure of a model previously constructed in collaboration with S. Nandi to explain the quark and lepton masses and mixings in a particular neutrino scenario. The U(1)_F family symmetry can be made anomaly-free with the introduction of one conjugate pair of SO(10)-singlet neutrinos with the same U(1)_F charge. Due to a plethora of conjugate pairs of supermultiplets, the model develops a Landau singularity within a factor of 1.5 above the GUT scale. With the imposition of a Z_2 discrete symmetry and under certain conditions, all higgsino triplets can be made superheavy while just one pair of higgsino doublets remains light and results in mass matrix textures previously obtained from the bottom-up approach. Diametrically opposite splitting of the first and third family scalar quark and lepton masses away from the second family ones results from the nonuniversal D-term contributions.

  19. The C-terminal RG dipeptide repeats of the spliceosomal Sm proteins D1 and D3 contain symmetrical dimethylarginines, which form a major B-cell epitope for anti-Sm autoantibodies.

    PubMed

    Brahms, H; Raymackers, J; Union, A; de Keyser, F; Meheus, L; Lührmann, R

    2000-06-02

    The Sm proteins B/B', D1, D2, D3, E, F, and G are components of the small nuclear ribonucleoproteins U1, U2, U4/U6, and U5 that are essential for the splicing of pre-mRNAs in eukaryotes. D1 and D3 are among the most common antigens recognized by anti-Sm autoantibodies, an autoantibody population found exclusively in patients afflicted with systemic lupus erythematosus. Here we demonstrate by protein sequencing and mass spectrometry that all arginines in the C-terminal arginine-glycine (RG) dipeptide repeats of the human Sm proteins D1 and D3, isolated from HeLa small nuclear ribonucleoproteins, contain symmetrical dimethylarginines (sDMAs), a posttranslational modification thus far only identified in the myelin basic protein. The further finding that human D1 individually overexpressed in baculovirus-infected insect cells contains asymmetrical dimethylarginines suggests that the symmetrical dimethylation of the RG repeats in D1 and D3 is dependent on the assembly status of D1 and D3. In antibody binding studies, 10 of 11 anti-Sm patient sera tested, as well as the monoclonal antibody Y12, reacted with a chemically synthesized C-terminal peptide of D1 containing sDMA, but not with peptides containing asymmetrically modified or nonmodified arginines. These results thus demonstrate that the sDMA-modified C terminus of D1 forms a major linear epitope for anti-Sm autoantibodies and Y12 and further suggest that posttranslational modifications of Sm proteins play a role in the etiology of systemic lupus erythematosus.

  20. Freeze-in production of sterile neutrino dark matter in U(1){sub B−L} model

    SciTech Connect

    Biswas, Anirban; Gupta, Aritra

    2016-09-27

    With the advent of new and more sensitive direct detection experiments, scope for a thermal WIMP explanation of dark matter (DM) has become extremely constricted. The non-observation of thermal WIMP in these experiments has put a strong upper bound on WIMP-nucleon scattering cross section and within a few years it is likely to overlap with the coherent neutrino-nucleon cross section. Hence in all probability, DM may have some non-thermal origin. In this work we explore in detail this possibility of a non-thermal sterile neutrino DM within the framework of U(1){sub B−L} model. The U(1){sub B−L} model on the other hand is a well-motivated and minimal way of extending the standard model so that it can explain the neutrino masses via Type-I see-saw mechanism. We have shown, besides explaining the neutrino mass, it can also accommodate a non-thermal sterile neutrino DM with correct relic density. In contrast with the existing literature, we have found that W{sup ±} decay can also be a dominant production mode of the sterile neutrino DM. To obtain the comoving number density of dark matter, we have solved here a coupled set of Boltzmann equations considering all possible decay as well as annihilation production modes of the sterile neutrino dark matter. The framework developed here though has been done for a U(1){sub B−L} model, can be applied quite generally for any models with an extra neutral gauge boson and a fermionic non-thermal dark matter.

  1. Instantons in 2D U(1) Higgs model and 2D CP(N-1) sigma models

    NASA Astrophysics Data System (ADS)

    Lian, Yaogang

    2007-12-01

    In this thesis I present the results of a study of the topological structures of 2D U(1) Higgs model and 2D CP N-1 sigma models. Both models have been studied using the overlap Dirac operator construction of topological charge density. The overlap operator provides a more incisive probe into the local topological structure of gauge field configurations than the traditional plaquette-based operator. In the 2D U(1) Higgs model, we show that classical instantons with finite sizes violate the negativity of topological charge correlator by giving a positive contribution to the correlator at non-zero separation. We argue that instantons in 2D U(1) Higgs model must be accompanied by large quantum fluctuations in order to solve this contradiction. In 2D CPN-1 sigma models, we observe the anomalous scaling behavior of the topological susceptibility chi t for N ≤ 3. The divergence of chi t in these models is traced to the presence of small instantons with a radius of order a (= lattice spacing), which are directly observed on the lattice. The observation of these small instantons provides detailed confirmation of Luscher's argument that such short-distance excitations, with quantized topological charge, should be the dominant topological fluctuations in CP1 and CP 2, leading to a divergent topological susceptibility in the continuum limit. For the CPN-1 models with N > 3 the topological susceptibility is observed to scale properly with the mass gap. Another topic presented in this thesis is an implementation of the Zolotarev optimal rational approximation for the overlap Dirac operator. This new implementation has reduced the time complexity of the overlap routine from O(N3 ) to O(N), where N is the total number of sites on the lattice. This opens up a door to more accurate lattice measurements in the future.

  2. Spontaneous compactification and coupling constants in a geometric model for SU(2)×U(1) with gravity

    NASA Astrophysics Data System (ADS)

    Nahmad-Achar, E.; Rosenbaum, M.; Bautista, R.; Mucio, J.

    1990-07-01

    A fiber-bundle treatment for Kaluza-Klein-type geometric unification of gravitation with the bosonic sector of the standard electroweak theory was presented by Rosenbaum et al. Here we show that it admits spontaneously compactified solutions where the dimensions of the internal space are of the order of the Planck length. Furthermore, the model is able to predict a numerical value for the ratio of the SU(2) and U(1) coupling constants at the energy where both compactification and the unification of gravitational with electroweak interactions would occur, and this value is in agreement with that obtained from applying the renormalization group to the standard model.

  3. SU(3){sub c} x SU(3){sub L} x U(1){sub X} models with four families

    SciTech Connect

    Benavides, Richard H.; Ponce, William A.; Giraldo, Yithsbey

    2010-07-01

    In the context of the local gauge group SU(3){sub c} x SU(3){sub L} x U(1){sub X}, we look for possible four family models, where all the particles carry ordinary electric charges. Thirteen different anomaly-free fermion structures emerge, out of which only two are realistic. For the simplest physical structure, we calculate the charged and neutral weak currents and the tree-level Fermion masses. We also look for new sources of flavor changing neutral currents in the quark sector in connection with the upcoming experimental results at the Large Hadron Collider.

  4. Analysis of Site Response at U1A Hole at the Nevada Test Site From Weak Motion Readings

    SciTech Connect

    Hutchings, L; Furrey, L

    2002-05-21

    We utilize weak motion recordings to evaluate the site response at the U1A hole, Nevada Test site to determine the effect on potential ground motion at the drift of the U1A hole 962 ft deep. We estimated the site response amplification of ground motion at the surface relative to the drift with the spectral ratio method. We utilized Fourier amplitude and absolute acceleration response spectra, and confined our study to frequencies of 0.5 to 25.0 Hz (.04 to 2.0 s periods). We identified 8 earthquakes in the area that were recorded at the bottom and top of the hole that were used for spectral ratios. We calculated the average and one standard deviation of ratios from all the events. Examining the data, we found that: (1) Fourier amplitude spectral ratios provided more detailed information on the site response than the absolute acceleration response that can be directly related to the effect of large earthquakes. (2) plots of the Fourier amplitude spectra for most of the recorded earthquakes show evidence for a spectral hole in the downhole recordings. This is due to downward reflected energy from the surface. This is not evident in absolute acceleration response records. (3) Fourier amplitude spectral ratios show a relative amplification at the surface of about a factor of eight for frequencies between about 9 to 15 Hz (.07 to .ll s periods) due to the spectral hole. (4) The free surface results in an amplification of about a factor of 2 for frequencies of about 13.0 to 25.0 Hz (.04 to .08 s periods). (5) The geology results in an amplification of about a factor 2 of the surface relative to the bottom for frequencies 1.0 to 25.0 Hz (0.04 to 1.0 s period). (6) A full site response function is provided as a function of frequency from the Fourier amplitude spectral ratios. This includes the effect of the spectral hole, free surface effect, and geologic amplification. It shows that strong ground motion would be diminished at the bottom of the U1A hole by a factor of .5 to

  5. Sterile neutrino dark matter with gauged U(1){sub B-L} and a low reheating temperature

    SciTech Connect

    Khalil, Shaaban; Seto, Osamu

    2009-04-17

    Sterile right-handed neutrinos can be naturally embedded in a low scale gauged U(1){sub B-L} extension of the standard model. We show that, within a low reheating scenario, such a neutrino can be produced via a novel manner, namely scattering through Z' gauge boson, and becomes an interesting dark matter candidate. In addition, we show that if the neutrino mass is of the order of MeV, then it accounts for the measured dark matter relic density and also accommodates the observed flux of 511 keV photons from the galactic bulge.

  6. Non-singlet Q-deformed N = (1 , 0) and N = (1 , 1 / 2) U(1) actions

    NASA Astrophysics Data System (ADS)

    De Castro, A.; Quevedo, L.

    2006-08-01

    In this Letter we construct N = (1 , 0) and N = (1 , 1 / 2) non-singlet Q-deformed supersymmetric U (1) actions in components. We obtain an exact expression for the enhanced supersymmetry action by turning off particular degrees of freedom of the deformation tensor. We analyze the behavior of the action upon restoring weekly some of the deformation parameters, obtaining a non-trivial interaction term between a scalar and the gauge field, breaking the supersymmetry down to N = (1 , 0). Additionally, we present the corresponding set of unbroken supersymmetry transformations. We work in harmonic superspace in four Euclidean dimensions.

  7. AAPM TG-43U1 formalism adaptation and Monte Carlo dosimetry simulations of multiple-radionuclide brachytherapy sources

    SciTech Connect

    Nuttens, V.E.; Lucas, S.

    2006-04-15

    This paper presents a preliminary study on multiple-radionuclide sources for brachytherapy. An adaptation of the AAPM TG-43U1 formalism is proposed in order to derive the dosimetry parameters of multiple-radionuclide sources from mono-radionuclides. The adapted formalism is applied to a bi-radionuclide case with the help of Monte Carlo calculations (MCNPX 2.5.0). InterSource{sup TM} seed loaded with {sup 103}Pd and {sup 125}I was chosen. This combination promotes a higher dose rate than InterSource{sup 125} (loaded with {sup 125}I) and deeper tissue penetration than InterSource{sup 103} (loaded with {sup 103}Pd) while reducing the dose at long distance (beyond 2.5 cm) relative to InterSource{sup 125}. In conclusion, this work shows the benefits of combining different radionuclides inside the same seed and proposes an adaptation of the AAPM TG-43U1 formalism for the implementation of multiple-radionuclide sources in current treatment planning systems.

  8. Affinity and Specificity of Protein U1A-RNA Complex Formation Based on an Additive Component Free Energy Model

    PubMed Central

    Kormos, Bethany L.; Benitex, Yulia; Baranger, Anne M.; Beveridge, David L.

    2007-01-01

    Summary A MM-GBSA computational protocol was used successfully to account for wild type U1A-RNA and F56 U1A mutant experimental binding free energies. The trend in mutant binding free energies compared to wild type is well-reproduced. Following application of a linear-response-like equation to scale the various energy components, the binding free energies agree quantitatively with observed experimental values. Conformational adaptation contributes to the binding free energy for both the protein and the RNA in these systems. Small differences in ΔGs are the result of different and sometimes quite large relative contributions from various energetic components. Residual free energy decomposition indicates differences not only at the site of mutation, but throughout the entire protein. MM-GBSA and ab initio calculations performed on model systems suggest that stacking interactions may nearly, but not completely, account for observed differences in mutant binding affinities. This study indicates that there may be different underlying causes of ostensibly similar experimentally observed binding affinities of different mutants, and thus recommends caution in the interpretation of binding affinities and specificities purely by inspection. PMID:17603075

  9. SU(4){sub L} x U(1){sub X} three-family model for the electroweak interaction

    SciTech Connect

    Sanchez, Luis A.; Wills-Toro, Luis A.; Zuluaga, Jorge I.

    2008-02-01

    An extension of the gauge group SU(2){sub L} x U(1){sub Y} of the standard model to the symmetry group SU(4){sub L} x U(1){sub X} (3-4-1 for short) is presented. The model does not contain exotic electric charges and anomaly cancellation is achieved with a family of quarks transforming differently from the other two, thus leading to FCNC. By introducing a discrete Z{sub 2} symmetry we obtain a consistent fermion mass spectrum, and avoid unitarity violation of the Cabibbo-Kobayashi-Maskawa mixing matrix arising from the mixing of ordinary and exotic quarks. The neutral currents coupled to all neutral vector bosons are studied, and by using CERN LEP and SLAC Linear Collider data at Z-pole and atomic parity violation data, we bound parameters of the model related to tree-level Z-Z{sup '} mixing. These parameters are further constrained by using experimental input from neutral meson mixing in the analysis of sources of FCNC present in the model. Constraints coming from the contribution of exotic particles to the one-loop oblique electroweak parameters S, T and U are also briefly discussed. Finally, a comparison is done of the predictions of different classes of 3-4-1 models without exotic electric charges.

  10. A cytoplasmically anchored nuclear protein interferes specifically with the import of nuclear proteins but not U1 snRNA

    PubMed Central

    1993-01-01

    A cytoplasmically anchored mutant SV40 T antigen, FS T antigen, was shown previously to interfere specifically with the nuclear import of a heterologous nuclear protein, adenovirus 5 fiber protein, in cultured monkey cells (Schneider, J., C. Schindewolf, K. van Zee, and E. Fanning. 1988. Cell. 54:117-125; van Zee, K., F. Appel, and E. Fanning. 1991. Mol. Cell. Biol. 11:5137-5146). In this report, we demonstrate that FS T antigen also interferes with the nuclear import of adenovirus E1A and a peptide-albumin conjugate bearing multiple copies of the T antigen nuclear localization signal, but not with the import of U1 snRNA. A kinetic analysis indicates that nuclear import of the albumin- peptide conjugate is inhibited only when high intracellular concentrations of FS T antigen are reached. After microinjection into the cytoplasm of cultured cells, purified FS T antigen protein does not accumulate at the nuclear periphery, but rather is distributed in a punctate pattern throughout the cytoplasm. These data support a model in which cytoplasmic anchoring of FS T antigen enables the mutant protein to sequester and titrate out a cellular factor which is required for nuclear protein but not U1 snRNA import. PMID:8468344

  11. Double-target Antisense U1snRNAs Correct Mis-splicing Due to c.639+861C>T and c.639+919G>A GLA Deep Intronic Mutations

    PubMed Central

    Ferri, Lorenzo; Covello, Giuseppina; Caciotti, Anna; Guerrini, Renzo; Denti, Michela Alessandra; Morrone, Amelia

    2016-01-01

    Fabry disease is a rare X-linked lysosomal storage disorder caused by deficiency of the α-galactosidase A (α-Gal A) enzyme, which is encoded by the GLA gene. GLA transcription in humans produces a major mRNA encoding α-Gal A and a minor mRNA of unknown function, which retains a 57-nucleotide-long cryptic exon between exons 4 and 5, bearing a premature termination codon. NM_000169.2:c.639+861C>T and NM_000169.2:c.639+919G>A GLA deep intronic mutations have been described to cause Fabry disease by inducing overexpression of the alternatively spliced mRNA, along with a dramatic decrease in the major one. Here, we built a wild-type GLA minigene and two minigenes that carry mutations c.639+861C>T and c.639+919G>A. Once transfected into cells, the minigenes recapitulate the molecular patterns observed in patients, at the mRNA, protein, and enzymatic level. We constructed a set of specific double-target U1asRNAs to correct c.639+861C>T and c.639+919G>A GLA mutations. Efficacy of U1asRNAs in inducing the skipping of the cryptic exon was evaluated upon their transient co-transfection with the minigenes in COS-1 cells, by real-time polymerase chain reaction (PCR), western blot analysis, and α-Gal A enzyme assay. We identified a set of U1asRNAs that efficiently restored α-Gal A enzyme activity and the correct splicing pathways in reporter minigenes. We also identified a unique U1asRNA correcting both mutations as efficently as the mutation-specific U1asRNAs. Our study proves that an exon skipping-based approach recovering α-Gal A activity in the c.639+861C>T and c.639+919G>A GLA mutations is active. PMID:27779620

  12. Double-target Antisense U1snRNAs Correct Mis-splicing Due to c.639+861C>T and c.639+919G>A GLA Deep Intronic Mutations.

    PubMed

    Ferri, Lorenzo; Covello, Giuseppina; Caciotti, Anna; Guerrini, Renzo; Denti, Michela Alessandra; Morrone, Amelia

    2016-01-01

    Fabry disease is a rare X-linked lysosomal storage disorder caused by deficiency of the α-galactosidase A (α-Gal A) enzyme, which is encoded by the GLA gene. GLA transcription in humans produces a major mRNA encoding α-Gal A and a minor mRNA of unknown function, which retains a 57-nucleotide-long cryptic exon between exons 4 and 5, bearing a premature termination codon. NM_000169.2:c.639+861C>T and NM_000169.2:c.639+919G>A GLA deep intronic mutations have been described to cause Fabry disease by inducing overexpression of the alternatively spliced mRNA, along with a dramatic decrease in the major one. Here, we built a wild-type GLA minigene and two minigenes that carry mutations c.639+861C>T and c.639+919G>A. Once transfected into cells, the minigenes recapitulate the molecular patterns observed in patients, at the mRNA, protein, and enzymatic level. We constructed a set of specific double-target U1asRNAs to correct c.639+861C>T and c.639+919G>A GLA mutations. Efficacy of U1asRNAs in inducing the skipping of the cryptic exon was evaluated upon their transient co-transfection with the minigenes in COS-1 cells, by real-time polymerase chain reaction (PCR), western blot analysis, and α-Gal A enzyme assay. We identified a set of U1asRNAs that efficiently restored α-Gal A enzyme activity and the correct splicing pathways in reporter minigenes. We also identified a unique U1asRNA correcting both mutations as efficently as the mutation-specific U1asRNAs. Our study proves that an exon skipping-based approach recovering α-Gal A activity in the c.639+861C>T and c.639+919G>A GLA mutations is active.

  13. Double-target Antisense U1snRNAs Correct Mis-splicing Due to c.639+861C>T and c.639+919G>A GLA Deep Intronic Mutations.

    PubMed

    Ferri, Lorenzo; Covello, Giuseppina; Caciotti, Anna; Guerrini, Renzo; Denti, Michela Alessandra; Morrone, Amelia

    2016-10-25

    Fabry disease is a rare X-linked lysosomal storage disorder caused by deficiency of the α-galactosidase A (α-Gal A) enzyme, which is encoded by the GLA gene. GLA transcription in humans produces a major mRNA encoding α-Gal A and a minor mRNA of unknown function, which retains a 57-nucleotide-long cryptic exon between exons 4 and 5, bearing a premature termination codon. NM_000169.2:c.639+861C>T and NM_000169.2:c.639+919G>A GLA deep intronic mutations have been described to cause Fabry disease by inducing overexpression of the alternatively spliced mRNA, along with a dramatic decrease in the major one. Here, we built a wild-type GLA minigene and two minigenes that carry mutations c.639+861C>T and c.639+919G>A. Once transfected into cells, the minigenes recapitulate the molecular patterns observed in patients, at the mRNA, protein, and enzymatic level. We constructed a set of specific double-target U1asRNAs to correct c.639+861C>T and c.639+919G>A GLA mutations. Efficacy of U1asRNAs in inducing the skipping of the cryptic exon was evaluated upon their transient co-transfection with the minigenes in COS-1 cells, by real-time polymerase chain reaction (PCR), western blot analysis, and α-Gal A enzyme assay. We identified a set of U1asRNAs that efficiently restored α-Gal A enzyme activity and the correct splicing pathways in reporter minigenes. We also identified a unique U1asRNA correcting both mutations as efficently as the mutation-specific U1asRNAs. Our study proves that an exon skipping-based approach recovering α-Gal A activity in the c.639+861C>T and c.639+919G>A GLA mutations is active.

  14. Role of IgE immune complexes in the regulation of HIV-1 replication and increased cell death of infected U1 monocytes: involvement of CD23/Fc epsilon RII-mediated nitric oxide and cyclic AMP pathways.

    PubMed Central

    Ouaaz, F.; Ruscetti, F. W.; Dugas, B.; Mikovits, J.; Agut, H.; Debré, P.; Mossalayi, M. D.

    1996-01-01

    BACKGROUND: IgE/anti-IgE immune complexes (IgE-IC) induce the release of multiple mediators from monocytes/macrophages and the monocytic cell line U937 following the ligation of the low-affinity Fc epsilon receptors (Fc epsilon RII/CD23). These effects are mediated through an accumulation of cAMP and the generation of L-arginine-dependent nitric oxide (NO). Since high IgE levels predict more rapid progression to acquired immunodeficiency syndrome, we attempted to define the effects of IgE-IC on human immunodeficiency virus (HIV) production in monocytes. MATERIALS AND METHODS: Two variants of HIV-1 chronically infected monocytic U1 cells were stimulated with IgE-IC and virus replication was quantified. NO and cAMP involvement was tested through the use of agonistic and antagonistic chemicals of these two pathways. RESULTS: IgE-IC induced p24 production by U1 cells with low-level constitutive expression of HIV-1 mRNAs and extracellular HIV capsid protein p24 levels (U1low), upon their pretreatment with interleukin 4 (IL-4) or IL-13. This effect was due to the crosslinking of CD23, as it was reversed by blocking the IgE binding site on CD23. The IgE-IC effect could also be mimicked by crosslinking of CD23 by a specific monoclonal antibody. p24 induction by IgE-IC was then shown to be due to CD23-mediated stimulation of cAMP, NO, and tumor necrosis factor alpha (TNF alpha) generation. In another variant of U1 cells with > 1 log higher constitutive production of p24 levels (U1high), IgE-IC addition dramatically decreased all cell functions tested and accelerated cell death. This phenomenon was reversed by blocking the nitric oxide generation. CONCLUSIONS: These data point out a regulatory role of IgE-IC on HIV-1 production in monocytic cells, through CD23-mediated stimulation of cAMP and NO pathways. IgE-IC can also stimulate increased cell death in high HIV producing cells through the NO pathway. Images FIG. 1 FIG. 2 FIG. 5 PMID:8900533

  15. Two topics in nonperturbative lattice field theories: The U(1) quantum link model and perfect actions for scalar theories

    NASA Astrophysics Data System (ADS)

    Tsapalis, Antonios S.

    This thesis deals with two topics in lattice field theories. In the first part we discuss aspects of renormalization group flow and non-perturbative improvement of actions for scalar theories regularized on a lattice. We construct a perfect action, an action which is free of lattice artifacts, for a given theory. It is shown how a good approximation to the perfect action-referred to as classically perfect-can be constructed based on a well-defined blocking scheme for the O(3) non-linear σ-model. We study the O(N) non- linear σ-model in the large-N limit and derive analytically its perfect action. This action is applied to the O(3) model on a square lattice. The Wolff cluster algorithm is used to simulate numerically the system. We perform scaling tests and discuss the scaling properties of the large- N inspired perfect action as opposed to the standard and the classically perfect action. In the second part we present a new formulation for a quantum field theory with Abelian gauge symmetry. A Hamiltonian is constructed on a four-dimensional Euclidean space-time lattice which is invariant under local transformations. The model is formulated as a 5- dimensional path integral of discrete variables. We argue that dimensional reduction will allow us to study the behavior of the standard compact U(1) gauge theory in 4-d. Based on the idea of the loop- cluster algorithm for quantum spins, we present the construction of a flux-cluster algorithm for the U(1) quantum link model for the spin-1/2 quantization of the electric flux. It is shown how improved estimators for Wilson loop expectation values can be defined. This is important because the Wilson loops are traditionally used to identify confining and Coulomb phases in gauge theories. Our study indicates that the spin-1/2 U(1) quantum link model is strongly coupled for all bare coupling values we examined. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)

  16. Stable SUSY breaking model with O(10) eV gravitino from combined D-term gauge mediation and U(1)' mediation

    SciTech Connect

    Nakayama, Yu; Nakayama, Yu

    2007-12-17

    We show a calculable example of stable supersymmetry (SUSY) breaking modelswith O(10) eV gravitino mass based on the combination of D-term gauge mediationand U(1)' mediation. A potential problem of the negative mass squared for theSUSY standard model (SSM) sfermions in the D-term gauge mediation is solvedby the contribution from the U(1)' mediation. On the other hand, the splittingbetween the SSM gauginos and sfermions in the U(1)' mediation iscircumvented bythe contributions from the D-term gauge mediation. Since the U(1)' mediation doesnot introduce any new SUSY vacua, we achieve a completely stable model underthermal effects. Our model, therefore, has no cosmological difficulty.

  17. Note on the formulation of thermosensitive and mucoadhesive vaginal hydrogels containing the miniCD4 M48U1 as anti-HIV-1 microbicide.

    PubMed

    Bouchemal, Kawthar; Frelichowska, Justyna; Martin, Loïc; Lievin-Le Moal, Vanessa; Le Grand, Roger; Dereuddre-Bosquet, Nathalie; Djabourov, Madeleine; Aka-Any-Grah, Armelle; Koffi, Armand; Ponchel, Gilles

    2013-10-01

    The miniCD4 M48U1 was formulated into thermosensitive and mucoadhesive pluronic(®) hydrogels as anti-HIV-1 microbicide. The release kinetics of M48U1 from F127/HPMC (20/1 wt%) and F127/F68/HPMC (22.5/2.5/1 wt%) studied during 24h by using Franz diffusion cells showed that HEC hydrogel (1.5 wt%) used as control released 93% of the peptide, while about 25% of M48U1 remained in pluronic(®) hydrogels. The formulation of M48U1 in pluronic(®) hydrogels ensures a local delivery because no diffusion of the peptide was detected through vaginal Cynomolgus macaque mucosa using Ussing chamber. Finally, toxicological studies showed no significant difference in the HeLa cell viability of the pluronic(®) hydrogels in comparison with HEC and phosphate buffer saline.

  18. Gauged U(1) Lμ -Lτ model in light of muon g - 2 anomaly, neutrino mass and dark matter phenomenology

    NASA Astrophysics Data System (ADS)

    Patra, Sudhanwa; Rao, Soumya; Sahoo, Nirakar; Sahu, Narendra

    2017-04-01

    Gauged U(1) Lμ -Lτ model has been advocated for a long time in light of muon g - 2 anomaly, which is a more than 3σ discrepancy between the experimental measurement and the standard model prediction. We augment this model with three right-handed neutrinos (Ne ,Nμ ,Nτ) and a vector-like singlet fermion (χ) to explain simultaneously the non-zero neutrino masses and dark matter content of the Universe, while satisfying the anomalous muon g - 2 constraints. We find that the model suffers stringent constraints from the simultaneous explanation of neutrino trident production and muon g - 2 anomaly. In a large region of the parameter space, where contribution to muon g - 2 anomaly comes partially and yet not ruled out by neutrino trident production, the model can explain the positron excess, observed at PAMELA, Fermi-LAT and AMS-02 through dark matter annihilation, while satisfying the relic density and direct detection limits.

  19. Spontaneous mass generation and the small dimensions of the Standard Model gauge groups U(1), SU(2) and SU(3)

    NASA Astrophysics Data System (ADS)

    Llanes-Estrada, Felipe J.; García, Guillermo; Guerrero Rojas, Jesús

    2017-01-01

    The gauge symmetry of the Standard Model is U(1) xSU(2)L xSU(3) for unknown reasons. One aspect that can be addressed is the low dimensionality of all its subgroups. Why not much larger groups like SU(7) or for that matter, SP(38) or E7? We observe that fermions charged under large groups acquire much bigger dynamical masses, all things being equal at a high e.g. GUT scale, than ordinary quarks. Should such multicharged fermions exist, they are too heavy to be observed today and have either decayed early on (if they couple to the rest of the Standard Model) or become reliquial dark matter (if they don't). The result follows easily from strong antiscreening of the running coupling for the larger group together with scaling properties of the Dyson-Schwinger equation for the fermion mass.

  20. Spontaneous mass generation and the small dimensions of the Standard Model gauge groups U(1), SU(2) and SU(3)

    NASA Astrophysics Data System (ADS)

    García Fernández, Guillermo; Guerrero Rojas, Jesús; Llanes-Estrada, Felipe J.

    2017-02-01

    The gauge symmetry of the Standard Model is SU(3)c × SU(2)L × U(1)Y for unknown reasons. One aspect that can be addressed is the low dimensionality of all its subgroups. Why not much larger groups like SU (7), or for that matter, SP (38) or E7? We observe that fermions charged under large groups acquire much bigger dynamical masses, all things being equal at a high e.g. GUT scale, than ordinary quarks. Should such multicharged fermions exist, they are too heavy to be observed today and have either decayed early on (if they couple to the rest of the Standard Model) or become reliquial dark matter (if they don't). The result follows from strong antiscreening of the running coupling for those larger groups (with an appropriately small number of flavors) together with scaling properties of the Dyson-Schwinger equation for the fermion mass.

  1. Fragmentation of 120 and 200 MeV u(-1)(4)He ions in water and PMMA targets.

    PubMed

    Rovituso, M; Schuy, C; Weber, U; Brons, S; Cortés-Giraldo, M A; La Tessa, C; Piasetzky, E; Izraeli, D; Schardt, D; Toppi, M; Scifoni, E; Krämer, M; Durante, M

    2017-02-21

    Recently, the use of (4)He particles in cancer radiotherapy has been reconsidered as they potentially represent a good compromise between protons and (12)C ions. The first step to achieve this goal is the development of a dedicated treatment planning system, for which basic physics information such as the characterization of the beam lateral scattering and fragmentation cross sections are required. In the present work, the attenuation of (4)He primary particles and the build-up of secondary charged fragments at various depths in water and polymethyl methacrylate were investigated experimentally for 120 and 200 MeV u(-1) beams delivered by the synchrotron at the Heidelberg Ion-Beam Therapy Center, Heidelberg. Species and isotope identification was accomplished combining energy loss and time-of-flight measurements. Differential yields and energy spectra of all fragments types were recorded between 0° and 20° with respect to the primary beam direction.

  2. Proof of the local mass-angular momenta inequality for U{(1)}^{2} invariant black holes

    NASA Astrophysics Data System (ADS)

    Alaee, Aghil; Kunduri, Hari K.

    2015-08-01

    We consider initial data for extreme vacuum asymptotically flat black holes with {{R}}× U{(1)}2 symmetry. Such geometries are critical points of a mass functional defined for a wide class of asymptotically flat, ‘(t-{φ }i)’ symmetric maximal initial data for the vacuum Einstein equations. We prove that the above extreme geometries are local minima of mass among nearby initial data (with the same interval structure) with fixed angular momenta. Thus the ADM mass of nearby data m≥slant f({J}1,{J}2) for some function f depending on the interval structure. The proof requires that the initial data of the critical points satisfy certain conditions that are satisfied by the extreme Myers-Perry and extreme black ring data.

  3. String completion of an SU(3)c ⊗ SU(3)L ⊗ U(1)X electroweak model

    NASA Astrophysics Data System (ADS)

    Addazi, Andrea; Valle, J. W. F.; Vaquera-Araujo, C. A.

    2016-08-01

    The extended electroweak SU(3)c ⊗ SU(3)L ⊗ U(1)X symmetry framework "explaining" the number of fermion families is revisited. While 331-based schemes can not easily be unified within the conventional field theory sense, we show how to do it within an approach based on D-branes and (un)oriented open strings, on Calabi-Yau singularities. We show how the theory can be UV-completed in a quiver setup, free of gauge and string anomalies. Lepton and baryon numbers are perturbatively conserved, so neutrinos are Dirac-type, and their lightness results from a novel TeV scale seesaw mechanism. Dynamical violation of baryon number by exotic instantons could induce neutron-antineutron oscillations, with proton decay and other dangerous R-parity violating processes strictly forbidden.

  4. Chiral quark dynamics and topological charge: The role of the Ramond-Ramond U(1) gauge field in holographic QCD

    NASA Astrophysics Data System (ADS)

    Thacker, H. B.; Xiong, Chi; Kamat, Ajinkya S.

    2011-11-01

    The Witten-Sakai-Sugimoto construction of holographic QCD in terms of D4 color branes and D8 flavor branes in type IIA string theory is used to investigate the role of topological charge in the chiral dynamics of quarks in QCD. The QCD theta term arises from a compactified five-dimensional Chern-Simons term on the D4 branes. This term couples the QCD topological charge to the Ramond-Ramond (RR) U(1) gauge field of type IIA string theory. For large Nc the contribution of instantons (D0 branes) is suppressed, and the nonzero topological susceptibility of pure-glue QCD is attributed to the presence of D6 branes, which constitute magnetic sources of the RR gauge field. The topological charge of QCD is required, by an anomaly inflow argument, to coincide in space-time with the intersection of the D6 branes and the D4 color branes. This clarifies the relation between D6 branes and the coherent, codimension-one topological charge membranes observed in QCD Monte Carlo calculations. Using open-string/closed-string duality, we interpret a quark loop (represented by a D4-D8 open-string loop) in terms of closed-string exchange between color and flavor branes. The role of the RR gauge field in quark-antiquark annihilation processes is discussed. RR exchange in the s-channel generates a 4-quark contact term which produces an η' mass insertion and provides an explanation for the observed spin-parity structure of the Okubo-Zweig-Iizuka rule. The (log⁡DetU)2 form of the U(1) anomaly emerges naturally. RR exchange in the t-channel of the qq¯ scattering amplitude produces a Nambu-Jona-Lasinio interaction which may provide a mechanism for spontaneous breaking of SU(Nf)×SU(Nf).

  5. Position-dependent inhibition of the cleavage step of pre-mRNA 3'-end processing by U1 snRNP.

    PubMed

    Vagner, S; Rüegsegger, U; Gunderson, S I; Keller, W; Mattaj, I W

    2000-02-01

    The 3' ends of most eukaryotic pre-mRNAs are generated by 3' endonucleolytic cleavage and subsequent polyadenylation. 3'-end formation can be influenced positively or negatively by various factors. In particular, U1 snRNP acts as an inhibitor when bound to a 5' splice site located either upstream of the 3'-end formation signals of bovine papilloma virus (BPV) late transcripts or downstream of the 3'-end processing signals in the 5' LTR of the HIV-1 provirus. Previous work showed that in BPV it is not the first step, 3' cleavage, that is affected by U1 snRNP, but rather the second step, polyadenylation, that is inhibited. Since in HIV-1 the biological requirement is to produce transcripts that read through the 5' LTR cleavage site rather than being cleaved there, this mechanism seemed unlikely to apply. The obvious difference between the two examples was the relative orientation of the 3'-end formation signals and the U1 snRNP-binding site. In vitro assays were therefore used to assess the effect of U1 snRNP bound at various locations relative to a cleavage/polyadenylation site on the 3' cleavage reaction. U1 snRNP was found to inhibit cleavage when bound to a 5' splice site downstream of the cleavage/polyadenylation site, as in the HIV-1 LTR. U1 snRNP binding at this location was shown not to affect the recruitment of multiple cleavage/polyadenylation factors to the cleavage substrate, indicating that inhibition is unlikely to be due to steric hindrance. Interactions between U1A, U1 70K, and poly(A) polymerase, which mediate the effect of U1 snRNP on polyadenylation of other pre-mRNAs, were shown not to be required for cleavage inhibition. Therefore, U1 snRNP bound to a 5' splice site can inhibit cleavage and polyadenylation in two mechanistically different ways depending on whether the 5' splice site is located upstream or downstream of the cleavage site.

  6. Neurotoxicity in Sri Lankan Russell's Viper (Daboia russelii) Envenoming is Primarily due to U1-viperitoxin-Dr1a, a Pre-Synaptic Neurotoxin.

    PubMed

    Silva, Anjana; Kuruppu, Sanjaya; Othman, Iekhsan; Goode, Robert J A; Hodgson, Wayne C; Isbister, Geoffrey K

    2017-01-01

    Russell's vipers are snakes of major medical importance in Asia. Russell's viper (Daboia russelii) envenoming in Sri Lanka and South India leads to a unique, mild neuromuscular paralysis, not seen in other parts of the world where the snake is found. This study aimed to identify and pharmacologically characterise the major neurotoxic components of Sri Lankan Russell's viper venom. Venom was fractionated using size exclusion chromatography and reverse-phase high-performance liquid chromatography (RP-HPLC). In vitro neurotoxicities of the venoms, fractions and isolated toxins were measured using chick biventer and rat hemidiaphragm preparations. A phospholipase A2 (PLA2) toxin, U1-viperitoxin-Dr1a (13.6 kDa), which constitutes 19.2 % of the crude venom, was isolated and purified using HPLC. U1-viperitoxin-Dr1a produced concentration-dependent in vitro neurotoxicity abolishing indirect twitches in the chick biventer nerve-muscle preparation, with a t 90 of 55 ± 7 min only at 1 μM. The toxin did not abolish responses to acetylcholine and carbachol indicating pre-synaptic neurotoxicity. Venom, in the absence of U1-viperitoxin-Dr1a, did not induce in vitro neurotoxicity. Indian polyvalent antivenom, at the recommended concentration, only partially prevented the neurotoxic effects of U1-viperitoxin-Dr1a. Liquid chromatography mass spectrometry analysis confirmed that U1-viperitoxin-Dr1a was the basic S-type PLA2 toxin previously identified from this venom (NCBI-GI: 298351762; SwissProt: P86368). The present study demonstrates that neurotoxicity following Sri Lankan Russell's viper envenoming is primarily due to the pre-synaptic neurotoxin U1-viperitoxin-Dr1a. Mild neurotoxicity observed in severely envenomed Sri Lankan Russell's viper bites is most likely due to the low potency of U1-viperitoxin-Dr1a, despite its high relative abundance in the venom.

  7. Lattice Parameter Behavior with Different Nd and O Concentrations in (U1-yNdy)O2±x Solid Solution

    DOE PAGES

    Lee, Seung Min; Knight, Travis W.; Voit, Stwart L.; ...

    2016-02-02

    The solid solution of (U1-yFPy)O-2±x, has the same fluorite structure as UO2±x lambda, and the lattice parameter is affected by dissolved fission product and oxygen concentrations. We investigated the relation between the lattice parameter and the concentrations of neodymium and oxygen in the fluorite structure of (U1-yNdy)O2±x using X-ray diffraction. Moreover, the lattice parameter behavior in the (U1-yNdy)O2±x, solid solution shows a linear change as a function of the oxygen-to-metal ratio and solubility of neodymium. The lattice parameter depends on the radii of ions forming the fluorite structure and also can be expressed by a particular rule (modified Vegard's law).more » Furthermore, the numerical analyses of the lattice parameters for the stoichiometric and nonstoichionietric solid solutions were conducted, and the lattice parameter model for the (U1-yNdy)O2±x, solid solution was assessed. There is a very linear relationship between the lattice parameter and the Nd and O concentration for the stoichiometry and nonstoichiometry of the (U1-yNdy)O2±x solid solution was verified.« less

  8. Controlled calculation of the thermal conductivity for a spinon Fermi surface coupled to a U(1) gauge field

    SciTech Connect

    Freire, Hermann

    2014-10-15

    Motivated by recent transport measurements on the candidate spin-liquid phase of the organic triangular lattice insulator EtMe{sub 3}Sb[Pd(dmit){sub 2}]{sub 2}, we perform a controlled calculation of the thermal conductivity at intermediate temperatures in a spin liquid system where a spinon Fermi surface is coupled to a U(1) gauge field. The present computation builds upon the double expansion approach developed by Mross et al. (2010) for small ϵ=z{sub b}−2 (where z{sub b} is the dynamical critical exponent of the gauge field) and large number of fermionic species N. Using the so-called memory matrix formalism that most crucially does not assume the existence of well-defined quasiparticles at low energies in the system, we calculate the temperature dependence of the thermal conductivity κ of this model due to non-critical Umklapp scattering of the spinons for a finite N and small ϵ. Then we discuss the physical implications of such theoretical result in connection with the experimental data available in the literature.

  9. Phenomenology of an SU(2) × SU(2) × U(1) model with lepton-flavour non-universality

    NASA Astrophysics Data System (ADS)

    Boucenna, Sofiane M.; Celis, Alejandro; Fuentes-Martín, Javier; Vicente, Avelino; Virto, Javier

    2016-12-01

    We investigate a gauge extension of the Standard Model in light of the observed hints of lepton universality violation in b → cℓν and b → sℓ + ℓ - decays at BaBar, Belle and LHCb. The model consists of an extended gauge group SU(2)1 × SU(2)2 × U(1) Y which breaks spontaneously around the TeV scale to the electroweak gauge group. Fermion mixing effects with vector-like fermions give rise to potentially large new physics contributions in flavour transitions mediated by W' and Z' bosons. This model can ease tensions in B-physics data while satisfying stringent bounds from flavour physics, and electroweak precision data. Possible ways to test the proposed new physics scenario with upcoming experimental measurements are discussed. Among other predictions, the ratios R M = Γ( B → M μ + μ -) /Γ( B → Me + e -), with M = K * , ϕ, are found to be reduced with respect to the Standard Model expectation R M ≃ 1.

  10. Boson stars in a theory of complex scalar fields coupled to the U(1) gauge field and gravity

    NASA Astrophysics Data System (ADS)

    Kumar, Sanjeev; Kulshreshtha, Usha; Shankar Kulshreshtha, Daya

    2014-08-01

    We study boson shells and boson stars in a theory of a complex scalar field coupled to the U(1) gauge field {{A}_{\\mu }} and Einstein gravity with the potential V(|\\Phi |)\\;:=\\frac{1}{2}{{m}^{2}}{{\\left( |\\Phi |+a \\right)}^{2}}. This could be considered either as a theory of a massive complex scalar field coupled to an electromagnetic field and gravity in a conical potential, or as a theory in the presence of a potential that is an overlap of a parabolic and conical potential. Our theory has a positive cosmological constant (\\Lambda :=4\\pi G{{m}^{2}}{{a}^{2}}). Boson stars are found to come in two types, having either ball-like or shell-like charge density. We studied the properties of these solutions and also determined their domains of existence for some specific values of the parameters of the theory. Similar solutions have also been obtained by Kleihaus, Kunz, Laemmerzahl and List, in a V-shaped scalar potential.

  11. Computational study of the energetics of charge and cation mixing in U1-xCexO₂

    DOE PAGES

    Hanken, B. E.; Stanek, C. R.; Grønbech-Jensen, N.; ...

    2011-08-26

    The formalism of electronic density-functional theory (DFT), with Hubbard-U corrections (DFT+U), is employed in a computational study of the energetics of fluorite-structured U1-xCexO₂ mixtures. The computational approach makes use of a procedure which facilitates convergence of the calculations to multiple self-consistent DFT+U solutions for a given cation arrangement, corresponding to different charge states for the U and Ce ions in several prototypical cation arrangements. Results indicate a significant dependence of the structural and energetic properties on the nature of both charge and cation ordering. With the effective Hubbard-U parameters that reproduce well the measured oxidation-reduction energies for urania and ceria,more » we find that charge transfer between U⁴⁺ and Ce⁴⁺ ions, leading to the formation of U⁵⁺ and Ce³⁺, gives rise to an increase in the mixing energy in the range of 4–14 kJ/mol of the formula unit, depending on the nature of the cation ordering. The results suggest that although charge transfer between uranium and cerium ions is disfavored energetically, it is likely to be entropically stabilized at the high temperatures relevant to the processing and service of urania-based solid solutions.« less

  12. Energy criterion and dynamical symmetry breaking in a SU(3){sub L} x U(1){sub X} extension of the standard model

    SciTech Connect

    Doff, A.

    2007-08-01

    The coupling constants g{sub L} and g{sub X} of some versions of the SU(3){sub L} x U(1){sub X} extension of the standard model are related through to relationship g{sub X}{sup 2}/g{sub L}{sup 2}=sin{sup 2}{theta}{sub W}/(1-4sin{sup 2}{theta}{sub W}). This fact suggest that the SU(3){sub L} x U(1){sub X} gauge symmetry in this class of models can be broken dynamically to the standard model at TeV scale without requiring the introduction of fundamental scalars. This possibility was investigated by Das and Jain who considered the only first version of this class of models. In this brief report we discuss an energy criterion to verify the most probable version of the SU(3){sub L} x U(1){sub X} model that is realized in nature.

  13. Quench dynamics of the three-dimensional U(1) complex field theory: Geometric and scaling characterizations of the vortex tangle

    NASA Astrophysics Data System (ADS)

    Kobayashi, Michikazu; Cugliandolo, Leticia F.

    2016-12-01

    We present a detailed study of the equilibrium properties and stochastic dynamic evolution of the U(1)-invariant relativistic complex field theory in three dimensions. This model has been used to describe, in various limits, properties of relativistic bosons at finite chemical potential, type II superconductors, magnetic materials, and aspects of cosmology. We characterize the thermodynamic second-order phase transition in different ways. We study the equilibrium vortex configurations and their statistical and geometrical properties in equilibrium at all temperatures. We show that at very high temperature the statistics of the filaments is the one of fully packed loop models. We identify the temperature, within the ordered phase, at which the number density of vortex lengths falls off algebraically and we associate it to a geometric percolation transition that we characterize in various ways. We measure the fractal properties of the vortex tangle at this threshold. Next, we perform infinite rate quenches from equilibrium in the disordered phase, across the thermodynamic critical point, and deep into the ordered phase. We show that three time regimes can be distinguished: a first approach toward a state that, within numerical accuracy, shares many features with the one at the percolation threshold; a later coarsening process that does not alter, at sufficiently low temperature, the fractal properties of the long vortex loops; and a final approach to equilibrium. These features are independent of the reconnection rule used to build the vortex lines. In each of these regimes we identify the various length scales of the vortices in the system. We also study the scaling properties of the ordering process and the progressive annihilation of topological defects and we prove that the time-dependence of the time-evolving vortex tangle can be described within the dynamic scaling framework.

  14. A New Fate of a Warped 5D FLRW Model with a U(1) Scalar Gauge Field

    NASA Astrophysics Data System (ADS)

    Slagter, Reinoud Jan; Pan, Supriya

    2016-09-01

    If we live on the weak brane with zero effective cosmological constant in a warped 5D bulk spacetime, gravitational waves and brane fluctuations can be generated by a part of the 5D Weyl tensor and carries information of the gravitational field outside the brane. We consider on a cylindrical symmetric warped FLRW background a U(1) self-gravitating scalar field coupled to a gauge field without bulk matter. It turns out that brane fluctuations can be formed dynamically, due to the modified energy-momentum tensor components of the scalar-gauge field ("cosmic string"). As a result, we find that the late-time behavior could significantly deviate from the standard evolution of the universe. The effect is triggered by the time-dependent warpfactor with two branches of the form ± 1/√{τ r}√{(c_1e^{√{2τ } t}+c_2e^{-√{2τ } t})(c_3e^{√{2τ } r}+c_4e^{-√{2τ } r})} ( with τ , c_i constants) and the modified brane equations comparable with a dark energy effect. This is a brane-world mechanism, not present in standard 4D FLRW, where the large disturbances are rapidly damped as the expansion proceed. Because gravity can propagate in the bulk, the cosmic string can build up a huge angle deficit (or mass per unit length) by the warpfactor and can induce massive KK-modes felt on the brane. Disturbances in the spatial components of the stress-energy tensor cause cylindrical symmetric waves, amplified due to the presence of the bulk space and warpfactor. They could survive the natural damping due to the expansion of the universe. It turns out that one of the metric components becomes singular at the moment the warp factor develops an extremum. This behavior could have influence on the possibility of a transition from acceleration to deceleration or vice versa.

  15. Gauge bosons masses in a SU(2){sub TC} x SU(3){sub L} x U(1){sub X} extension of the standard model

    SciTech Connect

    Doff, A.

    2010-06-01

    In this brief report we explore the full realization of the dynamical symmetry breaking of an 3-3-1 model to U(1){sub em} considering a model based on SU(2){sub TC} x SU(3){sub L} x U(1){sub X}. We compute the mass generated for the charged and neutral gauge bosons of the model that result from the symmetry breaking, and verify the equivalence between a 3-3-1 model with a scalar content formed by the set of the fundamental scalar bosons {chi},{rho} and {eta} with a 3-3-1 model where the dynamical symmetry breaking is implanted by the system formed by the set of composite bosons {Phi}{sub T},{Phi}{sub TC(1)} and {Phi}{sub TC(2)}. In this model the minimal composite scalar content is fixed by the condition of the cancellation of triangular anomaly in the technicolor (TC) sector.

  16. Semidirect product gauge group [SU(3){sub c}xSU(2){sub L}]xU(1){sub Y} and quantization of hypercharge

    SciTech Connect

    Hattori, Chuichiro; Matsunaga, Mamoru; Matsuoka, Takeo

    2011-01-01

    In the standard model the hypercharges of quarks and leptons are not determined by the gauge group SU(3){sub c}xSU(2){sub L}xU(1){sub Y} alone. We show that, if we choose the semidirect product group [SU(3){sub c}xSU(2){sub L}]xU(1){sub Y} as its gauge group, the hyperchages are settled to be n/6 mod Z(n=0,1,3,4). In addition, the conditions for gauge-anomaly cancellation give strong constraints. As a result, the ratios of the hypercharges are uniquely determined and the gravitational anomaly is automatically canceled. The standard charge assignment to quarks and leptons can be properly reproduced. For exotic matter fields their hypercharges are also discussed.

  17. The linked units of 5S rDNA and U1 snDNA of razor shells (Mollusca: Bivalvia: Pharidae).

    PubMed

    Vierna, J; Jensen, K T; Martínez-Lage, A; González-Tizón, A M

    2011-08-01

    The linkage between 5S ribosomal DNA and other multigene families has been detected in many eukaryote lineages, but whether it provides any selective advantage remains unclear. In this work, we report the occurrence of linked units of 5S ribosomal DNA (5S rDNA) and U1 small nuclear DNA (U1 snDNA) in 10 razor shell species (Mollusca: Bivalvia: Pharidae) from four different genera. We obtained several clones containing partial or complete repeats of both multigene families in which both types of genes displayed the same orientation. We provide a comprehensive collection of razor shell 5S rDNA clones, both with linked and nonlinked organisation, and the first bivalve U1 snDNA sequences. We predicted the secondary structures and characterised the upstream and downstream conserved elements, including a region at -25 nucleotides from both 5S rDNA and U1 snDNA transcription start sites. The analysis of 5S rDNA showed that some nontranscribed spacers (NTSs) are more closely related to NTSs from other species (and genera) than to NTSs from the species they were retrieved from, suggesting birth-and-death evolution and ancestral polymorphism. Nucleotide conservation within the functional regions suggests the involvement of purifying selection, unequal crossing-overs and gene conversions. Taking into account this and other studies, we discuss the possible mechanisms by which both multigene families could have become linked in the Pharidae lineage. The reason why 5S rDNA is often found linked to other multigene families seems to be the result of stochastic processes within genomes in which its high copy number is determinant.

  18. The (IR-)relevance of the Gribov ambiguity in SU(2)×U(1) gauge theories with fundamental Higgs matter

    SciTech Connect

    Capri, M.A.L.; Dudal, D.; Guimaraes, M.S.; Justo, I.F.; Sorella, S.P.; and others

    2014-04-15

    It is well accepted that dealing with the Gribov ambiguity has a major impact on correlation functions in gauge-fixed Yang–Mills theories, in particular in the low momentum regime where standard perturbation theory based on the Faddeev–Popov approach fails. Recent results, derived from functional tools (Dyson–Schwinger equations or exact RG) or the effective Gribov–Zwanziger action method, pointed towards e.g. gauge boson correlation functions that are not compatible with the properties of observable degrees of freedom. Although such an observation is a welcome feature for gauge theories exhibiting confinement, it would be a discomfort for gauge theories supplemented with Higgs fields, cf. the experimental success of the electroweak model based on a SU(2)×U(1) gauge group. The purpose of this short note is to assure that the effective action resolution to the Gribov ambiguity reduces to the standard Faddeev–Popov method in the perturbative regime of sufficiently small coupling/large Higgs condensate, thereby not compromising the physical particle spectrum of massive gauge bosons and a massless photon for the SU(2)×U(1) gauge–Higgs model. The closer the theory gets to the limit of vanishing Higgs condensate, the more the Gribov problem resurfaces with all its consequences. We give some speculations w.r.t. the Fradkin–Shenker insights about the phase diagram. -- Highlights: •Gribov horizon influences gauge propagators in a strong-coupling regime. •No influence of Gribov horizon in weak-coupling. •Inclusion of U(1) factor leads to very rich behavior of propagators.

  19. Muon Spin Relaxation Evidence for the U(1) Quantum Spin-Liquid Ground State in the Triangular Antiferromagnet YbMgGaO_{4}.

    PubMed

    Li, Yuesheng; Adroja, Devashibhai; Biswas, Pabitra K; Baker, Peter J; Zhang, Qian; Liu, Juanjuan; Tsirlin, Alexander A; Gegenwart, Philipp; Zhang, Qingming

    2016-08-26

    Muon spin relaxation (μSR) experiments on single crystals of the structurally perfect triangular antiferromagnet YbMgGaO_{4} indicate the absence of both static long-range magnetic order and spin freezing down to 0.048 K in a zero field. Below 0.4 K, the μ^{+} spin relaxation rates, which are proportional to the dynamic correlation function of the Yb^{3+} spins, exhibit temperature-independent plateaus. All these μSR results unequivocally support the formation of a gapless U(1) quantum spin liquid ground state in the triangular antiferromagnet YbMgGaO_{4}.

  20. Experimental oxygen potentials for U1-yPryO2±x and thermodynamic assessment of the U-Pr-O system

    NASA Astrophysics Data System (ADS)

    McMurray, J. W.; Silva, C. M.

    2016-03-01

    Thermogravimetric analysis (TGA) was used to determine the oxygen potentials of fluorite urania-praseodymia (U1-yPryO2±x) solid solutions for y = 0.10 and 0.20 between 1000 and 1500 °C. A thermodynamic assessment of U-Pr-O system was performed using the CALPHAD (CALculation of PHAse Diagrams) method. The models well reproduce the TGA measurements and the computed phase relations are in good agreement with those proposed from an X-ray diffraction investigation.

  1. Experimental oxygen potentials of U1-yPryO2± x and thermodynamic assessment of the U-Pr-O system

    DOE PAGES

    McMurray, Jake W.; Silva, Chinthaka M.

    2015-12-09

    Thermogravimetric analysis (TGA) was used to determine the oxygen potentials of fluorite urania-praseodymia (U1-yPryO2± x) solid solutions for y = 0.10 and 0.20 between 1000 and 1500 °C. A thermodynamic assessment of U-Pr-O system was performed using the CALPHAD (CALculation of PHAse Diagrams) method. Furthermore, the models well reproduce the TGA measurements and the computed phase relations are in good agreement with those proposed from an X-ray diffraction investigation.

  2. Efficient utilization of hemicellulose and cellulose in alkali liquor-pretreated corncob for bioethanol production at high solid loading by Spathaspora passalidarum U1-58.

    PubMed

    Yu, Hai; Guo, Jian; Chen, Yefu; Fu, Gengxin; Li, Baozhong; Guo, Xuewu; Xiao, Dongguang

    2017-02-11

    The bioethanol fermentation of pretreated corncob was investigated using Spathaspora passalidarum U1-58, which simultaneously utilizes glucose and xylose for high-efficiency ethanol production. Two approaches, namely, separate hydrolysis and co-fermentation (SHCF) and simultaneous saccharification and co-fermentation (SSCF), were optimized to test the ethanol fermentation potential of U1-58. The highest ethanol titer of 42.46g/L and yield of 72.12% were acquired in SHCF, whereas 53.24g/L ethanol and yield of 75.35% were obtained in SSCF at solid-to-liquid ratio of 1:5 (w/v). Approximately 86.20% of cellulose and 82.99% of hemicellulose were consumed in SSCF after 96h, and at least 10.49g/L ethanol was produced from hemicellulose, which corresponded to 37.59% of the theoretical yield. Compared with the published cellulosic ethanol fermentation cases, the present work presented high ethanol titer and yield, and cellulose and hemicellulose could be efficiently utilized for ethanol production.

  3. Free-Spinning-Tunnel Investigation of a 1/25-Scale Model of the Chance Vought F8U-1P Airplane

    NASA Technical Reports Server (NTRS)

    Browman, James S., Jr.; Healy, Frederick M.

    1959-01-01

    An investigation has been made in the Langley 20-foot free-spinning tunnel on a 1/25-scale dynamic model to determine the spin and recovery characteristics of the Chance Vought F8U-1P airplane. Results indicated that the F8U-IP airplane would have spin-recovery characteristics similar to the XF8U-1 design, a model of which was tested and the results of the tests reported in NACA Research Memorandum SL56L31b. The results indicate that some modification in the design, or some special technique for recovery, is required in order to insure satisfactory recovery from fully developed erect spins. The recommended recovery technique for the F8U-lP will be full rudder reversal and movement of ailerons full with the spin (stick right in a right spin) with full deflection of the wing leading- edge flap. Inverted spins will be difficult to obtain and any inverted spin obtained should be readily terminated by full rudder reversal to oppose the yawing rotation and neutralization of the longitudinal and lateral controls. In an emergency, the same size parachute recommended for the XFBU-1 airplane will be adequate for termination of the spin: a stable parachute 17.7 feet in diameter (projected) with a drag coefficient of 1.14 (based on projected diameter) and a towline length of 36.5 feet.

  4. Interaction of hnRNP A1 with snRNPs and pre-mRNAs: evidence for a possible role of A1 RNA annealing activity in the first steps of spliceosome assembly.

    PubMed Central

    Buvoli, M; Cobianchi, F; Riva, S

    1992-01-01

    The in vitro interaction of recombinant hnRNP A1 with purified snRNPs and with pre-mRNAs was investigated. We show that protein A1 can stably bind U2 and U4 snRNP but not U1. Oligo-RNAse H cleavage of U2 nucleotides involved in base pairing with the branch site, totally eliminates the A1-U2 interaction. RNase T1 protection and immunoprecipitation experiments demonstrate that recombinant protein A1 specifically binds the 3'-end regions of both beta-globin and Ad-2 introns. However, while on the beta-globin intron only binding to the polypyrimidine tract was observed, on the Ad-2 intron a 32 nt fragment encompassing the branch point and the AG splice-site dinucleotide was bound and protected. Such protection was drastically reduced in the presence of U2 snRNP. Altogether these results indicate that protein A1 can establish a different pattern of association with different pre-mRNAs and support the hypothesis that this protein could play a role in the annealing of U2 to the branch site and hence in the early events of pre-splicing complex assembly. Images PMID:1329035

  5. POC1A truncation mutation causes a ciliopathy in humans characterized by primordial dwarfism.

    PubMed

    Shaheen, Ranad; Faqeih, Eissa; Shamseldin, Hanan E; Noche, Ramil R; Sunker, Asma; Alshammari, Muneera J; Al-Sheddi, Tarfa; Adly, Nouran; Al-Dosari, Mohammed S; Megason, Sean G; Al-Husain, Muneera; Al-Mohanna, Futwan; Alkuraya, Fowzan S

    2012-08-10

    Primordial dwarfism (PD) is a phenotype characterized by profound growth retardation that is prenatal in onset. Significant strides have been made in the last few years toward improved understanding of the molecular underpinning of the limited growth that characterizes the embryonic and postnatal development of PD individuals. These include impaired mitotic mechanics, abnormal IGF2 expression, perturbed DNA-damage response, defective spliceosomal machinery, and abnormal replication licensing. In three families affected by a distinct form of PD, we identified a founder truncating mutation in POC1A. This gene is one of two vertebrate paralogs of POC1, which encodes one of the most abundant proteins in the Chlamydomonas centriole proteome. Cells derived from the index individual have abnormal mitotic mechanics with multipolar spindles, in addition to clearly impaired ciliogenesis. siRNA knockdown of POC1A in fibroblast cells recapitulates this ciliogenesis defect. Our findings highlight a human ciliopathy syndrome caused by deficiency of a major centriolar protein.

  6. U1-RNP and Toll-like receptors in the pathogenesis of mixed connective tissue diseasePart II. Endosomal TLRs and their biological significance in the pathogenesis of mixed connective tissue disease.

    PubMed

    Paradowska-Gorycka, Agnieszka

    2015-01-01

    Mixed connective tissue disease (MCTD) is a chronic autoimmune immunopathological disease of unknown etiology, which is characterized by the presence of various clinical symptoms and the presence of autoantibodies against U1-RNP particles. The U1-RNP component engages immune cells and their receptors in a complex network of interactions that ultimately lead to autoimmunity, inflammation, and tissue injury. The anti-U1-RNP autoantibodies form an immune complex with self-RNA, present in MCTD serum, which can act as endosomal Toll-like receptor (TLR) ligands. Inhibition of TLRs by nucleic acids is a promising area of research for the development of novel therapeutic strategies against pathogenic infection, tumorigenesis and autoimmunity. In this review we summarize current knowledge of endogenous TLRs and discuss their biological significance in the pathogenesis of MCTD. In part I we described the structure, biological function and significance of the U1-RNP complex in MCTD.

  7. Complementary test of the dark matter self-interaction in dark U(1) model by direct and indirect dark matter detection

    SciTech Connect

    Chen, Chian-Shu; Lin, Guey-Lin; Lin, Yen-Hsun E-mail: glin@cc.nctu.edu.tw

    2016-01-01

    The halo dark matter (DM) can be captured by the Sun if its final velocity after the collision with a nucleus in the Sun is less than the escape velocity. We consider a selfinteracting dark matter (SIDM) model where U(1) gauge symmetry is introduced to account for the DM self-interaction. Such a model naturally leads to isospin violating DM-nucleon interaction, although isospin symmetric interaction is still allowed as a special case. We present the IceCube-PINGU 2σ sensitivity to the parameter range of the above model with 5 years of search for neutrino signature from DM annihilation in the Sun. This indirect detection complements the direct detection by probing those SIDM parameter ranges which are either the region for very small m{sub χ} or the region opened up due to isospin violations.

  8. Complementary test of the dark matter self-interaction in dark U(1) model by direct and indirect dark matter detection

    SciTech Connect

    Chen, Chian-Shu; Lin, Guey-Lin; Lin, Yen-Hsun

    2016-01-07

    The halo dark matter (DM) can be captured by the Sun if its final velocity after the collision with a nucleus in the Sun is less than the escape velocity. We consider a selfinteracting dark matter (SIDM) model where U(1) gauge symmetry is introduced to account for the DM self-interaction. Such a model naturally leads to isospin violating DM-nucleon interaction, although isospin symmetric interaction is still allowed as a special case. We present the IceCube-PINGU 2σ sensitivity to the parameter range of the above model with 5 years of search for neutrino signature from DM annihilation in the Sun. This indirect detection complements the direct detection by probing those SIDM parameter ranges which are either the region for very small m{sub χ} or the region opened up due to isospin violations.

  9. Phenomenology of the SU(3){sub c}xSU(3){sub L}xU(1){sub X} model with exotic charged leptons

    SciTech Connect

    Salazar, Juan C.; Ponce, William A.; Gutierrez, Diego A.

    2007-04-01

    A phenomenological analysis of the three-family model based on the local gauge group SU(3){sub c}xSU(3){sub L}xU(1){sub X} with exotic charged leptons, is carried out. Instead of using the minimal scalar sector able to break the symmetry in a proper way, we introduce an alternative set of four Higgs scalar triplets, which combined with an anomaly-free discrete symmetry, produce quark and charged lepton mass spectrum without hierarchies in the Yukawa coupling constants. We also embed the structure into a simple gauge group and show some conditions to achieve a low energy gauge coupling unification, avoiding possible conflict with proton decay bounds. By using experimental results from the CERN-LEP, SLAC linear collider, and atomic parity violation data, we update constraints on several parameters of the model.

  10. Signals of extra gauge bosons and exotic leptons in SU(6){sub {ital L}}{direct_product}U(1){sub {ital Y}}

    SciTech Connect

    Gaitan-Lozano, R.; Hernandez-Galeana, A.; Tomas, S.A.; Ponce, W.A.; Zepeda, A. |||

    1995-06-01

    We study some of the consequences of the SU(6){sub {ital L}}{direct_product}U(1){sub {ital Y}} model of unification of electroweak interactions and families with a horizontal gauge group SU(2){sub {ital H}}, paying special attention to processes with flavor-changing neutral currents. We compute at the tree level the decays {ital K}{sup +}{r_arrow}{pi}{sup +}{mu}{sup +}{ital e}{sup {minus}}, {ital K}{sub {ital L}}{sup 0}{r_arrow}{mu}{sup +}{ital e}{sup {minus}}, and {mu}{sup {minus}}{r_arrow}{ital e}{sup {minus}}{bar {nu}}{sub {ital e}}{nu}{sub {mu}} from which we obtain lower bounds for the mass of the horizontal gauge boson associated with FCNC`s. Finally we obtain limits on the mixing between ordinary and exotic charged leptons.

  11. Relations de Dispersion et Diffusion des Glueballs et des Mesons dans la Theorie de Jauge U(1)(2+1) Compacte

    NASA Astrophysics Data System (ADS)

    Ahmed, Chaara El Mouez

    Nous avons etudie les relations de dispersion et la diffusion des glueballs et des mesons dans le modele U(1)_{2+1} compact. Ce modele a ete souvent utilise comme un simple modele de la chromodynamique quantique (QCD), parce qu'il possede le confinement ainsi que les etats de glueballs. Par contre, sa structure mathematique est beaucoup plus simple que la QCD. Notre methode consiste a diagonaliser l'Hamiltonien de ce modele dans une base appropriee de graphes et sur reseau impulsion, afin de generer les relations de dispersion des glueballs et des mesons. Pour la diffusion, nous avons utilise la methode dependante du temps pour calculer la matrice S et la section efficace de diffusion des glueballs et des mesons. Les divers resultats obtenus semblent etre en accord avec les travaux anterieurs de Hakim, Alessandrini et al., Irving et al., qui eux, utilisent plutot la theorie des perturbations en couplage fort, et travaillent sur un reseau espace-temps.

  12. Depression of superconducting and antiferromagnetic states in the Dy-rich (U 1- xDy x)Ni 2B 2C solid solutions

    NASA Astrophysics Data System (ADS)

    Gonçalves, António P.; Pereira, Laura C. J.; Kuznietz, Moshe; Almeida, Manuel; Silva, Paulo A. S.; Godinho, Margarida

    2000-06-01

    Polycrystalline Dy-rich (U 1- xDy x)Ni 2B 2C solid solutions ( x=0.97, 0.95, 0.90) were prepared, adopting LuNi 2B 2C-type structure. AC-susceptibility and magnetization studies show that Dy substitution by U (decreasing x) affects the superconducting (SC) and antiferromagnetic (AF) transitions of DyNi 2B 2C [initial magnetic order at 16.3(3) K, AF at 10.4(3) K, SC at ≅6 K], lowering the magnetic transition temperatures, with AF order disappearing for x<0.90. There is no clear evidence for a SC state in the materials down to the lower-temperature limit of 2 K.

  13. Room-temperature oxidation of hypostoichiometric uranium-plutonium mixed oxides U1-yPuyO2-x - A depth-selective approach

    NASA Astrophysics Data System (ADS)

    Vauchy, Romain; Robisson, Anne-Charlotte; Belin, Renaud C.; Martin, Philippe M.; Scheinost, Andreas C.; Hodaj, Fiqiri

    2015-10-01

    In the present work, TGA, XAS and XRD were used to evidence the spontaneous oxidation of biphasic U1-yPuyO2-x samples, with y = 0.28 and 0.45, at room temperature and upon exposure to low moisture and oxygen contents. The oxidation occurs within very short timescales (e.g. O/M ratio increasing from 1.94 to 1.98 within ∼1 μm surface layer in ∼50 h). The combined use of these three complementary methods offered a depth-selective approach from the sample's bulk to its surface and allowed a thorough understanding of the underlying processes involved during the formation of the oxidized layer and of its thickening with time. We believe our results to be of interest in the prospect of fabricating hypo-stoichiometric uranium-plutonium mixed oxides since mastering the oxygen content is a crucial point for many of the fuel properties.

  14. In situ study of the solid-state formation of U(1-x)Am(x)O(2±δ) solid solution.

    PubMed

    Lebreton, Florent; Belin, Renaud C; Prieur, Damien; Delahaye, Thibaud; Blanchart, Philippe

    2012-09-03

    In order to reduce the nuclear waste inventory and radiotoxicity, U(1-x)Am(x)O(2±δ) materials are promising fuels for heterogeneous transmutation. In this context, they are generally fabricated from UO(2+δ) and AmO(2-δ) dioxide powders. In the subsequent solid solution, americium is assumed to be trivalent whereas uranium exhibits a mixed-valence (+IV/+V) state. However, no formation mechanisms were ever evidenced and, more particularly, it was not possible to know whether the reduction of Am(IV) to Am(III) occurs before the solid-solution formation, or only once it is established. In this study, we used high-temperature X-ray diffraction on a UO(2±δ)/AmO(2-δ) (15 mol %) mixture to observe in situ the formation of the U(1-x)Am(x)O(2±δ) solid solution. We show that UO(2+δ) is, at relatively low temperature (<700 K), oxidized to U(4)O(9-δ), which is likely to be caused by oxygen release from the simultaneous AmO(2-δ) reduction to cubic Am(2)O(3±δ). Cubic Am(2)O(3+δ) then transforms to hexagonal Am(2)O(3) at 1300 K. Thus, the initial Am(IV) is fully reduced to Am(III) before the solid solution starts forming at 1740 K. The UO(2) fluorite phase vanishes after 4 h at 1970 K, indicating that the formation of the solid solution is completed, which proves that this solid solution is formed after the complete reduction of Am(IV) to Am(III).

  15. Clinical association of mixed connective tissue disease and granulomatosis with polyangiitis: a case report and systematic screening of anti-U1RNP and anti-PR3 auto-antibody double positivity in ten European hospitals.

    PubMed

    Tubery, Amandine; Fortenfant, Françoise; Combe, Bernard; Abreu, Isabelle; Bossuyt, Xavier; Chretien, Pascale; Desplat-Jégo, Sophie; Fabien, Nicole; Hue, Sophie; Johanet, Catherine; Lakomy, Daniela; Vincent, Thierry; Daïen, Claire I

    2016-12-01

    We report here the case of a 50-years-old man treated for mixed connective tissue disease (MCTD) positive for anti-U1 ribonucleoprotein (U1RNP) antibodies who secondarily developed a granulomatosis with polyangiitis (GPA) associated with anti-proteinase 3 anti-neutrophil cytoplasmic antibodies (PR3-ANCA). We then evaluated the frequency of the association between anti-U1RNP and anti-PR3-ANCA antibodies by a systematic retrospective study in ten European hospitals. Overall, out of 11,921 samples analyzed for both auto-antibodies, 18 cases of anti-U1RNP and anti-PR3-ANCA double positivity were found and only one patient presented with both MCTD and GPA symptoms. Our retrospective analysis indicates that anti-U1RNP and anti-PR3-ANCA antibodies double positivity is infrequent and very rarely associated with both MTCD and GPA. Our observation describes for the first time the coexistence of MTCD and severe GPA in a Caucasian patient. Association of anti-U1RNP and ANCA antibodies was rarely reported in the literature. Eleven cases of MCTD and ANCA vasculitis have been reported to date, with only two cases with anti-PR3-ANCA association, and only one vasculitis. The seven other cases reported in the literature presented with an association of MCTD and microscopic polyangiitis which appears to be a more frequent presentation than MTCD associated with GPA.

  16. P-23 Highlights 6/10/12: Cygnus Dual Beam Radiographic Facility Refurbishment completed at U1A tunnel in Nevada NNSS meeting Level 2 milestone

    SciTech Connect

    Deyoung, Anemarie; Smith, John R.

    2012-05-03

    A moratorium was placed on U.S. underground nuclear testing in 1992. In response, the Stockpile Stewardship Program was created to maintain readiness of the existing nuclear inventory through several efforts such as computer modeling, material analysis, and subcritical nuclear experiments (SCEs). As in the underground test era, the Nevada National Security Site (NNSS), formerly the Nevada Test Site, provides a safe and secure environment for SCEs by the nature of its isolated and secure facilities. A major tool for SCE diagnosis installed in the 05 drift laboratory is a high energy x-ray source used for time resolved imaging. This tool consists of two identical sources (Cygnus 1 and Cygnus 2) and is called the Cygnus Dual Beam Radiographic Facility (Figs. 2-6). Each Cygnus machine has 5 major elements: Marx Generator, Pulse Forming Line (PFL), Coaxial Transmission Line (CTL), 3-cell Inductive Voltage Adder (IVA), and Rod Pinch Diode. Each machine is independently triggered and may be fired in separate tests (staggered mode), or in a single test where there is submicrosecond separation between the pulses (dual mode). Cygnus must operate as a single shot machine since on each pulse the diode electrodes are destroyed. The diode is vented to atmosphere, cleaned, and new electrodes are inserted for each shot. There is normally two shots per day on each machine. Since its installation in 2003, Cygnus has participated in: 4 Subcritical Experiments (Armando, Bacchus, Barolo A, and Barolo B), a 12 shot plutonium physics series (Thermos), and 2 plutonium step wedge calibration series (2005, 2011), resulting in well over 1000 shots. Currently the Facility is in preparation for 2 SCEs scheduled for this calendar year - Castor and Pollux. Cygnus has performed well during 8 years of operations at NNSS. Many improvements in operations and performance have been implemented during this time. Throughout its service at U1a, major maintenance and replacement of many hardware items

  17. In vitro transcription of a Drosophila U1 small nuclear RNA gene requires TATA box-binding protein and two proximal cis-acting elements with stringent spacing requirements.

    PubMed Central

    Zamrod, Z; Tyree, C M; Song, Y; Stumph, W E

    1993-01-01

    Transcription of a Drosophila U1 small nuclear RNA gene was functionally analyzed in cell extracts derived from 0- to 12-h embryos. Two promoter elements essential for efficient initiation of transcription in vitro by RNA polymerase II were identified. The first, termed PSEA, is located between positions -41 and -61 relative to the transcription start site, is crucial for promoter activity, and is the dominant element for specifying the transcription initiation site. PSEA thus appears to be functionally homologous to the proximal sequence element of vertebrate small nuclear RNA genes. The second element, termed PSEB, is located at positions -25 to -32 and is required for an efficient level of transcription initiation because mutation of PSEB, or alteration of the spacing between PSEA and PSEB, severely reduced transcriptional activity relative to that of the wild-type promoter. Although the PSEB sequence does not have any obvious sequence similarity to a TATA box, conversion of PSEB to the canonical TATA sequence dramatically increased the efficiency of the U1 promoter and simultaneously relieved the requirement for the upstream PSEA. Despite these effects, introduction of the TATA sequence into the U1 promoter had no effect on the choice of start site or on the RNA polymerase II specificity of the promoter. Finally, evidence is presented that the TATA box-binding protein is required for transcription from the wild-type U1 promoter as well as from the TATA-containing U1 promoter. Images PMID:8355718

  18. Ditching Tests of a 1/8-Scale Model of the Chance Vought XF6U-1 Airplane, TED No. NACA DE319

    NASA Technical Reports Server (NTRS)

    Fisher, Lloyd J., Jr.; McBride, Ellis E.

    1953-01-01

    Tests were made with a 1/8-scale dynamically similar model of the Chance Vought XF6U-1 airplane to study its behavior when ditched. The model was ditched in calm water at the Langley tank no. 2 monorail. Various landing attitudes, speeds, and conditions of damage were simulated. The behavior of the model was determined from visual observations, by recording time histories of the accelerations, and by taking motion pictures of the ditchings. From the results of the tests it was concluded that the airplane should be ditched at the near-stall, tail-down attitude (12 deg). The flaps should be fully extended to obtain the lowest possible landing speed. The wing-tip tanks should be jettisoned. The underside of the fuselage will be critically damaged in a ditching and the airplane will dive violently after a run of about three fuselage lengths. Maximum longitudinal decelerations up to about 7g and maximum vertical accelerations up to about 5g will be encountered.

  19. Thermochemistry of rare earth doped uranium oxides LnxU1-xO2-0.5x+y (Ln = La, Y, Nd)

    NASA Astrophysics Data System (ADS)

    Zhang, Lei; Navrotsky, Alexandra

    2015-10-01

    Lanthanum, yttrium, and neodymium doped uranium dioxide samples in the fluorite structure have been synthesized, characterized in terms of metal ratio and oxygen content, and their enthalpies of formation measured by high temperature oxide melt solution calorimetry. For oxides doped with 10-50 mol % rare earth (Ln) cations, the formation enthalpies from constituent oxides (LnO1.5, UO2 and UO3 in a reaction not involving oxidation or reduction) become increasingly exothermic with increasing rare earth content, while showing no significant dependence on the varying uranium oxidation state. The oxidation enthalpy of LnxU1-xO2-0.5x+y is similar to that of UO2 to UO3 for all three rare earth doped systems. Though this may suggest that the oxidized uranium in these systems is energetically similar to that in the hexavalent state, thermochemical data alone can not constrain whether the uranium is present as U5+, U6+, or a mixture of oxidation states. The formation enthalpies from elements calculated from the calorimetric data are generally consistent with those from free energy measurements.

  20. Parity oscillations and photon correlation functions in the Z2-U (1 ) Dicke model at a finite number of atoms or qubits

    NASA Astrophysics Data System (ADS)

    Yi-Xiang, Yu; Ye, Jinwu; Zhang, CunLin

    2016-08-01

    Four standard quantum optics models, that is, the Rabi, Dicke, Jaynes-Cummings, and Tavis-Cummings models, were proposed by physicists many decades ago. Despite their relative simple forms and many previous theoretical works, their physics at a finite N , especially inside the superradiant regime, remain unknown. In this work, by using the strong-coupling expansion and exact diagonalization (ED), we study the Z2-U(1 ) Dicke model with independent rotating-wave coupling g and counterrotating-wave coupling g' at a finite N . This model includes the four standard quantum optics models as its various special limits. We show that in the superradiant phase, the system's energy levels are grouped into doublets with even and odd parity. Any anisotropy β =g'/g ≠1 leads to the oscillation of parities in both the ground and excited doublets as the atom-photon coupling strength increases. The oscillations will be pushed to the infinite coupling strength in the isotropic Z2 limit β =1 . We find nearly perfect agreement between the strong-coupling expansion and the ED in the superradiant regime when β is not too small. We also compute the photon correlation functions, squeezing spectrum, and number correlation functions that can be measured by various standard optical techniques.

  1. Application of the UMACS process to highly dense U1-xAmxO2±δ MABB fuel fabrication for the DIAMINO irradiation

    NASA Astrophysics Data System (ADS)

    Delahaye, Thibaud; Lebreton, Florent; Horlait, Denis; Herlet, Nathalie; Dehaudt, Philippe

    2013-01-01

    The DIAMINO irradiation program aims to assess the influence of Am content and microstructure on He release and fuel swelling for different irradiation temperatures during heterogeneous transmutation in the OSIRIS reactor. Such irradiation programs call for ceramic fuels compliant with strict specifications. In the case of the DIAMINO experiment, Am-bearing blanket fuels with two compositions (U1-xAmxO2±δ (x = 0.075, 0.15)) and two microstructures (dense and porous) were selected, corresponding with four sample sets. Porous samples (<85%TD) were fabricated using a process previously developed for a similar irradiation program while a new dedicated process, UMACS, was developed and applied to produce dense samples. Despite americium presence, this process, based on conventional sintering, produces samples with high density (˜96%TD) close to that usually obtained for UO2. In the case of Minor Actinide Bearing Blankets (MABB), such a result has never been obtained reproducibly even with reactive sintering or impregnation methods.

  2. Longitudinal Trim and Tumble Characteristics of a 0.057-Scale Model of the Chance Vought XF7U-1 Airplane, TED NO. NACA DE311

    NASA Technical Reports Server (NTRS)

    Bryant, Robert L.

    1948-01-01

    Based on results of longitudinal trim and tumble tests of a 0.057-scale model of the Chance Vought XF7U-1 airplane, the following conclusions regarding the trim and tumble characteristics of the airplane have been drawn: 1. The airplane will not trim at any unusual or uncontrolled angles of attack. 2. The airplane will not tumble with the center of gravity located forward of 24 percent of the mean aerodynamic chord. When the center of gravity is located at 24 percent of the mean aerodynamic chord and slats are extended and elevators are deflected full up, the airplane may tumble if given an external positive pitching moment. 3. The tumbling motion obtained will be readily terminated by deflecting the elevators full down so as to oppose the rotation. 4. The accelerations encountered during an established tumble may be dangerous to the pilot and, therefore, action should be taken to terminate a tumble immediately upon its inception. 5. Simultaneous opening of two wing-tip parachutes having diameters of 4 feet or larger and having drag coefficients of approximately 0.7 will effectively terminate the tumble. 6. Model results indicate that the pilot will not be struck by the airplane if it becomes necessary to leave the airplane during a tumble. The pilot may require aid from an ejection-seat arrangement.

  3. Fabrication and characterization of U1-xAmxO2±δ compounds with high americium contents (x = 0.3, 0.4 and 0.5)

    NASA Astrophysics Data System (ADS)

    Lebreton, Florent; Horlait, Denis; Delahaye, Thibaud; Blanchart, Philippe

    2013-08-01

    Mixed uranium-americium oxides are considered promising compounds for americium transmutation in fast neutron reactors. A better understanding of these materials and of the U-Am-O phase diagram is, however, needed. Though many results in the literature describe U1-xAmxO2±δ (x ⩽ 0.2) compounds, very few studies concern higher Am contents. In this context, this article reports the fabrication method of U1-xAmxO2±δ (0.3 ⩽ x ⩽ 0.5) and their preliminary characterization, notably by X-ray diffraction.

  4. Belt-hierarchic structure of th ring, satellite and planet systems: prediction S/2001 U1 and others objects in Solar system

    NASA Astrophysics Data System (ADS)

    Barkin, Yu. V.

    2003-04-01

    BELT-HIERARCHIC STRUCTURE OF THE RING, SATELLITE AND PLANET SYSTEMS: PREDICTION S/2001 U1 AND OTHERS OBJECTS IN SOLAR SYSTEM Yu.V.Barkin Sternberg Astronomical Institute, Moscow, Russia, barkin@sai.msu.ru Structure regularities of the planet and satellite systems have been studied. Statistic analysis of the distribution of the major semi-axes of the orbits of the planets, comets and centaurs of the Solar system, satellite and ring systems of Jupiter, Saturn, Neptune and Uran, exoplanet systems of the pulsars PSR 1257+12, PSR 1828-11 and of the main consequence star Ups And was fulfilled. The following empirical regularities were described [1]: 1) the bodies of systems are combined into hierarchic groups and main from them combine 5 companions; 2) differences of the major semi-axes of the neighboring orbits for bodies of every group are constant; 4) for main neighboring hierarchic group these distances are distinguished in 6 times increasing to external grope; 5) the filling of the gropes and some present changes in their structure are caused by the past catastrophes in corresponding systems. The special method of reconstruction of the catastrophes which had place in the life of the Solar system (SS) was developed. Suggested method has let us to explain uniformly observed values of the major semi-axes and average values of eccentricities of the planets. In particular the Pancul’s hypothesis about Jupiter formation from two giant protoplanets (Jupiter I and Jupiter II) was confirmed. The new empirical law of the filling of the orbits of the regular groups of the planets or satellites (or rings structures) of the hierarchic ordered systems of celestial bodies was established. It was shown that sum number of bodies is proportional to the value of catastrophic value of the eccentricities which are same for first, second ,.... and fifth orbits of all gropes. The theoretical numbers of bodies for pointed orbits practically coincide with their observed numbers in main

  5. Fully Coupled Modeling of Burnup-Dependent (U1- y , Pu y )O2- x Mixed Oxide Fast Reactor Fuel Performance

    NASA Astrophysics Data System (ADS)

    Liu, Rong; Zhou, Wenzhong; Zhou, Wei

    2016-03-01

    During the fast reactor nuclear fuel fission reaction, fission gases accumulate and form pores with the increase of fuel burnup, which decreases the fuel thermal conductivity, leading to overheating of the fuel element. The diffusion of plutonium and oxygen with high temperature gradient is also one of the important fuel performance concerns as it will affect the fuel material properties, power distribution, and overall performance of the fuel pin. In order to investigate these important issues, the (U1- y Pu y )O2- x fuel pellet is studied by fully coupling thermal transport, deformation, oxygen diffusion, fission gas release and swelling, and plutonium redistribution to evaluate the effects on each other with burnup-dependent models, accounting for the evolution of fuel porosity. The approach was developed using self-defined multiphysics models based on the framework of COMSOL Multiphysics to manage the nonlinearities associated with fast reactor mixed oxide fuel performance analysis. The modeling results showed a consistent fuel performance comparable with the previous results. Burnup degrades the fuel thermal conductivity, resulting in a significant fuel temperature increase. The fission gas release increased rapidly first and then steadily with the burnup increase. The fuel porosity increased dramatically at the beginning of the burnup and then kept constant as the fission gas released to the fuel free volume, causing the fuel temperature to increase. Another important finding is that the deviation from stoichiometry of oxygen affects greatly not only the fuel properties, for example, thermal conductivity, but also the fuel performance, for example, temperature distribution, porosity evolution, grain size growth, fission gas release, deformation, and plutonium redistribution. Special attention needs to be paid to the deviation from stoichiometry of oxygen in fuel fabrication. Plutonium content will also affect the fuel material properties and performance

  6. Molecular Cytogenetic Analysis of the European Hake Merluccius merluccius (Merlucciidae, Gadiformes): U1 and U2 snRNA Gene Clusters Map to the Same Location.

    PubMed

    García-Souto, Daniel; Troncoso, Tomás; Pérez, Montse; Pasantes, Juan José

    2015-01-01

    The European hake (Merluccius merluccius) is a highly valuable and intensely fished species in which a long-term alive stock has been established in captivity for aquaculture purposes. Due to their huge economic importance, genetic studies on hakes were mostly focused on phylogenetic and phylogeographic aspects; however chromosome numbers are still not described for any of the fifteen species in the genus Merluccius. In this work we report a chromosome number of 2n = 42 and a karyotype composed of three meta/submetacentric and 18 subtelo/telocentric chromosome pairs. Telomeric sequences appear exclusively at both ends of every single chromosome. Concerning rRNA genes, this species show a single 45S rDNA cluster at an intercalary location on the long arm of subtelocentric chromosome pair 12; the single 5S rDNA cluster is also intercalary to the long arm of chromosome pair 4. While U2 snRNA gene clusters map to a single subcentromeric position on chromosome pair 13, U1 snRNA gene clusters seem to appear on almost all chromosome pairs, but showing bigger clusters on pairs 5, 13, 16, 17 and 19. The brightest signals on pair 13 are coincident with the single U2 snRNA gene cluster signals. Therefore, the use of these probes allows the unequivocal identification of at least 7 of the chromosome pairs that compose the karyotype of Merluccius merluccius thus opening the way to integrate molecular genetics and cytological data on the study of the genome of this important species.

  7. Monte Carlo simulations of the relative biological effectiveness for DNA double strand breaks from 300 MeV u-1 carbon-ion beams

    NASA Astrophysics Data System (ADS)

    Huang, Y. W.; Pan, C. Y.; Hsiao, Y. Y.; Chao, T. C.; Lee, C. C.; Tung, C. J.

    2015-08-01

    Monte Carlo simulations are used to calculate the relative biological effectiveness (RBE) of 300 MeV u-1 carbon-ion beams at different depths in a cylindrical water phantom of 10 cm radius and 30 cm long. RBE values for the induction of DNA double strand breaks (DSB), a biological endpoint closely related to cell inactivation, are estimated for monoenergetic and energy-modulated carbon ion beams. Individual contributions to the RBE from primary ions and secondary nuclear fragments are simulated separately. These simulations are based on a multi-scale modelling approach by first applying the FLUKA (version 2011.2.17) transport code to estimate the absorbed doses and fluence energy spectra, then using the MCDS (version 3.10A) damage code for DSB yields. The approach is efficient since it separates the non-stochastic dosimetry problem from the stochastic DNA damage problem. The MCDS code predicts the major trends of the DSB yields from detailed track structure simulations. It is found that, as depth is increasing, RBE values increase slowly from the entrance depth to the plateau region and change substantially in the Bragg peak region. RBE values reach their maxima at the distal edge of the Bragg peak. Beyond this edge, contributions to RBE are entirely from nuclear fragments. Maximum RBE values at the distal edges of the Bragg peak and the spread-out Bragg peak are, respectively, 3.0 and 2.8. The present approach has the flexibility to weight RBE contributions from different DSB classes, i.e. DSB0, DSB+ and DSB++.

  8. Black hole physics from two-dimensional dilaton gravity based on the SL(2,[ital R])/U(1) coset model

    SciTech Connect

    Nojiri, S. ); Oda, I. Faculty of Science, Department of Physics, Ochanomizu University, 1-1, Otsuka 2, Bunkyo-ku, Tokyo 112 )

    1994-04-15

    We analyze the quantum two-dimensional dilaton gravity model, which is described by the SL(2,[ital R])/U(1) gauged Wess-Zumino-Witten model deformed by a (1,1) operator. We show that the curvature singularity does not appear when the central charge [ital c][sub matter] of the matter fields is given by 22[lt][ital c][sub matter][lt]24. When 22[lt][ital c][sub matter][lt]24, the matter shock waves, whose energy-momentum tensors are given by [ital T][sub matter][proportional to][delta]([ital x][sup +][minus][ital x][sub 0][sup +]), create a kind of wormholes, i.e., causally disconnected regions. Most of the quantum information in past null infinity is lost in future null infinity but the lost information would be carried by the wormholes. We also discuss the problem of defining the mass of quantum black holes. On the basis of the argument by Regge and Teitelboim, we show that the ADM mass measured by the observer who lives in one of the asymptotically flat regions is finite and does not vanish in general. On the other hand, the Bondi mass is ill defined in this model. Instead of the Bondi mass, we consider the mass measured by observers who live in an asymptotically flat region at first. A class of observers finds the mass of the black hole created by a shock wave changes as the observers' proper time goes by, i.e., they observe Hawking radiation. The measured mass vanishes after the infinite proper time and the black hole evaporates completely. Therefore the total Hawking radiation is positive even when [ital N][lt]24.

  9. Molecular Cytogenetic Analysis of the European Hake Merluccius merluccius (Merlucciidae, Gadiformes): U1 and U2 snRNA Gene Clusters Map to the Same Location

    PubMed Central

    García-Souto, Daniel; Troncoso, Tomás; Pérez, Montse; Pasantes, Juan José

    2015-01-01

    The European hake (Merluccius merluccius) is a highly valuable and intensely fished species in which a long-term alive stock has been established in captivity for aquaculture purposes. Due to their huge economic importance, genetic studies on hakes were mostly focused on phylogenetic and phylogeographic aspects; however chromosome numbers are still not described for any of the fifteen species in the genus Merluccius. In this work we report a chromosome number of 2n = 42 and a karyotype composed of three meta/submetacentric and 18 subtelo/telocentric chromosome pairs. Telomeric sequences appear exclusively at both ends of every single chromosome. Concerning rRNA genes, this species show a single 45S rDNA cluster at an intercalary location on the long arm of subtelocentric chromosome pair 12; the single 5S rDNA cluster is also intercalary to the long arm of chromosome pair 4. While U2 snRNA gene clusters map to a single subcentromeric position on chromosome pair 13, U1 snRNA gene clusters seem to appear on almost all chromosome pairs, but showing bigger clusters on pairs 5, 13, 16, 17 and 19. The brightest signals on pair 13 are coincident with the single U2 snRNA gene cluster signals. Therefore, the use of these probes allows the unequivocal identification of at least 7 of the chromosome pairs that compose the karyotype of Merluccius merluccius thus opening the way to integrate molecular genetics and cytological data on the study of the genome of this important species. PMID:26716701

  10. Langley Full-Scale Tunnel Investigation of a 1/3-Scale Model of the Chance Vought XF5U-1 Airplane

    NASA Technical Reports Server (NTRS)

    Lange, Roy H.; Cocke, Bennie W., Jr.; Proterra, Anthony J.

    1946-01-01

    The results of an investigation of a 1/3-scale model of the Chance Vought XF5U-1 airplane in the Langley full-scale tunnel are presented in this report. The maximum lift and stalling characteristics of several model configurations, the longitudinal stability characteristics of the model, and the effectiveness of the control surfaces were determined with the propellers removed. The propulsive characteristics, the effect of propeller operation on the lift, and the static thrust of the model propellers were determined at several propeller-blade angles. The results with the propellers removed showed that the maximum lift coefficient of the complete model configuration was only 0.97 was compared with the value of 1.31 for the model configuration in which the engine-air ducts and canopy are removed. The model with the propellers removed (normal center-of-gravity position) has a positive static margin, stick fixed, varying from 5 to 13 percent of the mean aerodynamic chord throughout the unstalled range of lift coefficients. The unit horizontal tail is sufficiently powerful to trim the airplane with the propellers removed throughout the unstalled range of lift coefficients. The peak propulsive efficiencies for beta = 20 degrees and beta = 30 degrees were increased 7 percent at C(sub L) congruent to 0.67 and 20 percent at C(sub L) congruent to 0.74, respectively, with the propellers rotating upward in the center than with the propellers rotating downward in the center. Indications are that the minimum forward-flight speed of the airplane for full-power operation at sea level will be about 90 miles per hour. Decreasing the weight and increasing the power reduced this value of minimum speed and there were no indications from the results of a lower limit to the minimum speed.

  11. Free-Spinning-Tunnel Tests of a 1/16-Scale Model of the Chance Vought XF5U-1 Airplane, TED No. NACA 2349

    NASA Technical Reports Server (NTRS)

    White, Richard P.

    1947-01-01

    Spin tests of a 1/16-scale model of the Chance Vought XF5U-1 airplane have been performed in the Langley 20-foot free-spinning tunnel. The effect of control position and movement upon the erect and inverted spin and recovery characteristics ae well as the effects of propellers, of stability flaps, and of various revisions to the design configuration have been determined for the normal fighter loading. The investigation also included spin recovery parachute, tumbling, and pilot-escape tests. For the original design configuration, with or without windmilling propellers, the recovery characteristics of the model were considered unsatisfactory. Increasing the maximum upward deflection of the ailavators from 45 deg to 65 deg resulted in greatly improved recovery characteristics. Dimensional revisions to the original airplane configuration, which satisfactorily improved the general spin and recovery characteristics of the model, consisted of: (1) a supplementary vertical tail 34 inches by 59 inches (full-scale) attached to a boom 80 inches aft of the trailing edge of the airplane in the plane of symmetry, (2) a large semispan undersurface spoiler placed along the airplane quarter-chord line and opened on the outboard side in a spin, or (3) two additional vertical tails 64 inches by 52 inches (full-scale) located at the tips of the ailavators. A satisfactory parachute arrangement for emergency spin recovery from demonstration spins was found to be an arrangement consisting of a 13.3-foot parachute attached by a 30-foot towline to the arresting gear mast on the airplane and opened simultaneously with an 8-foot parachute on the outboard end of the wing attached by a 3-foot towline. Tests indicated that pilot escape from a spin would be extremely hazardous unless the pilot is mechanically ejected from the cockpit. Model tumbling tests indicated that the airplane would not tumble.

  12. Free-Spinning Tunnel Tests of a 1/20-Scale Model of the Chance Vought XF6U-1 Airplane, TED No. NACA 2390

    NASA Technical Reports Server (NTRS)

    Klinar, Walter J.

    1946-01-01

    A spin investigation has been conducted in the Langley 20-foot free-spinning tunnel on a 1/20-scale model of the Chance Vought XF6U-1 airplane, The effects of control settings and movements upon the erect and inverted spin and recovery characteristics of the model were determined for the normal-fighter condition. The investigation also included tests for the take-off fighter condition (wing-tip tanks plus fuel added) spin-recovery parachutes, and simulated pilot escape. In general, for the normal-fighter condition, the model was extremely oscillatory in roll, pitch, and yaw. The angles of the fuselage varied from extremely flat to inverted attitudes, and the model rotated with the rudder in a series of short turns and glides. Recoveries by rudder reversal were rapid but the model would immediately go into a spin in the other direction. Recoveries by merely neutralizing the rudder were satisfactory when the elevator and ailerons were set to neutral, the ensuing flight path being a steep glide. Thus, it is recommended that all controls be neutralized for safe recovery from spins obtained on the airplane. With the external wing-tip tanks installed, the spins were somewhat less oscillatory in roll but recovery could not be obtained unless full-down elevator was used in conjunction with the rudder. If a spin is entered inadvertently with the full-scale airplane with external wing-tip tanks installed and if recovery is not imminent after a recovery attempt is made, it is recommended that the tanks be jettisoned and the controls neutralized.

  13. Free-Spinning-Tunnel Tests of a 0.057-Scale Model of the Chance Vought XF7U-1 Airplane

    NASA Technical Reports Server (NTRS)

    Daughtridge, Lee T., Jr.

    1948-01-01

    An investigation of the spin and recovery characteristics of a 0.057-scale model of the Chance Vought XF7U-1 airplane has been conducted in the Langley 20-foot free-spinning tunnel. The effects of control settings and movements on the erect and inverted spin and recovery characteristics were determined, as were also the effects of extending the wing slats, of center-of-gravity movement, and-of variation in the mass distribution. The investigation also included wing-tip spin-recovery-parachute tests, pilot-escape tests, and rudder-control-force tests. The investigation indicated that the spin and recovery characteristics of the airplane will be satisfactory for all conditions. It was found that a single 4.24-foot (full-scale) parachute when opened alone from the outboard wing tip or two 8.77-foot (full-scale) parachutes when opened simultaneously, one from each wing tip, would effect satisfactory emergency recoveries (the drag coefficients of the parachutes, based on the surface area of the parachute, were 0.83 and 0.70 for the 4.24- and 8.77-foot parachutes, respectively). The towline length in both cases was 25 feet (full scale). Tests results showed that, if the pilot should have to leave the airplane during a spin, he should jump from the outboard side (left side in a right spin) of the cockpit. The rudder-control force necessary for recovery from a spin was found to be rather high but appeared to be within the upper limits of a pilot's capabilities.

  14. Composite bound states and broken U(1) symmetry in the chemical-master-equation derivation of the Gray-Scott model.

    PubMed

    Cooper, Fred; Ghoshal, Gourab; Pérez-Mercader, Juan

    2013-10-01

    We give a first principles derivation of the stochastic partial differential equations that describe the chemical reactions of the Gray-Scott model (GS): U+2V →[λ]3V and V → [μ]P, U → [ν]Q, with a constant feed rate for U. We find that the conservation of probability ensured by the chemical master equation leads to a modification of the usual differential equations for the GS model, which now involves two composite fields and also intrinsic noise terms. One of the composites is ψ(1) = φ(v)(2), where {φ(v)}(η) =v is the concentration of the species V and the averaging is over the internal noise η(u,v,ψ(1)). The second composite field is the product of three fields χ = λφ(u)φ(v)(2) and requires a noise source to ensure probability conservation. A third composite ψ(2) = φ(u)φ(v) can also be identified from the noise-induced reactions. The Hamiltonian that governs the time evolution of the many-body wave function, associated with the master equation, has a broken U(1) symmetry related to particle number conservation. By expanding around the (broken symmetry) zero-energy solution of the Hamiltonian (by performing a Doi shift) one obtains from our path integral formulation the usual reaction diffusion equation, at the classical level. The Langevin equations that are derived from the chemical master equation have multiplicative noise sources for the density fields φ(u), φ(v),χ that induce higher-order processes such as n → n scattering for n>3. The amplitude of the noise acting on φ(v) is itself stochastic in nature.

  15. Dynamics of the Q2Π1u(1 ) state studied from the isotope effect on the cross sections for the formation of the 2 p atom pair in the photoexcitation of H2 and D2

    NASA Astrophysics Data System (ADS)

    Hosaka, Kouichi; Shiino, Kennichi; Nakanishi, Yuko; Odagiri, Takeshi; Kitajima, Masashi; Kouchi, Noriyuki

    2016-06-01

    The absolute values of the cross section for formation of a 2 p atom pair in the photoexcitation of H2 and D2 are measured against the incident photon energy in the range of doubly excited states by means of the coincidence detection of two Lyman-α photons. The cross-section curves are explained only by the contribution of the doubly excited Q2Π1u(1 ) state. The isotope effect on the oscillator strengths of 2 p +2 p pair formation for H2 and D2 from the Q2Π1u(1 ) state is almost the same as that on the oscillator strengths of 2 s +2 p pair formation from the Q2Π1u(1 ) state obtained by our group [T. Odagiri et al., Phys. Rev. A 84, 053401 (2011), 10.1103/PhysRevA.84.053401]. This channel independence indicates that both isotope effects are dominated by the early dynamics of the Q2Π1u(1 ) state, before reaching the branching point into 2 p +2 p pair formation and 2 s +2 p pair formation.

  16. Z- Z' mixing and Z-mediated FCNCs in SU(3) C × SU(3) L × U(1) X models

    NASA Astrophysics Data System (ADS)

    Buras, Andrzej J.; De Fazio, Fulvia; Girrbach-Noe, Jennifer

    2014-08-01

    Most of the existing analyses of flavour changing neutral current processes (FCNC) in the 331 models, based on the gauge group SU(3) C × SU(3) L × U(1) X , are fully dominated by tree-level exchanges of a new heavy neutral gauge boson Z'. However, due to the Z - Z' mixing also corresponding contributions from Z boson are present. As the Z - Z' mixing is estimated generally in Z' models to be at most , the latter contributions are usually neglected. The paucity of relevant parameters in 331 models allows to check whether this neglect is really justified in these concrete models. We calculate the impact of these contributions on Δ F = 2 processes and rare K, B s and B d decays for different values of a parameter β, which distinguishes between various 331 models and for different fermion representations under the SU(3) L group. We find a general expression for the Z - Z' mixing in terms β, M Z , M Z' and tan , familiar from 2 Higgs Doublet models, that differs from the one quoted in the literature. We study in particular the models with β = ± n/ with n = 1 , 2 which have recently been investigated by us in the context of new data on B s, d → μ + μ - and B d → K *( K) μ + μ -. We find that these new contributions can indeed be neglected in the case of Δ F = 2 transitions and decays, like B d → K * μ + μ -, where they are suppressed by the small vectorial Z coupling to charged leptons. However, the contributions of tree-level Z exchanges to decays sensitive to axial-vector couplings, like B s, d → μ + μ - and B d → Kμ + μ -, and those with neutrinos in the final state, like b → sν transitions, K + → π + ν and K L → π 0 ν cannot be generally neglected with size of Z contributions depending on β, tan and M Z' . We analyze how our recent results on FCNCs in 331 models, in particular correlations between various observables, are modified by these new contributions. As a byproduct we analyze for the first time the ratio ɛ' /ɛ in

  17. Raman study on structure of U1-yGdyO2-x (y=0.005, 0.01, 0.03, 0.05 and 0.1) solid solutions

    NASA Astrophysics Data System (ADS)

    Lee, Jeongmook; Kim, Jandee; Youn, Young-Sang; Liu, Nazhen; Kim, Jong-Goo; Ha, Yeong-Keong; Shoesmith, David W.; Kim, Jong-Yun

    2017-04-01

    The U1-yGdyO2-x solid solutions with y = 0.005, 0.01, 0.03, 0.05 and 0.1 were characterized by Raman spectroscopy to investigate the defect structure induced by oxygen vacancies. The oxygen deficiencies of solid solutions were estimated by the relation between the doping level and a lattice parameter calculated from X-ray diffraction patterns. Raman mode shifts to higher wavenumber with increasing doping level showed that crystal lattice disorder due to oxygen vacancies. The frequency shifts and relative ratio of Raman modes were enabled to be the indicator for composition, defect and oxygen vacancy of U1-yGdyO2-x solid solutions.

  18. Mechanisms and Regulation of Alternative Pre-mRNA Splicing

    PubMed Central

    Lee, Yeon

    2015-01-01

    Precursor messenger RNA (pre-mRNA) splicing is a critical step in the posttranscriptional regulation of gene expression, providing significant expansion of the functional proteome of eukaryotic organisms with limited gene numbers. Split eukaryotic genes contain intervening sequences or introns disrupting protein-coding exons, and intron removal occurs by repeated assembly of a large and highly dynamic ribonucleoprotein complex termed the spliceosome, which is composed of five small nuclear ribonucleoprotein particles, U1, U2, U4/U6, and U5. Biochemical studies over the past 10 years have allowed the isolation as well as compositional, functional, and structural analysis of splicing complexes at distinct stages along the spliceosome cycle. The average human gene contains eight exons and seven introns, producing an average of three or more alternatively spliced mRNA isoforms. Recent high-throughput sequencing studies indicate that 100% of human genes produce at least two alternative mRNA isoforms. Mechanisms of alternative splicing include RNA–protein interactions of splicing factors with regulatory sites termed silencers or enhancers, RNA–RNA base-pairing interactions, or chromatin-based effects that can change or determine splicing patterns. Disease-causing mutations can often occur in splice sites near intron borders or in exonic or intronic RNA regulatory silencer or enhancer elements, as well as in genes that encode splicing factors. Together, these studies provide mechanistic insights into how spliceosome assembly, dynamics, and catalysis occur; how alternative splicing is regulated and evolves; and how splicing can be disrupted by cis- and trans-acting mutations leading to disease states. These findings make the spliceosome an attractive new target for small-molecule, antisense, and genome-editing therapeutic interventions. PMID:25784052

  19. Functional stabilization of an RNA recognition motif by a noncanonical N-terminal expansion.

    PubMed

    Netter, Catharina; Weber, Gert; Benecke, Heike; Wahl, Markus C

    2009-07-01

    RNA recognition motifs (RRMs) constitute versatile macromolecular interaction platforms. They are found in many components of spliceosomes, in which they mediate RNA and protein interactions by diverse molecular strategies. The human U11/U12-65K protein of the minor spliceosome employs a C-terminal RRM to bind hairpin III of the U12 small nuclear RNA (snRNA). This interaction comprises one side of a molecular bridge between the U11 and U12 small nuclear ribonucleoprotein particles (snRNPs) and is reminiscent of the binding of the N-terminal RRMs in the major spliceosomal U1A and U2B'' proteins to hairpins in their cognate snRNAs. Here we show by mutagenesis and electrophoretic mobility shift assays that the beta-sheet surface and a neighboring loop of 65K C-terminal RRM are involved in RNA binding, as previously seen in canonical RRMs like the N-terminal RRMs of the U1A and U2B'' proteins. However, unlike U1A and U2B'', some 30 residues N-terminal of the 65K C-terminal RRM core are additionally required for stable U12 snRNA binding. The crystal structure of the expanded 65K C-terminal RRM revealed that the N-terminal tail adopts an alpha-helical conformation and wraps around the protein toward the face opposite the RNA-binding platform. Point mutations in this part of the protein had only minor effects on RNA affinity. Removal of the N-terminal extension significantly decreased the thermal stability of the 65K C-terminal RRM. These results demonstrate that the 65K C-terminal RRM is augmented by an N-terminal element that confers stability to the domain, and thereby facilitates stable RNA binding.

  20. Thermosensitive and Mucoadhesive Pluronic-Hydroxypropylmethylcellulose Hydrogel Containing the Mini-CD4 M48U1 Is a Promising Efficient Barrier against HIV Diffusion through Macaque Cervicovaginal Mucus

    PubMed Central

    Aka-Any-Grah, Armelle; Dereuddre-Bosquet, Nathalie; Martin, Loïc; Lievin-Le-Moal, Vanessa; Le Grand, Roger; Nicolas, Valérie; Gibellini, Davide; Lembo, David; Poüs, Christian; Koffi, Armand; Ponchel, Gilles

    2015-01-01

    To be efficient, vaginal microbicide hydrogels should form a barrier against viral infections and prevent virus spreading through mucus. Multiple particle tracking was used to quantify the mobility of 170-nm fluorescently labeled COOH-modified polystyrene particles (COOH-PS) into thermosensitive hydrogels composed of amphiphilic triblock copolymers with block compositions EOn-POm-EOn (where EO refers to ethylene oxide and PO to propylene oxide) containing mucoadhesive hydroxypropylmethylcellulose (HPMC). COOH-PS were used to mimic the size and the surface charge of HIV-1. Analysis of COOH-PS trajectories showed that particle mobility was decreased by Pluronic hydrogels in comparison with cynomolgus macaque cervicovaginal mucus and hydroxyethylcellulose hydrogel (HEC; 1.5% by weight [wt%]) used as negative controls. Formulation of the peptide mini-CD4 M48U1 used as an anti-HIV-1 molecule into a mixture of Pluronic F127 (20 wt%) and HPMC (1 wt%) did not affect its anti-HIV-1 activity in comparison with HEC hydrogel. The 50% inhibitory concentration (IC50) was 0.53 μg/ml (0.17 μM) for M48U1-HEC and 0.58 μg/ml (0.19 μM) for M48U1-F127-HPMC. The present work suggests that hydrogels composed of F127-HPMC (20/1 wt%, respectively) can be used to create an efficient barrier against particle diffusion in comparison to conventional HEC hydrogels. PMID:25645853

  1. Thermosensitive and mucoadhesive pluronic-hydroxypropylmethylcellulose hydrogel containing the mini-CD4 M48U1 is a promising efficient barrier against HIV diffusion through macaque cervicovaginal mucus.

    PubMed

    Bouchemal, Kawthar; Aka-Any-Grah, Armelle; Dereuddre-Bosquet, Nathalie; Martin, Loïc; Lievin-Le-Moal, Vanessa; Le Grand, Roger; Nicolas, Valérie; Gibellini, Davide; Lembo, David; Poüs, Christian; Koffi, Armand; Ponchel, Gilles

    2015-04-01

    To be efficient, vaginal microbicide hydrogels should form a barrier against viral infections and prevent virus spreading through mucus. Multiple particle tracking was used to quantify the mobility of 170-nm fluorescently labeled COOH-modified polystyrene particles (COOH-PS) into thermosensitive hydrogels composed of amphiphilic triblock copolymers with block compositions EOn-POm-EOn (where EO refers to ethylene oxide and PO to propylene oxide) containing mucoadhesive hydroxypropylmethylcellulose (HPMC). COOH-PS were used to mimic the size and the surface charge of HIV-1. Analysis of COOH-PS trajectories showed that particle mobility was decreased by Pluronic hydrogels in comparison with cynomolgus macaque cervicovaginal mucus and hydroxyethylcellulose hydrogel (HEC; 1.5% by weight [wt%]) used as negative controls. Formulation of the peptide mini-CD4 M48U1 used as an anti-HIV-1 molecule into a mixture of Pluronic F127 (20 wt%) and HPMC (1 wt%) did not affect its anti-HIV-1 activity in comparison with HEC hydrogel. The 50% inhibitory concentration (IC50) was 0.53 μg/ml (0.17 μM) for M48U1-HEC and 0.58 μg/ml (0.19 μM) for M48U1-F127-HPMC. The present work suggests that hydrogels composed of F127-HPMC (20/1 wt%, respectively) can be used to create an efficient barrier against particle diffusion in comparison to conventional HEC hydrogels.

  2. Human UBL5 protein interacts with coilin and meets the Cajal bodies.

    PubMed

    Svéda, Martin; Castorálová, Markéta; Lipov, Jan; Ruml, Tomáš; Knejzlík, Zdeněk

    2013-06-28

    UBL5 protein, a structural homologue of ubiquitin, was shown to be involved in pre-mRNA splicing and transcription regulation in yeast and Caenorhabditis elegans, respectively. However, role of the UBL5 human orthologue is still elusive. In our study, we observed that endogenous human UBL5 that was localized in the nucleus, partially associates with Cajal bodies (CBs), nuclear domains where spliceosomal components are assembled. Simultaneous expression of exogenous UBL5 and coilin resulted in their nuclear colocalization in HeLa cells. The ability of UBL5 to interact with coilin was proved by GST pull-down assay using coilin that was either in vitro translated or extracted from HEK293T cells. Further, our results showed that the UBL5-coilin interaction was not influenced by coilin phosphorylation. These results suggest that UBL5 could be targeted to CBs via its interaction with coilin. Relation between human UBL5 protein and CBs is in the agreement with current observations about yeast orthologue Hub1 playing important role in alternative splicing.

  3. Human UBL5 protein interacts with coilin and meets the Cajal bodies

    SciTech Connect

    Švéda, Martin; Častorálová, Markéta; Lipov, Jan; Ruml, Tomáš; Knejzlík, Zdeněk

    2013-06-28

    Highlights: •Localization of the UBL5 protein in Hela cells was determined by fluorescence microscopy and biochemical fractionation. •Colocalization of UBL5 with Cajal bodies was observed. •Interaction of UBL5 with coilin was proven by pull-down. -- Abstract: UBL5 protein, a structural homologue of ubiquitin, was shown to be involved in pre-mRNA splicing and transcription regulation in yeast and Caenorhabditis elegans, respectively. However, role of the UBL5 human orthologue is still elusive. In our study, we observed that endogenous human UBL5 that was localized in the nucleus, partially associates with Cajal bodies (CBs), nuclear domains where spliceosomal components are assembled. Simultaneous expression of exogenous UBL5 and coilin resulted in their nuclear colocalization in HeLa cells. The ability of UBL5 to interact with coilin was proved by GST pull-down assay using coilin that was either in vitro translated or extracted from HEK293T cells. Further, our results showed that the UBL5–coilin interaction was not influenced by coilin phosphorylation. These results suggest that UBL5 could be targeted to CBs via its interaction with coilin. Relation between human UBL5 protein and CBs is in the agreement with current observations about yeast orthologue Hub1 playing important role in alternative splicing.

  4. Two Routes to Genetic Suppression of RNA Trimethylguanosine Cap Deficiency via C-Terminal Truncation of U1 snRNP Subunit Snp1 or Overexpression of RNA Polymerase Subunit Rpo26.

    PubMed

    Qiu, Zhicheng R; Schwer, Beate; Shuman, Stewart

    2015-04-24

    The trimethylguanosine (TMG) caps of small nuclear (sn) RNAs are synthesized by the enzyme Tgs1 via sequential methyl additions to the N2 atom of the m(7)G cap. Whereas TMG caps are inessential for Saccharomyces cerevisiae vegetative growth at 25° to 37°, tgs1∆ cells that lack TMG caps fail to thrive at 18°. The cold-sensitive defect correlates with ectopic stoichiometric association of nuclear cap-binding complex (CBC) with the residual m(7)G cap of the U1 snRNA and is suppressed fully by Cbc2 mutations that weaken cap binding. Here, we show that normal growth of tgs1∆ cells at 18° is also restored by a C-terminal deletion of 77 amino acids from the Snp1 subunit of yeast U1 snRNP. These results underscore the U1 snRNP as a focal point for TMG cap function in vivo. Casting a broader net, we conducted a dosage suppressor screen for genes that allowed survival of tgs1∆ cells at 18°. We thereby recovered RPO26 (encoding a shared subunit of all three nuclear RNA polymerases) and RPO31 (encoding the largest subunit of RNA polymerase III) as moderate and weak suppressors of tgs1∆ cold sensitivity, respectively. A structure-guided mutagenesis of Rpo26, using rpo26∆ complementation and tgs1∆ suppression as activity readouts, defined Rpo26-(78-155) as a minimized functional domain. Alanine scanning identified Glu89, Glu124, Arg135, and Arg136 as essential for rpo26∆ complementation. The E124A and R135A alleles retained tgs1∆ suppressor activity, thereby establishing a separation-of-function. These results illuminate the structure activity profile of an essential RNA polymerase component.

  5. Thorium effect on the oxidation of uranium: Photoelectron spectroscopy (XPS/UPS) and cyclic voltammetry (CV) investigation on (U1 - xThx)O2 (x = 0 to 1) thin films

    NASA Astrophysics Data System (ADS)

    Cakir, P.; Eloirdi, R.; Huber, F.; Konings, R. J. M.; Gouder, T.

    2017-01-01

    Thin films of U1- xThxO2 (x = 0 to 1) have been deposited via reactive DC sputter technique and characterized by X-ray/Ultra-violet Photoelectron Spectroscopy (XPS/UPS), X-ray Powder Diffractometer (XRD) and Cyclic Voltammetry (CV) in order to understand the effect of Thorium on the oxidation mechanism. During the deposition, the competition between uranium and thorium for oxidation showed that thorium has a much higher affinity for oxygen. Deposition conditions, time and temperature were also the subject of this study, to look at the homogeneity and the stability of the films. While core level and valence band spectra were not altered by the time of deposition, temperature was affecting the oxidation state of uranium and the valence band due to the mobility increase of oxygen through the film. X-ray diffraction patterns, core level spectra obtained for U1 - xThxO2 versus the composition showed that lattice parameters follow the Vegard's law and together with the binding energies of U-4f and Th-4f are in good agreement with literature data obtained on bulk compounds. To study the effect of thorium on the oxidation of U1 - xThxO2 films, we used CV experiments at neutral pH of a NaCl solution in contact with air. The results indicated that thorium has an effect on the uranium oxidation as demonstrated by the decrease of the current of the oxidation peak of uranium. XPS measurements made before and after the CV, showed a relative enrichment of thorium at the extent of uranium at the surface supporting the formation at a longer term of a thorium protective layer at the surface of uranium-thorium mixed oxide.

  6. Human Immune Responses to Dengue Viruses.

    DTIC Science & Technology

    1985-08-01

    t-Ril 630 HuMAN IMMUNE RESPONSES TO DENGUE VIRUSES(U) 1 - MASSACHUSETTS UNIV MEDICAL SCHOOL WORCESTER F A ENNIS 01 AUGO 95 DAMDI-2-C-2233 UNCASSIFIED...Classification) (U) Human Immune Responses to Dengue Viruses 12. PERSONAL AUTHOR(S) Ennis, Francis A. 13a. TYPE OF REPORT 13b. TIME COVERED 14. DATE OF...on reverse if necessary and identify by block number) FIELD GROUP SUB-GROUP06 13 Virus; Dengue ; Arbovirus; Immunology 06 13 19. ABSTRACT (Continue on

  7. Abundant pseudogenes for small nuclear RNAs are dispersed in the human genome.

    PubMed Central

    Denison, R A; Van Arsdell, S W; Bernstein, L B; Weiner, A M

    1981-01-01

    We have cloned and partially characterized 24 loci from the human genome which are complementary to U1, U2, or U3, the three major species of small nuclear RNA (snRNA) in HeLa cells. When compared to the known U1 (human) and U2 (rat) snRNA sequences, the DNA sequences we report here for the complementary regions from two of the clones, U1.11 and U2.7, reveal the presence of truncated and divergent gene copies. Furthermore, most if not all of the 24 cloned loci contain gene copies that are significantly divergent from the homologous HeLa snRNA species because DNA from every recombinant phage except U1.7 and U1.15 proved unable to form snRNA.DNA hybrids which protect full-length HeLa snRNA from ild digestion with ribonuclease T1. Hence, we refer to these loci as snRNA pseudogenes. In both clones U1.11 and U2.7, an element of the dominant middle repetitive DNA sequence family in the human genome, the Alu family, is located upstream from the snRNA pseudogene and in the same orientation. Alu elements in the same location and orientation relative to bona fide genes have previously been found in the human beta-globin gene cluster [Duncan, C. H., Biro, P. A., Choudary, P. V., Elder, J. T., Wang, R. C., Forget, G. B., deRiel, J. K. & Weissman, S. M. (1979) Proc. Natl. Acad. Sci. USA 76, 5095-5099]. We discuss the significance of these findings in relation to the nature of snRNA multigene families and other reported examples of pseudogenes. Images PMID:6165010

  8. Investigation of the Stability and Control Characteristics of a 1/10-Scale Model of the Chance Vought XF7U-1 Airplane in the Langley Free-Flight Tunnel, TED No. NACA DE306

    NASA Technical Reports Server (NTRS)

    Draper, John W.; Hewes, Donald E.

    1948-01-01

    At the request of the Bureau of Aeronautics, Navy Department, a stability and control investigation of a 1/10-scale model of the Chance Vought XF7U-1 airplane has been conducted in the Langley free-flight tunnel. Results of force end flight tests to determine the power-off stability and control characteristics of the model with slats retracted and extended are presented herein. The longitudinal and lateral stability characteristics were satisfactory for both the slats retracted and extended conditions over the lift range up to the stall. With the slats retracted, the stall was fairly gentle but the model rolled off out of control. With the slats extended, control could be maintained at the stall so that the wings could be kept level even as the model dropped.

  9. Composition of yeast snRNPs and snoRNPs in the absence of trimethylguanosine caps reveals nuclear cap binding protein as a gained U1 component implicated in the cold-sensitivity of tgs1Δ cells.

    PubMed

    Schwer, Beate; Erdjument-Bromage, Hediye; Shuman, Stewart

    2011-08-01

    Small nuclear and nucleolar RNAs that program pre-mRNA splicing and rRNA processing have a signature 5'-trimethylguanosine (TMG) cap. Whereas the mechanism of TMG synthesis by Tgs1 methyltransferase has been elucidated, we know little about whether or how RNP biogenesis, structure and function are perturbed when TMG caps are missing. Here, we analyzed RNPs isolated by tandem-affinity purification from TGS1 and tgs1Δ yeast strains. The protein and U-RNA contents of total SmB-containing RNPs were similar. Finer analysis revealed stoichiometric association of the nuclear cap-binding protein (CBP) subunits Sto1 and Cbc2 with otherwise intact Mud1- and Nam8-containing U1 snRNPs from tgs1Δ cells. CBP was not comparably enriched in Lea1-containing U2 snRNPs from tgs1Δ cells. Moreover, CBP was not associated with mature Nop58-containing C/D snoRNPs or mature Cbf5- and Gar1-containing H/ACA snoRNPs from tgs1Δ cells. The protein composition and association of C/D snoRNPs with the small subunit (SSU) processosome were not grossly affected by absence of TMG caps, nor was the composition of H/ACA snoRNPs. The cold-sensitive (cs) growth defect of tgs1Δ yeast cells could be suppressed by mutating the cap-binding pocket of Cbc2, suggesting that ectopic CBP binding to the exposed U1 m(7)G cap in tgs1Δ cells (not lack of TMG caps per se) underlies the cs phenotype.

  10. Anomalous U(1), Dark Matter and Asymmetry

    NASA Astrophysics Data System (ADS)

    Moynihan, Michael W.

    This dissertation uses ordinary least squares regression analysis to measure the impact of gasoline price changes on sprawl defined as land density of population, employment and light visible from space over multiple decades. Using census data compiled and normalized to 2000 boundaries in the Geolytics Neighborhood Change Database (NCDB) for the decennial census years 1970 through 2000 and energy price data published by the Energy Information Agency (EIA), it tests the effect of gasoline prices on eight population density-derived measures of sprawl for 72 Primary Metropolitan Statistical Areas and 48 states. Using data contained in the Zipcode Business Patterns (ZPB) database maintained by the Census Bureau, it tests the impact of gasoline prices published by ACCRA on a variety of employment dispersion measures of sprawl for Metropolitan Statistical Areas (MSAs). And using a dataset created by Burchfield et al of light visible from space, it tests the effect of gasoline prices published by ACCRA on the Burchfield et al sprawl index for 275 MSAs. The regressions control for a variety of socioeconomic, demographic, legal and physical variables and use instrumental variables and other techniques to test for causal relationships. The dissertation finds robust evidence that gasoline price changes did influence sprawl at the 95% confidence level over the periods studied with higher prices leading to less marginal sprawl and lower prices leading to more marginal sprawl. In turn, it discusses ways that policymakers might intervene using this pathway to influence sprawl, notably through the imposition of gasoline taxes.

  11. Interaction between chronically HIV-infected promonocytic cells and human umbilical vein endothelial cells: role of proinflammatory cytokines and chemokines in viral expression modulation

    PubMed Central

    Borghi, M O; Panzeri, P; Shattock, R; Sozzani, S; Dobrina, A; Meroni, P L

    2000-01-01

    HIV type 1 expression was significantly up-regulated in chronically infected promonocytic cell line (U1) co-cultured with human umbilical vein endothelial cells (HUVEC). Virus replication, evaluated as supernatant p24 release, was higher when U1 were co-cultured with IL-1β-activated HUVEC than with unstimulated HUVEC. When non-adherent U1 were removed from co-cultures, the remaining U1 cells adherent to the endothelial monolayer still showed enhanced HIV replication in comparison with an equal number of U1 cultured alone. While addition of adhesion molecule blocking antibodies (anti-intercellular adhesion molecule-1 (ICAM-1), -vascular cell adhesion molecule-1 (VCAM-1), -CD18 and -very late antigen-4 (VLA-4)) strongly inhibited adherence of U1 cells to endothelial monolayers, such treatment resulted in only a partial reduction in p24 release. Furthermore, HIV replication in U1 cells was enhanced on culture in HUVEC-conditioned media. Such data suggest that soluble mediators secreted by endothelial monolayers may modulate HIV-1 expression. Indeed, addition of cytokine and chemokine antagonists to both U1/HUVEC co-cultures and to U1 cultured in HUVEC-conditioned media clearly down-regulated p24 release. Anti-IL-6, anti-tumour necrosis factor-alpha (TNF-α) and, particularly, anti-MCP-1 MoAbs reduced p24 release, while anti-IL-8 polyclonal antiserum and IL-1 receptor antagonist (IL-1Ra) had no significant effect. Thus, the interaction between HUVEC and infected monocytic cells up-regulates HIV-1 replication predominantly through production of endothelium-derived soluble factors including MCP-1, TNF-α and IL-6. This phenomenon may influence the passage of HIV-1 from latency to productive replication and enhance virus spreading during physiological and/or pathological contact of monocytes with endothelium. PMID:10759769

  12. A zebrafish model of Poikiloderma with Neutropenia recapitulates the human syndrome hallmarks and traces back neutropenia to the myeloid progenitor

    PubMed Central

    Colombo, Elisa A.; Carra, Silvia; Fontana, Laura; Bresciani, Erica; Cotelli, Franco; Larizza, Lidia

    2015-01-01

    Poikiloderma with Neutropenia (PN) is an autosomal recessive genodermatosis characterized by early-onset poikiloderma, pachyonychia, hyperkeratosis, bone anomalies and neutropenia, predisposing to myelodysplasia. The causative C16orf57/USB1 gene encodes a conserved phosphodiesterase that regulates the stability of spliceosomal U6-RNA. The involvement of USB1 in splicing has not yet allowed to unveil the pathogenesis of PN and how the gene defects impact on skin and bone tissues besides than on the haematological compartment. We established a zebrafish model of PN using a morpholino-knockdown approach with two different splicing morpholinos. Both usb1-depleted embryos displayed developmental abnormalities recapitulating the signs of the human syndrome. Besides the pigmentation and osteochondral defects, usb1-knockdown caused defects in circulation, manifested by a reduced number of circulating cells. The overall morphant phenotype was also obtained by co-injecting sub-phenotypic dosages of the two morpholinos and could be rescued by human USB1 RNA. Integrated in situ and real-time expression analyses of stage-specific markers highlighted defects of primitive haematopoiesis and traced back the dramatic reduction in neutrophil myeloperoxidase to the myeloid progenitors showing down-regulated pu.1 expression. Our vertebrate model of PN demonstrates the intrinsic requirement of usb1 in haematopoiesis and highlights PN as a disorder of myeloid progenitors associated with bone marrow dysfunction. PMID:26522474

  13. Human SPF45, a Splicing Factor, Has Limited Expression in Normal Tissues, Is Overexpressed in Many Tumors, and Can Confer a Multidrug-Resistant Phenotype to Cells

    PubMed Central

    Sampath, Janardhan; Long, Pandy R.; Shepard, Robert L.; Xia, Xiaoling; Devanarayan, Viswanath; Sandusky, George E.; Perry, William L.; Dantzig, Anne H.; Williamson, Mark; Rolfe, Mark; Moore, Robert E.

    2003-01-01

    Our effort to identify novel drug-resistant genes in cyclophosphamide-resistant EMT6 mouse mammary tumors led us to the identification of SPF45. Simultaneously, other groups identified SPF45 as a component of the spliceosome that is involved in alternative splicing. We isolated the human homologue and examined the normal human tissue expression, tumor expression, and the phenotype caused by overexpression of human SPF45. Our analyses revealed that SPF45 is expressed in many, but not all, normal tissues tested with predominant expression in normal ductal epithelial cells of the breast, liver, pancreas, and prostate. Our analyses using tissue microarrays and sausages of tumors indicated that SPF45 is highly expressed in numerous carcinomas including bladder, breast, colon, lung, ovarian, pancreatic, and prostate. Interestingly, this study revealed that overexpression of SPF45 in HeLa, a cervical carcinoma cell line, resulted in drug resistance to doxorubicin and vincristine, two chemotherapeutic drugs commonly used in cancer. To our knowledge, this is the first study showing tumor overexpression of an alternate splicing factor resulting in drug resistance. PMID:14578179

  14. Cosmological Bounds of Sterile Neutrinos in a S U(3) C ⊗ S U(3) L ⊗ S U(3) R ⊗ U(1) N Model as Dark Matter Candidates

    NASA Astrophysics Data System (ADS)

    Ferreira, C. P.; Guzzo, M. M.; de Holanda, P. C.

    2016-08-01

    We study sterile neutrinos in an extension of the standard model, based on the gauge group S U(3) C ⊗ S U(3) L ⊗ S U(3) R ⊗ U(1) N , and use this model to illustrate how to apply cosmological limits to thermalized particles that decouple while relativistic. These neutrinos, N a L , can be dark matter candidates, with a kiloelectron volt mass range arising rather naturally in this model. We analyse the cosmological limits imposed by N e f f and dark matter abundance on these neutrinos. Assuming that these neutrinos have roughly equal masses and are not CDM, we conclude that the N e f f experimental value can be satisfied in some cases and the abundance constraint implies that these neutrinos are hot dark matter. With this information, we give upper bounds on the Yukawa coupling between the sterile neutrinos and a scalar field, the possible values of the VEV of this scalar field and lower bounds to the mass of one gauge boson of the model.

  15. Human Immune Responses to Dengue Viruses.

    DTIC Science & Technology

    1984-08-01

    ND-R171 381 HUR IMMUNE RESPONSES TO DENGUE VIRUSES(U) 1/1 MASSRCHUSETTS UNIY M9DICAL SCHOOL WORCESTER F R~ ENNIS RUG 94 DRMt17-2-C-2233 UNCLASSIFIED...Responses to Dengue Viruses Annual Report 0(August 1983-July 1984) Francis A. Ennis, M.D. August 1984 Supported by U.S. Army Medical Research and...3M1- NO. SON No. Frederick, Maryland 21701-5012 61102A 61102BSI0 AA 104 11. TITLE Oxkf* Samqy Oao" Human Immune Responses to Dengue Viruses 12. PERSON

  16. Protein composition of human mRNPs spliced in vitro and differential requirements for mRNP protein recruitment

    PubMed Central

    Merz, Christian; Urlaub, Henning; Will, Cindy L.; Lührmann, Reinhard

    2007-01-01

    The deposition of proteins onto newly spliced mRNAs has far reaching consequences for their subsequent metabolism. We affinity-purified spliced human mRNPs under physiological conditions from HeLa nuclear extract and present the first comprehensive inventory of their protein composition as determined by mass spectrometry. Several proteins previously not known to be mRNP-associated were detected, including the DEAD-box helicases DDX3, DDX5, and DDX9, and the ELG, hNHN1, BCLAF1, and TRAP150 proteins. The association of some of the newly identified mRNP proteins was shown to be splicing-dependent, but not to require EJC formation. Initial recruitment of EJC proteins to the spliceosome did not require an EJC binding platform at the −20/24 region of the 5′ exon. Finally, while recruitment of EJC proteins and stable EJC formation were not dependent on the cap binding complex, several of the newly identified mRNP proteins required the latter for their association with mRNPs. These results provide novel insights into the composition of spliced mRNPs and the requirements for the association of mRNP proteins with the newly spliced mRNA. PMID:17095540

  17. Longitudinal Stability and Control Characteristics of a Semispan Wind-Tunnel Model of the XF7U-1 Airplane and a Comparison with Complete-Model Wind-Tunnel Tests and Semispan-Model Wing-Flow Tests

    NASA Technical Reports Server (NTRS)

    Goodson, Kenneth W.; King, Thomas J., Jr.

    1949-01-01

    An investigation was conducted on an 0.08-scale semispan model of the Chance Vought XF7U-1 airplane in the Langley high-speed 7- by 10-foot tunnel in the Mach number range from 0.40 to 0.97. The results are compared with those obtained with an 0.08-scale sting-mounted complete model tested in the same tunnel and with an 0.026-scale semispan model tested by the wing-flow method. The lift-curve slopes obtained for the 0.08-scale semispan model and the 0.026-scale wing-flow model were in good agreement but both were generally lower than the values obtained for the sting model. The results of an unpublished investigation have shown that tunnel-wall boundary-layer and strut-leakage effects can came the difference noted between the lift-curve slopes of the sting and the semispan data. Fair agreement was obtained among the data of the three models as regard the variation of pitching-moment coefficients with lift coefficient. The agreement between the complete and the semispan models was more favorable with the vertical fine on, because the wall-boundary-layer and strut leakage effects were less severe. In the Mach number range between 0.94 and 0.97, ailavator-control reversal was indicated in the wing-flow data near zero lift; Whereas, these same trends were indicated in the larger scale semispan data at somewhat higher lift coefficients.

  18. Synthesis of 4-thiouridine, 6-thioinosine, and 6-thioguanosine 3',5'-O-bisphosphates as donor molecules for RNA ligation and their application to the synthesis of photoactivatable TMG-capped U1 snRNA fragments.

    PubMed

    Kadokura, M; Wada, T; Seio, K; Sekine, M

    2000-08-25

    4-Thiouridine, 6-thioguanosine, and 6-thioinosine 3',5'-bisphosphates (9, 20, and 28) were synthesized in good yields by considerably improved methods. In the former two compounds, uridine and 2-N-phenylacetylguanosine were converted via transient O-trimethylsilylation to the corresponding 4- and 6-O-benzenesulfonyl intermediates (2 and 13), which, in turn, were allowed to react with 2-cyanoethanethiol in the presence of N-methylpyrrolidine to give 4-thiouridine (3) and 2-N-phenylacetyl-6-thioguanosine derivatives (14), respectively. In situ dimethoxytritylation of these thionucleoside derivatives gave the 5'-masked products 4 and 15 in high overall yields from 1 and 11. 6-S-(2-Cyanoethyl)-5'-O-(4,4'-dimethoxytrityl)-6-thioinosine (23) was synthesized via substitution of the 5'-O-tritylated 6-chloropurine riboside derivative 22 with 2-cyanoethanethiol. These S-(2-cyanoethyl)thionucleosides were converted to the 2'-O-(tert-butyldimethylsilyl)ribonucleoside 3'-phosphoramidite derivatives 7, 18, and 26 or 3',5'-bisphosphate derivatives 8, 19, and 27. Treatment of 8, 19, and 27 with DBU gave thionucleoside 3',5'-bisphosphate derivatives 9, 20, and 28, which were found to be substrates of T4 RNA ligase. These thionucleoside 3',5'-bisphosphates were examined as donors for ligation with m3(2,2,7) G5'pppAmUmA, i.e., the 5'-terminal tetranucleotide fragment of U1 snRNA, The 4-thiouridine 3',5'-bisphosphate derivative 9 was found to serve as the most active substrate of T4 RNA ligase with a reaction efficiency of 96%.

  19. Longitudinal Stability and Control Characteristics of a Semispan Model of the XF7U-1 Tailless Airplane at Transonic Speeds by the NACA Wing-Flow Method, TED No. NACA DE307

    NASA Technical Reports Server (NTRS)

    Sawyer, Richard H.; Trant, James P., Jr.

    1947-01-01

    An investigation was made by the NACA wing-flow method to determine the longitudinal stability and control characteristics at transonic speeds of a semispan model of the XF7U-1 tailless airplane. The 25-percent chord line of the wing of the model was swept back 35 deg. The airfoil sections of the wing perpendicular to the 25-percent chord line were 12 percent thick. Measurements were made of the normal force and pitching moment through an angle-of-attack range from about -3 deg to 14 deg for several ailavator deflections at Mach numbers from 0.65 to about 1.08. The results of the tests indicated no adverse effects of compressibility up to a Mach number of at least 0.85 at low normal-force coefficients and small ailavator deflections. Up to a Mach number of 0.85, the neutral point at low normal-force coefficients was at about 25 percent of the mean aerodynamic chord and moved rearward irregularly to 41 or 42 percent with a further increase in Mach number to about 1.05. For deflections up to -8.0 percent, the ailavator was effective in changing the pitching moment except at Mach numbers from 0.93 to about 1.0 where ineffectiveness or reversal was indicated for deflections and normal-force coefficients. With -13.2 deg deflection at normal-force coefficients above about 0.3, reversal of ailavator effectiveness occurred at Mach numbers as low as 0.81. A nose-down trim change, which began at a Mach number of about 0.85, together with the loss in effectiveness of the ailavator, indicated that with increase in the Mach number from about 0.95 to 1.05 an abrupt ailavator movement of 5 deg or 6 deg first up and then down would be required to maintain level flight.

  20. Treatment Strategies for Human Arboviral Infections Applicable to Veterinary Medicine

    DTIC Science & Technology

    1992-06-16

    0 Lf Reprintod from Tropical Veterinary Medicine : Current Issues and Perspectives 1• • Volume 653 of the Annals of the New York Academy of Sciences...June 16, 1992 _ Treatment Strategies for Human = __ Arboviral Infections Applicable to I= ’ Veterinary Medicine = ! Chlh. MEIR KENDE (A) U •Department...A 3 0. C . U. 2 * >. U u U>1 it 020 ce*. 0. , -,r- 8 C- ed U a - .; U~u0.M KENDE: HUMAN ARBOVIRAL INFECTIONS AND VETERINARY MEDICINE 299 TABLE 2

  1. Effect of Various Modifications on Drag and Longitudinal Stability and Control Characteristics at Transonic Speeds of a Model of the XF7U-1 Tailless Airplane: NACA Wing-FLow Method, TED No. NACA DE 307

    NASA Technical Reports Server (NTRS)

    Sawyer, Richard H.; Trant, James P., Jr.

    1950-01-01

    An investigation was made by the NACA wing-flow method to determine the drag, pitching-moment, lift, and angle-of-attack characteristics at transonic speeds of various configurations of a semispan model of an early configuration of the XF7U-1 tailless airplane. The results of the tests indicated that for the basic configuration with undeflected ailavator, the zero-lift drag rise occurred at a Mach number of about 0.85 and that about a five-fold increase in drag occurred through the transonic speed range. The results of the tests also indicated that the drag increment produced by -8.0 degrees deflection of the ailavator increased with increase in normal-force coefficient and was smaller at speeds above than at speeds below the drag rise. The drag increment produced by 35 degree deflection of the speed brakes varied from 0.040 to 0.074 depending on the normal-force coefficient and Mach number. These values correspond to drag coefficients of about 0.40 and 0.75 based on speed-brake frontal area. Removal of the fin produced a small positive drag increment at a given normal-force coefficient at speeds during the drag rise. A large forward shift of the neutral-point location occurred at Mach numbers above about 0.90 upon removal of the fin, and also a considerable forward shift throughout the Mach number range occurred upon deflection of the speed brakes. Ailavator ineffectiveness or reversal at low deflections, similar to that determined in previous tests of the basic configuration of the model in the Mach number range from about 0.93 to 1.0, was found for the fin-off configuration and for the model equipped with skewed (more highly sweptback) hinge-line ailavators. With the speed brakes deflected, little or no loss in the incremental pitching moment produced by deflection of the ailavator from O degrees to -8.00 degrees occurred in the Mach number range from 0.85 to 1.0 in contrast to a considerable loss found in previous tests with the speed brakes off.

  2. The intronic splicing code: multiple factors involved in ATM pseudoexon definition.

    PubMed

    Dhir, Ashish; Buratti, Emanuele; van Santen, Maria A; Lührmann, Reinhard; Baralle, Francisco E

    2010-02-17

    Abundance of pseudo splice sites in introns can potentially give rise to innumerable pseudoexons, outnumbering the real ones. Nonetheless, these are efficiently ignored by the splicing machinery, a process yet to be understood completely. Although numerous 5' splice site-like sequences functioning as splicing silencers have been found to be enriched in predicted human pseudoexons, the lack of active pseudoexons pose a fundamental challenge to how these U1snRNP-binding sites function in splicing inhibition. Here, we address this issue by focusing on a previously described pathological ATM pseudoexon whose inhibition is mediated by U1snRNP binding at intronic splicing processing element (ISPE), composed of a consensus donor splice site. Spliceosomal complex assembly demonstrates inefficient A complex formation when ISPE is intact, implying U1snRNP-mediated unproductive U2snRNP recruitment. Furthermore, interaction of SF2/ASF with its motif seems to be dependent on RNA structure and U1snRNP interaction. Our results suggest a complex combinatorial interplay of RNA structure and trans-acting factors in determining the splicing outcome and contribute to understanding the intronic splicing code for the ATM pseudoexon.

  3. Retrohoming of a Mobile Group II Intron in Human Cells Suggests How Eukaryotes Limit Group II Intron Proliferation

    PubMed Central

    Truong, David M.; Hewitt, F. Curtis; Hanson, Joseph H.; Cui, Xiaoxia; Lambowitz, Alan M.

    2015-01-01

    Mobile bacterial group II introns are evolutionary ancestors of spliceosomal introns and retroelements in eukaryotes. They consist of an autocatalytic intron RNA (a “ribozyme”) and an intron-encoded reverse transcriptase, which function together to promote intron integration into new DNA sites by a mechanism termed “retrohoming”. Although mobile group II introns splice and retrohome efficiently in bacteria, all examined thus far function inefficiently in eukaryotes, where their ribozyme activity is limited by low Mg2+ concentrations, and intron-containing transcripts are subject to nonsense-mediated decay (NMD) and translational repression. Here, by using RNA polymerase II to express a humanized group II intron reverse transcriptase and T7 RNA polymerase to express intron transcripts resistant to NMD, we find that simply supplementing culture medium with Mg2+ induces the Lactococcus lactis Ll.LtrB intron to retrohome into plasmid and chromosomal sites, the latter at frequencies up to ~0.1%, in viable HEK-293 cells. Surprisingly, under these conditions, the Ll.LtrB intron reverse transcriptase is required for retrohoming but not for RNA splicing as in bacteria. By using a genetic assay for in vivo selections combined with deep sequencing, we identified intron RNA mutations that enhance retrohoming in human cells, but <4-fold and not without added Mg2+. Further, the selected mutations lie outside the ribozyme catalytic core, which appears not readily modified to function efficiently at low Mg2+ concentrations. Our results reveal differences between group II intron retrohoming in human cells and bacteria and suggest constraints on critical nucleotide residues of the ribozyme core that limit how much group II intron retrohoming in eukaryotes can be enhanced. These findings have implications for group II intron use for gene targeting in eukaryotes and suggest how differences in intracellular Mg2+ concentrations between bacteria and eukarya may have impacted the

  4. Retrohoming of a Mobile Group II Intron in Human Cells Suggests How Eukaryotes Limit Group II Intron Proliferation.

    PubMed

    Truong, David M; Hewitt, F Curtis; Hanson, Joseph H; Cui, Xiaoxia; Lambowitz, Alan M

    2015-08-01

    Mobile bacterial group II introns are evolutionary ancestors of spliceosomal introns and retroelements in eukaryotes. They consist of an autocatalytic intron RNA (a "ribozyme") and an intron-encoded reverse transcriptase, which function together to promote intron integration into new DNA sites by a mechanism termed "retrohoming". Although mobile group II introns splice and retrohome efficiently in bacteria, all examined thus far function inefficiently in eukaryotes, where their ribozyme activity is limited by low Mg2+ concentrations, and intron-containing transcripts are subject to nonsense-mediated decay (NMD) and translational repression. Here, by using RNA polymerase II to express a humanized group II intron reverse transcriptase and T7 RNA polymerase to express intron transcripts resistant to NMD, we find that simply supplementing culture medium with Mg2+ induces the Lactococcus lactis Ll.LtrB intron to retrohome into plasmid and chromosomal sites, the latter at frequencies up to ~0.1%, in viable HEK-293 cells. Surprisingly, under these conditions, the Ll.LtrB intron reverse transcriptase is required for retrohoming but not for RNA splicing as in bacteria. By using a genetic assay for in vivo selections combined with deep sequencing, we identified intron RNA mutations that enhance retrohoming in human cells, but <4-fold and not without added Mg2+. Further, the selected mutations lie outside the ribozyme catalytic core, which appears not readily modified to function efficiently at low Mg2+ concentrations. Our results reveal differences between group II intron retrohoming in human cells and bacteria and suggest constraints on critical nucleotide residues of the ribozyme core that limit how much group II intron retrohoming in eukaryotes can be enhanced. These findings have implications for group II intron use for gene targeting in eukaryotes and suggest how differences in intracellular Mg2+ concentrations between bacteria and eukarya may have impacted the

  5. Crystal Chemistry and Magnetism of Ternary Actinoid Boron Carbides UB 1- xC 1+ x and U 1- xMxB 2C with M = Sc, Lu, and Th

    NASA Astrophysics Data System (ADS)

    Rogl, P.; Rupp, B.; Felner, I.; Fischer, P.

    1993-06-01

    Within the homogeneous range of uranium monocarbide UB 1- xC 1+ x, the crystal structures of stoichiometric UBC and of the carbon-rich solid solution UB 0.78C 1.22, have been refined from single-crystal X-ray counter data. From X-ray analysis crystal symmetry in both cases is consistent with the centro-symmetric space group Cmcm and there are no indications of superstructure formation. In contrast to the fully ordered atom arrangement revealed for stoichiometric UBC ( a = 0.35899(4), b = 1.19781(12), c = 0.33474(3) nm), random occupation by boron and carbon atoms is observed for the boron site in UB 0.78C 1.22 ( a = 0.35752(4), b = 1.18584(3), c = 0.33881(4) nm). For 279(278) reflections (|F 0| > 3σ) the obtained reliability factors R x = ∑|ΔF|/∑| F0| were R x = 0.069 for UBC and R x = 0.050 for UB 0.78C 1.22. Neutron powder diffraction experiments at 9 and 295 K unambiguously revealed full occupancy by the nonmetal atoms in UB 0.78C 1.22 and prove the statistical occupation of B and C atoms in the B-sites. For the orthorhombic symmetry Cmcm, refinement was not better than R1 = 0.044. A model calculation in monoclinic symmetry C12/ m1, however, resulted in a significant reduction of the residual value to R1 = 0.030, releasing spatial constraints on the boron atoms. Thus the boron-boron chain in Cmcm (B-B = 0.1874 nm) is dissolved into boron pairs (B-B = 0.1706 nm) which are loosely bound at a distance of 0.2043 nm. The formation of C-B-B-C groups corresponds to the structure types of ThBC and Th 3B 2C 3. The magnetic behavior has been investigated in the temperature range from 4.2 K to 1000 K for UB 1- xC 1+ x (UBC-type) and U 1- xMxB 2C (ThB 2C-type for the high temperature modification and 1-UB 2C-type for the low temperature modification) with U partially substituted by Th or Sc, Lu. From magnetic susceptibilities, the alloys UB 1- xC 1+ x reveal temperature independent paramagnetism with typical intermediate valence fluctuation behavior ( TSF ˜ 350 K

  6. Human Development, Human Evolution.

    ERIC Educational Resources Information Center

    Smillie, David

    One of the truly remarkable events in human evolution is the unprecedented increase in the size of the brain of "Homo" over a brief span of 2 million years. It would appear that some significant selective pressure or opportunity presented itself to this branch of the hominid line and caused a rapid increase in the brain, introducing a…

  7. Humanizing the Humanities.

    ERIC Educational Resources Information Center

    Peters, Dennis

    1983-01-01

    Reviews some of the steps taken at Shoreline Community College to develop cooperative programs involving vocational and academic faculty, including the creation of a Humanities Advisory Council. Briefly describes some of the cooperative programs, e.g., symposia on critical issues in higher education, guest lectures, and high school outreach. (AYC)

  8. Humanity and human DNA.

    PubMed

    Mattei, Jean-François

    2012-10-01

    Genetics has marked the second half of the 20th century by addressing such formidable problems as the identification of our genes and their role, their interaction with the environment, and even their therapeutic uses. The identification of genes raises questions about differences between humans and non-humans, as well as about the evolution towards trans-humanism and post-humanism. In practise, however, the main question concerns the limits of prenatal genetic diagnosis, not only on account of the seriousness of the affections involved but also because of the choice to be made between following-up the medical indication and engaging in a systematic public health strategy aimed at eliminating children with certain handicaps. History reminds us that genetic science has already been misused by political forces influenced by the ideas of eugenics, particularly in the Nazi period. We may wonder whether it is reasonable to formulate a judgement on the life of a child yet to be born, merely on the basis of a DNA analysis. My experience as a practising geneticist and my involvement in French politics forces me to stress the dangers of a new eugenics hiding behind a medical mask. As demonstrated by epigenetics, human beings cannot be reduced to their DNA alone. In our society, one of the problems concerns individuals whose lives may be considered by some as simply not worth living. Another problem is the place and the social significance of the handicapped amongst us. Fortunately, recent progresses in gene therapy, biotherapy, and even pharmacology, appear to be opening up promising therapeutic perspectives. We should bear in mind that the chief vocation of medical genetics, which fully belongs to the art of medicine, is to heal and to cure. This is precisely where genetics should concentrate its efforts software.

  9. Changing nuclear landscape and unique PML structures during early epigenetic transitions of human embryonic stem cells.

    PubMed

    Butler, John T; Hall, Lisa L; Smith, Kelly P; Lawrence, Jeanne B

    2009-07-01

    The complex nuclear structure of somatic cells is important to epigenomic regulation, yet little is known about nuclear organization of human embryonic stem cells (hESC). Here we surveyed several nuclear structures in pluripotent and transitioning hESC. Observations of centromeres, telomeres, SC35 speckles, Cajal Bodies, lamin A/C and emerin, nuclear shape and size demonstrate a very different "nuclear landscape" in hESC. This landscape is remodeled during a brief transitional window, concomitant with or just prior to differentiation onset. Notably, hESC initially contain abundant signal for spliceosome assembly factor, SC35, but lack discrete SC35 domains; these form as cells begin to specialize, likely reflecting cell-type specific genomic organization. Concomitantly, nuclear size increases and shape changes as lamin A/C and emerin incorporate into the lamina. During this brief window, hESC exhibit dramatically different PML-defined structures, which in somatic cells are linked to gene regulation and cancer. Unlike the numerous, spherical somatic PML bodies, hES cells often display approximately 1-3 large PML structures of two morphological types: long linear "rods" or elaborate "rosettes", which lack substantial SUMO-1, Daxx, and Sp100. These occur primarily between Day 0-2 of differentiation and become rare thereafter. PML rods may be "taut" between other structures, such as centromeres, but clearly show some relationship with the lamina, where PML often abuts or fills a "gap" in early lamin A/C staining. Findings demonstrate that pluripotent hES cells have a markedly different overall nuclear architecture, remodeling of which is linked to early epigenomic programming and involves formation of unique PML-defined structures.

  10. Sperm-immobilizing monoclonal antibody to human seminal plasma antigens.

    PubMed Central

    Shigeta, M; Watanabe, T; Maruyama, S; Koyama, K; Isojima, S

    1980-01-01

    Rat spleen cells immunized to human azoospermic semen (a mixture of seminal plasma components) and mouse myeloma cells (P3/X63 Ag8U1; P3U1) (Marguilies et al., 1976) were successfully fused with polyethylene glycol (PEG 1500) and 19 of 89 fused cell cultures were found to produce sperm-immobilizing antibody. The cells that produced antibody indicating the highest sperm-immobilizing activity were distributed into wells for further recloning and 10 clones producing sperm-immobilizing antibody were established. The clone (1C4) producing the highest antibody titre was found to produce a large amount of IgG in culture supernatants and to contain a mixture of rat and mouse chromosomes. It was proved by immunodiffusion test that the monoclonal antibody was produced to the human seminal plasma antigen No. 7 which is common to human milk protein. Using this hybridoma which produced a large amount of monoclonal sperm-immobilizing antibody, a new method could be developed for purifying human seminal plasma antigen by immunoaffinity chromatography with bound antibody from the hybridoma. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 PMID:6783353

  11. An Investigation of the Aerodynamic Characteristics of an 0.08-Scale Model of the Chance Vought XF7U-1 Airplane in the Langley High-Speed 7- by 10-Foot Tunnel. Part III - Longitudinal-Control Characteristics TED No. NACA DE308. Part 3; Longitudinal-Control Characteristics, TED No. NACA DE308

    NASA Technical Reports Server (NTRS)

    Kuhn, Richard E.; King, Thomas J., Jr.

    1947-01-01

    Tests have been conducted in the Langley high speed 7- by 10-foot tunnel over a Mach number range from 0.40 to 0.91 to determine the stability and control characteristics of an 0,08-scale model of the Chance Vought XF7U-1 airplane. The longitudinal-control characteristics of the complete model are presented in the present report with a limited analysis of the results.

  12. An Investigation of the Aerodynamic Characteristics of an 0.08-Scale Model of the Chance Vought XF7U-1 Airplane in the Langley High-Speed 7- by 10-Foot Tunnel. Part I - Basic Longitudinal Stability Characteristics, TED No. NACA DE308. Part 1; Basic Longitudinal Stability Characteristics, TED No. NACA DE308

    NASA Technical Reports Server (NTRS)

    Kemp, William B., Jr.; Kuhn, Richard E.; Goodson, Kenneth W.

    1947-01-01

    The stability and control characteristics of an 0.08-scale model of the Chance Vought XF7U-1 airplane have been investigated over a Mach number range from 0.40 to 0.91. Results of the basic longitudinal tests of the complete model with undeflected control surfaces are given in the present report with a very limited analysis of the results.

  13. An Investigation of the Aerodynamic Characteristics of an 0.08-Scale Model of the Chance Vought XF7U-1 Airplane in the Langley High-Speed 7- by 10-Foot Tunnel. Part IV - Aileron Characteristics TED No. NACA DE308. Part 4; Aileron Characteristics, TED No. NACA DE308

    NASA Technical Reports Server (NTRS)

    Goodson, Kenneth W.; Myers, Boyd C., II

    1947-01-01

    Tests have been conducted in the Langley high-speed 7- by 10-foot tunnel over a Mach number range from 0.40 to 0.91 to determine the stability and control characteristics of an 0.08-scale model of the Chance Vought XF7U-1 airplane. The aileron characteristics of the complete model are presented in the present report with a very limited analysis of the results.

  14. The phylogenetically invariant ACAGAGA and AGC sequences of U6 small nuclear RNA are more tolerant of mutation in human cells than in Saccharomyces cerevisiae.

    PubMed Central

    Datta, B; Weiner, A M

    1993-01-01

    U6 small nuclear RNA (snRNA) is the most highly conserved of the five spliceosomal snRNAs that participate in nuclear mRNA splicing. The proposal that U6 snRNA plays a key catalytic role in splicing [D. Brow and C. Guthrie, Nature (London) 337:14-15, 1989] is supported by the phylogenetic conservation of U6, the sensitivity of U6 to mutation, cross-linking of U6 to the vicinity of the 5' splice site, and genetic evidence for extensive base pairing between U2 and U6 snRNAs. We chose to mutate the phylogenetically invariant 41-ACAGAGA-47 and 53-AGC-55 sequences of human U6 because certain point mutations within the homologous regions of Saccharomyces cerevisiae U6 selectively block the first or second step of mRNA splicing. We found that both sequences are more tolerant to mutation in human cells (assayed by transient expression in vivo) than in S. cerevisiae (assayed by effects on growth or in vitro splicing). These differences may reflect different rate-limiting steps in the particular assays used or differential reliance on redundant RNA-RNA or RNA-protein interactions. The ability of mutations in U6 nucleotides A-45 and A-53 to selectively block step 2 of splicing in S. cerevisiae had previously been construed as evidence that these residues might participate directly in the second chemical step of splicing; an indirect, structural role seems more likely because the equivalent mutations have no obvious phenotype in the human transient expression assay. Images PMID:8355689

  15. Spinal muscular atrophy phenotype is ameliorated in human motor neurons by SMN increase via different novel RNA therapeutic approaches.

    PubMed

    Nizzardo, Monica; Simone, Chiara; Dametti, Sara; Salani, Sabrina; Ulzi, Gianna; Pagliarani, Serena; Rizzo, Federica; Frattini, Emanuele; Pagani, Franco; Bresolin, Nereo; Comi, Giacomo; Corti, Stefania

    2015-06-30

    Spinal muscular atrophy (SMA) is a primary genetic cause of infant mortality due to mutations in the Survival Motor Neuron (SMN) 1 gene. No cure is available. Antisense oligonucleotides (ASOs) aimed at increasing SMN levels from the paralogous SMN2 gene represent a possible therapeutic strategy. Here, we tested in SMA human induced pluripotent stem cells (iPSCs) and iPSC-differentiated motor neurons, three different RNA approaches based on morpholino antisense targeting of the ISSN-1, exon-specific U1 small nuclear RNA (ExSpeU1), and Transcription Activator-Like Effector-Transcription Factor (TALE-TF). All strategies act modulating SMN2 RNA: ASO affects exon 7 splicing, TALE-TF increase SMN2 RNA acting on the promoter, while ExSpeU1 improves pre-mRNA processing. These approaches induced up-regulation of full-length SMN mRNA and differentially affected the Delta-7 isoform: ASO reduced this isoform, while ExSpeU1 and TALE-TF increased it. All approaches upregulate the SMN protein and significantly improve the in vitro SMA motor neurons survival. Thus, these findings demonstrate that therapeutic tools that act on SMN2 RNA are able to rescue the SMA disease phenotype. Our data confirm the feasibility of SMA iPSCs as in vitro disease models and we propose novel RNA approaches as potential therapeutic strategies for treating SMA and other genetic neurological disorders.

  16. Human Augmentics: augmenting human evolution.

    PubMed

    Kenyon, Robert V; Leigh, Jason

    2011-01-01

    Human Augmentics (HA) refers to technologies for expanding the capabilities, and characteristics of humans. One can think of Human Augmentics as the driving force in the non-biological evolution of humans. HA devices will provide technology to compensate for human biological limitations either natural or acquired. The strengths of HA lie in its applicability to all humans. Its interoperability enables the formation of ecosystems whereby augmented humans can draw from other realms such as "the Cloud" and other augmented humans for strength. The exponential growth in new technologies portends such a system but must be designed for interaction through the use of open-standards and open-APIs for system development. We discuss the conditions needed for HA to flourish with an emphasis on devices that provide non-biological rehabilitation.

  17. Human Rights/Human Needs.

    ERIC Educational Resources Information Center

    Canning, Cynthia

    1978-01-01

    The faculty of Holy Names High School developed an interdisciplinary human rights program with school-wide activities focusing on three selected themes: the United Nations Universal Declaration of Human Rights, in conjunction with Human Rights Week; Food; and Women. This article outlines major program activities. (SJL)

  18. Recognition of U1 and U2 small nuclear RNAs can be altered by a 5-amino-acid segment in the U2 small nuclear ribonucleoprotein particle (snRNP) B" protein and through interactions with U2 snRNP-A' protein.

    PubMed Central

    Bentley, R C; Keene, J D

    1991-01-01

    We have investigated the sequence elements influencing RNA recognition in two closely related small nuclear ribonucleoprotein particle (snRNP) proteins, U1 snRNP-A and U2 snRNP-B". A 5-amino-acid segment in the RNA-binding domain of the U2 snRNP-B" protein was found to confer U2 RNA recognition when substituted into the corresponding position in the U1 snRNP-A protein. In addition, B", but not A, was found to require the U2 snRNP-A' protein as an accessory factor for high-affinity binding to U2 RNA. The pentamer segment in B" that conferred U2 RNA recognition was not sufficient to allow the A' enhancement of U2 RNA binding by B", thus implicating other sequences in this protein-protein interaction. Sequence elements involved in these interactions have been localized to variable loops of the RNA-binding domain as determined by nuclear magnetic resonance spectroscopy (D. Hoffman, C.C. Query, B. Golden, S.W. White, and J.D. Keene, Proc. Natl. Acad. Sci. USA, in press). These findings suggest a role for accessory proteins in the formation of RNP complexes and pinpoint amino acid sequences that affect the specificity of RNA recognition in two members of a large family of proteins involved in RNA processing. Images PMID:1826042

  19. Escaping the Nuclear Confines: Signal-Dependent Pre-mRNA Splicing in Anucleate Platelets

    PubMed Central

    Denis, Melvin M.; Tolley, Neal D.; Bunting, Michaeline; Schwertz, Hansjörg; Jiang, Huimiao; Lindemann, Stephan; Yost, Christian C.; Rubner, Frederick J.; Albertine, Kurt H.; Swoboda, Kathryn J.; Fratto, Carolyn M.; Tolley, Emilysa; Kraiss, Larry W.; McIntyre, Thomas M.; Zimmerman, Guy A.

    2015-01-01

    Summary Platelets are specialized hemostatic cells that circulate in the blood as anucleate cytoplasts. We report that platelets unexpectedly possess a functional spliceosome, a complex that processes pre-mRNAs in the nuclei of other cell types. Spliceosome components are present in the cytoplasm of human megakaryocytes and in proplatelets that extend from megakaryocytes. Primary human platelets also contain essential spliceosome factors including small nuclear RNAs, splicing proteins, and endogenous pre-mRNAs. In response to integrin engagement and surface receptor activation, platelets precisely excise introns from interleukin-1β pre-mRNA, yielding a mature message that is translated into protein. Signal-dependent splicing is a novel function of platelets that demonstrates remarkable specialization in the regulatory repertoire of this anucleate cell. While this mechanism may be unique to platelets, it also suggests previously unrecognized diversity regarding the functional roles of the spliceosome in eukaryotic cells. PMID:16096058

  20. Escaping the nuclear confines: signal-dependent pre-mRNA splicing in anucleate platelets.

    PubMed

    Denis, Melvin M; Tolley, Neal D; Bunting, Michaeline; Schwertz, Hansjörg; Jiang, Huimiao; Lindemann, Stephan; Yost, Christian C; Rubner, Frederick J; Albertine, Kurt H; Swoboda, Kathryn J; Fratto, Carolyn M; Tolley, Emilysa; Kraiss, Larry W; McIntyre, Thomas M; Zimmerman, Guy A; Weyrich, Andrew S

    2005-08-12

    Platelets are specialized hemostatic cells that circulate in the blood as anucleate cytoplasts. We report that platelets unexpectedly possess a functional spliceosome, a complex that processes pre-mRNAs in the nuclei of other cell types. Spliceosome components are present in the cytoplasm of human megakaryocytes and in proplatelets that extend from megakaryocytes. Primary human platelets also contain essential spliceosome factors including small nuclear RNAs, splicing proteins, and endogenous pre-mRNAs. In response to integrin engagement and surface receptor activation, platelets precisely excise introns from interleukin-1beta pre-mRNA, yielding a mature message that is translated into protein. Signal-dependent splicing is a novel function of platelets that demonstrates remarkable specialization in the regulatory repertoire of this anucleate cell. While this mechanism may be unique to platelets, it also suggests previously unrecognized diversity regarding the functional roles of the spliceosome in eukaryotic cells.

  1. Teaching humanism.

    PubMed

    Stern, David T; Cohen, Jordan J; Bruder, Ann; Packer, Barbara; Sole, Allison

    2008-01-01

    As the "passion that animates authentic professionalism," humanism must be infused into medical education and clinical care as a central feature of medicine's professionalism movement. In this article, we discuss a current definition of humanism in medicine. We will also provide detailed descriptions of educational programs intended to promote humanism at a number of medical schools in the United States (and beyond) and identify the key factors that make these programs effective. Common elements of programs that effectively teach humanism include: (1) opportunities for students to gain perspective in the lives of patients; (2) structured time for reflection on those experiences; and (3) focused mentoring to ensure that these events convert to positive, formative learning experiences. By describing educational experiences that both promote and sustain humanism in doctors, we hope to stimulate the thinking of other medical educators and to disseminate the impact of these innovative educational programs to help the profession meet its obligation to provide the public with humanistic physicians.

  2. Human cloning and human dignity.

    PubMed

    Birnbacher, Dieter

    2005-03-01

    Judging from the official documents dealing with the moral and legal aspects of human reproductive cloning there seems to be a nearly worldwide consensus that reproductive cloning is incompatible with human dignity. The certainty of this judgement is, however, not matched by corresponding arguments. Is the incompatibility of reproductive with human dignity an ultimate moral intuition closed to further argument? The paper considers several ways by which the intuition might be connected with more familiar applications of the concept of human dignity, and argues that there is no such connection. It concludes that the central objections to human reproductive cloning are not objections relating to dignity but objections relating to risk, especially the risks imposed on children born in the course of testing the method's safety.

  3. Human rights

    PubMed Central

    Powell, J Enoch

    1977-01-01

    What are human rights? In this article Enoch Powell, MP (a former Conservative Minister of Health), approaches this question through a critical discussion of Article 25 (I) of the United Nations Universal Declaration of Human Rights. Professor R S Downie in his accompanying commentary analyses Mr Powell's statements and takes up in particular Mr Powell's argument that claiming rights for one person entails compulsion on another person. In Professor Downie's view there is nothing in Article 25 (I) that cannot embody acceptable moral rights, the commonly accepted interpretation of that Article of the UN Universal Declaration of Human Rights which many people think is wholly acceptable. PMID:604483

  4. Sequential autoantigenic determinants of the small nuclear ribonucleoprotein Sm D shared by human lupus autoantibodies and MRL lpr/lpr antibodies.

    PubMed

    James, J A; Mamula, M J; Harley, J B

    1994-12-01

    Autoantibodies directed against the Sm proteins of the spliceosome complex are found in approximately 25% of systemic lupus erythematosus (SLE) patients sera. To determine which regions of the Sm D polypeptide are involved in the lupus autoimmune response, binding to overlapping octapeptides of Sm D has been evaluated with sera from nine Sm D-positive patients, six patients with other autoimmune serology, and five normal human sera. Lupus patient sera which are Sm precipitin-positive bind various combinations of five regions of the peptide. The major antigenic region, Epitope 5 (REAVA(GR)10GGPRR), is bound by eight of nine Sm precipitin-positive sera tested. This region of Sm D shows significant sequence homology with Epstein-Barr nuclear antigen-1. To determine the fine specificity of the murine Sm response, four unique Sm D MoAbs derived from MRL lpr/lpr mice and three adult anti-Sm-positive MRL lpr/lpr mouse sera have been analysed. Two of these monoclonals, KSm 4 and Y12, as well as the MRL lpr/lpr sera tested, show binding with Epitope 5. Another of these monoclonals, KSm 2, binds octapeptides 84-91, DVEPKVKSKKREAVAG, which corresponds to Epitope 4 of this study. Antibodies from SLE patients with autoimmune serology other than anti-Sm bind the carboxyl glycine-arginine repeat (GR)10 peptides of Sm D. However, none of the antibodies tested from patients who do not have lupus and who have different autoimmune serology binds any of the Sm D octapeptides. Normal controls did not significantly bind any of the Sm D octapeptides. These results describe two major regions of shared antigenicity of Sm D between sera from SLE patients and MRL lpr/lpr mice, thereby establishing a basis for the cross-species similarity of autoimmunity to the Sm autoantigen in SLE.

  5. Structural basis for recruiting and shuttling of the spliceosomal deubiquitinase USP4 by SART3

    PubMed Central

    Park, Joon Kyu; Das, Tanuza; Song, Eun Joo; Kim, Eunice EunKyeong

    2016-01-01

    Squamous cell carcinoma antigen recognized by T-cells 3 (SART3) is a U4/U6 recycling factor as well as a targeting factor of USP4 and USP15. However, the details of how SART3 recognizes these deubiquitinases and how they get subsequently translocated into the nucleus are not known. Here, we present the crystal structures of the SART3 half-a-tetratricopeptide (HAT) repeat domain alone and in complex with the domain present in ubiquitin-specific protease (DUSP)-ubiquitin-like (UBL) domains of ubiquitin specific protease 4 (USP4). The 12 HAT repeats of SART3 are in two sub-domains (HAT-N and HAT-C) forming a dimer through HAT-C. USP4 binds SART3 at the opposite surface of the HAT-C dimer interface utilizing the β-structured linker between the DUSP and the UBL domains. The binding affinities of USP4 and USP15 to SART3 are 0.9 μM and 0.2 μM, respectively. The complex structure of SART3 nuclear localization signal (NLS) and importin-α reveals bipartite binding, and removal of SART3 NLS prevents the entry of USP4 (and USP15) into the nucleus and abrogates the subsequent deubiquitinase activity of USP4. PMID:27060135

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

    PubMed

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

    2017-01-02

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

  7. An Investigation of the Aerodynamic Characteristics of an 0.08-Scale Model of the Chance Vought XF7U-1 Airplane in the Langley High-Speed 7-by 10-Foot Tunnel: TED No. DE308. Part 6; Estimated High-Speed Flying Qualities

    NASA Technical Reports Server (NTRS)

    Donlan, Charles J.; Kuhn, Richard E.

    1948-01-01

    An analysis of the estimated high-speed flying qualities of the Chance Vought XF7U-1 airplane in the Mach number range from 0.40 to 0.91 has been made, based on tests of an 0.08-scale model of this airplane in the Langley high-speed 7- by 10-foot wind tunnel. The analysis indicates longitudinal control-position instability at transonic speeds, but the accompanying trim changes are not large. Control-position maneuvering stability, however, is present for all speeds. Longitudinal lateral control appear adequate, but the damping of the short-period longitudinal and lateral oscillations at high altitudes is poor and may require artificial damping.

  8. Quark masses, chiral symmetry, and the U(1) anomaly

    SciTech Connect

    Creutz, M.

    1996-09-17

    The author discusses the mass parameters appearing in the gauge theory of the strong interactions, concentrating on the two flavor case. He shows how the effect of the CP violating parameter {theta} is simply interpreted in terms of the state of the aether via an effective potential for meson fields. For degenerate flavors he shows that a first order phase transition is expected at {theta} = {pi}. The author speculates on the implications of this structure for Wilson`s lattice fermions.

  9. Underground storage tank 253-D1U1 Closure Plan

    SciTech Connect

    Mancieri, S.; Giuntoli, N.

    1993-09-01

    This report is a closure plan for a diesel fuel tank at the Lawrence Livermore National Laboratory. Included are maps of the site, work plans, and personnel information regarding training and qualification.

  10. Dual view on sliding phases in U (1 ) symmetric systems

    NASA Astrophysics Data System (ADS)

    Vayl, S.; Kuklov, A. B.; Oganesyan, V.

    2017-03-01

    The proposal of sliding phases (SP) is revisited from the perspective of duality. A generic argument is formulated as essentially a no-go theorem for SP in translationally invariant nonfrustrated systems with short-range interactions—classical or quantum. Its validity is demonstrated on an asymmetric bilayer and its multilayer variation models where the duality allows obtaining asymptotically exact analytical solution. This solution is in drastic contrast with the perturbative renormalization group prediction and is strongly supported by Monte Carlo simulations. An alternative path toward finding SP is suggested. Its key ingredient is a long-range gauge-type interaction suppressing the interlayer Josephson coupling.

  11. Higher U(1)-gerbe connections in geometric prequantization

    NASA Astrophysics Data System (ADS)

    Fiorenza, Domenico; Rogers, Christopher L.; Schreiber, Urs

    2016-07-01

    We promote geometric prequantization to higher geometry (higher stacks), where a prequantization is given by a higher principal connection (a higher gerbe with connection). We show fairly generally how there is canonically a tower of higher gauge groupoids and Courant groupoids assigned to a higher prequantization, and establish the corresponding Atiyah sequence as an integrated Kostant-Souriau ∞-group extension of higher Hamiltonian symplectomorphisms by higher quantomorphisms. We also exhibit the ∞-group cocycle which classifies this extension and discuss how its restrictions along Hamiltonian ∞-actions yield higher Heisenberg cocycles. In the special case of higher differential geometry over smooth manifolds, we find the L∞-algebra extension of Hamiltonian vector fields — which is the higher Poisson bracket of local observables — and show that it is equivalent to the construction proposed by the second author in n-plectic geometry. Finally, we indicate a list of examples of applications of higher prequantization in the extended geometric quantization of local quantum field theories and specifically in string geometry.

  12. Lattice QCD solution to the U(1) problem

    SciTech Connect

    Fukugita, M. ); Kuramashi, Y.; Okawa, M. , Tsukuba, Ibaraki 305 ); Ukawa, A. )

    1995-04-01

    It is shown in quenched lattice QCD that the mass splitting between [eta][prime] and a pion arises from gauge configurations with a nonzero topological charge [ital Q], its magnitude increasing for larger values of [vert bar][ital Q][vert bar]; the contribution from the disconnected quark loop is strongly hindered unless the topological charge is excited. This demonstrates the explicit relation between the large [eta][prime] meson mass and gauge field topology, which is in the line of the argument in the continuum of instantons and the 1/[ital N] expansion.

  13. Generalized gauge U(1) family symmetry for quarks and leptons

    NASA Astrophysics Data System (ADS)

    Kownacki, Corey; Ma, Ernest; Pollard, Nicholas; Zakeri, Mohammadreza

    2017-03-01

    If the standard model of quarks and leptons is extended to include three singlet right-handed neutrinos, then the resulting fermion structure admits an infinite number of anomaly-free solutions with just one simple constraint. Well-known examples satisfying this constraint are B- L, Lμ-Lτ, B- 3Lτ, etc. We derive this simple constraint, and discuss two new examples which offer some insights to the structure of mixing among quark and lepton families, together with their possible verification at the Large Hadron Collider.

  14. Electroweak Supersymmetry with an Approximate U(1)_PQ

    SciTech Connect

    Hall, L.J.; Watari, T.

    2004-05-12

    A predictive framework for supersymmetry at the TeV scale is presented, which incorporates the Ciafaloni-Pomarol mechanism for the dynamical determination of the \\mu parameter of the MSSM. It is replaced by (\\lambda S), where S is a singlet field, and the axion becomes a heavy pseudoscalar, G, by adding a mass, m_G, by hand. The explicit breaking of Peccei-Quinn (PQ) symmetry is assumed to be sufficiently weak at the TeV scale that the only observable consequence is the mass m_G. Three models for the explicit PQ breaking are given; but the utility of this framework is that the predictions for all physics at the electroweak scale are independent of the particular model for PQ breaking. Our framework leads to a theory similar to the MSSM, except that \\mu is predicted by the Ciafaloni-Pomarol relation, and there are light, weakly-coupled states in the spectrum. The production and cascade decay of superpartners at colliders occurs as in the MSSM, except that there is one extra stage of the cascade chain, with the next-to-LSP decaying to its"superpartner" and \\tilde{s}, dramatically altering the collider signatures for supersymmetry. The framework is compatible with terrestrial experiments and astrophysical observations for a wide range of m_G and. If G is as light as possible, 300 keV< m_G< 3 MeV, it can have interesting effects on the radiation energy density during the cosmological eras of nucleosynthesis and acoustic oscillation, leading to predictions for N_{\

  15. Nucleoplasmic organization of small nuclear ribonucleoproteins in cultured human cells

    PubMed Central

    1993-01-01

    The organization of eight small nuclear ribonucleoproteins (the U1, U2, U4, U5, and U6 RNAs previously studied by others and three additional snRNAs, U11, U12, and 7SK) has been investigated in cultured human cells by fluorescence in situ hybridization with antisense DNA and 2'-O- Me RNA oligonucleotides. Using highly sensitive digital imaging microscopy we demonstrate that all of these snRNAs are widespread throughout the nucleoplasm, but they are excluded from the nucleoli. In addition, the U2, U4, U5, U6, and U12 snRNAs are concentrated in discrete nuclear foci, known as coiled bodies, but U1 and 7SK are not. In addition to coiled bodies, a classic speckled pattern was observed in the nucleoplasm of monolayer-grown HeLa cells, whereas suspension- grown HeLa cells revealed a more diffuse nucleoplasmic labeling. Immunofluorescence staining using various snRNP-specific antisera shows complete agreement with that of their antisense snRNA oligonucleotide counterparts. Although U2 RNA is concentrated in coiled bodies, quantitation of the fluorescence signals from the U2 antisense probe reveals that the bulk of the U2 snRNP is located in the nucleoplasm. Furthermore, simultaneous visualization of the U2 snRNAs and the tandemly repeated U2 genes demonstrates that coiled bodies are not the sites of U2 transcription. PMID:8491767

  16. Human Infrastructure & Human Activity Detection

    DTIC Science & Technology

    2007-07-01

    researchers are developing sensors systems that detect footfalls (or gait ) [1, 2], speech, the spectral response of human skin, etc [3]. Little work has...cone shaped field of view. • Visible imagers can capture color or grayscale video for human gait detection and object recognition. • Infrared...his/her gait produces a unique signature [13]. Indirect means of detecting personnel include the usage of acoustic, seismic, magnetic, passive

  17. Human monkeypox.

    PubMed

    McCollum, Andrea M; Damon, Inger K

    2014-01-01

    Human monkeypox is a zoonotic Orthopoxvirus with a presentation similar to smallpox. Clinical differentiation of the disease from smallpox and varicella is difficult. Laboratory diagnostics are principal components to identification and surveillance of disease, and new tests are needed for a more precise and rapid diagnosis. The majority of human infections occur in Central Africa, where surveillance in rural areas with poor infrastructure is difficult but can be accomplished with evidence-guided tools and educational materials to inform public health workers of important principles. Contemporary epidemiological studies are needed now that populations do not receive routine smallpox vaccination. New therapeutics and vaccines offer hope for the treatment and prevention of monkeypox; however, more research must be done before they are ready to be deployed in an endemic setting. There is a need for more research in the epidemiology, ecology, and biology of the virus in endemic areas to better understand and prevent human infections.

  18. Human Interface to Netcentricity

    DTIC Science & Technology

    2006-06-01

    to human communication involves communications initiated by applications or devices for human consumption. Examples include intelligent agents...AKO) are all examples of human to machine communication. • Human to Human: Human to human communication in a net-centric environment can be...the discussion will center on providing options for improving human to human communication . It is our position that an emphasis on human to human

  19. Human Trafficking

    ERIC Educational Resources Information Center

    Wilson, David McKay

    2011-01-01

    The shadowy, criminal nature of human trafficking makes evaluating its nature and scope difficult. The U.S. State Department and anti-trafficking groups estimate that worldwide some 27 million people are caught in a form of forced servitude today. Public awareness of modern-day slavery is gaining momentum thanks to new abolitionist efforts. Among…

  20. Classical Humanities

    ERIC Educational Resources Information Center

    Goodwin, Donn; And Others

    1975-01-01

    This article reports on a pilot course in humanities team-taught by three teachers, two from a senior high-school and one from a junior high-school, in Brookfield, Wisconsin. The specific subject matter is Greek and Roman culture. The curriculum is outlined and the basic reading list is included. (CLK)

  1. Humanizing Calculus

    ERIC Educational Resources Information Center

    Cirillo, Michelle

    2007-01-01

    In this article, the author explores the history and the mathematics used by Newton and Leibniz in their invention of calculus. The exploration of this topic is intended to show students that mathematics is a human invention. Suggestions are made to help teachers incorporate the mathematics and the history into their own lessons. (Contains 3…

  2. Nothing Human

    ERIC Educational Resources Information Center

    Wharram, C. C.

    2014-01-01

    In this essay C. C. Wharram argues that Terence's concept of translation as a form of "contamination" anticipates recent developments in philosophy, ecology, and translation studies. Placing these divergent fields of inquiry into dialogue enables us read Terence's well-known statement "I am a human being--I deem nothing…

  3. Human Rights in the Humanities

    ERIC Educational Resources Information Center

    Harpham, Geoffrey

    2012-01-01

    Human rights are rapidly entering the academic curriculum, with programs appearing all over the country--including at Duke, Harvard, Northeastern, and Stanford Universities; the Massachusetts Institute of Technology; the Universities of Chicago, of Connecticut, of California at Berkeley, and of Minnesota; and Trinity College. Most of these…

  4. Human Locomotion

    PubMed Central

    Inman, Verne T.

    1966-01-01

    The development of bipedal plantigrade progression is a purely human, and apparently learned, accomplishment. Experimental findings confirm the hypothesis that the human body will integrate the motion of various segments of the body and control the activity of muscles to minimize energy expenditure. Movements which are integrated for this purpose include vertical displacement of the body, horizontal rotation of the pelvis, mediolateral pelvic tilt, flexion of the knee, plantar flexion of the ankle and foot, lateral displacement of the torso and rotation of the shoulder girdle. Raising and lowering the body results in gains and losses of potential energy, and acceleration and deceleration result in gains and losses of kinetic energy. The motions are so co-ordinated that a transfer of energy back and forth from kinetic to potential occurs during walking, which tends to minimize total energy expenditure as well as muscle work. ImagesFig. 1 PMID:5942660

  5. Humane reproduction.

    PubMed

    1974-03-01

    Discusses social, economic, and humane considerations in population control. Mental health aspects of controlled fertility are considered in relation to the family's psychosocial and material resources, the effects of reproduction on the individual the family, and community, and the advantages and disadvantages of controlled reproduction. A distinction between family planning and population control is outlined. It is suggested that there is hardly a single more effective tool for preventing psychological disorders than the prevention of unwanted pregnancies. Analyses of educational and medical services and methods of birth control are presented. A comprehensive neighborhood health station, which would consolidate these services, is suggested. It is concluded that humane programs of reproduction would lead to a reconciliation of biological drives with a responsible concern for the quality of life.

  6. Human genetics

    SciTech Connect

    Carlson, E.A.

    1984-01-01

    This text provides full and balanced coverage of the concepts requisite for a thorough understanding of human genetics. Applications to both the individual and society are integrated throughout the lively and personal narrative, and the essential principles of heredity are clearly presented to prepare students for informed participation in public controversies. High-interest, controversial topics, including recombinant DNA technology, oncogenes, embryo transfer, environmental mutagens and carcinogens, IQ testing, and eugenics encourage understanding of important social issues.

  7. Human Metapneumovirus.

    PubMed

    Schuster, Jennifer E; Williams, John V

    2014-10-01

    Human metapneumovirus (HMPV), a paramyxovirus identified in 2001, is a leading cause of respiratory tract infections in both children and adults. Seroprevalence studies demonstrate that the primary infection occurs before the age of 5 years, and humans are reinfected throughout life. The four subgroups of HMPV occur with year-to-year variability, and infection with one subgroup confers some serologic cross-protection. Experimental vaccines elicit a humoral response in both animal and human models and have been used to identify antigenic determinants. The main target of protective antibodies is the fusion (F) protein, although many of the remaining eight proteins are immunogenic. Monoclonal antibodies (mAbs) targeting the F protein are both protective and therapeutic in animal models. Most recently, the identification of broadly neutralizing antibodies against HMPV and respiratory syncytial virus demonstrates that common epitopes are present between the two viruses. Broadly neutralizing mAbs have significant clinical implications for prophylaxis and treatment of high-risk hosts as well as vaccine development.

  8. Human evolution.

    PubMed

    Wood, B

    1996-12-01

    The common ancestor of modern humans and the great apes is estimated to have lived between 5 and 8 Myrs ago, but the earliest evidence in the human, or hominid, fossil record is Ardipithecus ramidus, from a 4.5 Myr Ethiopian site. This genus was succeeded by Australopithecus, within which four species are presently recognised. All combine a relatively primitive postcranial skeleton, a dentition with expanded chewing teeth and a small brain. The most primitive species in our own genus, Homo habilis and Homo rudolfensis, are little advanced over the australopithecines and with hindsight their inclusion in Homo may not be appropriate. The first species to share a substantial number of features with later Homo is Homo ergaster, or 'early African Homo erectus', which appears in the fossil record around 2.0 Myr. Outside Africa, fossil hominids appear as Homo erectus-like hominids, in mainland Asia and in Indonesia close to 2 Myr ago; the earliest good evidence of 'archaic Homo' in Europe is dated at between 600-700 Kyr before the present. Anatomically modern human, or Homo sapiens, fossils are seen first in the fossil record in Africa around 150 Kyr ago. Taken together with molecular evidence on the extent of DNA variation, this suggests that the transition from 'archaic' to 'modern' Homo may have taken place in Africa.

  9. Human suffering.

    PubMed

    1992-12-01

    10 measures of quality of life are used to rank 141 countries in the International Human Suffering Index (HSI). The Index differentiates between extreme, high, moderate, and minimal levels of human suffering. Social welfare is the sum of 10 measures: life expectancy, daily caloric intake, clean drinking water, infant immunization, secondary school enrollment, gross national product per capita, the rate of inflation, communication technology (i.e., telephones), political freedom, and civil rights. Each measure is ranked between 0 and 10. The highest score indicates the greatest country stress, with the worst possible score being 100. About 1 billion people live in desperate poverty. Living conditions are the worst in Mozambique (93), followed by Somalia, Afghanistan, Haiti, and Sudan. Most of these countries also have high population growth. The most comfortable countries are Denmark (1), the Netherlands, Belgium, Switzerland, and Canada, which have low population growth. Total scores of 75 or greater (extreme human suffering) occur in 27 countries (20 in Africa, 16 in Asia, and Haiti) with 8% of the world's population (432 million people). High human suffering scores range between 50 and 74 and include 56 countries (24 in Africa, 16 in Asia, 15 in the Western Hemisphere, and 1 in Oceania) with 3.5 billion people. The number of countries in this grouping increased from 44 countries with 58% of world population in 1987. Moderate suffering scores range from 25-49. Countries with moderate suffering number 34 countries (9 in Europe, 13 in Asia, 8 in the Western Hemisphere, and 2 in Oceania and 2 in Africa) with 11.8% of world population (636 million). Over the preceding 5-year period the number of countries increased from 29 countries with 10% of world population. Minimal human suffering occurs in 24 countries (17 in Europe, Israel and Japan in Asia; Canada, the US, and Barbados in the Western Hemisphere; and Australia and New Zealand in Oceania) with 14.8% of world

  10. Human Capital, (Human) Capabilities and Higher Education

    ERIC Educational Resources Information Center

    Le Grange, L.

    2011-01-01

    In this article I initiate a debate into the (de)merits of human capital theory and human capability theory and discuss implications of the debate for higher education. Human capital theory holds that economic growth depends on investment in education and that economic growth is the basis for improving the quality of human life. Human capable…

  11. Infrared radiative decay dynamics from the γ 1u (3P2), H 1u (3P1), and 1u (1D2) ion-pair states of I2 observed by a perturbation facilitated optical-optical double resonance technique

    NASA Astrophysics Data System (ADS)

    Hoshino, Shoma; Araki, Mitsunori; Nakano, Yukio; Ishiwata, Takashi; Tsukiyama, Koichi

    2016-01-01

    We report the spectroscopic and temporal analyses on the amplified spontaneous emission (ASE) from the single rovibrational levels of the Ω = 1u ion-pair series, γ 1u (3P2), H 1u (3P1), and 1u (1D2), of I2 by using a perturbation facilitated optical-optical double resonance technique through the c 1 Π g ˜ B 3 Π ( 0u + ) hyperfine mixed valence state as the intermediate state. The ASE detected in the infrared region was assigned to the parallel transitions from the Ω = 1u ion-pair states down to the nearby Ω = 1g ion-pair states. The subsequent ultraviolet (UV) fluorescence from the Ω = 1g states was also observed and the relative vibrational populations in the Ω = 1g states were derived through the Franck-Condon simulation of the intensity pattern of the vibrational progression. In the temporal profiles of the UV fluorescence, an obvious delay in the onset of the fluorescence was recognized after the excitation laser pulse. These results revealed that ASE is a dominant energy relaxation process between the Ω = 1u and 1g ion-pair states of I2. Finally, the lifetimes of the relevant ion-pair states were evaluated by temporal analyses of the UV fluorescence. The propensity was found which was the longer lifetime in the upper level of the ASE transitions tends to give intense ASE.

  12. Human Heredity: Genetic Mechanisms in Humans.

    ERIC Educational Resources Information Center

    Blank, C. E.

    1988-01-01

    Discussed are some of the uncertainties in human genetic mechanisms that are often presented as dogma in Biology textbooks. Presented is a brief historical background and illustrations involving chromosome abnormality in humans and linkage studies in humans. (CW)

  13. Human Astroviruses

    PubMed Central

    Pintó, Rosa M.; Guix, Susana

    2014-01-01

    SUMMARY Human astroviruses (HAtVs) are positive-sense single-stranded RNA viruses that were discovered in 1975. Astroviruses infecting other species, particularly mammalian and avian, were identified and classified into the genera Mamastrovirus and Avastrovirus. Through next-generation sequencing, many new astroviruses infecting different species, including humans, have been described, and the Astroviridae family shows a high diversity and zoonotic potential. Three divergent groups of HAstVs are recognized: the classic (MAstV 1), HAstV-MLB (MAstV 6), and HAstV-VA/HMO (MAstV 8 and MAstV 9) groups. Classic HAstVs contain 8 serotypes and account for 2 to 9% of all acute nonbacterial gastroenteritis in children worldwide. Infections are usually self-limiting but can also spread systemically and cause severe infections in immunocompromised patients. The other groups have also been identified in children with gastroenteritis, but extraintestinal pathologies have been suggested for them as well. Classic HAstVs may be grown in cells, allowing the study of their cell cycle, which is similar to that of caliciviruses. The continuous emergence of new astroviruses with a potential zoonotic transmission highlights the need to gain insights on their biology in order to prevent future health threats. This review focuses on the basic virology, pathogenesis, host response, epidemiology, diagnostic assays, and prevention strategies for HAstVs. PMID:25278582

  14. Human schistosomiasis

    PubMed Central

    Colley, Daniel G; Bustinduy, Amaya L; Secor, W Evan; King, Charles H

    2015-01-01

    Human schistosomiasis—or bilharzia—is a parasitic disease caused by trematode flukes of the genus Schistosoma. By conservative estimates, at least 230 million people worldwide are infected with Schistosoma spp. Adult schistosome worms colonise human blood vessels for years, successfully evading the immune system while excreting hundreds to thousands of eggs daily, which must either leave the body in excreta or become trapped in nearby tissues. Trapped eggs induce a distinct immune-mediated granulomatous response that causes local and systemic pathological effects ranging from anaemia, growth stunting, impaired cognition, and decreased physical fitness, to organ-specific effects such as severe hepatosplenism, periportal fibrosis with portal hypertension, and urogenital inflammation and scarring. At present, preventive public health measures in endemic regions consist of treatment once every 1 or 2 years with the isoquinolinone drug, praziquantel, to suppress morbidity. In some locations, elimination of transmission is now the goal; however, more sensitive diagnostics are needed in both the field and clinics, and integrated environmental and health-care management will be needed to ensure elimination. PMID:24698483

  15. Human schistosomiasis.

    PubMed

    Colley, Daniel G; Bustinduy, Amaya L; Secor, W Evan; King, Charles H

    2014-06-28

    Human schistosomiasis--or bilharzia--is a parasitic disease caused by trematode flukes of the genus Schistosoma. By conservative estimates, at least 230 million people worldwide are infected with Schistosoma spp. Adult schistosome worms colonise human blood vessels for years, successfully evading the immune system while excreting hundreds to thousands of eggs daily, which must either leave the body in excreta or become trapped in nearby tissues. Trapped eggs induce a distinct immune-mediated granulomatous response that causes local and systemic pathological effects ranging from anaemia, growth stunting, impaired cognition, and decreased physical fitness, to organ-specific effects such as severe hepatosplenism, periportal fibrosis with portal hypertension, and urogenital inflammation and scarring. At present, preventive public health measures in endemic regions consist of treatment once every 1 or 2 years with the isoquinolinone drug, praziquantel, to suppress morbidity. In some locations, elimination of transmission is now the goal; however, more sensitive diagnostics are needed in both the field and clinics, and integrated environmental and health-care management will be needed to ensure elimination.

  16. Dosimetric characterization of model Cs-1 Rev2 cesium-131 brachytherapy source in water phantoms and human tissues with MCNP5 Monte Carlo simulation.

    PubMed

    Wang, Jianhua; Zhang, Hualin

    2008-04-01

    A recently developed alternative brachytherapy seed, Cs-1 Rev2 cesium-131, has begun to be used in clinical practice. The dosimetric characteristics of this source in various media, particularly in human tissues, have not been fully evaluated. The aim of this study was to calculate the dosimetric parameters for the Cs-1 Rev2 cesium-131 seed following the recommendations of the AAPM TG-43U1 report [Rivard et al., Med. Phys. 31, 633-674 (2004)] for new sources in brachytherapy applications. Dose rate constants, radial dose functions, and anisotropy functions of the source in water, Virtual Water, and relevant human soft tissues were calculated using MCNP5 Monte Carlo simulations following the TG-43U1 formalism. The results yielded dose rate constants of 1.048, 1.024, 1.041, and 1.044 cGy h(-1) U(-1) in water, Virtual Water, muscle, and prostate tissue, respectively. The conversion factor for this new source between water and Virtual Water was 1.02, between muscle and water was 1.006, and between prostate and water was 1.004. The authors' calculation of anisotropy functions in a Virtual Water phantom agreed closely with Murphy's measurements [Murphy et al., Med. Phys. 31, 1529-1538 (2004)]. Our calculations of the radial dose function in water and Virtual Water have good agreement with those in previous experimental and Monte Carlo studies. The TG-43U1 parameters for clinical applications in water, muscle, and prostate tissue are presented in this work.

  17. An Investigation of the Aerodynamic Characteristics of an 0.08-Scale Model of the Chance Vought XF7U-1 Airplane in the Langley High-Speed 7- by 10-Foot Tunnel. Part V - Wing-Alone Tests and Effect of Modifications to the Vertical Fins, Speed Brakes, and Fuselage TED No. NACA DE308. Part V; Wing-Alone Tests and Effect of Modifications to the Vertical Fins, Speed Brakes, and Fuselage, TED No. NACA DE308

    NASA Technical Reports Server (NTRS)

    Kuhri, Richard E.; Myers, Boyd C., II

    1947-01-01

    Tests have been conducted in the Langley high-speed 7- by 10-foot tunnel over a Mach number range from 0.40 to 0.91 to determine the stability and control characteristics of an 0.08-scale model of the Chance Vought XF7U-1 airplane. The wing-alone tests and the effect of the various vertical-fin modifications, speed-brake modifications, and fuselage modifications on the aerodynamic characteristics in pitch and yaw are presented in the present paper with a limited analysis of the results. Also included are tuft studies of the flow for some of the modifications tested.

  18. Absorption Oscillator Strengths for the c4‧1Σu+(3, 4, 6)-X1Σg+(v‧‧), b‧1Σu+(10, 13, 20)-X1Σg+(v‧‧), and c5‧1Σu+(1)-X1Σg+(v‧‧) Progressions in N2

    NASA Astrophysics Data System (ADS)

    Lavín, C.; Velasco, A. M.

    2016-01-01

    Absorption oscillator strengths, calculated with the molecular quantum defect orbital method, for the c4'1 Σu+(3)-X1Σg+ (v'' = 0-12), c4'1Σu+(4) -X1Σg+(v'' = 0-12), c4'1Σu+(6) -X1Σg+(v'' = 0-12), b'1Σu+(10) -X1Σg+(v'' = 0-12), b'1Σu+(13) -X1Σg+(v'' = 0-12), b'1Σu+(20) -X1Σg+(v'' = 0-12), and c5'1Σu+(1) -X1Σg+(v'' = 0-12) bands of molecular nitrogen are reported. The Rydberg-valence interaction between states of 1Σu+ symmetry has been treated through an interaction matrix that includes vibrational coupling. Due to the homogeneous interaction, the intensity distribution of the bands within each progression deviates from the Franck-Condon predictions. The present results for vibronic transitions from the X1Σg+(0) ground state agree rather well with reported high-resolution measurements. As far as we know, f-values for bands originating from v″ > 0 vibrational levels of the electronic ground state are reported here for the first time. These data may be useful in the interpretation of the extreme ultraviolet spectra from Earth’s and Titan's atmospheres, in which several bands of the c4'(3), c4', and c4'(6) progressions have been identified.

  19. The Digital Humanities as a Humanities Project

    ERIC Educational Resources Information Center

    Svensson, Patrik

    2012-01-01

    This article argues that the digital humanities can be seen as a humanities project in a time of significant change in the academy. The background is a number of scholarly, educational and technical challenges, the multiple epistemic traditions linked to the digital humanities, the potential reach of the field across and outside the humanities,…

  20. NATO Human View Architecture and Human Networks

    NASA Technical Reports Server (NTRS)

    Handley, Holly A. H.; Houston, Nancy P.

    2010-01-01

    The NATO Human View is a system architectural viewpoint that focuses on the human as part of a system. Its purpose is to capture the human requirements and to inform on how the human impacts the system design. The viewpoint contains seven static models that include different aspects of the human element, such as roles, tasks, constraints, training and metrics. It also includes a Human Dynamics component to perform simulations of the human system under design. One of the static models, termed Human Networks, focuses on the human-to-human communication patterns that occur as a result of ad hoc or deliberate team formation, especially teams distributed across space and time. Parameters of human teams that effect system performance can be captured in this model. Human centered aspects of networks, such as differences in operational tempo (sense of urgency), priorities (common goal), and team history (knowledge of the other team members), can be incorporated. The information captured in the Human Network static model can then be included in the Human Dynamics component so that the impact of distributed teams is represented in the simulation. As the NATO militaries transform to a more networked force, the Human View architecture is an important tool that can be used to make recommendations on the proper mix of technological innovations and human interactions.

  1. Building artificial humans to understand humans.

    PubMed

    Ishiguro, Hiroshi; Nishio, Shuichi

    2007-01-01

    If we could build an android as a very humanlike robot, how would we humans distinguish a real human from an android? The answer to this question is not so easy. In human-android interaction, we cannot see the internal mechanism of the android, and thus we may simply believe that it is a human. This means that a human can be defined from two perspectives: one by organic mechanism and the other by appearance. Further, the current rapid progress in artificial organs makes this distinction confusing. The approach discussed in this article is to create artificial humans with humanlike appearances. The developed artificial humans, an android and a geminoid, can be used to improve understanding of humans through psychological and cognitive tests conducted using the artificial humans. We call this new approach to understanding humans android science.

  2. Human Rhinoviruses

    PubMed Central

    Lamson, Daryl M.; St. George, Kirsten; Walsh, Thomas J.

    2013-01-01

    Human rhinoviruses (HRVs), first discovered in the 1950s, are responsible for more than one-half of cold-like illnesses and cost billions of dollars annually in medical visits and missed days of work. Advances in molecular methods have enhanced our understanding of the genomic structure of HRV and have led to the characterization of three genetically distinct HRV groups, designated groups A, B, and C, within the genus Enterovirus and the family Picornaviridae. HRVs are traditionally associated with upper respiratory tract infection, otitis media, and sinusitis. In recent years, the increasing implementation of PCR assays for respiratory virus detection in clinical laboratories has facilitated the recognition of HRV as a lower respiratory tract pathogen, particularly in patients with asthma, infants, elderly patients, and immunocompromised hosts. Cultured isolates of HRV remain important for studies of viral characteristics and disease pathogenesis. Indeed, whether the clinical manifestations of HRV are related directly to viral pathogenicity or secondary to the host immune response is the subject of ongoing research. There are currently no approved antiviral therapies for HRVs, and treatment remains primarily supportive. This review provides a comprehensive, up-to-date assessment of the basic virology, pathogenesis, clinical epidemiology, and laboratory features of and treatment and prevention strategies for HRVs. PMID:23297263

  3. 5'-Terminal nucleotide variations in human cytoplasmic tRNAHisGUG and its 5'-halves.

    PubMed

    Shigematsu, Megumi; Kirino, Yohei

    2017-02-01

    Transfer RNAs (tRNAs) are fundamental adapter components of translational machinery. tRNAs can further serve as a source of tRNA-derived noncoding RNAs that play important roles in various biological processes beyond translation. Among all species of tRNAs, tRNA(HisGUG) has been known to uniquely contain an additional guanosine residue at the -1 position (G-1) of its 5'-end. To analyze this -1 nucleotide in detail, we developed a TaqMan qRT-PCR method that can distinctively quantify human mature cytoplasmic tRNA(HisGUG) containing G-1, U-1, A-1, or C-1 or lacking the -1 nucleotide (starting from G1). Application of this method to the mature tRNA fraction of BT-474 breast cancer cells revealed the presence of tRNA(HisGUG) containing U-1 as well as the one containing G-1 Moreover, tRNA lacking the -1 nucleotide was also detected, thus indicating the heterogeneous expression of 5'-tRNA(HisGUG) variants. A sequence library of sex hormone-induced 5'-tRNA halves (5'-SHOT-RNAs), identified via cP-RNA-seq of a BT-474 small RNA fraction, also demonstrated the expression of 5'-tRNA(HisGUG) halves containing G-1, U-1, or G1 as 5'-terminal nucleotides. Although the detected 5'-nucleotide species were identical, the relative abundances differed widely between mature tRNA and 5'-half from the same BT-474 cells. The majority of mature tRNAs contained the -1 nucleotide, whereas the majority of 5'-halves lacked this nucleotide, which was biochemically confirmed using a primer extension assay. These results reveal the novel identities of tRNA(HisGUG) molecules and provide insights into tRNA(HisGUG) maturation and the regulation of tRNA half production.

  4. Human Factors in Human-Systems Integration

    NASA Technical Reports Server (NTRS)

    Fitts, David J.; Sandor, Aniko; Litaker, Harry L., Jr.; Tillman, Barry

    2008-01-01

    Any large organization whose mission is to design and develop systems for humans, and train humans needs a well-developed integration and process plan to deal with the challenges that arise from managing multiple subsystems. Human capabilities, skills, and needs must be considered early in the design and development process, and must be continuously considered throughout the development lifecycle. This integration of human needs within system design is typically formalized through a Human-Systems Integration (HSI) program. By having an HSI program, an institution or organization can reduce lifecycle costs and increase the efficiency, usability, and quality of its products because human needs have been considered from the beginning.

  5. Identification of Novel Tumor Suppressor Genes in Human Breast Cancer Using Nonsense-Mediated mRNA Decay Inhibition (NMDI)-Microarray Analysis

    DTIC Science & Technology

    2007-08-01

    of apoptosis and regulating heat shock protein Beta- 2 -microglobulin B2M Del CT in (CT)4 nt 37–44 LoVo MHC class I receptor activity Abbreviations...inappropriate location by interaction with components of the spliceosome that remained associated with the 2 downstream exon - exon junction following splicing...valid OMB control number. PLEASE DO NOT RETURN YOUR FORM TO THE ABOVE ADDRESS. 1. REPORT DATE 01-08-2007 2 . REPORT TYPE Final 3. DATES COVERED

  6. Xe2 gerade Rydberg states observed in the afterglow of a microplasma by laser spectroscopy of a^3 {Σ }_u^ + ( {1_u,O_u^ - }) absorption in the green (545-555 nm) and near-infrared (675-800 nm)

    NASA Astrophysics Data System (ADS)

    Wagner, C. J.; Galvin, T. C.; Eden, J. G.

    2014-06-01

    Bound←bound transitions of the Xe dimer at small internuclear separation (R < 4.0 Å) have been observed in the 545-555 nm and 675-800 nm spectral regions by laser spectroscopy in the afterglow of a pulsed Xe microplasma with a volume of ˜160 nl. Transient suppression of Xe2 A^1 {Σ }_u^ + ( {O_u^ + }) to X^1 {Σ }_g^ + ( {O_g^ + }) emission in the vacuum ultraviolet (˜172 nm), induced by laser excitation of {Ω }_g leftarrow a^3 {Σ }_u^ + ( {1_u,O_u^ - }) [Rydberg←Rydberg] transitions of the molecule, has confirmed the existence of structure between 720 and 770 nm (reported by Killeen and Eden [J. Chem. Phys. 84, 6048 (1986)]) but also reveals red-degraded vibrational bands extending to wavelengths beyond 800 nm. Spectral simulations based on calculations of Franck-Condon factors for assumed {Ω }_g leftarrow a^3 {Σ }_u^ + transitions involving Ω = 0±,1 gerade Rydberg states suggest that the upper level primarily responsible for the observed spectrum is an Ω = 1 state correlated, in the separated atom limit, with Xe(5p6 1S0) + Xe(5p5 6p) and built on a predominantly A2Π3/2g molecular ion core. Specifically, the spectroscopic constants for the upper state of the 1_g leftarrow 1_u,O_u^ ± absorptive transitions are determined to be Te = 13 000 ± 150 cm-1, ω _e^' = 120 ± 10 cm^{ - 1}, ω _e^' x_e^' = 1.1 ± 0.4 cm^{ - 1}, De = 3300 ± 300 cm-1, and {Δ }R_e = R_e^' - R_e^' ' } = 0.3 ± 0.1 {Å} which are in general agreement with the theoretical predictions of the pseudopotential hole-particle formalism, developed by Jonin and Spiegelmann [J. Chem. Phys. 117, 3059 (2002)], for both the (5)1g and ( 3)O_g^ + states of Xe2. These spectra exhibit the most extensive vibrational development, and provide evidence for the first molecular core-switching transition, observed to date for any of the rare gas dimers at small R (<4 Ǻ). Experiments in the green (545-555 nm) also provide improved absorption spectra, relative to data reported in 1986 and 1999

  7. Humane Education: An Overview.

    ERIC Educational Resources Information Center

    Whitlock, Eileen S.; Westerlund, Stuart R.

    This booklet traces the historical development of human education as it has been instilled into the young people of America from colonial times to the present and provides a future prognosis of humaneness in the schools. Humane education promotes humane behavior and is an important part of the humane movement in the United States, although until…

  8. Human Research Risk Management

    NASA Video Gallery

    Crew health and performance is critical to successful human exploration beyond low Earth orbit. The Human Research Program (HRP) investigates and mitigates the highest risks to human health and per...

  9. Sequences more than 500 base pairs upstream of the human U3 small nuclear RNA gene stimulate the synthesis of U3 RNA in frog oocytes

    SciTech Connect

    Suh, D.; Reddy, R. ); Wright, D. )

    1991-06-04

    Small nuclear RNA (snRNA) genes contain strong promoters capable of initiating transcription once every 4 s. Studies on the human U1 snRNA gene, carried out in other laboratories, showed that sequences within 400 bp of the 5' flanking region are sufficient for maximal levels of transcription both in vivo and in frog oocytes (reviewed in Dahlberg and Lund (1988)). The authors studied the expression of a human U3 snRNA gene by injecting 5' deletion mutants into frog oocytes. The results show that sequences more than 500 bp upstream of the U3 snRNA gene have a 2-3-fold stimulatory effect on the U3 snRNA synthesis. These results indicate that the human U3 snRNA gene is different from human U1 snRNA gene in containing regulatory elements more than 500 bp upstream. The U3 snRNA gene upstream sequences contain an AluI homologous sequence in the {minus}1,200 region; these AluI sequences were transcribed in vitro and in frog oocytes but were not detectable in Hela cells.

  10. Engineered human vaccines

    SciTech Connect

    Sandhu, J.S. . Div. of Immunology and Neurobiology)

    1994-01-01

    The limitations of human vaccines in use at present and the design requirements for a new generation of human vaccines are discussed. The progress in engineering of human vaccines for bacteria, viruses, parasites, and cancer is reviewed, and the data from human studies with the engineered vaccines are discussed, especially for cancer and AIDS vaccines. The final section of the review deals with the possible future developments in the field of engineered human vaccines and the requirement for effective new human adjuvants.

  11. Human-machine interactions

    DOEpatents

    Forsythe, J. Chris; Xavier, Patrick G.; Abbott, Robert G.; Brannon, Nathan G.; Bernard, Michael L.; Speed, Ann E.

    2009-04-28

    Digital technology utilizing a cognitive model based on human naturalistic decision-making processes, including pattern recognition and episodic memory, can reduce the dependency of human-machine interactions on the abilities of a human user and can enable a machine to more closely emulate human-like responses. Such a cognitive model can enable digital technology to use cognitive capacities fundamental to human-like communication and cooperation to interact with humans.

  12. Origins of De Novo Genes in Human and Chimpanzee

    PubMed Central

    Ruiz-Orera, Jorge; Hernandez-Rodriguez, Jessica; Chiva, Cristina; Sabidó, Eduard; Kondova, Ivanela; Bontrop, Ronald; Marqués-Bonet, Tomàs; Albà, M.Mar

    2015-01-01

    The birth of new genes is an important motor of evolutionary innovation. Whereas many new genes arise by gene duplication, others originate at genomic regions that did not contain any genes or gene copies. Some of these newly expressed genes may acquire coding or non-coding functions and be preserved by natural selection. However, it is yet unclear which is the prevalence and underlying mechanisms of de novo gene emergence. In order to obtain a comprehensive view of this process, we have performed in-depth sequencing of the transcriptomes of four mammalian species—human, chimpanzee, macaque, and mouse—and subsequently compared the assembled transcripts and the corresponding syntenic genomic regions. This has resulted in the identification of over five thousand new multiexonic transcriptional events in human and/or chimpanzee that are not observed in the rest of species. Using comparative genomics, we show that the expression of these transcripts is associated with the gain of regulatory motifs upstream of the transcription start site (TSS) and of U1 snRNP sites downstream of the TSS. In general, these transcripts show little evidence of purifying selection, suggesting that many of them are not functional. However, we find signatures of selection in a subset of de novo genes which have evidence of protein translation. Taken together, the data support a model in which frequently-occurring new transcriptional events in the genome provide the raw material for the evolution of new proteins. PMID:26720152

  13. Origins of De Novo Genes in Human and Chimpanzee.

    PubMed

    Ruiz-Orera, Jorge; Hernandez-Rodriguez, Jessica; Chiva, Cristina; Sabidó, Eduard; Kondova, Ivanela; Bontrop, Ronald; Marqués-Bonet, Tomàs; Albà, M Mar

    2015-12-01

    The birth of new genes is an important motor of evolutionary innovation. Whereas many new genes arise by gene duplication, others originate at genomic regions that did not contain any genes or gene copies. Some of these newly expressed genes may acquire coding or non-coding functions and be preserved by natural selection. However, it is yet unclear which is the prevalence and underlying mechanisms of de novo gene emergence. In order to obtain a comprehensive view of this process, we have performed in-depth sequencing of the transcriptomes of four mammalian species--human, chimpanzee, macaque, and mouse--and subsequently compared the assembled transcripts and the corresponding syntenic genomic regions. This has resulted in the identification of over five thousand new multiexonic transcriptional events in human and/or chimpanzee that are not observed in the rest of species. Using comparative genomics, we show that the expression of these transcripts is associated with the gain of regulatory motifs upstream of the transcription start site (TSS) and of U1 snRNP sites downstream of the TSS. In general, these transcripts show little evidence of purifying selection, suggesting that many of them are not functional. However, we find signatures of selection in a subset of de novo genes which have evidence of protein translation. Taken together, the data support a model in which frequently-occurring new transcriptional events in the genome provide the raw material for the evolution of new proteins.

  14. What Are the Humanities?

    ERIC Educational Resources Information Center

    Broderick, Francis

    A working definition of the humanities and characteristics of a liberally educated person are specified. The humanities embrace areas of human knowledge that possess these elements: central concern for human beings rather than for the processes of nature or the structures of society; primary focus on the individual rather than on the group;…

  15. Cooperation in human teaching.

    PubMed

    Kruger, Ann Cale

    2015-01-01

    Kline's evolutionary analysis of teaching provides welcome reframing for cross-species comparisons. However, theory based on competition cannot explain the transmission of human cultural elements that were collectively created. Humans evolved in a cultural niche and teaching-learning coevolved to transmit culture. To study human cultural variation in teaching, we need a more articulated theory of this distinctively human engagement.

  16. Visualizing Humans by Computer.

    ERIC Educational Resources Information Center

    Magnenat-Thalmann, Nadia

    1992-01-01

    Presents an overview of the problems and techniques involved in visualizing humans in a three-dimensional scene. Topics discussed include human shape modeling, including shape creation and deformation; human motion control, including facial animation and interaction with synthetic actors; and human rendering and clothing, including textures and…

  17. Special Section: Human Rights

    ERIC Educational Resources Information Center

    Frydenlund, Knut; And Others

    1978-01-01

    Eleven articles examine human rights in Europe. Topics include unemployment, human rights legislation, role of the Council of Europe in promoting human rights, labor unions, migrant workers, human dignity in industralized societies, and international violence. Journal available from Council of Europe, Directorate of Press and Information, 67006…

  18. Human Research Program Opportunities

    NASA Technical Reports Server (NTRS)

    Kundrot, Craig E.

    2014-01-01

    The goal of HRP is to provide human health and performance countermeasures, knowledge, technologies, and tools to enable safe, reliable, and productive human space exploration. The Human Research Program was designed to meet the needs of human space exploration, and understand and reduce the risk to crew health and performance in exploration missions.

  19. [Deregulation of pre-messenger RNA splicing and rare diseases].

    PubMed

    de la Grange, Pierre

    2016-12-01

    Most of protein-coding human genes are subjected to alternative pre-mRNA splicing. This mechanism is highly regulated to precisely modulate detection of specific splice sites. This regulation is under control of the spliceosome and several splicing factors are also required to modulate the alternative usage of splice sites. Splicing factors and spliceosome components recognize splicing signals and regulatory sequences of the pre-mRNAs. These splicing sequences make splicing susceptible to polymorphisms and mutations. Examples of associations between human rare diseases and defects in pre-messenger RNA splicing are accumulating. Although many alterations are caused by mutations in splicing sequence (i.e., cis acting mutations), recent studies described the disruptive impact of mutations within spliceosome components or splicing factors (i.e., trans acting mutations). Following growing of knowledge regarding splicing regulation, several approaches have been developed to compensate for the effect of deleterious mutations and to restore sufficient amounts of functional protein.

  20. ISS Payload Human Factors

    NASA Technical Reports Server (NTRS)

    Ellenberger, Richard; Duvall, Laura; Dory, Jonathan

    2016-01-01

    The ISS Payload Human Factors Implementation Team (HFIT) is the Payload Developer's resource for Human Factors. HFIT is the interface between Payload Developers and ISS Payload Human Factors requirements in SSP 57000. ? HFIT provides recommendations on how to meet the Human Factors requirements and guidelines early in the design process. HFIT coordinates with the Payload Developer and Astronaut Office to find low cost solutions to Human Factors challenges for hardware operability issues.

  1. Preference for human eyes in human infants.

    PubMed

    Dupierrix, Eve; de Boisferon, Anne Hillairet; Méary, David; Lee, Kang; Quinn, Paul C; Di Giorgio, Elisa; Simion, Francesca; Tomonaga, Masaki; Pascalis, Olivier

    2014-07-01

    Despite evidence supporting an early attraction to human faces, the nature of the face representation in neonates and its development during the first year after birth remain poorly understood. One suggestion is that an early preference for human faces reflects an attraction toward human eyes because human eyes are distinctive compared with other animals. In accord with this proposal, prior empirical studies have demonstrated the importance of the eye region in face processing in adults and infants. However, an attraction for the human eye has never been shown directly in infants. The current study aimed to investigate whether an attraction for human eyes would be present in newborns and older infants. With the use of a preferential looking time paradigm, newborns and 3-, 6-, 9-, and 12-month-olds were simultaneously presented with a pair of nonhuman primate faces (chimpanzees and Barbary macaques) that differed only by the eyes, thereby pairing a face with original nonhuman primate eyes with the same face in which the eyes were replaced by human eyes. Our results revealed that no preference was observed in newborns, but a preference for nonhuman primate faces with human eyes emerged from 3months of age and remained stable thereafter. The findings are discussed in terms of how a preference for human eyes may emerge during the first few months after birth.

  2. Economics of human trafficking.

    PubMed

    Wheaton, Elizabeth M; Schauer, Edward J; Galli, Thomas V

    2010-01-01

    Because freedom of choice and economic gain are at the heart of productivity, human trafficking impedes national and international economic growth. Within the next 10 years, crime experts expect human trafficking to surpass drug and arms trafficking in its incidence, cost to human well-being, and profitability to criminals (Schauer and Wheaton, 2006: 164-165). The loss of agency from human trafficking as well as from modern slavery is the result of human vulnerability (Bales, 2000: 15). As people become vulnerable to exploitation and businesses continually seek the lowest-cost labour sources, trafficking human beings generates profit and a market for human trafficking is created. This paper presents an economic model of human trafficking that encompasses all known economic factors that affect human trafficking both across and within national borders. We envision human trafficking as a monopolistically competitive industry in which traffickers act as intermediaries between vulnerable individuals and employers by supplying differentiated products to employers. In the human trafficking market, the consumers are employers of trafficked labour and the products are human beings. Using a rational-choice framework of human trafficking we explain the social situations that shape relocation and working decisions of vulnerable populations leading to human trafficking, the impetus for being a trafficker, and the decisions by employers of trafficked individuals. The goal of this paper is to provide a common ground upon which policymakers and researchers can collaborate to decrease the incidence of trafficking in humans.

  3. Mobile Bacterial Group II Introns at the Crux of Eukaryotic Evolution.

    PubMed

    Lambowitz, Alan M; Belfort, Marlene

    2015-02-01

    This review focuses on recent developments in our understanding of group II intron function, the relationships of these introns to retrotransposons and spliceosomes, and how their common features have informed thinking about bacterial group II introns as key elements in eukaryotic evolution. Reverse transcriptase-mediated and host factor-aided intron retrohoming pathways are considered along with retrotransposition mechanisms to novel sites in bacteria, where group II introns are thought to have originated. DNA target recognition and movement by target-primed reverse transcription infer an evolutionary relationship among group II introns, non-LTR retrotransposons, such as LINE elements, and telomerase. Additionally, group II introns are almost certainly the progenitors of spliceosomal introns. Their profound similarities include splicing chemistry extending to RNA catalysis, reaction stereochemistry, and the position of two divalent metals that perform catalysis at the RNA active site. There are also sequence and structural similarities between group II introns and the spliceosome's small nuclear RNAs (snRNAs) and between a highly conserved core spliceosomal protein Prp8 and a group II intron-like reverse transcriptase. It has been proposed that group II introns entered eukaryotes during bacterial endosymbiosis or bacterial-archaeal fusion, proliferated within the nuclear genome, necessitating evolution of the nuclear envelope, and fragmented giving rise to spliceosomal introns. Thus, these bacterial self-splicing mobile elements have fundamentally impacted the composition of extant eukaryotic genomes, including the human genome, most of which is derived from close relatives of mobile group II introns.

  4. Mice with human livers.

    PubMed

    Grompe, Markus; Strom, Stephen

    2013-12-01

    Animal models are used to study many aspects of human disease and to test therapeutic interventions. However, some very important features of human biology cannot be replicated in animals, even in nonhuman primates or transgenic rodents engineered with human genes. Most human microbial pathogens do not infect animals and the metabolism of many xenobiotics is different between human beings and animals. The advent of transgenic immune-deficient mice has made it possible to generate chimeric animals harboring human tissues and cells, including hepatocytes. The liver plays a central role in many human-specific biological processes and mice with humanized livers can be used to model human metabolism, liver injury, gene regulation, drug toxicity, and hepatotropic infections.

  5. Human dignity, bioethics, and human rights.

    PubMed

    Häyry, Matti; Takala, Tuija

    2005-09-01

    The authors analyse and assess the Universal Draft Declaration on Bioethics and Human Rights published by UNESCO. They argue that the Draft has two main weaknesses. It unnecessarily confines the scope of bioethics to life sciences and their practical applications. And it fails to spell out the intended role of human dignity in international ethical regulation.

  6. A genome-wide siRNA screen for regulators of tumor suppressor p53 activity in human non-small lung cancer cells identifies components of the RNA splicing machinery as targets for anticancer treatment.

    PubMed

    Siebring-van Olst, Ellen; Blijlevens, Maxime; de Menezes, Renee X; van der Meulen-Muileman, Ida H; Smit, Egbert F; van Beusechem, Victor W

    2017-03-13

    Reinstating wild-type tumor suppressor p53 activity could be a valuable option for the treatment of cancer. To contribute to development of new treatment options for non-small cell lung cancer (NSCLC), we performed genome-wide siRNA screens for determinants of p53 activity in NSCLC cells. We identified many genes not previously known to be involved in regulating p53 activity. Silencing p53 pathway inhibitor genes was associated with loss of cell viability. The largest functional gene cluster influencing p53 activity was mRNA splicing. Prominent p53 activation was observed upon silencing of specific spliceosome components, rather than by general inhibition of the spliceosome. Ten genes were validated as inhibitors of p53 activity in multiple NSCLC cell lines: genes encoding the Ras-pathway activator SOS1, the zinc finger protein TSHZ3, the mitochondrial membrane protein COX16 and the spliceosome components SNRPD3, SF3A3, SF3B1, SF3B6, XAB2, CWC22 and HNRNPL. Silencing these genes generally increased p53 levels, with distinct effects on CDKN1A expression, induction of cell cycle arrest and cell death. Silencing spliceosome components was associated with alternative splicing of MDM4 mRNA, which could contribute to activation of p53. In addition, silencing splice factors was particularly effective in killing NSCLC cells, albeit in a p53-independent manner. Interestingly, silencing SNRPD3 and SF3A3 exerted much stronger cytotoxicity to NSCLC cells than to lung fibroblasts, suggesting that these genes could represent useful therapeutic targets. This article is protected by copyright. All rights reserved.

  7. The spliceosome-associated protein Nrl1 suppresses homologous recombination-dependent R-loop formation in fission yeast

    PubMed Central

    Aronica, Lucia; Kasparek, Torben; Ruchman, David; Marquez, Yamile; Cipak, Lubos; Cipakova, Ingrid; Anrather, Dorothea; Mikolaskova, Barbora; Radtke, Maximilian; Sarkar, Sovan; Pai, Chen-Chun; Blaikley, Elizabeth; Walker, Carol; Shen, Kuo-Fang; Schroeder, Renee; Barta, Andrea; Forsburg, Susan L.; Humphrey, Timothy C.

    2016-01-01

    The formation of RNA–DNA hybrids, referred to as R-loops, can promote genome instability and cancer development. Yet the mechanisms by which R-loops compromise genome instability are poorly understood. Here, we establish roles for the evolutionarily conserved Nrl1 protein in pre-mRNA splicing regulation, R-loop suppression and in maintaining genome stability. nrl1Δ mutants exhibit endogenous DNA damage, are sensitive to exogenous DNA damage, and have defects in homologous recombination (HR) repair. Concomitantly, nrl1Δ cells display significant changes in gene expression, similar to those induced by DNA damage in wild-type cells. Further, we find that nrl1Δ cells accumulate high levels of R-loops, which co-localize with HR repair factors and require Rad51 and Rad52 for their formation. Together, our findings support a model in which R-loop accumulation and subsequent DNA damage sequesters HR factors, thereby compromising HR repair at endogenously or exogenously induced DNA damage sites, leading to genome instability. PMID:26682798

  8. An illustration of the clinical relevance of detecting human antimouse antibody interference by affinity chromatography.

    PubMed

    Koper, N P; Massuger, L F; Thomas, C M; Beyer, C; Crooy, M J

    1999-10-01

    Elevated Cancer antigen 125 (CA 125) serum concentrations (up to 221 kU/1) were measured in a 39 year old woman with a positive family history of breast cancer. The serum determinations were performed with the automated Immulite OM-MA chemiluminescent enzyme immunoassay system (Diagnostic Products). Laparoscopic evaluation of the ovaries did not reveal any abnormalities. CA 125 measurements in the same patient using the automated IMx immunoassay system (Abbott) demonstrated normal serum levels. Using a previously reported chromatography procedure IgG type human antimouse antibody activity was found to be present in the serum samples explaining the falsely elevated levels. To prevent this interference the manufacturer modified the assay system by replacing the monoclonal M11 detection antibody with a rabbit polyclonal antibody. Using the modified OM-MA CA 125 assay results were comparable with the IMx values.

  9. Human Papillomavirus (HPV) Vaccines

    MedlinePlus

    ... Directory Cancer Prevention Overview Research Human Papillomavirus (HPV) Vaccines On This Page What are human papillomaviruses? Which ... infections? Can HPV infections be prevented? What HPV vaccines are available? Who should get the HPV vaccines? ...

  10. Telling the Human Story.

    ERIC Educational Resources Information Center

    Richardson, Miles

    1987-01-01

    Proposes that one of the fundamental human attributes is telling stories. Explores the debate on whether Neanderthals possessed language ability. Discusses the role of the "human story" in teaching anthropology. (DH)

  11. Mining human antibody repertoires

    PubMed Central

    2010-01-01

    Human monoclonal antibodies (mAbs) have become drugs of choice for the management of an increasing number of human diseases. Human antibody repertoires provide a rich source for human mAbs. Here we review the characteristics of natural and non-natural human antibody repertoires and their mining with non-combinatorial and combinatorial strategies. In particular, we discuss the selection of human mAbs from naïve, immune, transgenic and synthetic human antibody repertoires using methods based on hybridoma technology, clonal expansion of peripheral B cells, single-cell PCR, phage display, yeast display and mammalian cell display. Our reliance on different strategies is shifting as we gain experience and refine methods to the efficient generation of human mAbs with superior pharmacokinetic and pharmacodynamic properties. PMID:20505349

  12. The Growing Human Population.

    ERIC Educational Resources Information Center

    Keyfitz, Nathan

    1989-01-01

    Discusses the issue of human population. Illustrates the projections of the growing human population in terms of developed and less developed countries. Describes the family planning programs in several countries. Lists three references for further reading. (YP)

  13. Human genomic variation

    PubMed Central

    Disotell, Todd R

    2000-01-01

    The recent completion and assembly of the first draft of the human genome, which combines samples from several ethnically diverse males and females, provides preliminary data on the extent of human genetic variation. PMID:11178257

  14. Indicators: Human Disturbance

    EPA Pesticide Factsheets

    Human disturbance is a measure of the vulnerability of aquatic resources to a variety of harmful human activities such as tree removal, road building, construction near shorelines/streambanks, and artificial hardening of lakeshores with retaining walls.

  15. Human assisted robotic exploration

    NASA Astrophysics Data System (ADS)

    Files, B. T.; Canady, J.; Warnell, G.; Stump, E.; Nothwang, W. D.; Marathe, A. R.

    2016-05-01

    In support of achieving better performance on autonomous mapping and exploration tasks by incorporating human input, we seek here to first characterize humans' ability to recognize locations from limited visual information. Such a characterization is critical to the design of a human-in-the-loop system faced with deciding whether and when human input is useful. In this work, we develop a novel and practical place-recognition task that presents humans with video clips captured by a navigating ground robot. Using this task, we find experimentally that human performance does not seem to depend on factors such as clip length or familiarity with the scene and also that there is significant variability across subjects. Moreover, we find that humans significantly outperform a state-of-the-art computational solution to this problem, suggesting the utility of incorporating human input in autonomous mapping and exploration techniques.

  16. Human Papillomavirus (HPV) Vaccine

    MedlinePlus

    Why get vaccinated?HPV vaccine prevents infection with human papillomavirus (HPV) types that are associated with cause ... at http://www.cdc.gov/hpv. HPV Vaccine (Human Papillomavirus) Information Statement. U.S. Department of Health and ...

  17. Human Melioidosis, Malawi, 2011

    PubMed Central

    Katangwe, Thembi; Purcell, Janet; Bar-Zeev, Naor; Denis, Brigitte; Montgomery, Jacqui; Alaerts, Maaike; Heyderman, Robert Simon; Dance, David A.B.; Kennedy, Neil; Feasey, Nicholas

    2013-01-01

    A case of human melioidosis caused by a novel sequence type of Burkholderia pseudomallei occurred in a child in Malawi, southern Africa. A literature review showed that human cases reported from the continent have been increasing. PMID:23735189

  18. Human bites (image)

    MedlinePlus

    Human bites present a high risk of infection. Besides the bacteria which can cause infection, there is ... the wound extends below the skin. Anytime a human bite has broken the skin, seek medical attention.

  19. Pathfinder: Humans in space

    NASA Technical Reports Server (NTRS)

    Anderson, John L.

    1988-01-01

    Viewgraphs are presented on the Pathfinder program. Information is given on human exploration of the solar system, technical requirements interfaces, program objectives, space suits, human performance, man-machine systems, space habitats, life support systems, and artificial gravity

  20. Human productivity program definition

    NASA Technical Reports Server (NTRS)

    Cramer, D. B.

    1985-01-01

    The optimization of human productivity on the space station within the existing resources and operational constraints is the aim of the Human Productivity Program. The conceptual objectives of the program are as follows: (1) to identify long lead technology; (2) to identify responsibility for work elements; (3) to coordinate the development of crew facilities and activities; and (4) to lay the foundation for a cost effective approach to improving human productivity. Human productivity work elements are also described and examples are presented.

  1. Regulated nucleo-cytoplasmic shuttling of human aci-reductone dioxygenase (hADI1) and its potential role in mRNA processing.

    PubMed

    Gotoh, Isamu; Uekita, Takamasa; Seiki, Motoharu

    2007-01-01

    Bacterial aci-reductone dioxygenase (ARD), a member of the cupin superfamily, has evolutionarily primitive protein folding and functions in the methionine recycling pathway. Recently, a human ARD orthologue (human ADI1, hADI1) has been identified and exhibits functions other than ARD activity. The hADI1 localizes mainly to the cytoplasm, but a substantial fraction is nuclear, suggesting functions in both cellular compartments. In this study, we report that nucleo-cytoplasmic transport of hADI1 is regulated by a non-canonical nuclear export signal (NES) located in the N-terminal region of hADI1. The NES is composed of multiple basic amino-acid residues instead of the canonical leucine-rich sequence. Nuclear export of hADI1 was not mediated by CRM1, a major transporter that binds to leucine-rich NES. Substitution of the basic residues with alanines abolished NES activity. Mutant hADI1 accumulated in the nucleus and formed speckles frequently observed with splicing factors and some transcription factors. Indeed, hADI1 specifically co-localized with the splicing factor U1-70K to the nucleus but not with another splicing factor, SC35. U1-70K over-expression induced nuclear accumulation of hADI1. Nuclear hADI1 expression significantly altered the splicing pattern of the adenovirus E1A mini-gene, which generates multiple alternatively spliced transcripts. Thus, hADI1 may have acquired a novel role in nuclear mRNA processing possibly by modulating U1-70K-related functions, an activity negatively regulated by a non-classical NES sequence.

  2. Human Rights Resource Catalogue.

    ERIC Educational Resources Information Center

    Zambrano, Elias, Comp.

    This document provides information about 25 programs/brochures which focus on human rights topics. Specific topics include: (1) counselor preparation; (2) multicultural awareness; (3) abuse and neglect; (4) Acquired Immune Deficiency Syndrome; (5) self-awareness; (6) human rights awareness and human rights of students; (7) cultural diversity; (8)…

  3. The Virtual Physiological Human

    PubMed Central

    Coveney, Peter V.; Diaz, Vanessa; Hunter, Peter; Kohl, Peter; Viceconti, Marco

    2011-01-01

    The Virtual Physiological Human is synonymous with a programme in computational biomedicine that aims to develop a framework of methods and technologies to investigate the human body as a whole. It is predicated on the transformational character of information technology, brought to bear on that most crucial of human concerns, our own health and well-being.

  4. Robotics of human movements.

    PubMed

    van der Smagt, Patrick; Grebenstein, Markus; Urbanek, Holger; Fligge, Nadine; Strohmayr, Michael; Stillfried, Georg; Parrish, Jonathon; Gustus, Agneta

    2009-01-01

    The construction of robotic systems that can move the way humans do, with respect to agility, stability and precision, is a necessary prerequisite for the successful integration of robotic systems in human environments. We explain human-centered views on robotics, based on the three basic ingredients (1) actuation; (2) sensing; and (3) control, and formulate detailed examples thereof.

  5. Whose Human Rights?

    ERIC Educational Resources Information Center

    Rendel, Margherita

    During the last 50 years, principles, institutions, and policies of human rights have been developed worldwide. This book brings together European and international conventions on human rights, the rights of women, and the users and uses of education, and places them in their wider context. It examines issues in how human rights work, the ways in…

  6. [Eugenics and human cloning].

    PubMed

    Boloz, W

    2001-01-01

    Because of legislative bans there are still no reports of human cloning. However eager public debate is currently running, concerning medical, legal, social and ethical aspects of human cloning. Arguments for and against human cloning are presented. An important argument against cloning is the danger of eugenic tendencies connected with cloning, which could lead to genetic discrimination.

  7. Humanities in the Community.

    ERIC Educational Resources Information Center

    Vendler, Helen

    1982-01-01

    In order that the humanities survive in America and that they find a place in the American community, learning should begin with arts. It is by the natural reciprocity between the arts and the humanities that the humanities can be made most accessible in the community. (MLW)

  8. Production Of Human Antibodies

    NASA Technical Reports Server (NTRS)

    Sammons, David W.; Neil, Garry A.

    1993-01-01

    Process for making human monoclonal antibodies based on combination of techniques. Antibodies made active against specific antigen. Process involves in vivo immunization of human B lymphocyte cells in mice. B cells of interest enriched in vitro before fusion. Method potentially applicable to any antigen. Does not rely on use of Epstein-Barr virus at any step. Human lymphocytes taken from any source.

  9. A Human Rights Glossary.

    ERIC Educational Resources Information Center

    Flowers, Nancy

    1998-01-01

    Presents a human rights glossary that includes definitions of basic terms, treaties, charters, and groups/organizations that have been featured in previous articles in this edition of "Update on Law-Related Education"; the human rights terms have been compiled as part of the celebration of the Universal Declaration of Human Rights…

  10. ATP-dependent unwinding of U4/U6 snRNAs by the Brr2 helicase requires the C terminus of Prp8.

    PubMed

    Maeder, Corina; Kutach, Alan K; Guthrie, Christine

    2009-01-01

    The spliceosome is a highly dynamic machine requiring multiple RNA-dependent ATPases of the DExD/H-box family. A fundamental unanswered question is how their activities are regulated. Brr2 function is necessary for unwinding the U4/U6 duplex, a step essential for catalytic activation of the spliceosome. Here we show that Brr2-dependent dissociation of U4/U6 snRNAs in vitro is activated by a fragment from the C terminus of the U5 snRNP protein Prp8. In contrast to its helicase-stimulating activity, this fragment inhibits Brr2 U4/U6-dependent ATPase activity. Notably, U4/U6 unwinding activity is not stimulated by fragments carrying alleles of prp8 that in humans confers an autosomal dominant form of retinitis pigmentosa. Because Brr2 activity must be restricted to prevent premature catalytic activation, our results have important implications for fidelity maintenance in the spliceosome.

  11. Humanism in emergency medicine.

    PubMed

    Rosenzweig, S

    1993-09-01

    Emergency medicine has not yet appropriated "humanism" as a term of its own. Medical humanism needs to be interpreted in a way that is consistent with the practical goals of emergency medicine. In this essay, humanism in emergency medicine is defined by identifying the dehumanizing aspects of sudden illness and exploring of ways for sustaining the humanity of emergency department patients. Excerpts from Dr Oliver Sacks' autobiographical work A Leg to Stand On give voice to the human needs created by sudden illness and its treatment.

  12. Human Mitochondrial Protein Database

    National Institute of Standards and Technology Data Gateway

    SRD 131 Human Mitochondrial Protein Database (Web, free access)   The Human Mitochondrial Protein Database (HMPDb) provides comprehensive data on mitochondrial and human nuclear encoded proteins involved in mitochondrial biogenesis and function. This database consolidates information from SwissProt, LocusLink, Protein Data Bank (PDB), GenBank, Genome Database (GDB), Online Mendelian Inheritance in Man (OMIM), Human Mitochondrial Genome Database (mtDB), MITOMAP, Neuromuscular Disease Center and Human 2-D PAGE Databases. This database is intended as a tool not only to aid in studying the mitochondrion but in studying the associated diseases.

  13. Biological Races in Humans

    PubMed Central

    Templeton, Alan R.

    2013-01-01

    Races may exist in humans in a cultural sense, but biological concepts of race are needed to access their reality in a non-species-specific manner and to see if cultural categories correspond to biological categories within humans. Modern biological concepts of race can be implemented objectively with molecular genetic data through hypothesis-testing. Genetic data sets are used to see if biological races exist in humans and in our closest evolutionary relative, the chimpanzee. Using the two most commonly used biological concepts of race, chimpanzees are indeed subdivided into races but humans are not. Adaptive traits, such as skin color, have frequently been used to define races in humans, but such adaptive traits reflect the underlying environmental factor to which they are adaptive and not overall genetic differentiation, and different adaptive traits define discordant groups. There are no objective criteria for choosing one adaptive trait over another to define race. As a consequence, adaptive traits do not define races in humans. Much of the recent scientific literature on human evolution portrays human populations as separate branches on an evolutionary tree. A tree-like structure among humans has been falsified whenever tested, so this practice is scientifically indefensible. It is also socially irresponsible as these pictorial representations of human evolution have more impact on the general public than nuanced phrases in the text of a scientific paper. Humans have much genetic diversity, but the vast majority of this diversity reflects individual uniqueness and not race. PMID:23684745

  14. Human Milk Banking.

    PubMed

    Haiden, Nadja; Ziegler, Ekhard E

    2016-01-01

    Human milk banks play an essential role by providing human milk to infants who would otherwise not be able to receive human milk. The largest group of recipients are premature infants who derive very substantial benefits from it. Human milk protects premature infants from necrotizing enterocolitis and from sepsis, two devastating medical conditions. Milk banks collect, screen, store, process, and distribute human milk. Donating women usually nurse their own infants and have a milk supply that exceeds their own infants' needs. Donor women are carefully selected and are screened for HIV-1, HIV-2, human T-cell leukemia virus 1 and 2, hepatitis B, hepatitis C, and syphilis. In the milk bank, handling, storing, processing, pooling, and bacterial screening follow standardized algorithms. Heat treatment of human milk diminishes anti-infective properties, cellular components, growth factors, and nutrients. However, the beneficial effects of donor milk remain significant and donor milk is still highly preferable in comparison to formula.

  15. Human rights and bioethics.

    PubMed

    Barilan, Y M; Brusa, M

    2008-05-01

    In the first part of this article we survey the concept of human rights from a philosophical perspective and especially in relation to the "right to healthcare". It is argued that regardless of meta-ethical debates on the nature of rights, the ethos and language of moral deliberation associated with human rights is indispensable to any ethics that places the victim and the sufferer in its centre. In the second part we discuss the rise of the "right to privacy", particularly in the USA, as an attempt to make the element of personal free will dominate over the element of basic human interest within the structure of rights and when different rights seem to conflict. We conclude by discussing the relationship of human rights with moral values beyond the realm of rights, mainly human dignity, free will, human rationality and response to basic human needs.

  16. An unanticipated early function of DEAD-box ATPase Prp28 during commitment to splicing is modulated by U5 snRNP protein Prp8

    PubMed Central

    Price, Argenta M.; Görnemann, Janina; Guthrie, Christine; Brow, David A.

    2014-01-01

    The stepwise assembly of the highly dynamic spliceosome is guided by RNA-dependent ATPases of the DEAD-box family, whose regulation is poorly understood. In the canonical assembly model, the U4/U6.U5 triple snRNP binds only after joining of the U1 and, subsequently, U2 snRNPs to the intron-containing pre-mRNA. Catalytic activation requires the exchange of U6 for U1 snRNA at the 5′ splice site, which is promoted by the DEAD-box protein Prp28. Because Prp8, an integral U5 snRNP protein, is thought to be a central regulator of DEAD-box proteins, we conducted a targeted search in Prp8 for cold-insensitive suppressors of a cold-sensitive Prp28 mutant, prp28-1. We identified a cluster of suppressor mutations in an N-terminal bromodomain-like sequence of Prp8. To identify the precise defect in prp28-1 strains that is suppressed by the Prp8 alleles, we analyzed spliceosome assembly in vivo and in vitro. Surprisingly, in the prp28-1 strain, we observed a block not only to spliceosome activation but also to one of the earliest steps of assembly, formation of the ATP-independent commitment complex 2 (CC2). The Prp8 suppressor partially corrected both the early assembly and later activation defects of prp28-1, supporting a role for this U5 snRNP protein in both the ATP-independent and ATP-dependent functions of Prp28. We conclude that the U5 snRNP has a role in the earliest events of assembly, prior to its stable incorporation into the spliceosome. PMID:24231520

  17. Human research subjects as human research workers.

    PubMed

    Lynch, Holly Fernandez

    2014-01-01

    Biomedical research involving human subjects has traditionally been treated as a unique endeavor, presenting special risks and demanding special protections. But in several ways, the regulatory scheme governing human subjects research is counter-intuitively less protective than the labor and employment laws applicable to many workers. This Article relies on analogical and legal reasoning to demonstrate that this should not be the case; in a number of ways, human research subjects ought to be fundamentally recast as human research workers. Like other workers protected under worklaw, biomedical research subjects often have interests that diverge from those in positions of control but little bargaining power for change. Bearing these important similarities in mind, the question becomes whether there is any good reason to treat subjects and protected workers differently as a matter of law. With regard to unrestricted payment, eligibility for a minimum wage, compensation for injury, and rights to engage in concerted activity, the answer is no and human subjects regulations ought to be revised accordingly.

  18. Integrated Environmental Modelling: human decisions, human challenges

    USGS Publications Warehouse

    Glynn, Pierre D.

    2015-01-01

    Integrated Environmental Modelling (IEM) is an invaluable tool for understanding the complex, dynamic ecosystems that house our natural resources and control our environments. Human behaviour affects the ways in which the science of IEM is assembled and used for meaningful societal applications. In particular, human biases and heuristics reflect adaptation and experiential learning to issues with frequent, sharply distinguished, feedbacks. Unfortunately, human behaviour is not adapted to the more diffusely experienced problems that IEM typically seeks to address. Twelve biases are identified that affect IEM (and science in general). These biases are supported by personal observations and by the findings of behavioural scientists. A process for critical analysis is proposed that addresses some human challenges of IEM and solicits explicit description of (1) represented processes and information, (2) unrepresented processes and information, and (3) accounting for, and cognizance of, potential human biases. Several other suggestions are also made that generally complement maintaining attitudes of watchful humility, open-mindedness, honesty and transparent accountability. These suggestions include (1) creating a new area of study in the behavioural biogeosciences, (2) using structured processes for engaging the modelling and stakeholder communities in IEM, and (3) using ‘red teams’ to increase resilience of IEM constructs and use.

  19. Complexities of 5'splice site definition: implications in clinical analyses.

    PubMed

    De Conti, Laura; Skoko, Natasa; Buratti, Emanuele; Baralle, Marco

    2012-06-01

    In higher eukaryotes, the 5' splice site (5'ss) is initially recognized through an RNA-RNA interaction by U1 small nuclear ribonucleoprotein (U1 snRNP). This event represents one of the key steps in initial spliceosomal assembly and many disease-associated mutations in humans often disrupt this process. Beside base pair complementarity, 5'ss recognition can also be modified by additional factors such as RNA secondary structures or the specific binding of other nuclear proteins. In this work, we have focused on investigating a few examples of changes detected within the 5'ss in patients, that would not be immediately considered "disease causing mutations". We show that the splicing outcome of very similar mutations can be very different due to variations in trans-acting factor(s) interactions and specific context influences. Using several NF1 donor sites and SELEX approaches as experimental models, we have examined the binding properties of particular sequence motifs such as GGGU found in donor sites, and how the sequence context can change their interaction with hnRNPs such as H/F and A1/A2. Our results clearly show that even minor differences in local nucleotide context can differentially affect the binding ability of these factors to the GGGU core. Finally, using a previously identified mutation in KCNH2 that resulted in intron retention we show how very similar 5'ss mutations found in patients can have a very different splicing outcome due to the neighbouring sequence context, thus highlighting the general need to approach splicing problems with suitable experimental approaches.

  20. [The embryo, the human and the humanized].

    PubMed

    Roa, A

    1992-03-01

    Since the moment of fecundation the human embryo is endowed with the properties of unity and uniqueness and its existence is therefore inviolable. Disputing arguments against this thesis are analyzed. Recent views of some biologists negate the human character to the embryo since the essence of a human being would be its cultural nature and ability to communicate. However, the embryo contains all the genetic information that will allow him to develop the ability to communicate. Any attempt to separate the 3 moments of time, past present and future is a definitive violation of ethics. A basic foundation of ethics is that present and future are implicit in the past and vice-versa. Finally, the idea that the unwanted child is not a cultural being should be discarded.