Science.gov

Sample records for 17s u2 snrnp

  1. 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.

  2. Multiple pathways in nuclear transport: the import of U2 snRNP occurs by a novel kinetic pathway

    PubMed Central

    1991-01-01

    Protein import to the nucleus is a signal-mediated process that exhibits saturation kinetics. We investigated whether signal bearing proteins compete with U2 and U6 snRNPs during import. When injected into Xenopus oocytes, saturating concentrations of P(Lys)-BSA, a protein bearing multiple nuclear localization signals from SV40 large T- antigen, reduce the rate of [125I]P(Lys)-BSA and of [125I]nucleoplasmin import, consistent with their competing for and sharing the same limiting component of the import apparatus. In contrast, saturating concentrations of P(Lys)-BSA do not reduce the rate of HeLa [32P]U2 snRNP assembly or import. The import of U6 snRNP is also competed by P(Lys)-BSA. We conclude that U2 snRNP is imported into oocyte nuclei by a kinetic pathway that is distinct from the one followed by P(Lys)-BSA, nucleoplasmin, and U6 snRNP. PMID:1824847

  3. Leucine periodicity of U2 small nuclear ribonucleoprotein particle (snRNP) A' protein is implicated in snRNP assembly via protein-protein interactions.

    PubMed Central

    Fresco, L D; Harper, D S; Keene, J D

    1991-01-01

    Recombinant A' protein could be reconstituted into U2 small nuclear ribonucleoprotein particles (snRNPs) upon addition to HeLa cell extracts as determined by coimmunoprecipitation and particle density; however, direct binding to U2 RNA could not be demonstrated except in the presence of the U2 snRNP B" protein. Mutational analysis indicated that a central core region of A' was required for particle reconstitution. This region consists of five tandem repeats of approximately 24 amino acids each that exhibit a periodicity of leucine and asparagine residues that is distinct from the leucine zipper. Similar leucine-rich (Leu-Leu motif) repeats are characteristic of a diverse array of soluble and membrane-associated proteins from yeasts to humans but have not been reported previously to reside in nuclear proteins. Several of these proteins, including Toll, chaoptin, RNase/angiogenin inhibitors, lutropin-choriogonadotropin receptor, carboxypeptidase N, adenylyl cyclase, CD14, and human immunodeficiency virus type 1 Rev, may be involved in protein-protein interactions. Our findings suggest that in cell extracts the Leu-Leu motif of A' is required for reconstitution with U2 snRNPs and perhaps with other components involved in splicing through protein-protein interactions. Images PMID:1825347

  4. 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

  5. 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

  6. The gene for human U2 snRNP auxiliary factor small 35-kDa subunit (U2AF1) maps to the progressive myoclonus epilepsy (EPM1) critical region on chromosome 21q22.3

    SciTech Connect

    Lalioti, M.D.; Rossier, C.; Antonarakis, S.E.

    1996-04-15

    We used targeted exon trapping to clone portions of genes from human chromosome 21q22.3. One trapped sequence showed complete homology with the cDNA of human U2AF{sup 35} (M96982; HGM-approved nomenclature U2AF1), which encodes for the small 35-kDa subunit of the U2 snRNP auxiliary factor. Using the U2AF1 cDNA as a probe, we mapped this gene to cosmid Q15D2, a P1, and YAC 350F7 of the Chumakov et al. contig, close to the cystathionine-{beta}-synthase gene (CBS) on 21q22.3. This localization was confirmed by PCR using oligonucleotides from the 3{prime} UTR and by FISH. As U2AF1 associated with a number of different factors during mRNA splicing, overexpression in trisomy 21 individuals could contribute to some Down syndrome phenotypes by interfering with the splicing process. Furthermore, because this gene maps in the critical region for the progressive myoclonus epilepsy I locus (EPM1), mutation analysis will be carried out in patients to evaluate the potential role of U2AF1 as a candidate for EPM1. 24 refs., 1 fig.

  7. 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

  8. Thermodynamic studies on Cs 4U 5O 17(s) and Cs 2U 2O 7(s) by emf and calorimetric measurements

    NASA Astrophysics Data System (ADS)

    Jayanthi, K.; Iyer, V. S.; Venugopal, V.

    1997-12-01

    The oxygen potentials over the phase field: Cs 4U 5O 17(s)+Cs 2U 2O 7(s)+Cs 2U 4O 12(s) was determined by measuring the emf values between 1048 and 1206 K using a solid oxide electrolyte galvanic cell. The oxygen potential existing over the phase field for a given temperature can be represented by: Δ μ(O 2) (kJ/mol) (±0.5)=-272.0+0.207 T (K). The differential thermal analysis showed that Cs 4U 5O 17(s) is stable in air up to 1273 K. The molar Gibbs energy formation of Cs 4U 5O 17(s) was calculated from the above oxygen potentials and can be given by, Δ fG0 (kJ/mol)±6=-7729+1.681 T (K). The enthalpy measurements on Cs 4U 5O 17(s) and Cs 2U 2O 7(s) were carried out from 368.3 to 905 K and 430 to 852 K respectively, using a high temperature Calvet calorimeter. The enthalpy increments, ( H0T- H0298), in J/mol for Cs 4U 5O 17(s) and Cs 2U 2O 7(s) can be represented by, H0T- H0298.15 (Cs 4U 5O 17) kJ/mol±0.9=-188.221+0.518 T (K)+0.433×10 -3T2 (K)-2.052×10 -5T3 (K) (368 to 905 K) and H0T- H0298.15 (Cs 2U 2O 7) kJ/mol±0.5=-164.210+0.390 T (K)+0.104×10 -4T2 (K)+0.140×10 5(1/ T (K)) (411 to 860 K). The thermal properties of Cs 4U 5O 17(s) and Cs 2U 2O 7(s) were derived from the experimental values. The enthalpy of formation of (Cs 4U 5O 17, s) at 298.15 K was calculated by the second law method and is: Δ fH0298.15=-7645.0±4.2 kJ/mol.

  9. Functional Cus1p Is Found with Hsh155p in a Multiprotein Splicing Factor Associated with U2 snRNA

    PubMed Central

    Pauling, Michelle Haynes; McPheeters, David S.; Ares, Manuel

    2000-01-01

    To explore the dynamics of snRNP structure and function, we have studied Cus1p, identified as a suppressor of U2 snRNA mutations in budding yeast. Cus1p is homologous to human SAP145, a protein present in the 17S form of the human U2 snRNP. Here, we define the Cus1p amino acids required for function in yeast. The segment of Cus1p required for binding to Hsh49p, a homolog of human SAP49, is contained within an essential region of Cus1p. Antibodies against Cus1p coimmunoprecipitate U2 snRNA, as well as Hsh155p, a protein homologous to human SAP155. Biochemical fractionation of splicing extracts and reconstitution of heat-inactivated splicing extracts from strains carrying a temperature-sensitive allele of CUS1 indicate that Cus1p and Hsh155p reside in a functional, high-salt-stable complex that is salt-dissociable from U2 snRNA. We propose that Cus1p, Hsh49p, and Hsh155p exist in a stable protein complex which can exchange with a core U2 snRNP and which is necessary for U2 snRNP function in prespliceosome assembly. The Cus1p complex shares functional as well as structural similarities with human SF3b. PMID:10688664

  10. 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

  11. 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

  12. Knocking Down Snrnp200 Initiates Demorphogenesis of Rod Photoreceptors in Zebrafish.

    PubMed

    Liu, Yuan; Chen, Xue; Qin, Bing; Zhao, Kanxing; Zhao, Qingshun; Staley, Jonathan P; Zhao, Chen

    2015-01-01

    Purpose. The small nuclear ribonucleoprotein 200 kDa (SNRNP200) gene is a fundamental component for precursor message RNA (pre-mRNA) splicing and has been implicated in the etiology of autosomal dominant retinitis pigmentosa (adRP). This study aims to determine the consequences of knocking down Snrnp200 in zebrafish. Methods. Expression of the Snrnp200 transcript in zebrafish was determined via whole mount in situ hybridization. Morpholino oligonucleotide (MO) aiming to knock down the expression of Snrnp200 was injected into zebrafish embryos, followed by analyses of aberrant splicing and expression of the U4/U6-U5 tri-small nuclear ribonucleoproteins (snRNPs) components and retina-specific transcripts. Systemic changes and retinal phenotypes were further characterized by histological study and immunofluorescence staining. Results. Snrnp200 was ubiquitously expressed in zebrafish. Knocking down Snrnp200 in zebrafish triggered aberrant splicing of the cbln1 gene, upregulation of other U4/U6-U5 tri-snRNP components, and downregulation of a panel of retina-specific transcripts. Systemic defects were found correlated with knockdown of Snrnp200 in zebrafish. Only demorphogenesis of rod photoreceptors was detected in the initial stage, mimicking the disease characteristics of RP. Conclusions. We conclude that knocking down Snrnp200 in zebrafish could alter regular splicing and expression of a panel of genes, which may eventually trigger rod defects.

  13. Knocking Down Snrnp200 Initiates Demorphogenesis of Rod Photoreceptors in Zebrafish

    PubMed Central

    Liu, Yuan; Chen, Xue; Qin, Bing; Zhao, Kanxing; Zhao, Qingshun; Staley, Jonathan P.; Zhao, Chen

    2015-01-01

    Purpose. The small nuclear ribonucleoprotein 200 kDa (SNRNP200) gene is a fundamental component for precursor message RNA (pre-mRNA) splicing and has been implicated in the etiology of autosomal dominant retinitis pigmentosa (adRP). This study aims to determine the consequences of knocking down Snrnp200 in zebrafish. Methods. Expression of the Snrnp200 transcript in zebrafish was determined via whole mount in situ hybridization. Morpholino oligonucleotide (MO) aiming to knock down the expression of Snrnp200 was injected into zebrafish embryos, followed by analyses of aberrant splicing and expression of the U4/U6-U5 tri-small nuclear ribonucleoproteins (snRNPs) components and retina-specific transcripts. Systemic changes and retinal phenotypes were further characterized by histological study and immunofluorescence staining. Results. Snrnp200 was ubiquitously expressed in zebrafish. Knocking down Snrnp200 in zebrafish triggered aberrant splicing of the cbln1 gene, upregulation of other U4/U6-U5 tri-snRNP components, and downregulation of a panel of retina-specific transcripts. Systemic defects were found correlated with knockdown of Snrnp200 in zebrafish. Only demorphogenesis of rod photoreceptors was detected in the initial stage, mimicking the disease characteristics of RP. Conclusions. We conclude that knocking down Snrnp200 in zebrafish could alter regular splicing and expression of a panel of genes, which may eventually trigger rod defects. PMID:26137319

  14. Molecular genetic analysis of the heterodimeric splicing factor U2AF: the RS domain on either the large or small Drosophila subunit is dispensable in vivo

    PubMed Central

    Rudner, David Z.; Breger, Kevin S.; Rio, Donald C.

    1998-01-01

    The pre-mRNA splicing factor U2AF (U2 snRNP auxiliary factor) has an essential role in 3′ splice site selection. U2AF binds the intron pyrimidine tract between the branchpoint and the 3′ splice site and recruits U2 snRNP to the branch site at an early step in spliceosome assembly. Human U2AF is a heterodimer composed of large (hU2AF65) and small (hU2AF35) subunits. Both subunits contain a domain enriched in arginine–serine dipeptide repeats termed an RS domain. The two U2AF RS domains have been assigned essential and independent roles in spliceosome assembly in vitro—the hU2AF65 RS domain is required to target U2 snRNP to the branch site and the hU2AF35 RS domain is necessary for protein–protein interactions with constitutive and alternative splicing factors. We have investigated the functional requirements for the RS domains on the Drosophila U2AF homolog in vivo. In sharp contrast to its essential role in U2 snRNP recruitment in vitro, the RS domain on the Drosophila large subunit homolog (dU2AF50) was completely dispensable in vivo. Prompted by this unexpected result, we analyzed the RS domain on the Drosophila small subunit homolog (dU2AF38). Despite its requirement for enhancer-dependent splicing activity in vitro, the dU2AF38 RS domain was also inessential in vivo. Finally, we have tested whether the Drosophila U2AF heterodimer requires any RS domain. Flies mutant for both the small and large subunits could not be rescued by dU2AF50ΔRS and dU2AF38ΔRS transgenes. Therefore, in contrast to the separate roles assigned to the U2AF RS domains in vitro, our genetic data suggest that they may have redundant functions in vivo. PMID:9531538

  15. Interaction between Subunits of Heterodimeric Splicing Factor U2AF Is Essential In Vivo

    PubMed Central

    Rudner, David Z.; Kanaar, Roland; Breger, Kevin S.; Rio, Donald C.

    1998-01-01

    The heterodimeric pre-mRNA splicing factor, U2AF (U2 snRNP auxiliary factor), plays a critical role in 3′ splice site selection. Although the U2AF subunits associate in a tight complex, biochemical experiments designed to address the requirement for both subunits in splicing have yielded conflicting results. We have taken a genetic approach to assess the requirement for the Drosophila U2AF heterodimer in vivo. We developed a novel Escherichia coli copurification assay to map the domain on the Drosophila U2AF large subunit (dU2AF50) that interacts with the Drosophila small subunit (dU2AF38). A 28-amino-acid fragment on dU2AF50 that is both necessary and sufficient for interaction with dU2AF38 was identified. Using the copurification assay, we scanned this 28-amino-acid interaction domain for mutations that abrogate heterodimer formation. A collection of these dU2AF50 point mutants was then tested in vivo for genetic complementation of a recessive lethal dU2AF50 allele. A mutation that completely abolished interaction with dU2AF38 was incapable of complementation, whereas dU2AF50 mutations that did not effect heterodimer formation rescued the recessive lethal dU2AF50 allele. Analysis of heterodimer formation in embryo extracts derived from these interaction mutant lines revealed a perfect correlation between the efficiency of subunit association and the ability to complement the dU2AF50 recessive lethal allele. These data indicate that Drosophila U2AF heterodimer formation is essential for viability in vivo, consistent with a requirement for both subunits in splicing in vitro. PMID:9528748

  16. 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

  17. Crystallization and preliminary X-ray analysis of a U2AF{sup 65} variant in complex with a polypyrimidine-tract analogue by use of protein engineering

    SciTech Connect

    Sickmier, E. Allen; Frato, Katherine E.; Kielkopf, Clara L.

    2006-05-01

    A complex of the essential splicing factor U2AF{sup 65} and a deoxyuridine oligonucleotide has been crystallized by modification of an interdomain linker. The large subunit of the essential pre-mRNA splicing factor U2 auxiliary factor (U2AF{sup 65}) binds the polypyrimidine tract near the 3′ splice site of pre-mRNA introns and directs the association of the U2 small nuclear ribonucleoprotein particle (U2 snRNP) of the spliceosome with the pre-mRNA. Protein engineering, in which the flexible linker region connecting tandem RNA-recognition motifs (RRMs) within the U2AF{sup 65} RNA-binding domain was partially deleted, allowed successful crystallization of the protein–nucleic acid complex. Cocrystals of a U2AF{sup 65} variant with a deoxyuridine dodecamer diffract X-rays to 2.9 Å resolution and contain one complex per asymmetric unit.

  18. 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

  19. Vought XO4U-2

    NASA Technical Reports Server (NTRS)

    1933-01-01

    Vought XO4U-2: A biplane scout, the Vought XO4U-2 was 'flown' in the NACA's 30 x 60 Full Scale Tunnel at the Langley Memorial Aeronautical Laboratory in early spring 1933. Part of these tests were to study the cooling of the Pratt & Whitney Twin Wasp radial engine. Other tests involved the relation of the slipstream to stability and control.

  20. The splicing factor U2AF65 stabilizes TRF1 protein by inhibiting its ubiquitin-dependent proteolysis

    SciTech Connect

    Kim, Jeonghee; Chung, In Kwon

    2014-01-17

    Highlights: •Identification of U2AF65 as a novel TRF1-interacting protein. •U2AF65 stabilizes TRF1 protein by inhibiting its ubiquitin-dependent proteolysis. •U2AF65 interferes with the interaction between TRF1 and Fbx4. •U2AF65 represents a new route for modulating TRF1 function at telomeres. -- Abstract: The human telomeric protein TRF1 is a component of the six-subunit protein complex shelterin, which provides telomere protection by organizing the telomere into a high-order structure. TRF1 functions as a negative regulator of telomere length by controlling the access of telomerase to telomeres. Thus, the cellular abundance of TRF1 at telomeres should be maintained and tightly regulated to ensure proper telomere function. Here, we identify U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor 65 (U2AF65), an essential pre-mRNA splicing factor, as a novel TRF1-interacting protein. U2AF65 interacts with TRF1 in vitro and in vivo and is capable of stabilizing TRF1 protein by inhibiting its ubiquitin-dependent proteolysis. We also found that U2AF65 interferes with the interaction between TRF1 and Fbx4, an E3 ubiquitin ligase for TRF1. Depletion of endogenous U2AF65 expression by short interfering RNA (siRNA) reduced the stability of endogenous TRF1 whereas overexpression of U2AF65 significantly extended the half-life of TRF1. These findings demonstrate that U2AF65 plays a critical role in regulating the level of TRF1 through physical interaction and ubiquitin-mediated proteolysis. Hence, U2AF65 represents a new route for modulating TRF1 function at telomeres.

  1. The cytoplasmic sites of the snRNP protein complexes are punctate structures that are responsive to changes in metabolism and intracellular architecture.

    PubMed

    Zieve, G W

    1999-02-25

    Five anti-Sm monoclonal antibodies, Y12, 7.13, KSm4, KSm6, and 128, stain similar discrete punctate structures distributed throughout the cytoplasm of hamster fibroblasts in addition to the expected intense nuclear staining. Several criteria suggest the cytoplasmic staining reflects the cytoplasmic pools of snRNP core proteins. The relative intensity of the cytoplasmic staining is similar to the 30% relative abundance of the cytoplasmic snRNP core proteins compared to the nuclear snRNP core proteins based on cell-fractionation studies. Moreover, the cytoplasmic staining is removed by the same extraction conditions that solubilize the pools of cytoplasmic snRNP core proteins. The cytoplasmic sites of staining are typically spherical but heterogeneous in diameter (0.2-0.5 microm). The larger particles greatly exceed the diameter of individual snRNP core particles and are likely to represent centers of many snRNP proteins or snRNP protein complexes. The staining, though punctate, is evenly dispersed throughout the cytoplasm with no evidence of major compartmentalization. The cytoplasmic staining pattern collapses into larger foci of intensely staining structures when cellular energy levels are depleted or when cells are exposed to hypertonic medium. Unlike the normal sites of snRNP protein cytoplasmic staining, these larger collapsed foci resist detergent extraction. These results suggest that the cytoplasmic staining identified with the anti-Sm monoclonal antibodies represents the large pools of snRNP core proteins in the cytoplasm.

  2. Molecular cloning of the cDNA for the human U2 snRNA-specific A' protein.

    PubMed Central

    Sillekens, P T; Beijer, R P; Habets, W J; van Verooij, W J

    1989-01-01

    The A' polypeptide is one of the protein constituents of the U2 snRNP particle. A potentially full-length cDNA clone containing the complete coding sequence for this U2 snRNP-specific protein was isolated by screening of a human lambda gt11 expression vector library with an autoimmune anti-(U1,U2)RNP serum. Monospecific antibodies, eluted from the 140-150 kD fusion protein of this cDNA recombinant, specifically recognized the A' protein on immunoblots and immunoprecipitated U2 snRNP particles from nuclear extracts. The identity of the clone was confirmed by in vitro translation of hybrid-selected mRNA or an RNA transcript synthesized from the cDNA insert. RNA blot analysis showed strong hybridization to a single polyadenylated transcript of 1.3 kb in human cells. The nucleotide sequence of the 1054 bp cDNA contains an open reading frame of 756 bp encoding a polypeptide of 255 amino acids with a predicted molecular weight of 28,444 D. The coding sequence is preceded by a 49 bp 5'-untranslated region and followed by a 226 bp 3'-untranslated region containing a single polyadenylation signal. Most striking feature of the deduced primary structure for the A' protein is a leucine-rich region in the amino-terminal half of the polypeptide. In contrast to the other U2 snRNP-specific protein B", the A' protein does not contain segments homologous to the RNP consensus sequences RNP1 and RNP2, common amino acid motifs found in several RNA-binding proteins. In the A' protein, however, the extremely hydrophilic carboxy terminus may constitute an RNA-binding moiety. Images PMID:2928112

  3. Ongoing U snRNP Biogenesis Is Required for the Integrity of Cajal Bodies

    PubMed Central

    Lemm, Ira; Girard, Cyrille; Kuhn, Andreas N.; Watkins, Nicholas J.; Schneider, Marc; Bordonné, Rémy

    2006-01-01

    Cajal bodies (CBs) have been implicated in the nuclear phase of the biogenesis of spliceosomal U small nuclear ribonucleoproteins (U snRNPs). Here, we have investigated the distribution of the CB marker protein coilin, U snRNPs, and proteins present in C/D box small nucleolar (sno)RNPs in cells depleted of hTGS1, SMN, or PHAX. Knockdown of any of these three proteins by RNAi interferes with U snRNP maturation before the reentry of U snRNA Sm cores into the nucleus. Strikingly, CBs are lost in the absence of hTGS1, SMN, or PHAX and coilin is dispersed in the nucleoplasm into numerous small foci. This indicates that the integrity of canonical CBs is dependent on ongoing U snRNP biogenesis. Spliceosomal U snRNPs show no detectable concentration in nuclear foci and do not colocalize with coilin in cells lacking hTGS1, SMN, or PHAX. In contrast, C/D box snoRNP components concentrate into nuclear foci that partially colocalize with coilin after inhibition of U snRNP maturation. We demonstrate by siRNA-mediated depletion that coilin is required for the condensation of U snRNPs, but not C/D box snoRNP components, into nucleoplasmic foci, and also for merging these factors into canonical CBs. Altogether, our data suggest that CBs have a modular structure with distinct domains for spliceosomal U snRNPs and snoRNPs. PMID:16687569

  4. 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

  5. snRNP protein expression enhances the formation of Cajal bodies containing p80-coilin and SMN.

    PubMed

    Sleeman, J E; Ajuh, P; Lamond, A I

    2001-12-01

    Splicing snRNPs (small nuclear ribonucleoproteins) are essential sub-units of the spliceosome. Here we report the establishment of stable cell lines expressing fluorescently tagged SmB, a core snRNP protein. Analysis of these stable cell lines has allowed us to characterize the nuclear pathway that leads to snRNP accumulation in nuclear speckles and has identified a limiting nucleolar step in the pathway that can be saturated by overexpression of Sm proteins. After nuclear import, newly assembled snRNPs accumulate first in a subset of Cajal bodies that contain both p80-coilin and the survival of motor neurons protein (SMN) and not in bodies that contain p80-coilin but lack SMN. Treatment of cells with leptomycin B (LMB) inhibits both the accumulation of snRNPs in nuclear bodies and their subsequent accumulation in speckles. The formation of Cajal bodies is enhanced by Sm protein expression and the assembly of new snRNPs. Formation of heterokaryons between HeLa cell lines expressing Sm proteins and primary cells that usually lack Cajal bodies results in the detection of Cajal bodies in primary cell nuclei. Transient over-expression of exogenous SmB alone is sufficient to induce correspondingly transient Cajal body formation in primary cells. These data indicate that the level of snRNP protein expression and snRNP assembly, rather than the expression levels of p80-coilin or SMN, may be a key trigger for Cajal body formation.

  6. A Proteomic Strategy Identifies Lysine Methylation of Splicing Factor snRNP70 by the SETMAR Enzyme.

    PubMed

    Carlson, Scott M; Moore, Kaitlyn E; Sankaran, Saumya M; Reynoird, Nicolas; Elias, Joshua E; Gozani, Or

    2015-05-08

    The lysine methyltransferase (KMT) SETMAR is implicated in the response to and repair of DNA damage, but its molecular function is not clear. SETMAR has been associated with dimethylation of histone H3 lysine 36 (H3K36) at sites of DNA damage. However, SETMAR does not methylate H3K36 in vitro. This and the observation that SETMAR is not active on nucleosomes suggest that H3K36 methylation is not a physiologically relevant activity. To identify potential non-histone substrates, we utilized a strategy on the basis of quantitative proteomic analysis of methylated lysine. Our approach identified lysine 130 of the mRNA splicing factor snRNP70 as a SETMAR substrate in vitro, and we show that the enzyme primarily generates monomethylation at this position. Furthermore, we show that SETMAR methylates snRNP70 Lys-130 in cells. Because snRNP70 is a key early regulator of 5' splice site selection, our results suggest a model in which methylation of snRNP70 by SETMAR regulates constitutive and/or alternative splicing. In addition, the proteomic strategy described here is broadly applicable and is a promising route for large-scale mapping of KMT substrates.

  7. 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.

  8. Cracking the control of RNA polymerase II elongation by 7SK snRNP and P-TEFb

    PubMed Central

    C. Quaresma, Alexandre J.; Bugai, Andrii; Barboric, Matjaz

    2016-01-01

    Release of RNA polymerase II (Pol II) from promoter-proximal pausing has emerged as a critical step regulating gene expression in multicellular organisms. The transition of Pol II into productive elongation requires the kinase activity of positive transcription elongation factor b (P-TEFb), which is itself under a stringent control by the inhibitory 7SK small nuclear ribonucleoprotein (7SK snRNP) complex. Here, we provide an overview on stimulating Pol II pause release by P-TEFb and on sequestering P-TEFb into 7SK snRNP. Furthermore, we highlight mechanisms that govern anchoring of 7SK snRNP to chromatin as well as means that release P-TEFb from the inhibitory complex, and propose a unifying model of P-TEFb activation on chromatin. Collectively, these studies shine a spotlight on the central role of RNA binding proteins (RBPs) in directing the inhibition and activation of P-TEFb, providing a compelling paradigm for controlling Pol II transcription with a non-coding RNA. PMID:27369380

  9. Core structure of the U6 snRNP at 1.7 Å resolution

    PubMed Central

    Montemayor, Eric J.; Curran, Elizabeth C.; Liao, Hong Hong; Andrews, Kristie L.; Treba, Christine N.; Butcher, Samuel E.; Brow, David A.

    2014-01-01

    The spliceosome is a dynamic assembly of five small nuclear ribonucleoproteins (snRNPs) that removes introns from eukaryotic pre-mRNA. U6 is the most conserved of the spliceosomal snRNAs and participates directly in catalysis. Here, we report the crystal structure of the Saccharomyces cerevisiae U6 snRNP core, containing most of U6 snRNA and all four RRM domains of the Prp24 protein. It reveals a unique interlocked RNP architecture that sequesters the 5′ splice site-binding bases of U6 snRNA. RRMs 1, 2 and 4 of Prp24 form an electropositive groove that binds double-stranded RNA and may nucleate annealing of U4 and U6 snRNAs. Substitutions in Prp24 that suppress a mutation in U6 localize to direct RNA-protein contacts. Our results provide the most complete view to date of a multi-RRM protein bound to RNA, and reveal striking co-evolution of protein and RNA structure. PMID:24837192

  10. Lower neurocognitive function in U-2 pilots

    PubMed Central

    Tate, David F.; Wood, Joe; Sladky, John H.; McDonald, Kent; Sherman, Paul M.; Kawano, Elaine S.; Rowland, Laura M.; Patel, Beenish; Wright, Susan N.; Hong, Elliot; Rasmussen, Jennifer; Willis, Adam M.; Kochunov, Peter V.

    2014-01-01

    Objective: Determine whether United States Air Force (USAF) U-2 pilots (U2Ps) with occupational exposure to repeated hypobaria had lower neurocognitive performance compared to pilots without repeated hypobaric exposure and whether U2P neurocognitive performance correlated with white matter hyperintensity (WMH) burden. Methods: We collected Multidimensional Aptitude Battery–II (MAB-II) and MicroCog: Assessment of Cognitive Functioning (MicroCog) neurocognitive data on USAF U2Ps with a history of repeated occupational exposure to hypobaria and compared these with control data collected from USAF pilots (AFPs) without repeated hypobaric exposure (U2Ps/AFPs MAB-II 87/83; MicroCog 93/80). Additional comparisons were performed between U2Ps with high vs low WMH burden. Results: U2Ps with repeated hypobaric exposure had significantly lower scores than control pilots on reasoning/calculation (U2Ps/AFPs 99.4/106.5), memory (105.5/110.9), information processing accuracy (102.1/105.8), and general cognitive functioning (103.5/108.5). In addition, U2Ps with high whole-brain WMH count showed significantly lower scores on reasoning/calculation (high/low 96.8/104.1), memory (102.9/110.2), general cognitive functioning (101.5/107.2), and general cognitive proficiency (103.6/108.8) than U2Ps with low WMH burden (high/low WMH mean volume 0.213/0.003 cm3 and mean count 14.2/0.4). Conclusion: In these otherwise healthy, highly functioning individuals, pilots with occupational exposure to repeated hypobaria demonstrated lower neurocognitive performance, albeit demonstrable on only some tests, than pilots without repeated exposure. Furthermore, within the U2P population, higher WMH burden was associated with lower neurocognitive test performance. Hypobaric exposure may be a risk factor for subtle changes in neurocognition. PMID:25008397

  11. 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

  12. 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

  13. Electronic structure of U2PtC2 and U2RhC2

    DOE PAGES

    Ronning, F.; Zhu, J. -X.

    2015-03-18

    In this study, we present density functional theory calculations within the generalized gradient approximation of U2RhC2 and U2PtC2. We find the calculated density of states are significantly less than that measured by specific heat indicating the need for electronic correlations. The mass enhancement found for U2PtC2 is m*/mband ≈ 4.

  14. 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.

  15. 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.

  16. Autosomal-dominant retinitis pigmentosa caused by a mutation in SNRNP200, a gene required for unwinding of U4/U6 snRNAs.

    PubMed

    Zhao, Chen; Bellur, Deepti L; Lu, Shasha; Zhao, Feng; Grassi, Michael A; Bowne, Sara J; Sullivan, Lori S; Daiger, Stephen P; Chen, Li Jia; Pang, Chi Pui; Zhao, Kanxing; Staley, Jonathan P; Larsson, Catharina

    2009-11-01

    Mutations in genes associated with the U4/U6-U5 small nuclear ribonucleoprotein (snRNP) complex of the spliceosome are implicated in autosomal-dominant retinitis pigmentosa (adRP), a group of progressive retinal degenerative disorders leading to visual impairment, loss of visual field, and even blindness. We recently assigned a locus (RP33) for adRP to 2cen-q12.1, a region that harbors the SNRNP200 gene encoding hBrr2, another U4/U6-U5 snRNP component that is required for unwinding of U4/U6 snRNAs during spliceosome activation and for disassembly of the spliceosome. Here, we report the identification of a missense mutation, c.3260C>T (p.S1087L), in exon 25 of the SNRNP200 gene in an RP33-linked family. The c.3260C>T substitution showed complete cosegregation with the retinitis pigmentosa (RP) phenotype over four generations, but was absent in a panel of 400 controls. The p.S1087L mutation and p.R1090L, another adRP-associated allele, reside in the "ratchet" helix of the first of two Sec63 domains implicated in the directionality and processivity of nucleic acid unwinding. Indeed, marked defects in U4/U6 unwinding, but not U4/U6-U5 snRNP assembly, were observed in budding yeast for the analogous mutations (N1104L and R1107L) of the corresponding Brr2p residues. The linkage of hBrr2 to adRP suggests that the mechanism of pathogenesis for splicing-factor-related RP may fundamentally derive from a defect in hBrr2-dependent RNA unwinding and a consequent defect in spliceosome activation.

  17. 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

  18. 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.

  19. 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.

  20. 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

  1. Transcriptomic comparison of Drosophila snRNP biogenesis mutants reveals mutant-specific changes in pre-mRNA processing: implications for spinal muscular atrophy.

    PubMed

    Garcia, Eric L; Wen, Ying; Praveen, Kavita; Matera, A Gregory

    2016-08-01

    Survival motor neuron (SMN) functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs) that catalyze pre-mRNA splicing. Here, we used disruptions in Smn and two additional snRNP biogenesis genes, Phax and Ars2, to classify RNA processing differences as snRNP-dependent or gene-specific in Drosophila Phax and Smn mutants exhibited comparable reductions in snRNAs, and comparison of their transcriptomes uncovered shared sets of RNA processing changes. In contrast, Ars2 mutants displayed only small decreases in snRNA levels, and RNA processing changes in these mutants were generally distinct from those identified in Phax and Smn animals. Instead, RNA processing changes in Ars2 mutants support the known interaction of Ars2 protein with the cap-binding complex, as splicing changes showed a clear bias toward the first intron. Bypassing disruptions in snRNP biogenesis, direct knockdown of spliceosomal proteins caused similar changes in the splicing of snRNP-dependent events. However, these snRNP-dependent events were largely unaltered in three Smn mutants expressing missense mutations that were originally identified in human spinal muscular atrophy (SMA) patients. Hence, findings here clarify the contributions of Phax, Smn, and Ars2 to snRNP biogenesis in Drosophila, and loss-of-function mutants for these proteins reveal differences that help disentangle cause and effect in SMA model flies.

  2. [Application of VNTR D17S30 locus polymorphism in the paternity test].

    PubMed

    Feng, M; Feng, Z; Lu, Q; Zhang, Y; Yang, Y; Ji, Y; Chen, R

    1998-01-01

    A sensitive and rapid PCR-based technique was adopted to genotype the VNTR D17S30 locus. It was confirmed through the genetic analysis of 20 normal families that the inheritance of D17S30 locus coincides with Mendelian law as simple co-dominant. Retrospective analysis of 100 paternity cases demonstrated that D17S30 locus could be used in forensic paternity test in our country. The exclusion probability estimated from allele frequencies of D17S30 locus (74.04%) does not differ significantly from the observed rate of exclusion (80.00%) in these cases. In all excluded paternity cases there are two in which the exclusion evidence is solely provided by the D17S30 locus.

  3. Lupus autoantibodies to native DNA cross-react with the A and D SnRNP polypeptides.

    PubMed Central

    Reichlin, M; Martin, A; Taylor-Albert, E; Tsuzaka, K; Zhang, W; Reichlin, M W; Koren, E; Ebling, F M; Tsao, B; Hahn, B H

    1994-01-01

    Antibodies to native DNA (nDNA) in sera from patients with systemic lupus erythematosus have been found to frequently correlate with antibodies to the A and D SnRNP proteins measured in Western blot assays. 40 of 54 SLE (74.1%) sera with anti-nDNA bound to A and D proteins, while 9 of 113 sera (8%) without anti-nDNA bound the A and D proteins, P < 10(-8) by Fisher's exact test. Antibodies to nDNA correlated closely with anti-A and anti-D in seven of eight patients followed sequentially, r = 0.7865. Nine human polyclonal anti-nDNA populations were isolated from DNA cellulose columns. Seven reacted equally with A and D, and two reacted predominantly with D. Two of three murine monoclonal anti-DNA antibodies isolated from NZB/NZW F1 hybrid mice bound A and D equally in Western blot with a titer > 1/40,000. These reactions were directed to the unfolded A and D proteins measurable in Western blot since these monoclonals (and several of the human anti-nDNA populations) failed to react with native U1RNP in ELISA or in RNA immunoprecipitation experiments. These newly recognized cross reactions of anti-nDNA may amplify the immune response to DNA and be part of the original immunogenic drive. Images PMID:8282818

  4. 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

  5. Developmental regulation of an snRNP core protein epitope during pig embryogenesis and after nuclear transfer for cloning.

    PubMed

    Prather, R S; Rickords, L F

    1992-10-01

    The appearance and stabilization of a core protein epitope of the snRNP is developmentally regulated during pig embryogenesis. The epitope recognized by the monoclonal antibody Y12 is present in the germinal vesicle of mature oocytes and interphase nuclei of late 4-cell stage (24 to 30 hours post cleavage to the 4-cell stage) to blastocyst stage embryos. There was no antibody localization within pronuclei, or nuclei of 2-cell or early 4-cell stage embryos. Zygotes or 2-cell stage embryos cultured in the presence of alpha-amanitin to the late 4-cell stage showed no immunoreactivity, whereas control embryos had immunoreactivity. Thus antibody localization was correlated with RNA synthesis and RNA processing that begins by 24 hours post cleavage to the 4-cell stage. A final experiment showed no detectable immunoreactivity in 16-cell stage nuclei that had been transferred to enucleated activated meiotic metaphase II oocytes. Since immunoreactivity is associated with active RNA synthesis and RNA processing, it suggests that the 16-cell stage nucleus, which is RNA synthetically active, does not process RNA after nuclear transfer to an enucleated activated meiotic metaphase II oocyte.

  6. U2 And NASA Create Video To Celebrate Collaboration

    NASA Video Gallery

    NASA and U2 released a commemorative video highlighting a year's worth of collaboration in space and on the Irish rock band's 360 Degree tour. U2 approached NASA in 2009 with an idea to include a d...

  7. 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.

  8. 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

  9. The Drosophila Gene for Antizyme Requires Ribosomal Frameshifting for Expression and Contains an Intronic Gene for snRNP Sm D3 on the Opposite Strand

    PubMed Central

    Ivanov, Ivaylo P.; Simin, Karl; Letsou, Anthea; Atkins, John F.; Gesteland, Raymond F.

    1998-01-01

    Previously, a Drosophila melanogaster sequence with high homology to the sequence for mammalian antizyme (ornithine decarboxylase antizyme) was reported. The present study shows that homology of this coding sequence to its mammalian antizyme counterpart also extends to a 5′ open reading frame (ORF) which encodes the amino-terminal part of antizyme and overlaps the +1 frame (ORF2) that encodes the carboxy-terminal three-quarters of the protein. Ribosomes shift frame from the 5′ ORF to ORF2 with an efficiency regulated by polyamines. At least in mammals, this is part of an autoregulatory circuit. The shift site and 23 of 25 of the flanking nucleotides which are likely important for efficient frameshifting are identical to their mammalian homologs. In the reverse orientation, within one of the introns of the Drosophila antizyme gene, the gene for snRNP Sm D3 is located. Previously, it was shown that two closely linked P-element transposon insertions caused the gutfeeling phenotype of embryonic lethality and aberrant neuronal and muscle cell differentiation. The present work shows that defects in either snRNP Sm D3 or antizyme, or both, are likely causes of the phenotype. PMID:9488472

  10. SMN is essential for the biogenesis of U7 snRNP and 3′-end formation of histone mRNAs

    PubMed Central

    Tisdale, Sarah; Lotti, Francesco; Saieva, Luciano; Van Meerbeke, James P.; Crawford, Thomas O.; Sumner, Charlotte J.; Mentis, George Z.; Pellizzoni, Livio

    2013-01-01

    Spinal muscular atrophy (SMA) is a neurodegenerative disease caused by a deficiency in the survival motor neuron (SMN) protein. SMN mediates the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs) and possibly other RNPs. Here we investigated SMN requirement for the biogenesis and function of U7—an snRNP specialized in the 3′-end formation of replication-dependent histone mRNAs that normally are not polyadenylated. We show that SMN deficiency impairs U7 snRNP assembly and decreases U7 levels in mammalian cells. The SMN-dependent U7 reduction affects endonucleolytic cleavage of histone mRNAs leading to abnormal accumulation of 3′-extended and polyadenylated transcripts, followed by downstream changes in histone gene expression. Importantly, SMN deficiency induces defects of histone mRNA 3′-end formation in both SMA mice and human patients. These findings demonstrate that SMN is essential for U7 biogenesis and histone mRNA processing in vivo, and identify a novel RNA pathway disrupted in SMA. PMID:24332368

  11. 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.

  12. Dinoflagellate 17S rRNA sequence inferred from the gene sequence: Evolutionary implications

    PubMed Central

    Herzog, Michel; Maroteaux, Luc

    1986-01-01

    We present the complete sequence of the nuclear-encoded small-ribosomal-subunit RNA inferred from the cloned gene sequence of the dinoflagellate Prorocentrum micans. The dinoflagellate 17S rRNA sequence of 1798 nucleotides is contained in a family of 200 tandemly repeated genes per haploid genome. A tentative model of the secondary structure of P. micans 17S rRNA is presented. This sequence is compared with the small-ribosomal-subunit rRNA of Xenopus laevis (Animalia), Saccharomyces cerevisiae (Fungi), Zea mays (Planta), Dictyostelium discoideum (Protoctista), and Halobacterium volcanii (Monera). Although the secondary structure of the dinoflagellate 17S rRNA presents most of the eukaryotic characteristics, it contains sufficient archaeobacterial-like structural features to reinforce the view that dinoflagellates branch off very early from the eukaryotic lineage. PMID:16578795

  13. Dinoflagellate 17S rRNA sequence inferred from the gene sequence: Evolutionary implications.

    PubMed

    Herzog, M; Maroteaux, L

    1986-11-01

    We present the complete sequence of the nuclear-encoded small-ribosomal-subunit RNA inferred from the cloned gene sequence of the dinoflagellate Prorocentrum micans. The dinoflagellate 17S rRNA sequence of 1798 nucleotides is contained in a family of 200 tandemly repeated genes per haploid genome. A tentative model of the secondary structure of P. micans 17S rRNA is presented. This sequence is compared with the small-ribosomal-subunit rRNA of Xenopus laevis (Animalia), Saccharomyces cerevisiae (Fungi), Zea mays (Planta), Dictyostelium discoideum (Protoctista), and Halobacterium volcanii (Monera). Although the secondary structure of the dinoflagellate 17S rRNA presents most of the eukaryotic characteristics, it contains sufficient archaeobacterial-like structural features to reinforce the view that dinoflagellates branch off very early from the eukaryotic lineage.

  14. Building Customized University-to-Business (U2B) Partnerships

    ERIC Educational Resources Information Center

    Irvine, George; Verma, Lisa

    2013-01-01

    Continuing education (CE) units throughout the United States have successfully built University-to-Business (U2B) partnerships to provide greater value to their community partners and to increase revenue for the university. Our experience in building U2B partnerships and feedback from our partners--businesses, corporations, state agencies, and…

  15. Prp40 pre-mRNA processing factor 40 homolog B (PRPF40B) associates with SF1 and U2AF65 and modulates alternative pre-mRNA splicing in vivo

    PubMed Central

    Becerra, Soraya; Montes, Marta; Hernández-Munain, Cristina

    2015-01-01

    The first stable complex formed during the assembly of spliceosomes onto pre-mRNA substrates in mammals includes U1 snRNP, which recognizes the 5′ splice site, and the splicing factors SF1 and U2AF, which bind the branch point sequence, polypyrimidine tract, and 3′ splice site. The 5′ and 3′ splice site complexes are thought to be joined together by protein–protein interactions mediated by factors that ensure the fidelity of the initial splice site recognition. In this study, we identified and characterized PRPF40B, a putative mammalian ortholog of the U1 snRNP-associated yeast splicing factor Prp40. PRPF40B is highly enriched in speckles with a behavior similar to splicing factors. We demonstrated that PRPF40B interacts directly with SF1 and associates with U2AF65. Accordingly, PRPF40B colocalizes with these splicing factors in the cell nucleus. Splicing assays with reporter minigenes revealed that PRPF40B modulates alternative splice site selection. In the case of Fas regulation of alternative splicing, weak 5′ and 3′ splice sites and exonic sequences are required for PRPF40B function. Placing our data in a functional context, we also show that PRPF40B depletion increased Fas/CD95 receptor number and cell apoptosis, which suggests the ability of PRPF40B to alter the alternative splicing of key apoptotic genes to regulate cell survival. PMID:25605964

  16. Release of positive transcription elongation factor b (P-TEFb) from 7SK small nuclear ribonucleoprotein (snRNP) activates hexamethylene bisacetamide-inducible protein (HEXIM1) transcription.

    PubMed

    Liu, Pingyang; Xiang, Yanhui; Fujinaga, Koh; Bartholomeeusen, Koen; Nilson, Kyle A; Price, David H; Peterlin, B Matija

    2014-04-04

    By phosphorylating negative elongation factors and the C-terminal domain of RNA polymerase II (RNAPII), positive transcription elongation factor b (P-TEFb), which is composed of CycT1 or CycT2 and CDK9, activates eukaryotic transcription elongation. In growing cells, it is found in active and inactive forms. In the former, free P-TEFb is a potent transcriptional coactivator. In the latter, it is inhibited by HEXIM1 or HEXIM2 in the 7SK small nuclear ribonucleoprotein (snRNP), which contains, additionally, 7SK snRNA, methyl phosphate-capping enzyme (MePCE), and La-related protein 7 (LARP7). This P-TEFb equilibrium determines the state of growth and proliferation of the cell. In this study, the release of P-TEFb from the 7SK snRNP led to increased synthesis of HEXIM1 but not HEXIM2 in HeLa cells, and this occurred only from an unannotated, proximal promoter. ChIP with sequencing revealed P-TEFb-sensitive poised RNA polymerase II at this proximal but not the previously annotated distal HEXIM1 promoter. Its immediate upstream sequences were fused to luciferase reporters and were found to be responsive to many P-TEFb-releasing compounds. The superelongation complex subunits AF4/FMR2 family member 4 (AFF4) and elongation factor RNA polymerase II 2 (ELL2) were recruited to this proximal promoter after P-TEFb release and were required for its transcriptional effects. Thus, P-TEFb regulates its own equilibrium in cells, most likely to maintain optimal cellular homeostasis.

  17. Superconformal mechanics in S U (2 |1 ) superspace

    NASA Astrophysics Data System (ADS)

    Ivanov, E.; Sidorov, S.; Toppan, F.

    2015-04-01

    Using the worldline S U (2 |1 ) superfield approach, we construct N =4 superconformally invariant actions for the d =1 multiplets (1 ,4 ,3 ) and (2 ,4 ,2 ). The S U (2 |1 ) superfield framework automatically implies the trigonometric realization of the superconformal symmetry and the harmonic oscillator term in the corresponding component actions. We deal with the general N =4 superconformal algebra D (2 ,1 ;α ) and its central-extended α =0 and α =-1 p s u (1 ,1 |2 )⊕s u (2 ) descendants. We capitalize on the observation that D (2 ,1 ;α ) at α ≠0 can be treated as a closure of its two s u (2 |1 ) subalgebras, one of which defines the superisometry of the S U (2 |1 ) superspace, while the other is related to the first one through the reflection of μ , the parameter of contraction to the flat N =4 ,d =1 superspace. This closure property and its α =0 analog suggest a simple criterion for the S U (2 |1 ) invariant actions to be superconformal: they should be even functions of μ . We find that the superconformal actions of the multiplet (2 ,4 ,2 ) exist only at α =-1 ,0 and are reduced to a sum of the free sigma-model-type action and the conformal superpotential yielding, respectively, the oscillator potential ˜μ2 and the standard conformal inverse-square potential in the bosonic sector. The sigma-model action in this case can be constructed only on account of nonzero central charge in the superalgebra s u (1 ,1 |2 ).

  18. Suppression of superconductivity and resistivity anomaly in Rh17S15 by cobalt substitution.

    PubMed

    Daou, Ramzy; Berthebaud, David; Maignan, Antoine

    2017-02-22

    The chalcogenide superconductor Rh17S15 is known for having an upper critical field of nearly twice the Pauli limit and an unusual temperature dependence of the resistivity. When doped with small amounts of cobalt, superconductivity in Rh17-x Co x S15 (0  <  x  <  3) is systematically suppressed. We explore the evolution of the electrical transport properties from 2-300 K as a function of x. We identify three temperature regimes which are differently affected by doping. The disappearance of an electron-like contribution to the transport at low temperature is correlated with the suppression of superconductivity.

  19. Suppression of superconductivity and resistivity anomaly in Rh17S15 by cobalt substitution

    NASA Astrophysics Data System (ADS)

    Daou, Ramzy; Berthebaud, David; Maignan, Antoine

    2017-02-01

    The chalcogenide superconductor Rh17S15 is known for having an upper critical field of nearly twice the Pauli limit and an unusual temperature dependence of the resistivity. When doped with small amounts of cobalt, superconductivity in Rh17-x Co x S15 (0  <  x  <  3) is systematically suppressed. We explore the evolution of the electrical transport properties from 2-300 K as a function of x. We identify three temperature regimes which are differently affected by doping. The disappearance of an electron-like contribution to the transport at low temperature is correlated with the suppression of superconductivity.

  20. Epidermal surface antigen (MS17S1) is highly conserved between mouse and human

    SciTech Connect

    Cho, Y.J.; Chema, D.; Cho, M.

    1995-05-20

    A mouse monoclonal antibody ECS-1 raised to human keratinocytes detects a 35-kDa epidermal surface antigen (ESA) and causes keratinocyte dissociation in vitro. ECS-1 stains skin of 16-day mouse embryo and 8- to 9-week human fetus. Mouse Esa cDNA encodes a 379-amino-acid protein that is 99.2% identical to the human, differing at only 3 amino acids. The gene (M17S1) was mapped to mouse chromosome 11, highlighting the conserved linkage synteny existing between human chromosome 17 and mouse chromosome 11. Although the nude locus has been mapped to the same region of chromosome 11, no abnormalities in protein, mRNA, or cDNA or genomic sequences were detected in nude mice. However, both nude and control mice were found to have a second Esa mRNA transcript that conserves amino acid sequence and molecular weight. The mouse and human 5{prime} and 3{prime} untranslated sequences are conserved. Similar RNA folding patterns of the 5{prime} untranslated region are predicted despite a 91-bp insertion in the mouse. These data suggest that both the function and the regulation of ESA protein are of importance and that Esa (M17S1) is not the nude locus gene. 42 refs., 7 figs., 3 tabs.

  1. U-2 Pilot Post-Mission Fatigue Questionnaire

    DTIC Science & Technology

    2014-10-01

    prolonged mission duration of up to 12 hours. This research investigates factors that contribute to subjective fatigue and explores fatigue countermeasure...an average of 3.07 (± 0.75) hours prior to takeoff and an average mission duration of 9.81 (± 0.48 hours), resulting in a total time awake at landing...strategies are in place to prevent increases in fatigue in prolonged U-2 missions; however, changes in mission duration , mission frequency, and/or

  2. Radiative neutrino model with S U (2 )L triplet fields

    NASA Astrophysics Data System (ADS)

    Nomura, Takaaki; Okada, Hiroshi; Orikasa, Yuta

    2016-12-01

    We propose a loop-induced neutrino mass model, in which we introduce several exotic fermions and bosons with an S U (2 )L multiplet, and discuss various phenomenologies such as lepton flavor violations, the muon anomalous magnetic moment, nonstandard interacting neutrinoless double beta decay, the relic density of dark matter, and the possibility of the spin-independent direct detection searches, imposing the constraints of oblique parameters. And we show a benchmark point to satisfy all the constraints and discuss our predictions.

  3. Fam118B, a newly identified component of Cajal bodies, is required for Cajal body formation, snRNP biogenesis and cell viability.

    PubMed

    Li, Yujing; Fong, Ka-Wing; Tang, Mengfan; Han, Xin; Gong, Zihua; Ma, Wenbin; Hebert, Michael; Songyang, Zhou; Chen, Junjie

    2014-05-01

    Cajal bodies are specialized and dynamic compartments in the nucleus that are involved in the biogenesis of small nuclear ribonucleoproteins (snRNPs). Because of the dynamic and varied roles of Cajal bodies, it is of great interest to identify the components of Cajal bodies to better understand their functions. We performed a genome-wide screen to identify proteins that colocalize with coilin, the marker protein of Cajal bodies. In this study, we identified and characterized Fam118B as a newly discovered component of Cajal bodies. Fam118B is widely expressed in a variety of cell lines derived from various origins. Overexpression of Fam118B changes the canonical morphology of Cajal bodies, whereas depletion of Fam118B disrupts the localization of components of Cajal bodies, including coilin, the survival of motor neuron protein (SMN) and the Sm protein D1 (SmD1, also known as SNRPD1). Moreover, depletion of Fam118B reduces splicing capacity and inhibits cell proliferation. In addition, Fam118B associates with coilin and SMN proteins. Fam118B depletion reduces symmetric dimethylarginine modification of SmD1, which in turn diminishes the binding of SMN to this Sm protein. Taken together, these data indicate that Fam118B, by regulating SmD1 symmetric dimethylarginine modification, plays an important role in Cajal body formation, snRNP biogenesis and cell viability.

  4. 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

  5. U-2 Spy Plane With Fictitious NASA Markings

    NASA Technical Reports Server (NTRS)

    1960-01-01

    After Francis Gary Powers was shot down over the Soviet Union during a CIA spy flight on May 1. 1960, NASA issued a press release with a cover story about a U-2 conducting weather research that may have strayed off course after the pilot reported difficulties with his oxygen equipment. To bolster the cover-up, a U-2 was quickly painted in NASA markings, with a fictitious NASA serial number, and put on display for the news media at the NASA Flight Research Center at Edwards Air Force Base on May 6, 1960. The U-2 cover story in 1956 was that it was an NACA plane to conduct high-altitude weather research. But various observers doubted this story from the beginning. Certainly the Soviets did not believe it once the aircraft began overflying their territory. The NASA cover story quickly blew up in the agency's face when both Gary Powers and aircraft wreckage were displayed by the Soviet Union, proving that it was a reconnaissance aircraft. This caused embarrassment for several top NASA officials.

  6. Interactions of U2 Gene Loci and Their Nuclear Transcripts with Cajal (Coiled) Bodies: Evidence for PreU2 within Cajal Bodies

    PubMed Central

    Smith, Kelly P.; Lawrence, Jeanne Bentley

    2000-01-01

    The Cajal (coiled) body (CB) is a structure enriched in proteins involved in mRNA, rRNA, and snRNA metabolism. CBs have been shown to interact with specific histone and snRNA gene loci. To examine the potential role of CBs in U2 snRNA metabolism, we used a variety of genomic and oligonucleotide probes to visualize in situ newly synthesized U2 snRNA relative to U2 loci and CBs. Results demonstrate that long spacer sequences between U2 coding repeats are transcribed, supporting other recent evidence that U2 transcription proceeds past the 3′ box. The presence of bright foci of this U2 locus RNA differed between alleles within the same nucleus; however, this did not correlate with the loci's association with a CB. Experiments with specific oligonucleotide probes revealed signal for preU2 RNA within CBs. PreU2 was also detected in the locus-associated RNA foci, whereas sequences 3′ of preU2 were found only in these foci, not in CBs. This suggests that a longer primary transcript is processed before entry into CBs. Although this work shows that direct contact of a U2 locus with a CB is not simply correlated with RNA at that locus, it provides the first evidence of new preU2 transcripts within CBs. We also show that, in contrast to CBs, SMN gems do not associate with U2 gene loci and do not contain preU2. Because other evidence indicates that preU2 is processed in the cytoplasm before assembly into snRNPs, results point to an involvement of CBs in modification or transport of preU2 RNA. PMID:10982395

  7. Ocean Chlorophyll Studies from a U-2 Aircraft Platform

    NASA Technical Reports Server (NTRS)

    Kim, H. H.; Mcclain, C. R.; Blaine, L. R.; Hart, W. D.; Atkinson, L. P.; Yoder, J. A.

    1979-01-01

    Chlorophyll gradient maps of large ocean areas were generated from U-2 ocean color scanner data obtained over test sites in the Pacific and Atlantic Oceans. The delineation of oceanic features using the upward radiant intensity relies on an analysis method which presupposes that radiation backscattered from the atmosphere and ocean surface can be properly modeled using a measurement made at 778 nm. An estimation of the chlorophyll concentration was performed by properly ratioing radiances measured at 472 nm and 548 nm after removing the atmospheric effects. The correlation between the remotely sensed data and in-situ surface chlorophyll measurements was validated in two sets of data. The results show that the correlation between the in-situ measured chlorophyll and the derived quantity is a negative exponential function and the correlation coefficient was calculated to be -0.965.

  8. Hydrogen absorption-desorption properties of U 2Ti

    NASA Astrophysics Data System (ADS)

    Takuya, Yamamoto; Satoru, Tanaka; Michio, Yamawaki

    1990-02-01

    Hydrogen absorption-desorption properties of U 2Ti intermetallic compound was examined over the temperature range of 298 to 973 K and at hydrogen pressures below 10 5 Pa. It absorbs hydrogen up to 7.6 atoms per F.U. (formula unit) by two step reactions and hence each desorption isotherm is separated into two plateau regions. In the first plateau, a newly-found ternary hydride is formed, where the hydrogen concentration, cH, reaches 2.4 H atoms/F.U. In the second plateau, UH 3 is formed and cH reaches 7.6 H atoms/F.U. The specimen is disintegrated into fine powder in the second plateau, while in the first plateau the ternary hydride which was identified to be UTi 2H x, ( x = 4.8 to 6.2) showed high durability against powdering. It is predicted that UTi 2 can be suitable material for tritium storage.

  9. Alternative splicing of U2AF1 reveals a shared repression mechanism for duplicated exons

    PubMed Central

    Kralovicova, Jana; Vorechovsky, Igor

    2017-01-01

    The auxiliary factor of U2 small nuclear ribonucleoprotein (U2AF) facilitates branch point (BP) recognition and formation of lariat introns. The gene for the 35-kD subunit of U2AF gives rise to two protein isoforms (termed U2AF35a and U2AF35b) that are encoded by alternatively spliced exons 3 and Ab, respectively. The splicing recognition sequences of exon 3 are less favorable than exon Ab, yet U2AF35a expression is higher than U2AF35b across tissues. We show that U2AF35b repression is facilitated by weak, closely spaced BPs next to a long polypyrimidine tract of exon Ab. Each BP lacked canonical uridines at position -2 relative to the BP adenines, with efficient U2 base-pairing interactions predicted only for shifted registers reminiscent of programmed ribosomal frameshifting. The BP cluster was compensated by interactions involving unpaired cytosines in an upstream, EvoFold-predicted stem loop (termed ESL) that binds FUBP1/2. Exon Ab inclusion correlated with predicted free energies of mutant ESLs, suggesting that the ESL operates as a conserved rheostat between long inverted repeats upstream of each exon. The isoform-specific U2AF35 expression was U2AF65-dependent, required interactions between the U2AF-homology motif (UHM) and the α6 helix of U2AF35, and was fine-tuned by exon Ab/3 variants. Finally, we identify tandem homologous exons regulated by U2AF and show that their preferential responses to U2AF65-related proteins and SRSF3 are associated with unpaired pre-mRNA segments upstream of U2AF-repressed 3′ss. These results provide new insights into tissue-specific subfunctionalization of duplicated exons in vertebrate evolution and expand the repertoire of exon repression mechanisms that control alternative splicing. PMID:27566151

  10. Wild-Type U2AF1 Antagonizes the Splicing Program Characteristic of U2AF1-Mutant Tumors and Is Required for Cell Survival

    PubMed Central

    Fei, Dennis Liang; Motowski, Hayley; Chatrikhi, Rakesh; Gao, Shaojian; Kielkopf, Clara L.; Varmus, Harold

    2016-01-01

    We have asked how the common S34F mutation in the splicing factor U2AF1 regulates alternative splicing in lung cancer, and why wild-type U2AF1 is retained in cancers with this mutation. A human lung epithelial cell line was genetically modified so that U2AF1S34F is expressed from one of the two endogenous U2AF1 loci. By altering levels of mutant or wild-type U2AF1 in this cell line and by analyzing published data on human lung adenocarcinomas, we show that S34F-associated changes in alternative splicing are proportional to the ratio of S34F:wild-type gene products and not to absolute levels of either the mutant or wild-type factor. Preferential recognition of specific 3′ splice sites in S34F-expressing cells is largely explained by differential in vitro RNA-binding affinities of mutant versus wild-type U2AF1 for those same 3′ splice sites. Finally, we show that lung adenocarcinoma cell lines bearing U2AF1 mutations do not require the mutant protein for growth in vitro or in vivo. In contrast, wild-type U2AF1 is required for survival, regardless of whether cells carry the U2AF1S34F allele. Our results provide mechanistic explanations of the magnitude of splicing changes observed in U2AF1-mutant cells and why tumors harboring U2AF1 mutations always retain an expressed copy of the wild-type allele. PMID:27776121

  11. Mutation in the splicing factor Hprp3p linked to retinitis pigmentosa impairs interactions within the U4/U6 snRNP complex.

    PubMed

    Gonzalez-Santos, Juana Maria; Cao, Huibi; Duan, Rongqi Cathleen; Hu, Jim

    2008-01-15

    Mutations in PRPF3, a gene encoding the essential pre-mRNA splicing factor Hprp3p, have been identified in patients with autosomal dominant retinitis pigmentosa type 18 (RP18). Patients with RP18 have one of two single amino acid substitutions, Pro493Ser or Thr494Met, at the highly conserved Hprp3p C-terminal region. Pro493Ser occurs sporadically, whereas Thr494Met is observed in several unlinked RP families worldwide. The latter mutation also alters a potential recognition motif for phosphorylation by casein kinase II (CKII). To understand the molecular basis of RP18, we examined the consequences of Thr494Met mutation on Hprp3p molecular interactions with components of the U4/U6.U5 small nuclear ribonucleoprotein particles (snRNPs) complex. Since numerous mutations causing human diseases change pre-mRNA splice sites, we investigated whether Thr494Met substitution affects the processing of PRPF3 mRNA. We found that Thr494Met does not affect PRPF3 mRNA processing, indicating that the mutation may exert its effect primarily at the protein level. We used small hairpin RNAs to specifically silence the endogenous PRPF3 while simultaneously expressing HA-tagged Thr494Met. We demonstrated that the C- but not N-terminal region of Hprp3p is indeed phosphorylated by CKII in vitro and in cells. CKII-mediated Hprp3p phosphorylation was significantly reduced by Thr494Met mutation. Consequently, the Hprp3p C-terminal region is rendered partially defective in its association with itself, Hprp4p, and U4/U6 snRNA. Our findings provide new insights into the biology of Hprp3p and suggest that the loss of Hprp3p phosphorylation at Thr494 is a key step for initiating Thr494Met aberrant interactions within U4/U6 snRNP complex and that these are likely linked to the RP18 phenotype.

  12. The Role of U2AF1 Mutations in the Pathogenesis of Myelodysplastic Syndromes

    DTIC Science & Technology

    2015-10-01

    to U2AF1(WT). We validated several homologous dysregulated junctions (i.e., across species) in MDS patient bone marrow samples that have mutant ...U2AF1(S34F) versus U2AF1(WT). Together, these results suggest that mutant U2AF1 expression contributes to the altered hematopoiesis and pre-mRNA...whether the U2AF1(S34F) mutation alters hematopoiesis in vivo. We will inducibly express wild-type and S34F mutant (resulting from the most common

  13. Genomic functions of U2AF in constitutive and regulated splicing.

    PubMed

    Wu, Tongbin; Fu, Xiang-Dong

    2015-01-01

    The U2AF heterodimer is generally accepted to play a vital role in defining functional 3' splice sites in pre-mRNA splicing. Given prevalent mutations in U2AF, particularly in the U2AF1 gene (which encodes for the U2AF35 subunit) in blood disorders and other human cancers, there are renewed interests in these classic splicing factors to further understand their regulatory functions in RNA metabolism in both physiological and disease settings. We recently reported that U2AF has a maximal capacity to directly bind ˜88% of functional 3' splice sites in the human genome and that numerous U2AF binding events also occur in various exonic and intronic locations, thus providing additional mechanisms for the regulation of alternative splicing besides their traditional role in titrating weak splice sites in the cell. These findings, coupled with the existence of multiple related proteins to both U2AF65 and U2AF35, beg a series of questions on the universal role of U2AF in functional 3' splice site definition, their binding specificities in vivo, potential mechanisms to bypass their requirement for certain intron removal events, contribution of splicing-independent functions of U2AF to important cellular functions, and the mechanism for U2AF mutations to invoke specific diseases in humans.

  14. 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.

  15. Lower Neurocognitive Function in U-2 Pilots: Relationship to White Matter Hyperintensities

    DTIC Science & Technology

    2014-07-09

    repeated occupational exposure to hypobaria and compared these with control data collected from USAF pilots ( AFPs ) without repeated hypobaric exposure...U2Ps/ AFPs MAB-II 87/83; Micro- Cog 93/80). Additional comparisons were performed between U2Ps with high vs low WMH burden. U2Ps with repeated...hypobaric exposure had significantly lower scores than control pilots on reasoning/calculation (U2Ps/ AFPs 99.4/106.5), memory (105.5/110.9), information

  16. A Conditional Role of U2AF in Splicing of Introns with Unconventional Polypyrimidine Tracts▿ †

    PubMed Central

    Sridharan, Vinod; Singh, Ravinder

    2007-01-01

    Recognition of polypyrimidine (Py) tracts typically present between the branch point and the 3′ splice site by the large subunit of the essential splicing factor U2AF is a key early step in pre-mRNA splicing. Diverse intronic sequence arrangements exist, however, including 3′ splice sites lacking recognizable Py tracts, which raises the question of how general the requirement for U2AF is for various intron architectures. Our analysis of fission yeast introns in vivo has unexpectedly revealed that whereas introns lacking Py tracts altogether remain dependent on both subunits of U2AF, introns with long Py tracts, unconventionally positioned upstream of branch points, are unaffected by U2AF inactivation. Nevertheless, mutation of these Py tracts causes strong dependence on the large subunit U2AF59. We also find that Py tract diversity influences the requirement for the conserved C-terminal domain of U2AF59 (RNA recognition motif 3), which has been implicated in protein-protein interactions with other splicing factors. Together, these results suggest that in addition to Py tract binding by U2AF, supplementary mechanisms of U2AF recruitment and 3′ splice site identification exist to accommodate diverse intron architectures, which have gone unappreciated in biochemical studies of model pre-mRNAs. PMID:17709389

  17. Structure and Properties of Some Layered U2O5 Phases: A Density Functional Theory Study.

    PubMed

    Molinari, Marco; Brincat, Nicholas A; Allen, Geoffrey C; Parker, Stephen C

    2017-04-05

    U2O5 is the boundary composition between the fluorite and the layered structures of the UO2→3 system and the least studied oxide in the group. δ-U2O5 is the only layered structure proposed so far experimentally, although evidence of fluorite-based phases has also been reported. Our DFT work explores possible structures of U2O5 stoichiometry by starting from existing M2O5 structures (where M is an actinide or transition metal) and replacing the M ions with uranium ions. For all structures, we predicted structural and electronic properties including bulk moduli and band gaps. The majority of structures were found to be less stable than δ-U2O5. U2O5 in the R-Nb2O5 structure was found to be a competitive structure in terms of stability, whereas U2O5 in the Np2O5 structure was found to be the most stable overall. Indeed, by including the vibrational contribution to the free energy using the frequencies obtained from the optimized unit cells we predict that Np2O5 structured U2O5 is the most thermodynamically stable under ambient conditions. δ-U2O5 only becomes more stable at high temperatures and/or pressures. This suggests that a low-temperature synthesis route should be tested and so potentially opens a new avenue of research for pentavalent uranium oxides.

  18. Mutant U2AF1 Expression Alters Hematopoiesis and Pre-mRNA Splicing In Vivo

    PubMed Central

    Shirai, Cara Lunn; Ley, James N.; White, Brian S.; Kim, Sanghyun; Tibbitts, Justin; Shao, Jin; Ndonwi, Matthew; Wadugu, Brian; Duncavage, Eric J.; Okeyo-Owuor, Theresa; Liu, Tuoen; Griffith, Malachi; McGrath, Sean; Magrini, Vincent; Fulton, Robert S.; Fronick, Catrina; O’Laughlin, Michelle; Graubert, Timothy A.; Walter, Matthew J.

    2015-01-01

    SUMMARY Heterozygous somatic mutations in the spliceosome gene U2AF1 occur in ~11% of patients with myelodysplastic syndromes (MDS), the most common adult myeloid malignancy. It is unclear how these mutations contribute to disease. We examined in vivo hematopoietic consequences of the most common U2AF1 mutation using a doxycycline-inducible transgenic mouse model. Mice expressing mutant U2AF1(S34F) display altered hematopoiesis and changes in pre-mRNA splicing in hematopoietic progenitor cells by whole transcriptome analysis (RNA-seq). Integration with human RNA-seq datasets determined that common mutant U2AF1-induced splicing alterations are enriched in RNA processing genes, ribosomal genes, and recurrently-mutated MDS and acute myeloid leukemia-associated genes. These findings support the hypothesis that mutant U2AF1 alters downstream gene isoform expression, thereby contributing to abnormal hematopoiesis in MDS patients. PMID:25965570

  19. R2U2: Monitoring and Diagnosis of Security Threats for Unmanned Aerial Systems

    NASA Technical Reports Server (NTRS)

    Schumann, Johann; Moosbruger, Patrick; Rozier, Kristin Y.

    2015-01-01

    We present R2U2, a novel framework for runtime monitoring of security properties and diagnosing of security threats on-board Unmanned Aerial Systems (UAS). R2U2, implemented in FPGA hardware, is a real-time, REALIZABLE, RESPONSIVE, UNOBTRUSIVE Unit for security threat detection. R2U2 is designed to continuously monitor inputs from the GPS and the ground control station, sensor readings, actuator outputs, and flight software status. By simultaneously monitoring and performing statistical reasoning, attack patterns and post-attack discrepancies in the UAS behavior can be detected. R2U2 uses runtime observer pairs for linear and metric temporal logics for property monitoring and Bayesian networks for diagnosis of security threats. We discuss the design and implementation that now enables R2U2 to handle security threats and present simulation results of several attack scenarios on the NASA DragonEye UAS.

  20. RLIM interacts with Smurf2 and promotes TGF-{beta} induced U2OS cell migration

    SciTech Connect

    Huang, Yongsheng; Yang, Yang; Gao, Rui; Yang, Xianmei; Yan, Xiaohua; Wang, Chenji; Jiang, Sirui; Yu, Long

    2011-10-14

    Highlights: {yields} RLIM directly binds to Smurf2. {yields} RLIM enhances TGF-{beta} responsiveness in U2OS cells. {yields} RLIM promotes TGF-{beta} driven migration of osteosarcoma U2OS cells. -- Abstract: TGF-{beta} (transforming growth factor-{beta}), a pleiotropic cytokine that regulates diverse cellular processes, has been suggested to play critical roles in cell proliferation, migration, and carcinogenesis. Here we found a novel E3 ubiquitin ligase RLIM which can directly bind to Smurf2, enhancing TGF-{beta} responsiveness in osteosarcoma U2OS cells. We constructed a U2OS cell line stably over-expressing RLIM and demonstrated that RLIM promoted TGF-{beta}-driven migration of U2OS cells as tested by wound healing assay. Our results indicated that RLIM is an important positive regulator in TGF-{beta} signaling pathway and cell migration.

  1. Unlimited Horizons: Design and Development of the U-2. [NASA Aeronautics Book Series

    NASA Technical Reports Server (NTRS)

    Merlin, Peter W.

    2015-01-01

    This book describes the creation, history, design, and research value of the U-2 program. It also describes the involvement of NACA, as a cover story, and the later use by NASA of these aircraft as environmental research platforms.

  2. The flavonoid luteolin enhances doxorubicin-induced autophagy in human osteosarcoma U2OS cells

    PubMed Central

    Zhang, Baoliang; Yu, Xin; Xia, Hong

    2015-01-01

    Luteolin (LUT), a flavone, which is universally present as constituent of medicinal plants as well as some vegetables and spices, has been demonstrated display specific anti-carcinogenic effects. However, the mechanisms by which LUT inhibits human osteosarcoma growth remain unknown. The effects of LUT on cell growth in human osteosarcoma U2OS cells were measured by MTT assay and flowcytometry. The effects of LUT on morphological markers of autophagy in U2OS were analyzed by fluorescence microscopy and electron microscopy. Autophagic markers, beclin1 and LC3 were detected by western blotting. Here, we found that LUT induced autophagy in U2OS and acted as an enhancer to sensitize doxorubicin (DOX)-mediated autophagy signaling. The combined treatment of LUT and DOX greatly decreases the growth of U2OS, showing synergistic cytotoxicity. Our results indicate that LUT in combination with DOX maybe a novel strategy for the treatment of human osteosarcoma. PMID:26629003

  3. 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

  4. Factors associated with a purine-rich exonic splicing enhancer sequence in Xenopus oocyte nucleus

    SciTech Connect

    Masuyama, Kaoru; Taniguchi, Ichiro; Okawa, Katsuya; Ohno, Mutsuhito . E-mail: hitoohno@virus.kyoto-u.ac.jp

    2007-08-03

    Purine-rich exonic splicing enhancers (ESEs) stimulate splicing of the adjacent introns with suboptimal splice sites. To elucidate the mechanism regarding ESEs, factors specifically associated with ESEs in HeLa cell nuclear extracts were previously investigated, and shown to include SR (serine/arginine-rich) proteins. However, factors associated with ESEs in vivo have not yet been explored. Here we show that a GAA repeat RNA sequence, a typical ESE, is associated in Xenopus oocyte nuclei with at least one SR protein, SF2/ASF, as was expected. Moreover, components of SF3a/b complexes, U2 snRNA, and U2AF{sup 65} were also found to be associated with the ESE in the nucleus. Since SF3a/b complexes are the constituents of the 17S U2 snRNP, these results suggest that the 17S U2 snRNP is associated with the ESE in the nucleus, probably through bridging interactions of U2AF and SR proteins. The identified factors may represent a functional splicing enhancer complex in vivo.

  5. P elements inserted in the vicinity of or within the Drosophila snRNP SmD3 gene nested in the first intron of the Ornithine Decarboxylase Antizyme gene affect only the expression of SmD3.

    PubMed Central

    Schenkel, Heide; Hanke, Susanne; De Lorenzo, Cécilia; Schmitt, Rolf; Mechler, Bernard M

    2002-01-01

    The Drosophila gene for snRNP SmD3 (SmD3) is contained in reverse orientation within the first intron of the Ornithine Decarboxylase Antizyme (AZ) gene. Previous studies show that two closely linked P elements cause the gutfeeling phenotype characterized by embryonic lethality and aberrant neuronal and muscle cell differentiation. However, the exact nature of the gene(s) affected in the gutfeeling phenotype remained unknown. This study shows that a series of P inserts located within the 5'-untranslated region (5'-UTR) of SmD3 or its promoter affects only the expression of SmD3. Our analysis reveals that the gutfeeling phenotype associated with P elements inserted in the 5'-UTR of SmD3 results from amorphic or strongly hypomorphic mutations. In contrast, P inserts in the SmD3 promoter region reduce the expression of SmD3 without abolishing it and produce larval lethality with overgrown imaginal discs, brain hemispheres, and hematopoietic organs. The lethality of these mutations could be rescued by an SmD3+ transgene. Finally, inactivation of AZ was obtained by complementing with SmD3+ the deficiency Df(2R)guf(lex47) that uncovers both SmD3 and AZ. Interestingly, AZ inactivation causes a new phenotype characterized by late larval lethality and atrophy of the brain, imaginal discs, hematopoietic organs, and salivary glands. PMID:12072471

  6. A Natural Product from Polygonum cuspidatum Sieb. Et Zucc. Promotes Tat-Dependent HIV Latency Reversal through Triggering P-TEFb’s Release from 7SK snRNP

    PubMed Central

    Lu, Huasong; You, Hongchao; Ni, Man; Shan, Wenjun; Lin, Ting; Gao, Xiang; Chen, Haifeng; Zhou, Qiang; Xue, Yuhua

    2015-01-01

    The latent reservoirs of HIV represent a major impediment to eradication of HIV/AIDS. To overcome this problem, agents that can activate latent HIV proviruses have been actively sought after, as they can potentially be used in combination with the highly active antiretroviral therapy (HAART) to eliminate the latent reservoirs. Although several chemical compounds have been shown to activate latency, they are of limited use due to high toxicity and poor clinical outcomes. In an attempt to identify natural products as effective latency activators from traditional Chinese medicinal herbs that have long been widely used in human population, we have isolated procyanidin C-13,3',3"-tri-O-gallate (named as REJ-C1G3) from Polygonum cuspidatum Sieb. et Zucc., that can activate HIV in latently infected Jurkat T cells. REJ-C1G3 preferentially stimulates HIV transcription in a process that depends on the viral encoded Tat protein and acts synergistically with prostratin (an activator of the NF-κB pathway) or JQ1 (an inhibitor of Brd4) to activate HIV latency. Our mechanistic analyses further show that REJ-C1G3 accomplishes these tasks by inducing the release of P-TEFb, a host cofactor essential for Tat-activation of HIV transcription, from the cellular P-TEFb reservoir 7SK snRNP. PMID:26569506

  7. Recognition of the 3' splice site RNA by the U2AF heterodimer involves a dynamic population shift.

    PubMed

    Voith von Voithenberg, Lena; Sánchez-Rico, Carolina; Kang, Hyun-Seo; Madl, Tobias; Zanier, Katia; Barth, Anders; Warner, Lisa R; Sattler, Michael; Lamb, Don C

    2016-11-15

    An essential early step in the assembly of human spliceosomes onto pre-mRNA involves the recognition of regulatory RNA cis elements in the 3' splice site by the U2 auxiliary factor (U2AF). The large (U2AF65) and small (U2AF35) subunits of the U2AF heterodimer contact the polypyrimidine tract (Py-tract) and the AG-dinucleotide, respectively. The tandem RNA recognition motif domains (RRM1,2) of U2AF65 adopt closed/inactive and open/active conformations in the free form and when bound to bona fide Py-tract RNA ligands. To investigate the molecular mechanism and dynamics of 3' splice site recognition by U2AF65 and the role of U2AF35 in the U2AF heterodimer, we have combined single-pair FRET and NMR experiments. In the absence of RNA, the RRM1,2 domain arrangement is highly dynamic on a submillisecond time scale, switching between closed and open conformations. The addition of Py-tract RNA ligands with increasing binding affinity (strength) gradually shifts the equilibrium toward an open conformation. Notably, the protein-RNA complex is rigid in the presence of a strong Py-tract but exhibits internal motion with weak Py-tracts. Surprisingly, the presence of U2AF35, whose UHM domain interacts with U2AF65 RRM1, increases the population of the open arrangement of U2AF65 RRM1,2 in the absence and presence of a weak Py-tract. These data indicate that the U2AF heterodimer promotes spliceosome assembly by a dynamic population shift toward the open conformation of U2AF65 to facilitate the recognition of weak Py-tracts at the 3' splice site. The structure and RNA binding of the heterodimer was unaffected by cancer-linked myelodysplastic syndrome mutants.

  8. 16. DETAIL, VERTICAL MEMBER L2U2 FROM BELOW AND EAST. UNUSUALLY ...

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

    16. DETAIL, VERTICAL MEMBER L2-U2 FROM BELOW AND EAST. UNUSUALLY SHAPED DESIGN REFLECTS COLUMN STRESSES ALSO NOTE LACING, WHICH COMPRISES ANGLES RATHER THAN COMMON FLAT BARS - Coraopolis Bridge, Spanning Ohio River back channel at Ferree Street & Grand Avenue, Coraopolis, Allegheny County, PA

  9. Structure and Organization of the Engraulidae Family U2 snRNA: An Evolutionary Model Gene?

    PubMed

    Chairi, Hicham; Gonzalez, Laureana Rebordinos

    2015-04-01

    The U2 snRNA multigene family has been analyzed in four species of the Engraulidae family--Engraulis encrasicolus, Engraulis mordax, Engraulis ringens, and Engraulis japonicas--with the object of understanding more about the structure of this multigene family in these pelagic species and studying their phylogenetic relationships. The results showed that the cluster of this gene family in the Engraulis genus is formed by the U2-U5 snRNA with highly conserved sequences of mini- and micro-satellites, such as (CTGT)n, embedded downstream of the transcription unit; findings indicate that this gene family evolved following the concerted model. The phylogenetic analysis of the non-transcribed spacer of cluster U2-U5 snDNA in the 4 species showed that the sequences of the species E. encrasicolus and E. japonicus are closely related; these two are genetically close to E. mordax and slightly more distant from E. ringens. The data obtained by molecular analysis of U2-U5 snDNA and their secondary structure, with the presence of the micro-satellite (CTGT)n and mini-satellites, show clearly that the species E. encrasicolus and E. japonicus are closely related and would be older than E. mordax and E. ringens.

  10. Synthesis of phase-pure U2N3 microspheres and its decomposition into UN

    DOE PAGES

    Silva, Chinthaka M.; Hunt, Rodney Dale; Snead, Lance Lewis; ...

    2014-12-12

    Uranium mononitride (UN) is important as a nuclear fuel. Fabrication of UN in its microspherical form also has its own merits since the advent of the concept of accident-tolerant fuel, where UN is being considered as a potential fuel in the form of TRISO particles. But, not many processes have been well established to synthesize kernels of UN. Therefore, a process for synthesis of microspherical UN with a minimum amount of carbon is discussed herein. First, a series of single-phased microspheres of uranium sesquinitride (U2N3) were synthesized by nitridation of UO2+C microspheres at a few different temperatures. Resulting microspheres weremore » of low-density U2N3 and decomposed into low-density UN. The variation of density of the synthesized sesquinitrides as a function of its chemical composition indicated the presence of extra (interstitial) nitrogen atoms corresponding to its hyperstoichiometry, which is normally indicated as α-U2N3. Average grain sizes of both U2N3 and UN varied in a range of 1–2.5 μm. In addition, these had a considerably large amount of pore spacing, indicating the potential sinterability of UN toward its use as a nuclear fuel.« less

  11. Noble Gases in Giant Cluster IDP U2-20GCA

    NASA Astrophysics Data System (ADS)

    Pepin, R. O.; Palma, R. L.; Schlutter, D. J.; Brownlee, D. E.; Joswiak, D.

    2015-07-01

    Noble gas analyses of 15 particles from U2-20GCA reveal a suite of trapped 20Ne/22Ne ratios similar to HL-Ne, Q-Ne and SW-Ne. Highly spallogenic 21Ne/22Ne points to past residence in an environment of intense energetic proton radiation.

  12. Phenomenology of an S U (2 )1×S U (2 )2×U (1 )Y model at the LHC

    NASA Astrophysics Data System (ADS)

    Chen, Chuan-Hung; Nomura, Takaaki

    2017-01-01

    We investigate the implications of a minimal S U (2 ) gauge symmetry extension of the standard model at the LHC. To achieve the spontaneous symmetry breaking, a heavy Higgs doublet of the S U (2 ) is introduced. To obtain an anomaly-free model and the decays of new charged gauge bosons, we include a vectorlike quark doublet. We also employ a real scalar boson to dictate the heavy Higgs production via the gluon-gluon fusion processes. We find that the new gauge coupling and the masses of new gauge bosons can be strictly bounded by the electroweak ρ -parameter and dilepton resonance experiments at the LHC. We find that due to the new charged gauge boson enhancement, the cross sections for a heavy scalar boson to diphoton channel measured by ATLAS and CMS can be easily satisfied when the values of Yukawa couplings are properly taken. Furthermore, by adopting event simulation, we find that the significance of p p →(γ γ )H+jet , where the diphoton is from the heavy Higgs decay, can be over 4 σ when the luminosity is above 60 fb-1 .

  13. The ternary germanides UMnGe and U2Mn3Ge

    NASA Astrophysics Data System (ADS)

    Hoffmann, Rolf-Dieter; Pöttgen, Rainer; Chevalier, Bernard; Gaudin, Etienne; Matar, Samir F.

    2013-07-01

    The title compounds were prepared by induction levitation melting of the elemental components and subsequent annealing. UMnGe (Pnma, a = 686.12(9), b = 425.49(6) and c = 736.5(1) pm) adopts the orthorhombic structure of TiNiSi and U2Mn3Ge (P63/mmc, a = 524.3(2) and c = 799.2(3) pm) possesses the hexagonal Mg2Cu3Si-type structure (ordered variant of the hexagonal Laves phase MgZn2). Both structures were refined from X-ray powder data to residuals of RI = 0.021 and 0.014 for UMnGe and U2Mn3Ge, respectively. The manganese and germanium atoms in UMnGe build up a three-dimensional [MnGe] network of ordered Mn3Ge3 hexagons with Mn-Ge distances ranging from 248 to 259 pm. The uranium atoms are coordinated by two tilted Mn3Ge3 hexagons. The manganese atoms in U2Mn3Ge build up Kagomé networks with 252 and 272 pm Mn-Mn distances which are connected via the germanium atoms (254 pm Mn-Ge) to a three-dimensional network. A remarkable feature of the U2Mn3Ge structure is a short U-U distance of 278 pm between adjacent cavities of the [Mn3Ge] network. From DFT based electronic structure calculations both germanides are found more cohesive than the Laves phase UMn2, thus underpinning the substantial role of Mn-Ge bonding. Calculations for both germanides show ferrimagnetic ground states with antiparallel spin alignments between U and Mn. The valence bands show bonding characteristics for interactions of atoms of different chemical natures and significant Mn-Mn bonding in U2Mn3Ge. Preliminary investigation of UMnGe by magnetization measurements confirms an antiferromagnetic arrangement below TN = 240 K.

  14. Structure-guided U2AF65 variant improves recognition and splicing of a defective pre-mRNA

    PubMed Central

    Agrawal, Anant A.; McLaughlin, Krystle J.; Jenkins, Jermaine L.; Kielkopf, Clara L.

    2014-01-01

    Purine interruptions of polypyrimidine (Py) tract splice site signals contribute to human genetic diseases. The essential splicing factor U2AF65 normally recognizes a Py tract consensus sequence preceding the major class of 3′ splice sites. We found that neurofibromatosis- or retinitis pigmentosa-causing mutations in the 5′ regions of Py tracts severely reduce U2AF65 affinity. Conversely, we identified a preferred binding site of U2AF65 for purine substitutions in the 3′ regions of Py tracts. Based on a comparison of new U2AF65 structures bound to either A- or G-containing Py tracts with previously identified pyrimidine-containing structures, we expected to find that a D231V amino acid change in U2AF65 would specify U over other nucleotides. We found that the crystal structure of the U2AF65-D231V variant confirms favorable packing between the engineered valine and a target uracil base. The D231V amino acid change restores U2AF65 affinity for two mutated splice sites that cause human genetic diseases and successfully promotes splicing of a defective retinitis pigmentosa-causing transcript. We conclude that reduced U2AF65 binding is a molecular consequence of disease-relevant mutations, and that a structure-guided U2AF65 variant is capable of manipulating gene expression in eukaryotic cells. PMID:25422459

  15. Cleavage-induced termination in U2 snRNA gene expression

    SciTech Connect

    Nabavi, Sadeq; Nazar, Ross N.

    2010-03-12

    The maturation of many small nuclear RNAs is dependent on RNase III-like endonuclease mediated cleavage, which generates a loading site for the exosome complex that trims the precursor at its 3' end. Using a temperature sensitive Pac1 nuclease, here we show that the endonuclease cleavage is equally important in terminating the transcription of the U2 snRNA in Schizosaccharomyces pombe. Using a temperature sensitive Dhp1p 5' {yields} 3' exonuclease, we demonstrate that it also is an essential component of the termination pathway. Taken together the results support a 'reversed torpedoes' model for the termination and maturation of the U2 snRNA; the Pac1 endonuclease cleavage provides entry sites for the 3' and 5' exonuclease activities, leading to RNA maturation in one direction and transcript termination in the other.

  16. High altitude perspective. [cost-reimbursable services using NASA U-2 aircraft

    NASA Technical Reports Server (NTRS)

    1978-01-01

    The capabilities of the NASA Ames Center U-2 aircraft for research or experimental programs are described for such areas as Earth resources inventories; remote sensing data interpretation, electronic sensor research and development; satellite investigative support; stratospheric gas studies; and astronomy and astrophysics. The availability of this aircraft on a cost-reimbursable basis for use in high-altitude investigations that cannot be performed by the private sector is discussed.

  17. Cool aid? Health, wellbeing and place in the work of Bono and U2.

    PubMed

    Andrews, Gavin J; Kearns, Robin A; Kingsbury, Paul; Carr, Edward R

    2011-01-01

    Through a discussion of the sounds and statements of Bono and U2, this paper explores the ways in which music can work in particular spatial contexts, contributing towards both personal and population-wide health and wellbeing. We engage critically with the idea of celebrity diplomacy, and look beyond this notion to suggest ways in which the production, circulation and consumption of music warrants greater attention within the unfolding domain of health geography.

  18. Closure plan for Corrective Action Unit 109: U-2bu subsidence crater, Nevada Test Site, Nevada

    SciTech Connect

    1999-03-01

    The U-2bu subsidence crater, Corrective Action Unit 109, will be closed in accordance with the Resource Conservation and Recovery Act, the Nevada Division of Environmental Protection operational permit, and the Federal Facility Agreement and Consent Order. The U-2bu subsidence crater is located in Area 2 of the Nevada Test Site. It was created in 1971 by an underground nuclear test with the name Miniata. The crater has a diameter of 288 meters (944 feet) and an approximate depth of 35 meters (115 feet). Based on the results of the analyses reported in the site characterization report, the only constituents of concern in the U-2bu subsidence crater include leachable lead and total petroleum hydrocarbons. Closure activities will include the excavation and disposal of impacted soil from the top of the crater. Upon completion of excavation, verification samples will be collected to show that the leachable lead has been removed to concentrations below the regulatory action level. After sample results show that the lead has been removed, the excavated area will be backfilled and a soil flood diversion berm will be constructed as a best management practice. An independent registered professional engineer will certify the site was closed following the approved Closure Plan. Post-closure care is not warranted for this site because closure activities will involve removal of the Resource Conservation and Recovery Act constituents of concern.

  19. RCRA Part A permit characterization plan for the U-2bu subsidence crater. Revision 1

    SciTech Connect

    1998-04-01

    This plan presents the characterization strategy for Corrective Action Unit (CAU) 109, U-2bu Subsidence Crater (referred to as U-2bu) in Area 2 at the Nevada Test Site (NTS). The objective of the planned activities is to obtain sufficient characterization data for the crater soils and observed wastes under the conditions of the current Resource Conservation and Recovery Act (RCRA) Part A permit. The scope of the characterization plan includes collecting surface and subsurface soil samples with hand augers and for the purpose of site characterization. The sampling strategy is to characterize the study area soils and look for RCRA constituents. Observable waste soils and surrounding crater soils will be analyzed and evaluated according to RCRA closure criteria. Because of the status of the crater a RCRA Part A permit site, acquired radionuclide analyses will only be evaluated in regards to the health and safety of site workers and the disposition of wastes generated during site characterization. The U-2bu Subsidence Crater was created in 1971 by a Lawrence Livermore National Laboratory underground nuclear test, event name Miniata, and was used as a land-disposal unit for radioactive and hazardous waste from 1973 to 1988.

  20. Synthesis, characterization, in vitro antimicrobial, and U2OS tumoricidal activities of different coumarin derivatives

    PubMed Central

    2013-01-01

    Background Coumarin and its derivatives are biologically very active. It was found that the enhanced activities are dependent on the coumarin nucleus. Biological significance of these compounds include anti-bacterial, anti-thrombotic and vasodilatory, anti-mutagenic, lipoxygenase and cyclooxygenase inhibition, scavenging of reactive oxygen species, and anti-tumourigenic. Our interest in medicinal chemistry of dicoumarol compounds have been developed by keeping in view the importance of coumarins along with its derivatives in medicinal chemistry. All the synthesized compounds were fully characterized by spectroscopic and analytical techniques and were screened for antimicrobial and U2OS bone cancer activities. Results 4-hydroxycoumarin was derivatized by condensing with different aldehydes yielding the dicoumarol and translactonized products. Elemental analyses, ESI(+,−) MS, 1H and 13C{1H}-NMR, infrared spectroscopy and conductance studies were used to characterize the synthesized compounds which revealed the dicoumarol and dichromone structures for the compounds. The compounds were screened against U2OS cancerous cells and pathogenic micro organisms. The compounds with intermolecular H-bonding were found more active revealing a possible relationship among hydrogen bonding, cytotoxicity and antimicrobial activities. Conclusion Coumarin based drugs can be designed for the possible treatment of U2OS leukemia. PMID:23587363

  1. Magnetic anisotropy and spin-glass behavior in single crystalline U2PdSi3.

    PubMed

    Li, D X; Kimura, A; Haga, Y; Nimori, S; Shikama, T

    2011-02-23

    We present the magnetic and transport properties of single crystalline U(2)PdSi(3) measured with the magnetic field (H) (or measuring current, I) applied along two typical crystallographic directions, i.e. H ⊥ c-axis and H c-axis (or I ⊥ c-axis and I c-axis). For both directions, a spin-glass state is confirmed to form at low temperature with the same spin freezing temperature T(f) (=11.5 K), initial frequency shift δT(f) (=0.023) and activation energy E(a)/k(B) (=90.15 K) in zero dc field. Strong anisotropy in magnetic and transport behavior is found to be a significant feature of U(2)PdSi(3). The unusual ferromagnetic-like anomaly in ac susceptibility and dc magnetization curves around T(m)=71 K is observed in the case of H c-axis but not in the cases of H ⊥ c-axis. The characteristic temperature T(ir), below which evident irreversible magnetism originated from random spin freezing can be observed, shows much stronger field dependence for H ⊥ c-axis than for H c-axis. Moreover, an unusual finding is that the electrical resistivity measurements indicate the formation of magnetic Brillouin-zone boundary gaps and much larger magnetic scattering for I ⊥ c-axis, while the coherent-Kondo-effect-like behavior is obvious for I c-axis. We also emphasize that no resistivity minimum can be detected down to 2.5 K for either direction. The observed magnetic and transport behaviors are compared with those in polycrystalline U(2)PdSi(3) and other 2:1:3 intermetallic compounds.

  2. X-ray Structures of U2 snRNA-Branchpoint Duplexes Containing Conserved Pseudouridines

    SciTech Connect

    Lin,Y.; Kielkopf, C.

    2008-01-01

    A pseudouridine-modified region of the U2 small nuclear (sn)RNA anneals with the intronic branchpoint sequence and positions a bulged adenosine to serve as the nucleophile in the first chemical step of pre-mRNA splicing. We have determined three X-ray structures of RNA oligonucleotides containing the pseudouridylated U2 snRNA and the branchpoint consensus sequences. The expected adenosine branchpoint is extrahelical in a 1.65 Angstroms resolution structure containing the mammalian consensus sequence variant and in a 2.10 Angstroms resolution structure containing a shortened Saccharomyces cerevisiae consensus sequence. The adenosine adjacent to the expected branchpoint is extrahelical in a third structure, which contains the intact yeast consensus sequence at 1.57 Angstroms resolution. The hydration and base stacking interactions mediated by the U2 snRNA pseudouridines correlate with the identity of the unpaired adenosine. The expected adenosine bulge is associated with a well-stacked pseudouridine, which is linked via an ordered water molecule to a neighboring nucleotide. In contrast, the bulge of the adjacent adenosine shifts the base stacking and disrupts the water-mediated interactions of the pseudouridine. These structural differences may contribute to the ability of the pseudouridine modification to promote the bulged conformation of the branch site adenosine and to enhance catalysis by snRNAs. Furthermore, iodide binding sites are identified adjacent to the unconventional bulged adenosine, and the structure of the mammalian consensus sequence variant provides a high-resolution view of a hydrated magnesium ion bound in a similar manner to a divalent cation binding site of the group II intron.

  3. Structure and evolution of the U2 small nuclear RNA multigene family in primates: gene amplification under natural selection?

    PubMed Central

    Matera, A G; Weiner, A M; Schmid, C W

    1990-01-01

    The organization of U2 genes was compared in apes, Old World monkeys, and the prosimian galago. In humans and all apes (gibbon, orangutan, gorilla, and chimpanzee), the U2 genes were organized as a tandem repeat of a 6-kb element; however, the restriction maps of the 6-kb elements in these divergent species differed slightly, demonstrating that mechanisms must exist for maintaining sequence homogeneity within this tandem array. In Old World monkeys, the U2 genes were organized as a tandem repeat of an 11-kb element; the restriction maps of the 11-kb elements in baboon and two closely related macaques, bonnet and rhesus monkeys, also differed slightly, confirming that efficient sequence homogenization is an intrinsic property of the U2 tandem array. Interestingly, the 11-kb monkey repeat unit differed from the 6-kb hominid repeat unit by a 5-kb block of monkey-specific sequence. Finally, we found that the U2 genes of the prosimian galago were dispersed rather than tandemly repeated, suggesting that the hominid and Old World monkey U2 tandem arrays resulted from independent amplifications of a common ancestral U2 gene. Alternatively, the 5-kb monkey-specific sequence could have been inserted into the 6-kb array or deleted from the 11-kb array soon after divergence of the hominid and Old World monkey lineages. Images PMID:2233721

  4. The gene for pancreatic polypeptide (PPY) and the anonymous marker D17S78 are within 45 kb of each other on chromosome 17q21

    SciTech Connect

    Chandrasekharappa, S.C.; King, S.E.; Lee, Y.H.; Weber, B.L.; Collins, F.S. ); Friedman, L.; King, M.C. ); Welsch, P.; Bowcock, A.M. )

    1994-05-15

    A gene for early-onset breast and ovarian cancer (BRCA1) has been localized to a small region of chromosome 17q21. A combination of genetic linkage studies, radiation-reduced hybrid analysis, and physical mapping by FISH has identified several genes/markers that lie in this interval. Among these are the gene encoding pancreatic polypeptide (PPY) and a polymorphic marker at locus D17S78. Efforts to construct a physical map of this region by isolating a large number of yeast artificial chromosome (YAC) and cosmid clones demonstrate that PPY and D17S78 are present within the same cosmid clone, and therefore no farther than 45 kb apart. This observation takes on particular significance since it excludes a recently described BRCA1 candidate gene from the interval defined by meiotic mapping. Although PPY and D17S78 were found to be no farther than 45 kb apart, identification of a smaller fragment that hybridizes to both probes would indicate that these two are much closer. The probe p131 and the gene PPY were previously mapped to 17q21-q23 and to the proximal long arm of chromosome 17, respectively. The demonstration of the close proximity of these markers should allow them to be treated as a single locus in terms of long-range genomic mapping of this region, and the genomic clones isolated should serve as useful resources for the identification of the BRCA1 gene. Analysis of a large number of a familial and spordic breast and ovarian cancers has identified frequent loss of heterozygosity near the BRCA1 locus. A recent report has suggested the responsible interval lies just telomeric to PPY, and a suggested candidate gene (MCD) for BRCA1 was found to be somatically rearranged in two of several hundred sporadic breast tumors.

  5. Subjective experiences of watching stereoscopic Avatar and U2 3D in a cinema

    NASA Astrophysics Data System (ADS)

    Pölönen, Monika; Salmimaa, Marja; Takatalo, Jari; Häkkinen, Jukka

    2012-01-01

    A stereoscopic 3-D version of the film Avatar was shown to 85 people who subsequently answered questions related to sickness, visual strain, stereoscopic image quality, and sense of presence. Viewing Avatar for 165 min induced some symptoms of visual strain and sickness, but the symptom levels remained low. A comparison between Avatar and previously published results for the film U2 3D showed that sickness and visual strain levels were similar despite the films' runtimes. The genre of the film had a significant effect on the viewers' opinions and sense of presence. Avatar, which has been described as a combination of action, adventure, and sci-fi genres, was experienced as more immersive and engaging than the music documentary U2 3D. However, participants in both studies were immersed, focused, and absorbed in watching the stereoscopic 3-D (S3-D) film and were pleased with the film environments. The results also showed that previous stereoscopic 3-D experience significantly reduced the amount of reported eye strain and complaints about the weight of the viewing glasses.

  6. Structure and Reactivity of X-ray Amorphous Uranyl Peroxide, U2O7.

    PubMed

    Odoh, Samuel O; Shamblin, Jacob; Colla, Christopher A; Hickam, Sarah; Lobeck, Haylie L; Lopez, Rachel A K; Olds, Travis; Szymanowski, Jennifer E S; Sigmon, Ginger E; Neuefeind, Joerg; Casey, William H; Lang, Maik; Gagliardi, Laura; Burns, Peter C

    2016-04-04

    Recent accidents resulting in worker injury and radioactive contamination occurred due to pressurization of uranium yellowcake drums produced in the western U.S.A. The drums contained an X-ray amorphous reactive form of uranium oxide that may have contributed to the pressurization. Heating hydrated uranyl peroxides produced during in situ mining can produce an amorphous compound, as shown by X-ray powder diffraction of material from impacted drums. Subsequently, studtite, [(UO2)(O2)(H2O)2](H2O)2, was heated in the laboratory. Its thermal decomposition produced a hygroscopic anhydrous uranyl peroxide that reacts with water to release O2 gas and form metaschoepite, a uranyl-oxide hydrate. Quantum chemical calculations indicate that the most stable U2O7 conformer consists of two bent (UO2)(2+) uranyl ions bridged by a peroxide group bidentate and parallel to each uranyl ion, and a μ2-O atom, resulting in charge neutrality. A pair distribution function from neutron total scattering supports this structural model, as do (1)H- and (17)O-nuclear magnetic resonance spectra. The reactivity of U2O7 in water and with water in air is higher than that of other uranium oxides, and this can be both hazardous and potentially advantageous in the nuclear fuel cycle.

  7. Crystal structure of a model branchpoint-U2 snRNA duplex containing bulged adenosines.

    PubMed Central

    Berglund, J A; Rosbash, M; Schultz, S C

    2001-01-01

    Bulged nucleotides play a variety of important roles in RNA structure and function, frequently forming tertiary interactions and sometimes even participating in RNA catalysis. In pre-mRNA splicing, the U2 snRNA base pairs with the intron branchpoint sequence (BPS) to form a short RNA duplex that contains a bulged adenosine that ultimately serves as the nucleophile that attacks the 5' splice site. We have determined a 2.18-A resolution crystal structure of a self-complementary RNA designed to mimic the highly conserved yeast (Saccharomyces cerevisiae) branchpoint sequence (5'-UACUAACGUAGUA with the BPS italicized and the branchsite adenosine underlined) base paired with its complementary sequence from U2 snRNA. The structure shows a nearly ideal A-form helix from which two unpaired adenosines flip out. Although the adenosine adjacent to the branchsite adenosine is the one bulged out in the structure described here, either of these adenosines can serve as the nucleophile in mammalian but not in yeast pre-mRNA splicing. In addition, the packing of the bulged RNA helices within the crystal reveals a novel RNA tertiary interaction in which three RNA helices interact through bulged adenosines in the absence of any divalent metal ions. PMID:11350032

  8. Electronic transport in the ferromagnetic pyrochlore L u2V2O7 : Role of magnetization

    NASA Astrophysics Data System (ADS)

    Zhang, Xiaohang; Zhou, Haidong; Yu, Liuqi; Gardner, H. Jeffery; von Molnár, Stephan; Wiebe, Christopher; Xiong, Peng

    2015-05-01

    This paper reports on a study of the resistivity and Hall effect of the ferromagnetic pyrochlore L u2V2O7 . The temperature dependence of the resistivity of single crystalline L u2V2O7 exhibits overall activation behavior with a metalliclike exception at intermediate temperatures near the Curie temperature (TC). This temperature dependence bears a surprising resemblance to that of doped semiconductors. The ferromagnetic oxide shows a negative magnetoresistance (MR) which scales quadratically with the reduced magnetization at temperatures above TC; however, the scaling factor is significantly smaller than the value expected for a ferromagnetic system in the pure spin scattering regime, which suggests that other scattering processes may be at work. Concomitant with the negative MR, a distinct switch in the Hall resistivity slope is observed at temperatures near TC. Our analysis suggests that the nonlinear Hall effect is associated with a change in the effective carrier density at a constant critical magnetization induced by an external magnetic field. We argue that within a picture that incorporates high temperature activation transport with a magnetization-driven charge percolation transition, the observed complex electronic transport in the ferromagnetic pyrochlore can be quantitatively described.

  9. Closure Plan for Corrective Action Unit 109: U-2bu Subsidence Crater Nevada Test Site, Nevada

    SciTech Connect

    Shannon Parsons

    1999-03-01

    The U-2bu subsidence crater, Corrective Action Unit 109, will be closed in accordance with the Resource Conservation and Recovery Act, the Nevada Division of Environmental Protection operational permit, and the Federal Facilities Agreement and Consent Order. The U-2bu subsidence crater is located in Area 2 of the Nevada Test Site. It was created in 1971 by an underground nuclear test with the name Miniata. The crater has a diameter of 288 meters (944 feet) and an approximate depth of 35 meters (115 feet). The subsidence crater was used as a land disposal unit for radioactive and hazardous waste from 1973 to 1988. Site disposal history is supported by memorandums, letters, and personnel who worked at the Nevada Test Site at the time of active disposal. Closure activities will include the excavation and disposal of impacted soil form the tip of the crater. Upon completion of excavation, verification samples will be collected to show that lead has been removed to concentrations be low regulatory action level. The area will then be backfilled and a soil flood diversion berm will be constructed, and certified by an independent professional engineer as to having followed the approved Closure Plan.

  10. U-2 with fictitious NASA markings to support CIA cover story for pilot Gary Powers, shot down over S

    NASA Technical Reports Server (NTRS)

    1960-01-01

    After Francis Gary Powers was shot down over the Soviet Union during a CIA spy flight on 1 May 1960, NASA issued a press release with a cover story about a U-2 conducting weather research that may have strayed off course after the pilot 'reported difficulties with his oxygen equipment.' To bolster the cover-up, a U-2 was quickly painted in NASA markings, with a fictitious NASA serial number, and put on display for the news media at the NASA Flight Research Center at Edwards Air Force Base on 6 May 1960. The next day, Soviet Premier Nikita Kruschev exposed the cover-up by revealing that the pilot had been captured, and espionage equipment had been recovered from the wreckage. 7 May 1956 - NACA Director Dr. Hugh L. Dryden issues a press release stating that U-2 aircraft are conducting weather research for NACA with Air Force support from Watertown, Nevada. 22 May 1956 - A second press release is issued with cover story for U-2 aircraft operating overseas. 1 May 1960 - Francis Gary Powers is shot down near Sverdlovsk. 6 May 1960 - U-2 with fictitious NASA serial number and NASA markings is shown to news media to bolster cover story of NASA weather research flights with U-2. 7 May 1960 - Soviet Premier Kruschev announces capture and confession of Powers. 1960 - Dr. Hugh L. Dryden tells senate committee that some 200 U-2 flights carrying NASA weather instrumentation have taken place since 1956. 2 April 1971 - NASA receives two U-2C aircraft for high-altitude research.

  11. UHM–ULM interactions in the RBM39–U2AF65 splicing-factor complex

    SciTech Connect

    Stepanyuk, Galina A.; Serrano, Pedro; Peralta, Eigen; Farr, Carol L.; Axelrod, Herbert L.; Geralt, Michael; Das, Debanu; Chiu, Hsiu-Ju; Jaroszewski, Lukasz; Deacon, Ashley M.; Lesley, Scott A.; Elsliger, Marc-André; Godzik, Adam; Wilson, Ian A.; Wüthrich, Kurt; Salomon, Daniel R.; Williamson, James R.

    2016-03-24

    RNA-binding protein 39 (RBM39) is a splicing factor and a transcriptional co-activator of estrogen receptors and Jun/AP-1, and its function has been associated with malignant progression in a number of cancers. The C-terminal RRM domain of RBM39 belongs to the U2AF homology motif family (UHM), which mediate protein–protein interactions through a short tryptophan-containing peptide known as the UHM-ligand motif (ULM). Here, crystal and solution NMR structures of the RBM39-UHM domain, and the crystal structure of its complex with U2AF65-ULM, are reported. The RBM39–U2AF65 interaction was confirmed by co-immunoprecipitation from human cell extracts, by isothermal titration calorimetry and by NMR chemical shift perturbation experiments with the purified proteins. When compared with related complexes, such as U2AF35–U2AF65 and RBM39–SF3b155, the RBM39-UHM–U2AF65-ULM complex reveals both common and discriminating recognition elements in the UHM–ULM binding interface, providing a rationale for the known specificity of UHM–ULM interactions. This study therefore establishes a structural basis for specific UHM–ULM interactions by splicing factors such as U2AF35, U2AF65, RBM39 and SF3b155, and a platform for continued studies of intermolecular interactions governing disease-related alternative splicing in eukaryotic cells.

  12. RNA structure replaces the need for U2AF2 in splicing

    PubMed Central

    Lin, Chien-Ling; Taggart, Allison J.; Lim, Kian Huat; Cygan, Kamil J.; Ferraris, Luciana; Creton, Robbert; Huang, Yen-Tsung; Fairbrother, William G.

    2016-01-01

    RNA secondary structure plays an integral role in catalytic, ribosomal, small nuclear, micro, and transfer RNAs. Discovering a prevalent role for secondary structure in pre-mRNAs has proven more elusive. By utilizing a variety of computational and biochemical approaches, we present evidence for a class of nuclear introns that relies upon secondary structure for correct splicing. These introns are defined by simple repeat expansions of complementary AC and GT dimers that co-occur at opposite boundaries of an intron to form a bridging structure that enforces correct splice site pairing. Remarkably, this class of introns does not require U2AF2, a core component of the spliceosome, for its processing. Phylogenetic analysis suggests that this mechanism was present in the ancestral vertebrate lineage prior to the divergence of tetrapods from teleosts. While largely lost from land dwelling vertebrates, this class of introns is found in 10% of all zebrafish genes. PMID:26566657

  13. RNA structure replaces the need for U2AF2 in splicing.

    PubMed

    Lin, Chien-Ling; Taggart, Allison J; Lim, Kian Huat; Cygan, Kamil J; Ferraris, Luciana; Creton, Robbert; Huang, Yen-Tsung; Fairbrother, William G

    2016-01-01

    RNA secondary structure plays an integral role in catalytic, ribosomal, small nuclear, micro, and transfer RNAs. Discovering a prevalent role for secondary structure in pre-mRNAs has proven more elusive. By utilizing a variety of computational and biochemical approaches, we present evidence for a class of nuclear introns that relies upon secondary structure for correct splicing. These introns are defined by simple repeat expansions of complementary AC and GT dimers that co-occur at opposite boundaries of an intron to form a bridging structure that enforces correct splice site pairing. Remarkably, this class of introns does not require U2AF2, a core component of the spliceosome, for its processing. Phylogenetic analysis suggests that this mechanism was present in the ancestral vertebrate lineage prior to the divergence of tetrapods from teleosts. While largely lost from land dwelling vertebrates, this class of introns is found in 10% of all zebrafish genes.

  14. The splicing factor U2AF65 is functionally conserved in the thermotolerant deep-sea worm Alvinella pompejana.

    PubMed

    Henscheid, Kristy L; Shin, David S; Cary, S Craig; Berglund, J Andrew

    2005-03-10

    Due to their inherent stability, thermophilic bacteria and archaea serve as important resources for biochemical and biophysical analyses of many biological processes. Unfortunately, scientists characterizing eukaryote-specific processes, such as nuclear pre-mRNA splicing, are unable to take advantage of these sources of thermostable proteins. To identify and provide a source of thermostable eukaryotic proteins, we are characterizing splicing factors in the thermotolerant deep-sea vent polychaete, Alvinella pompejana. This worm, also known as the Pompeii worm, is found in the extreme environment of deep-sea hydrothermal vents, and is one of the most thermotolerant eukaryotic organisms known. We report on detailed analyses of U2AF65, the large subunit of the U2 small nuclear ribonucleoprotein auxiliary factor, an essential splicing factor important for intron definition and alternative splicing. The cloning and characterization of Pompeii U2AF65 show it is highly similar to human U2AF65 in sequence and function and is more thermostable than the human protein when bound to RNA in vitro. Notably, Pompeii U2AF65 can restore splicing in a human extract depleted of human U2AF. We also determine that the general splicing mechanisms and signal sequences are conserved in the Pompeii worm, an annelid which has previously been uncharacterized in terms of splicing factors and signals.

  15. Antibacterial Activity of Elephant Garlic and Its Effect against U2OS Human Osteosarcoma Cells

    PubMed Central

    Huang, Zehao; Ren, Jianwu

    2013-01-01

    Objective(s): The present study was designed to investigate the antibacterial function and pharmacological effect of elephant garlic (Allium ampeloprasum var. ampeloprasum) on U2OS human osteosarcoma cells. Materials and Methods: Seven kinds of bacteria were reconstituted, inoculated and tested in this research to evaluate elephant garlic antibacterial activity. By the means of FACS analysis, cell proliferation assay, confocal laser scanning microscopy and Transwell migration assays, the effect of elephant garlic against U2OS human osteosarcoma cells was unveiled. Rerults: The antimicrobial activity of elephant garlic was stronger than ampicillin when used against Escherichia coli, Bacillus subtilis, Bacillus thuringiensis, Staphylococcus actinomycetes, and gray actinomycetes. Even at a very low concentration (12.5%), elephant garlic still had an antibacterial effect on common bacteria E. coli and S. aureus. The G0/G1 ratio of elephant garlic treated group cells increased while S phase decreased. Elephant garlic extract inhibited the growth of human osteosarcoma cells, U2OS, through preventing the transition from G1 phase to S phase. It reduced osteosarcoma cell, U2OS, invasion ability and significantly increased the proportion of apoptosis. It significantly affected the cytoskeleton generation. Conclusion: Elephant garlic exhibits antibacterial property and has an inhibitory effect on osteosarcoma cells (U2OS) proliferation and cell activity, suggesting the mechanism of its anticancer effects on U2OS human osteosarcoma cells. PMID:24379966

  16. Structural Basis for Polypyrimidine Tract Recognition by the Essential Pre-mRNA Splicing Factor U2AF65

    SciTech Connect

    Sickmier,E.; Frato, K.; Shen, H.; Paranawithana, S.; Green, M.; Kielkopf, C.

    2006-01-01

    The essential pre-mRNA splicing factor, U2AF{sup 65}, guides the early stages of splice site choice by recognizing a polypyrimidine (Py)-tract consensus sequence near the 3'-splice site. Since Py-tracts are relatively poorly conserved in higher eukaryotes, U2AF{sup 65} is faced with the problem of specifying uridine-rich sequences, yet tolerating a variety of nucleotide substitutions found in natural Py-tracts. To better understand these apparently contradictory RNA binding characteristics, the X-ray structure of the U2AF{sup 65} RNA binding domain bound to a Py-tract composed of seven uridines has been determined at 2.5Angstroms resolution. Specific hydrogen bonds between U2AF{sup 65} and the uracil bases provide an explanation for polyuridine recognition. Flexible sidechains and bound water molecules form the majority of the base contacts, and potentially could rearrange when the U2AF{sup 65} structure adapts to different Py-tract sequences. The energetic importance of conserved residues for Py-tract binding is established by analysis of site-directed mutant U2AF{sup 65} proteins using surface plasmon resonance.

  17. Gadolinium chloride elicits apoptosis in human osteosarcoma U-2 OS cells through extrinsic signaling, intrinsic pathway and endoplasmic reticulum stress.

    PubMed

    Tsai, Yuh-Feng; Huang, Ching-Wen; Chiang, Jo-Hua; Tsai, Fuu-Jen; Hsu, Yuan-Man; Lu, Chi-Cheng; Hsiao, Chen-Yu; Yang, Jai-Sing

    2016-12-01

    Gadolinium (Gd) compounds are important as magnetic resonance imaging (MRI) contrast agents, and are potential anticancer agents. However, no report has shown the effect of gadolinium chloride (GdCl3) on osteosarcoma in vitro. The present study investigated the apoptotic mechanism of GdCl3 on human osteosarcoma U-2 OS cells. Our results indicated that GdCl3 significantly reduced cell viability of U-2 OS cells in a concentration-dependent manner. GdCl3 led to apoptotic cell shrinkage and DNA fragmentation in U-2 OS cells as revealed by morphologic changes and TUNEL staining. Colorimetric assay analyses also showed that activities of caspase-3, caspase-8, caspase-9 and caspase-4 occurred in GdCl3-treated U-2 OS cells. Pretreatment of cells with pan-caspase inhibitor (Z-VAD-FMK) and specific inhibitors of caspase-3/-8/-9 significantly reduced cell death caused by GdCl3. The increase of cytoplasmic Ca2+ level, ROS production and the decrease of mitochondria membrane potential (ΔΨm) were observed by flow cytometric analysis in U-2 OS cells after GdCl3 exposure. Western blot analyses demonstrated that the levels of Fas, FasL, cytochrome c, Apaf-1, GADD153 and GRP78 were upregulated in GdCl3-treated U-2 OS cells. In conclusion, death receptor, mitochondria-dependent and endoplasmic reticulum (ER) stress pathways contribute to GdCl3-induced apoptosis in U-2 OS cells. GdCl3 might have potential to be used in treatment of osteosarcoma patients.

  18. Useful to Usable (U2U): Transforming Climate Variability and Change Information for Cereal Crop Producers

    NASA Astrophysics Data System (ADS)

    Niyogi, D.; Andresen, J.

    2011-12-01

    Corn and soybean production contributes over $100 billion annually to the U.S. economy, most of which comes from the intensely cultivated corn-belt region of the Midwest. Successful crop production in this region is highly dependent on favorable temperatures and appropriate precipitation patters, making this industry vulnerable to changes in climate patterns. Though predictive models are constantly improving, there are gaps in our understanding of how different management practices can be used to help farmers adapt to changes in climate while maintaining economic viability. Furthermore, currently available tools and models are not meeting producers' needs, and little is known about the types of information they would like to access. Useful to Usable (U2U): Transforming Climate Variability and Change Information for Cereal Crop Producers is an integrated research and extension project that seeks to improve the resilience and profitability of farms in the North Central Region amid variable climate change through the development and dissemination of improved decision support tools, resource materials, and training. The goal is to work closely with producers to help them make better long-term plans on what, when and where to plant, and also how to manage crops for maximum yields and minimum environmental damage. The U2U team is composed of a uniquely qualified group of climatologists, crop modelers, agronomists, economists, and social scientists from 10 partner universities across the Midwest. Over the span of 5 years, collaborators will complete tasks associated with 5 objectives that will enhance the usability of climate information for the agricultural community and lead to more sustainable farming operations. First the team will produce research on the biophysical and economic impacts of different climate scenarios on corn and soybean yields in the North Central Region (objective 1) and conduct complementary research to understand how producers and advisors are

  19. A comparative proteomics study on matrix vesicles of osteoblast-like Saos-2 and U2-OS cells.

    PubMed

    Jiang, Liang; Cui, Yazhou; Luan, Jing; Zhou, Xiaoyan; Zhou, Xiaoying; Han, Jinxiang

    2013-05-01

    Matrix vesicles (MVs) play an important role in the initial stage of the process of bone mineralization, and are involved in multiple rare skeletal diseases with pathological mineralization or calcification. The aim of the study was to compare the proteomic profiling of osteoblast-like cells with and without mineralization ability (Saos-2 and U2-OS), and to identify novel mineralization-associated MV proteins. MVs were extracted using ExoQuick solution from mineralization-induced Saos-2 and U2-OS cells, and then were validated by transmission electron microscopy. A label-free quantitative proteomic method was used to compare the protein profiling of MVs from Saos-2 and U2-OS cells. Western-blots were used to confirm the expression of MVs proteins identified in proteomic studies. In our proteomic studies, we identified that 89 mineralization-related proteins were significantly up-regulated in Saos-2 MVs compared with U2-OS MVs. We further validated that two MVs proteins, protein kinase C α and ras-related protein Ral-A, were up-regulated in MVs of Saos-2 cells compared to those of U2-OS cells under mineralization-induction. Our findings suggest that protein kinase C α and ras-related protein Ral-A might be involved in bone mineralization as MVs components.

  20. Gap formation in the semimetal U 2Ru 2Sn: evidence from 119Sn NMR investigations

    NASA Astrophysics Data System (ADS)

    Baenitz, M.; Rabis, A.; Paschen, S.; Senthilkumaran, N.; Steglich, F.; Tran, V. H.; de V. du Plessis, P.; Strydom, A. M.

    2003-05-01

    We report measurements of the 119Sn nuclear spin-lattice relaxation rate 1/ T1 and the Knight shift K for polycrystalline U 2Ru 2Sn powder samples as a function of temperature. The T dependence of 1/ T1 is very similar to that of CeNiSn with the only difference that the temperature scale is increased roughly by a factor of 10. Therefore a first estimate gives a (pseudo-) gap value of Δ/k B≈140 K ( ≈14 K for CeNiSn). At low temperatures similar to CeNiSn a T1T=constant behaviour is observed which indicates the presence of a residual density of states at the Fermi level N( EF) in the pseudo-gap. Knight shift measurements on oriented polycrystalline powder samples show nearly no magnetic anisotropy, whereas the temperature dependence roughly follows the behaviour of the magnetic susceptibility. First investigations on the non-magnetic reference compound Th 2Ru 2Sn are also discussed.

  1. U2 8 + -intensity record applying a H2 -gas stripper cell

    NASA Astrophysics Data System (ADS)

    Barth, Winfried; Adonin, Aleksey; Düllmann, Christoph E.; Heilmann, Manuel; Hollinger, Ralph; Jäger, Egon; Khuyagbaatar, Jadambaa; Krier, Joerg; Scharrer, Paul; Vormann, Hartmut; Yakushev, Alexander

    2015-04-01

    To meet the Facility for Antiproton and Ion Research science requirements higher beam intensity has to be achieved in the present GSI-accelerator complex. For this an advanced upgrade program for the UNILAC is ongoing. Stripping is a key technology for all heavy ion accelerators. For this an extensive research and development program was carried out to optimize for high brilliance heavy ion operation. After upgrade of the supersonic N2 -gas jet (2007), implementation of high current foil stripping (2011) and preliminary investigation of H2 -gas jet operation (2012), recently (2014) a new H2 -gas cell using a pulsed gas regime synchronized with arrival of the beam pulse has been developed. An obviously enhanced stripper gas density as well as a simultaneously reduced gas load for the pumping system result in an increased stripping efficiency, while the beam emittance remains the same. A new record intensity (7.8 emA) for 238U2 8 + beams at 1.4 MeV /u has been achieved applying the pulsed high density H2 stripper target to a high intensity 238U4 + beam from the VARIS ion source with a newly developed extraction system. The experimental results are presented in detail.

  2. An Atlas of extraterrestrial particles collected with NASA U-2 aircraft, 1974 - 1976

    NASA Technical Reports Server (NTRS)

    Brownlee, D. E.; Tomandl, D.; Blanchard, M. B.; Ferry, G. V.; Kyte, F.

    1976-01-01

    Extraterrestrial particles collected during U-2 flights in the stratosphere were divided into four groups: chondritic, iron-sulfur--nickel, mafic silicates, and others. The chondritic aggregates are typically composed of Fe, Mg, Si, C, S, Ca, and Ni. Detectable levels of He-4 implanted from the solar wind occur in some. Olivine, spinel, and possibly pyrrhotite and a hydrated layered-lattice silicate were identified. The chondritic ablation particles contain no sulfur and appear to have been melted. Magnetite, olivine, and pyroxene were identified. The iron-sulfur-nickel type particles resemble meteoritic iron sulfide with a small amount of nickel, and contain magnetite and troilite. The mafic silicate type particles are iron magnesium silicate grains with clumps of chondritic aggregate particles adhering to their surfaces. Olivine and possibly pyrrhotite and pyroxene were identified. Most of the iron-nickel type particles are spherules and include taenite and wustite. The other type particles include nickel-iron mounds on spheroidal glassy-like grains having chondritic-like elemental abundances.

  3. On the oscillator realization of conformal U(2, 2) quantum particles and their particle-hole coherent states

    NASA Astrophysics Data System (ADS)

    Calixto, M.; Pérez-Romero, E.

    2014-08-01

    We revise the unireps. of U(2, 2) describing conformal particles with continuous mass spectrum from a many-body perspective, which shows massive conformal particles as compounds of two correlated massless particles. The statistics of the compound (boson/fermion) depends on the helicity h of the massless components (integer/half-integer). Coherent states (CS) of particle-hole pairs ("excitons") are also explicitly constructed as the exponential action of exciton (non-canonical) creation operators on the ground state of unpaired particles. These CS are labeled by points Z (2 × 2 complex matrices) on the Cartan-Bergman domain {D}_4=U(2,2)/U(2)^2, and constitute a generalized (matrix) version of Perelomov U(1, 1) coherent states labeled by points z on the unit disk {D}_1=U(1,1)/U(1)^2. First, we follow a geometric approach to the construction of CS, orthonormal basis, U(2, 2) generators and their matrix elements and symbols in the reproducing kernel Hilbert space H_λ ({D}_4) of analytic square-integrable holomorphic functions on {D}_4, which carries a unitary irreducible representation of U(2, 2) with index λ in {N} (the conformal or scale dimension). Then we introduce a many-body representation of the previous construction through an oscillator realization of the U(2, 2) Lie algebra generators in terms of eight boson operators with constraints. This particle picture allows us for a physical interpretation of our abstract mathematical construction in the many-body jargon. In particular, the index λ is related to the number 2(λ - 2) of unpaired quanta and to the helicity h = (λ - 2)/2 of each massless particle forming the massive compound.

  4. Structure of U2 snRNA genes of Arabidopsis thaliana and their expression in electroporated plant protoplasts

    PubMed Central

    Vankan, Pierre; Filipowicz, Witold

    1988-01-01

    We have characterized the U2 snRNA gene family in the higher plant Arabidopsis thaliana. It consists of 10-15 genes which do not appear to be closely clustered. Six of the U2 genes were sequenced and the structure of the Arabidopsis U2 RNA termini was determined in order to define the coding regions. Each of the genes codes for a distinct RNA differing from the others by 2-13 point mutations, localized in the 3' part of the 196 nt-long RNA. The upstream non-coding regions of all genes show strong sequence similarity in positions −81 to −1 and contain three highly conserved sequence elements: GTCCCACATCG (positions −78 to −68; 100% conservation), GTAGTATAAATA (−37 to −26) and CAANTC (−6 to −1). The coding regions are followed by the sequence CAN7-9AGTNNAA, a putative termination signal. The expression of three of the genes was studied in electroporated Orychophragmus violaceus and Nicotiana tabacum protoplasts. The genes, one of which contains a T → C change in the Sm antigen binding site, were actively transcribed and processed into U2 RNAs of the expected size and containing trimethylguanosine caps. Deletion analysis indicates that sequences upstream of the conserved −80 to −1 region are not important for transcription in protoplasts. The 5'-terminal parts of U2 RNAs from several monocot and dicot plants were sequenced. This region, containing the sequence implicated in base-pairing with the branch point in pre-mRNA introns, is identical in all U2 RNAs examined. Images PMID:16453831

  5. On the oscillator realization of conformal U(2, 2) quantum particles and their particle-hole coherent states

    SciTech Connect

    Calixto, M. Pérez-Romero, E.

    2014-08-01

    We revise the unireps. of U(2, 2) describing conformal particles with continuous mass spectrum from a many-body perspective, which shows massive conformal particles as compounds of two correlated massless particles. The statistics of the compound (boson/fermion) depends on the helicity h of the massless components (integer/half-integer). Coherent states (CS) of particle-hole pairs (“excitons”) are also explicitly constructed as the exponential action of exciton (non-canonical) creation operators on the ground state of unpaired particles. These CS are labeled by points Z (2×2 complex matrices) on the Cartan-Bergman domain D₄=U(2,2)/U(2)², and constitute a generalized (matrix) version of Perelomov U(1, 1) coherent states labeled by points z on the unit disk D₁=U(1,1)/U(1)². First, we follow a geometric approach to the construction of CS, orthonormal basis, U(2, 2) generators and their matrix elements and symbols in the reproducing kernel Hilbert space H{sub λ}(D₄) of analytic square-integrable holomorphic functions on D₄, which carries a unitary irreducible representation of U(2, 2) with index λϵN (the conformal or scale dimension). Then we introduce a many-body representation of the previous construction through an oscillator realization of the U(2, 2) Lie algebra generators in terms of eight boson operators with constraints. This particle picture allows us for a physical interpretation of our abstract mathematical construction in the many-body jargon. In particular, the index λ is related to the number 2(λ – 2) of unpaired quanta and to the helicity h = (λ – 2)/2 of each massless particle forming the massive compound.

  6. Exploring center strings in S U (2 ) and S U (3 ) relativistic Yang-Mills-Higgs models

    NASA Astrophysics Data System (ADS)

    Oxman, L. E.; Vercauteren, D.

    2017-01-01

    We develop numerical tools and apply them to solve the relativistic Yang-Mills-Higgs equations in a model where the S U (N ) symmetry is spontaneously broken to its center. In S U (2 ) and S U (3 ), we obtain the different field profiles for infinite and finite center strings, with end points at external monopole sources. Exploration of parameter space permits the detection of a region where the equations get Abelianized. Finally, a general parametrization of the color structure of S U (2 ) fields leads us to a reference point where an Abelian-like Bogomol'nyi-Prasad-Sommereld (BPS) bound is reconciled with N -ality.

  7. U(2)⁵ flavor symmetry and lepton universality violation in W→τν̄τ

    SciTech Connect

    Filipuzzi, Alberto; Portolés, Jorge; González-Alonso, Martín

    2012-06-26

    The seeming violation of universality in the τ lepton coupling to the W boson suggested by LEP-II data is studied using an effective field theory (EFT) approach. Within this framework we explore how this feature fits into the current constraints from electroweak precision observables using different assumptions about the flavor structure of New Physics, namely [U(2)×U(1)]⁵ and U(2)⁵. We show the importance of leptonic and semileptonic tau decay measurements, giving 3–4 TeV bounds on the New Physics effective scale at 90% C.L. We conclude under very general assumptions that it is not possible to accommodate this deviation from universality in the EFT framework, and thus such a signal could only be explained by the introduction of light degrees of freedom or New Physics strongly coupled at the electroweak scale.

  8. U(2)⁵ flavor symmetry and lepton universality violation in W→τν̄τ

    DOE PAGES

    Filipuzzi, Alberto; Portolés, Jorge; González-Alonso, Martín

    2012-06-26

    The seeming violation of universality in the τ lepton coupling to the W boson suggested by LEP-II data is studied using an effective field theory (EFT) approach. Within this framework we explore how this feature fits into the current constraints from electroweak precision observables using different assumptions about the flavor structure of New Physics, namely [U(2)×U(1)]⁵ and U(2)⁵. We show the importance of leptonic and semileptonic tau decay measurements, giving 3–4 TeV bounds on the New Physics effective scale at 90% C.L. We conclude under very general assumptions that it is not possible to accommodate this deviation from universality inmore » the EFT framework, and thus such a signal could only be explained by the introduction of light degrees of freedom or New Physics strongly coupled at the electroweak scale.« less

  9. GROMOS polarizable charge-on-spring models for liquid urea: COS/U and COS/U2.

    PubMed

    Lin, Zhixiong; Bachmann, Stephan J; van Gunsteren, Wilfred F

    2015-03-07

    Two one-site polarizable urea models, COS/U and COS/U2, based on the charge-on-spring model are proposed. The models are parametrized against thermodynamic properties of urea-water mixtures in combination with the polarizable COS/G2 and COS/D2 models for liquid water, respectively, and have the same functional form of the inter-atomic interaction function and are based on the same parameter calibration procedure and type of experimental data as used to develop the GROMOS biomolecular force field. Thermodynamic, dielectric, and dynamic properties of urea-water mixtures simulated using the polarizable models are closer to experimental data than using the non-polarizable models. The COS/U and COS/U2 models may be used in biomolecular simulations of protein denaturation.

  10. GROMOS polarizable charge-on-spring models for liquid urea: COS/U and COS/U2

    SciTech Connect

    Lin, Zhixiong; Bachmann, Stephan J.; Gunsteren, Wilfred F. van

    2015-03-07

    Two one-site polarizable urea models, COS/U and COS/U2, based on the charge-on-spring model are proposed. The models are parametrized against thermodynamic properties of urea-water mixtures in combination with the polarizable COS/G2 and COS/D2 models for liquid water, respectively, and have the same functional form of the inter-atomic interaction function and are based on the same parameter calibration procedure and type of experimental data as used to develop the GROMOS biomolecular force field. Thermodynamic, dielectric, and dynamic properties of urea-water mixtures simulated using the polarizable models are closer to experimental data than using the non-polarizable models. The COS/U and COS/U2 models may be used in biomolecular simulations of protein denaturation.

  11. The NASA Thunderstorm Overflight Program (TOP): Research in atmospheric electricity from an instrumented U-2 aircraft platform

    NASA Technical Reports Server (NTRS)

    Vaughan, O. H., Jr.

    1983-01-01

    An overview of the NASA Thunderstorm Overflight Program (TOP) is presented. The various instruments flown on the NASA U-2 aircraft, as well as the ground instrumentation used to collect optical and electronic signature from the lightning events, are discussed. Samples of some of the photographic and electronic signatures are presented. Approximately 6400 electronic data samples of optical pulses were collected and are being analyzed.

  12. Ancient Origin of the U2 Small Nuclear RNA Gene-Targeting Non-LTR Retrotransposons Utopia

    PubMed Central

    Kojima, Kenji K.

    2015-01-01

    Most non-long terminal repeat (non-LTR) retrotransposons encoding a restriction-like endonuclease show target-specific integration into repetitive sequences such as ribosomal RNA genes and microsatellites. However, only a few target-specific lineages of non-LTR retrotransposons are distributed widely and no lineage is found across the eukaryotic kingdoms. Here we report the most widely distributed lineage of target sequence-specific non-LTR retrotransposons, designated Utopia. Utopia is found in three supergroups of eukaryotes: Amoebozoa, SAR, and Opisthokonta. Utopia is inserted into a specific site of U2 small nuclear RNA genes with different strength of specificity for each family. Utopia families from oomycetes and wasps show strong target specificity while only a small number of Utopia copies from reptiles are flanked with U2 snRNA genes. Oomycete Utopia families contain an “archaeal” RNase H domain upstream of reverse transcriptase (RT), which likely originated from a plant RNase H gene. Analysis of Utopia from oomycetes indicates that multiple lineages of Utopia have been maintained inside of U2 genes with few copy numbers. Phylogenetic analysis of RT suggests the monophyly of Utopia, and it likely dates back to the early evolution of eukaryotes. PMID:26556480

  13. Ancient Origin of the U2 Small Nuclear RNA Gene-Targeting Non-LTR Retrotransposons Utopia.

    PubMed

    Kojima, Kenji K; Jurka, Jerzy

    2015-01-01

    Most non-long terminal repeat (non-LTR) retrotransposons encoding a restriction-like endonuclease show target-specific integration into repetitive sequences such as ribosomal RNA genes and microsatellites. However, only a few target-specific lineages of non-LTR retrotransposons are distributed widely and no lineage is found across the eukaryotic kingdoms. Here we report the most widely distributed lineage of target sequence-specific non-LTR retrotransposons, designated Utopia. Utopia is found in three supergroups of eukaryotes: Amoebozoa, SAR, and Opisthokonta. Utopia is inserted into a specific site of U2 small nuclear RNA genes with different strength of specificity for each family. Utopia families from oomycetes and wasps show strong target specificity while only a small number of Utopia copies from reptiles are flanked with U2 snRNA genes. Oomycete Utopia families contain an "archaeal" RNase H domain upstream of reverse transcriptase (RT), which likely originated from a plant RNase H gene. Analysis of Utopia from oomycetes indicates that multiple lineages of Utopia have been maintained inside of U2 genes with few copy numbers. Phylogenetic analysis of RT suggests the monophyly of Utopia, and it likely dates back to the early evolution of eukaryotes.

  14. The effect of Th substitution and of magnetic field on Kondo semiconducting behaviour in U2Ru2Sn

    NASA Astrophysics Data System (ADS)

    du Plessis, P. de V.; Strydom, A. M.; Troc, R.; Menon, L.

    2001-09-01

    Electrical resistivity, ρ(T), measurements on U2Ru2Sn show typical Kondo semiconducting behaviour, namely a ρ(T)~ln T behaviour at higher temperatures and an activation-like increase in ρ(T) below 20 K which indicates the opening of a small gap in the electronic density of states. The magnetic susceptibility, χ(T), of U2Ru2Sn has a maximum around 180 K which is characteristic of intermediate-valence behaviour. The χ(T) data for U2Ru2Sn have been fitted to the interconfigurational fluctuation model of Sales and Wohlleben giving a value of Tsf* = 155(2) K for the characteristic fluctuation temperature. Substituting as little as 5% Th for U leads to a ρ(T) variation reminiscent of that of a single-ion Kondo metal ρ(T) = ρ(0)[1- (π2/16)(T2/TK2)]. Values of TK = 79(1) and 113(1) K are respectively obtained for alloys with 5% and 10% Th substitution.

  15. RhoA/ROCK pathway inhibition by fasudil suppresses the vasculogenic mimicry of U2OS osteosarcoma cells in vitro.

    PubMed

    Xia, Yun; Cai, Xianyi; Fan, Jiquan; Zhang, Liling; Li, Zhenyu; Ren, Jinghua; Wu, Gang; Zhu, Fang

    2017-02-20

    GTPase RhoA and its downstream Rho-associated coiled-coil-containing protein kinases (ROCKs) are frequently overexpressed in human cancers. Inhibition of the RhoA/ROCK pathway blocks angiogenesis mediated by the vascular endothelial growth factor, which led us to investigate the role of this pathway in vasculogenic mimicry (VM) - a process by which aggressive cancer cells form vessel-like structures that provide adequate blood supply for tumor growth. We showed that the expression of RhoA and its effector kinases ROCK1/2 was much higher in human osteosarcoma (OS) tissues and the human OS cell line U2OS than in nontumorous tissues and cell line hFOB 1.19 using western blot analysis and real-time PCR. Inhibition of the RhoA/ROCK signaling pathway by the pharmacological inhibitor fasudil reduced vascular-like channels of U2OS cells in Matrigel. Furthermore, we used rhodamine-phalloidin immunofluorescence, wound healing assay, and transwell migration assay to examine the effect of fasudil on tumor cell plasticity and motility, both of which play key roles in VM formation. Finally, we explored the underlying mechanisms of fasudil-induced VM destruction. In this context, we showed that the RhoA/ROCK signaling pathway is a novel regulator in VM of U2OS OS cells and suggest that fasudil in conjunction with established treatments may present a novel therapeutic strategy for OS.

  16. Complementary DNA cloning, sequence analysis, and tissue transcription profile of a novel U2AF2 gene from the Chinese Banna mini-pig inbred line.

    PubMed

    Wang, S Y; Huo, J L; Miao, Y W; Cheng, W M; Zeng, Y Z

    2013-04-02

    U2 small nuclear RNA auxiliary factor 2 (U2AF2) is an important gene for pre-messenger RNA splicing in higher eukaryotes. In this study, the Banna mini-pig inbred line (BMI) U2AF2 coding sequence (CDS) was cloned, sequenced, and characterized. The U2AF2 complete CDS was amplified using the reverse transcription-polymerase chain reaction (RT-PCR) technique based on the conserved sequence information of cattle and known highly homologous swine expressed sequence tags. This novel gene was deposited into the National Center for Biotechnology Information database (Accession No. JQ839267). Sequence analysis revealed that the BMI U2AF2 coding sequence consisted of 1416 bp and encoded 471 amino acids with a molecular weight of 53.12 kDa. The protein sequence has high sequence homology with U2AF65 of 6 species - Homo sapiens (100%), Equus caballus (100%), Canis lupus (100%), Macaca mulatta (99.8%), Bos taurus (74.4%), and Mus musculus (74.4%). The phylogenetic tree analysis revealed that BMI U2AF65 has a closer genetic relationship with B. taurus U2AF65 than with U2AF65 of E. caballus, C. lupus, M. mulatta, H. sapiens, and M. musculus. RT-PCR analysis showed that BMI U2AF2 was most highly expressed in the brain; moderately expressed in the spleen, lung, muscle, and skin; and weakly expressed in the liver, kidney, and ovary. Its expression was nearly silent in the spinal cord, nerve fiber, heart, stomach, pancreas, and intestine. Three microRNA target sites were predicted in the CDS of BMI U2AF2 messenger RNA. Our results establish a foundation for further insight into this swine gene.

  17. Wnt10b Activates the Wnt, Notch and NFκB Pathways in U2OS Osteosarcoma Cells

    PubMed Central

    Mödder, Ulrike I.; Oursler, Merry Jo; Khosla, Sundeep; Monroe, David G.

    2011-01-01

    Although osteosarcoma represents the most common bone malignancy, the molecular and cellular mechanisms influencing its pathogenesis have remained elusive. Recent evidence has suggested that the Wnt signaling pathway may play a crucial role in osteosarcoma. This study employed a microarray approach to discover novel genes and pathways involved in Wnt signaling in osteosarcoma. We developed a Wnt10b-expressing cell line using the human U2OS osteosarcoma model (U2OS-Wnt10b) and performed microarray and pathway analyses using parental U2OS cells as control. Differential expression of 1003 genes encompassing 28 pathways was noted. The Wnt, NFκB and Notch pathways were chosen for further study based on their known importance in bone biology. Known Wnt-responsive genes Axin-2 (4.9-fold), CD44 (2.1-fold), endothelin-1 (4.2-fold) and sclerostin domain containing-1 (43-fold) were regulated by Wnt10b. The proinflammatory cytokines interleukin-1α and tumor necrosis factor-α, known inducers of NFκB, were upregulated both at the transcript and protein level, and NFκB reporter activity was stimulated 3.8-fold, confirming NFκB activation. Interestingly, genes involved in Notch signaling [Notch-1 (2.4-fold) and Jagged-1 (3.1-fold)] were upregulated, whereas the Notch inhibitor, lunatic fringe, was downregulated (8.2-fold). This resulted in the activation of the classic Notch-responsive genes, hairy and enhancer of split-1 (Hes-1; 2.2-fold) and hairy/enhancer-of-split related with YRPW motif-1 (Hey-1; 2.5-fold). A Hey-1 reporter construct was regulated 9.1-fold in U2OS-Wnt10b cells, confirming Notch activation. Interestingly, Wnt3a failed to induce the Notch and NFκB pathways, demonstrating Wnt-specificity. In conclusion, our data demonstrate that Wnt10b, but not Wnt3a, stimulates the NFκB and Notch pathways in U2OS osteosarcoma cells. PMID:21321991

  18. U2AF65 adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifs

    PubMed Central

    Jenkins, Jermaine L.; Agrawal, Anant A.; Gupta, Ankit; Green, Michael R.; Kielkopf, Clara L.

    2013-01-01

    Degenerate splice site sequences mark the intron boundaries of pre-mRNA transcripts in multicellular eukaryotes. The essential pre-mRNA splicing factor U2AF65 is faced with the paradoxical tasks of accurately targeting polypyrimidine (Py) tracts preceding 3′ splice sites while adapting to both cytidine and uridine nucleotides with nearly equivalent frequencies. To understand how U2AF65 recognizes degenerate Py tracts, we determined six crystal structures of human U2AF65 bound to cytidine-containing Py tracts. As deoxy-ribose backbones were required for co-crystallization with these Py tracts, we also determined two baseline structures of U2AF65 bound to the deoxy-uridine counterparts and compared the original, RNA-bound structure. Local structural changes suggest that the N-terminal RNA recognition motif 1 (RRM1) is more promiscuous for cytosine-containing Py tracts than the C-terminal RRM2. These structural differences between the RRMs were reinforced by the specificities of wild-type and site-directed mutant U2AF65 for region-dependent cytosine- and uracil-containing RNA sites. Small-angle X-ray scattering analyses further demonstrated that Py tract variations select distinct inter-RRM spacings from a pre-existing ensemble of U2AF65 conformations. Our results highlight both local and global conformational selection as a means for universal 3′ splice site recognition by U2AF65. PMID:23376934

  19. Salinomycin simultaneously induces apoptosis and autophagy through generation of reactive oxygen species in osteosarcoma U2OS cells.

    PubMed

    Kim, Sang-Hun; Choi, Young-Jun; Kim, Kwang-Youn; Yu, Sun-Nyoung; Seo, Young-Kyo; Chun, Sung-Sik; Noh, Kyung-Tae; Suh, Jeung-Tak; Ahn, Soon-Cheol

    2016-04-29

    Salinomycin, a polyether antibiotic, acts as a highly selective potassium ionophore. It was reported to anticancer activity on various cancer cell lines. In this study, salinomycin was examined on apoptosis and autophagy through generation of reactive oxygen species (ROS) in osteosarcoma U2OS cells. Apoptosis, autophagy, mitochondrial membrane potential (MMP) and ROS were analyzed using flow cytometry. Also, expressions of apoptosis- and autophagy-related proteins were determined by western blotting. As a result, salinomycin triggered apoptosis of U2OS cells, which was accompanied by change of MMP and cleavage of caspases-3 and poly (ADP-ribose) polymerase. And salinomycin increased the expression of autophagy-related protein and accumulation of acidic vesicular organelles (AVO). Salinomycin-induced ROS production promotes both apoptosis and autophagy, as evidenced by the result that treatment of N-acetyl-l-cysteine (NAC), a ROS scavenger, attenuated both apoptosis and autophagy. In addition, inhibition of autophagy by 3-methyladenine (3 MA) enhanced the salinoymcin-induced apoptosis. Taken together, these results suggested that salinomycin-induced autophagy, as a survival mechanism, might be a potential strategy through ROS regulation in cancer therapy.

  20. Polypyrimidine tract binding protein inhibits IgM pre-mRNA splicing by diverting U2 snRNA base-pairing away from the branch point.

    PubMed

    Zheng, Xuexiu; Cho, Sunghee; Moon, Heegyum; Loh, Tiing Jen; Oh, Huyn Kyung; Green, Michael R; Shen, Haihong

    2014-04-01

    The mouse immunoglobulin (IgM) pre-mRNA contains a splicing inhibitor that bears multiple binding sites for the splicing repressor polypyrimidine tract binding protein (PTB). Here we show that the inhibitor directs assembly of an ATP-dependent complex that contains PTB and U1 and U2 small nuclear RNAs (snRNAs). Unexpectedly, although U2 snRNA is present in the inhibitor complex, it is not base-paired to the branch point. We present evidence that inhibitor-bound PTB contacts U2 snRNA to promote base-pairing to an adjacent branch point-like sequence within the inhibitor, thereby preventing the U2 snRNA-branch point interaction and resulting in splicing repression. Our studies reveal a novel mechanism by which PTB represses splicing.

  1. A Gene Cluster Encoding Steps in Conversion of Naphthalene to Gentisate in Pseudomonas sp. Strain U2

    PubMed Central

    Fuenmayor, Sergio L.; Wild, Mark; Boyes, Alastair L.; Williams, Peter A.

    1998-01-01

    Pseudomonas sp. strain U2 was isolated from oil-contaminated soil in Venezuela by selective enrichment on naphthalene as the sole carbon source. The genes for naphthalene dioxygenase were cloned from the plasmid DNA of strain U2 on an 8.3-kb BamHI fragment. The genes for the naphthalene dioxygenase genes nagAa (for ferredoxin reductase), nagAb (for ferredoxin), and nagAc and nagAd (for the large and small subunits of dioxygenase, respectively) were located by Southern hybridizations and by nucleotide sequencing. The genes for nagB (for naphthalene cis-dihydrodiol dehydrogenase) and nagF (for salicylaldehyde dehydrogenase) were inferred from subclones by their biochemical activities. Between nagAa and nagAb were two open reading frames, homologs of which have also been identified in similar locations in two nitrotoluene-using strains (J. V. Parales, A. Kumar, R. E. Parales, and D. T. Gibson, Gene 181:57–61, 1996; W.-C. Suen, B. Haigler, and J. C. Spain, J. Bacteriol. 178:4926–4934, 1996) and a naphthalene-using strain (G. J. Zylstra, E. Kim, and A. K. Goyal, Genet. Eng. 19:257–269, 1997). Recombinant Escherichia coli strains with plasmids carrying this region were able to convert salicylate to gentisate, which was identified by a combination of gas chromatography-mass spectrometry and nuclear magnetic resonance. The first open reading frame, designated nagG, encodes a protein with characteristics of a Rieske-type iron-sulfur center homologous to the large subunits of dihydroxylating dioxygenases, and the second open reading frame, designated nagH, encodes a protein with limited homology to the small subunits of the same dioxygenases. Cloned together in E. coli, nagG, nagH, and nagAb, were able to convert salicylate (2-hydroxybenzoate) into gentisate (2,5-dihydroxybenzoate) and therefore encode a salicylate 5-hydroxylase activity. Single-gene knockouts of nagG, nagH, and nagAb demonstrated their functional roles in the formation of gentisate. It is proposed

  2. The new NCPSS BL19U2 beamline at the SSRF for small-angle X-ray scattering from biological macromolecules in solution1

    PubMed Central

    Li, Na; Li, Xiuhong; Wang, Yuzhu; Liu, Guangfeng; Zhou, Ping; Wu, Hongjin; Hong, Chunxia; Bian, Fenggang; Zhang, Rongguang

    2016-01-01

    The beamline BL19U2 is located in the Shanghai Synchrotron Radiation Facility (SSRF) and is its first beamline dedicated to biological material small-angle X-ray scattering (BioSAXS). The electrons come from an undulator which can provide high brilliance for the BL19U2 end stations. A double flat silicon crystal (111) monochromator is used in BL19U2, with a tunable monochromatic photon energy ranging from 7 to 15 keV. To meet the rapidly growing demands of crystallographers, biochemists and structural biologists, the BioSAXS beamline allows manual and automatic sample loading/unloading. A Pilatus 1M detector (Dectris) is employed for data collection, characterized by a high dynamic range and a short readout time. The highly automated data processing pipeline SASFLOW was integrated into BL19U2, with help from the BioSAXS group of the European Molecular Biology Laboratory (EMBL, Hamburg), which provides a user-friendly interface for data processing. The BL19U2 beamline was officially opened to users in March 2015. To date, feedback from users has been positive and the number of experimental proposals at BL19U2 is increasing. A description of the new BioSAXS beamline and the setup characteristics is given, together with examples of data obtained. PMID:27738413

  3. U2AF35(S34F) Promotes Transformation by Directing Aberrant ATG7 Pre-mRNA 3' End Formation.

    PubMed

    Park, Sung Mi; Ou, Jianhong; Chamberlain, Lynn; Simone, Tessa M; Yang, Huan; Virbasius, Ching-Man; Ali, Abdullah M; Zhu, Lihua Julie; Mukherjee, Siddhartha; Raza, Azra; Green, Michael R

    2016-05-19

    Recurrent mutations in the splicing factor U2AF35 are found in several cancers and myelodysplastic syndrome (MDS). How oncogenic U2AF35 mutants promote transformation remains to be determined. Here we derive cell lines transformed by the oncogenic U2AF35(S34F) mutant and identify aberrantly processed pre-mRNAs by deep sequencing. We find that in U2AF35(S34F)-transformed cells the autophagy-related factor 7 (Atg7) pre-mRNA is abnormally processed, which unexpectedly is not due to altered splicing but rather selection of a distal cleavage and polyadenylation (CP) site. This longer Atg7 mRNA is translated inefficiently, leading to decreased ATG7 levels and an autophagy defect that predisposes cells to secondary mutations, resulting in transformation. MDS and acute myeloid leukemia patient samples harboring U2AF35(S34F) have a similar increased use of the ATG7 distal CP site, and previous studies have shown that mice with hematopoietic cells lacking Atg7 develop an MDS-like syndrome. Collectively, our results reveal a basis for U2AF35(S34F) oncogenic activity.

  4. Involvement of recently cultured group U2 bacterium in ruminal fiber digestion revealed by coculture with Fibrobacter succinogenes S85.

    PubMed

    Fukuma, Naoki; Koike, Satoshi; Kobayashi, Yasuo

    2012-11-01

    In a previous study, we reported the ecological significance of uncultured bacterial group U2 in the rumen. In this study, the involvement of a recently cultured group U2 bacterium, strain R-25, in fiber digestion was tested in coculture with the fibrolytic bacterium Fibrobacter succinogenes S85. Dry matter (DM) digestion, growth and metabolites were examined in culture using rice straw as the carbon source. Although strain R-25 did not digest rice straw in monoculture, coculture of strain R-25 and F. succinogenes S85 showed enhanced DM digestion compared with that for F. succinogenes S85 monoculture (36.9 ± 0.6% vs. 32.8 ± 1.3%, P < 0.05). Growth of strain R-25 and production of the main metabolites, d-lactate (strain R-25) and succinate (F. succinogenes S85), were enhanced in the coculture. Enzyme assay showed increased activities of carboxymethylcellulase and xylanase in coculture of strain R-25 and F. succinogenes S85. Triculture including strain R-25, F. succinogenes S85 and Selenomonas ruminantium S137 showed a further increase in DM digestion (41.8 ± 0.8%, P < 0.05) with a concomitant increase in propionate, produced from the conversion of d-lactate and succinate. These results suggest that the positive interaction between strains R-25 and F. succinogenes S85 causes increased rice straw digestion.

  5. A genome landscape of SRSF3-regulated splicing events and gene expression in human osteosarcoma U2OS cells

    PubMed Central

    Ajiro, Masahiko; Jia, Rong; Yang, Yanqin; Zhu, Jun; Zheng, Zhi-Ming

    2016-01-01

    Alternative RNA splicing is an essential process to yield proteomic diversity in eukaryotic cells, and aberrant splicing is often associated with numerous human diseases and cancers. We recently described serine/arginine-rich splicing factor 3 (SRSF3 or SRp20) being a proto-oncogene. However, the SRSF3-regulated splicing events responsible for its oncogenic activities remain largely unknown. By global profiling of the SRSF3-regulated splicing events in human osteosarcoma U2OS cells, we found that SRSF3 regulates the expression of 60 genes including ERRFI1, ANXA1 and TGFB2, and 182 splicing events in 164 genes, including EP300, PUS3, CLINT1, PKP4, KIF23, CHK1, SMC2, CKLF, MAP4, MBNL1, MELK, DDX5, PABPC1, MAP4K4, Sp1 and SRSF1, which are primarily associated with cell proliferation or cell cycle. Two SRSF3-binding motifs, CCAGC(G)C and A(G)CAGCA, are enriched to the alternative exons. An SRSF3-binding site in the EP300 exon 14 is essential for exon 14 inclusion. We found that the expression of SRSF1 and SRSF3 are mutually dependent and coexpressed in normal and tumor tissues/cells. SRSF3 also significantly regulates the expression of at least 20 miRNAs, including a subset of oncogenic or tumor suppressive miRNAs. These data indicate that SRSF3 affects a global change of gene expression to maintain cell homeostasis. PMID:26704980

  6. Splice Variants of mda-7/IL-24 Differentially Affect Survival and Induce Apoptosis in U2OS Cells

    PubMed Central

    Whitaker, Erin L.; Filippov, Valery; Filippova, Maria; Guerrero-Juarez, Christian F.; Duerksen-Hughes, Penelope J.

    2011-01-01

    Interleukin-24 (mda-7/IL-24) is a cytokine in the IL-10 family that has received a great deal of attention for its properties as a tumor suppressor and as a potential treatment for cancer. In this study, we have identified and characterized five alternatively spliced isoforms of this gene. Several, but not all of these isoforms induce apoptosis in the osteosarcoma cell line U2OS, while none affect the survival of the non-cancerous NOK cell line. One of these isoforms, lacking three exons and encoding the N-terminal end of the mda-7/IL-24 protein sequence, caused levels of apoptosis that were higher than those caused by the full-length mda-7/IL-24 variant. Additionally, we found that the ratio of isoform expression can be modified by the splice factor SRp55. This regulation suggests that alternative splicing of mda-7/IL-24 is under tight control in the cell, and can be modified under various cellular conditions, such as DNA damage. In addition to providing new insights into the function of an important tumor suppressor gene, these findings may also point toward new avenues for cancer treatment. PMID:21843952

  7. Dzyaloshinskii-Morija interaction and local magnetic anisotropies in U2Pd2In : Ground state and metamagnetic transition

    NASA Astrophysics Data System (ADS)

    Sandratskii, L. M.

    2016-11-01

    U2Pd2In is the material where the elements of the geometrical frustration of the lattice coexist with strong spin-orbit coupling (SOC). The ground state of the system is a noncollinear planar magnetic structure with orthogonal atomic magnetic moments. There are three possible physical mechanisms that can lead to this nontrivial magnetic structure: frustrated isotropic exchange interaction, Dzyaloshinskii-Morija interaction (DMI), and magnetic anisotropy. Our first-principles calculations show that in the case where the SOC is neglected, and therefore the DMI and magnetic anisotropy are absent, the ground state structure is the collinear ferromagnetic one. The leading contribution to the stabilization of the magnetically compensated configuration of orthogonal atomic moments is provided by the local magnetic anisotropy of the U moments. A weaker DMI leads to the lifting of the degeneracy between the magnetic states with different local chirality. The established hierarchy of the interactions allows us to explain the metamagnetic phase transition in the in-plane external magnetic field. The analysis of the noncollinearity of the spin and orbital moments of the same U atom appearing in the applied external field show that the trend to the antiparallel orientation of the two atomic moments following from the third Hund's rule is much stronger than the trend to the parallel orientation of the moments due to the applied external magnetic field.

  8. Observation of an eclipse of U-3 Titania by U-2 Umbriel on December 8, 2007 with ESO-VLT

    NASA Astrophysics Data System (ADS)

    Arlot, J.-E.; Dumas, C.; Sicardy, B.

    2008-12-01

    Context: Equinox occurred on Uranus in 2007, allowing unique observations of mutual events of the satellites that occur every 42 years. On December 8, 2007, we observed an eclipse of Titania U-3 by Umbriel U-2. Aims: Our goal was to record an observation of very high accuracy in order to evaluate the quality of the available dynamical models of the motion of the satellites. Methods: Such an observation is challenging because of the faintness of the satellites, the vicinity of the bright planet Uranus, and the small amplitude of the magnitude drop observable during the eclipse. We recorded the event in K-band, using the ESO Very Large Telescope in Chile equipped with the NACO adaptive optics camera. Results: High signal/noise ratio images were obtained for the event making possible the determination of relative positions of the involved satellites. Comparing our results with theoretical models of the satellites motions, we obtain a valuable assessment of the accuracy of those models. Conclusions: Such observations provide important constraints on the orbits of the satellites. We discuss what is needed to improve existing dynamical models of the Uranian satellite system. These observations were made through the ESO run 080.C-03575 (A).

  9. Thermodynamic studies of studtite thermal decomposition pathways via amorphous intermediates UO3, U2O7, and UO4

    NASA Astrophysics Data System (ADS)

    Guo, Xiaofeng; Wu, Di; Xu, Hongwu; Burns, Peter C.; Navrotsky, Alexandra

    2016-09-01

    The thermal decomposition of studtite (UO2)O2(H2O)2·2H2O results in a series of intermediate X-ray amorphous materials with general composition UO3+x (x = 0, 0.5, 1). As an extension of a structural study on U2O7, this work provides detailed calorimetric data on these amorphous oxygen-rich materials since their energetics and thermal stability are unknown. These were characterized in situ by thermogravimetry, and mass spectrometry. Ex situ X-ray diffraction and infrared spectroscopy characterized their chemical bonding and local structures. This detailed characterization formed the basis for obtaining formation enthalpies by high temperature oxide melt solution calorimetry. The thermodynamic data demonstrate the metastability of the amorphous UO3+x materials, and explain their irreversible and spontaneous reactions to generate oxygen and form metaschoepite. Thus, formation of studtite in the nuclear fuel cycle, followed by heat treatment, can produce metastable amorphous UO3+x materials that pose the risk of significant O2 gas. Quantitative knowledge of the energy landscape of amorphous UO3+x was provided for stability analysis and assessment of conditions for decomposition.

  10. Thermodynamic studies of studtite thermal decomposition pathways via amorphous intermediates UO3, U2O7, and UO4

    DOE PAGES

    Guo, Xiaofeng; Wu, Di; Xu, Hongwu; ...

    2016-09-01

    The thermal decomposition of studtite (UO2)O2(H2O)2·2H2O results in a series of intermediate X-ray amorphous materials with general composition UO3+x (x = 0, 0.5, 1). As an extension of a structural study on U2O7, this work provides detailed calorimetric data on these amorphous oxygen-rich materials since their energetics and thermal stability are unknown. These were characterized in situ by thermogravimetry, and mass spectrometry. Ex situ X-ray diffraction and infrared spectroscopy characterized their chemical bonding and local structures. This detailed characterization formed the basis for obtaining formation enthalpies by high temperature oxide melt solution calorimetry. The thermodynamic data demonstrate the metastability ofmore » the amorphous UO3+x materials, and explain their irreversible and spontaneous reactions to generate oxygen and form metaschoepite. Thus, formation of studtite in the nuclear fuel cycle, followed by heat treatment, can produce metastable amorphous UO3+x materials that pose the risk of significant O2 gas. Quantitative knowledge of the energy landscape of amorphous UO3+x was provided for stability analysis and assessment of conditions for decomposition.« less

  11. Ultrafast carrier relaxation through Auger recombination in the topological insulator B i1.5S b0.5T e1.7S e1.3

    NASA Astrophysics Data System (ADS)

    Onishi, Yoshito; Ren, Zhi; Segawa, Kouji; Kaszub, Wawrzyniec; Lorenc, Maciej; Ando, Yoichi; Tanaka, Koichiro

    2015-02-01

    Ultrafast carrier dynamics have great significance for our understanding of the transport properties of the surface state in topological insulator (TI) materials. We report midinfrared pump-probe measurements on the intrinsic TI material B i1.5S b0.5T e1.7S e1.3 and show that the change in photoinduced reflectivity can be decomposed into a fast negative part and a slow positive part. Calculations of the dielectric function made at various carrier temperatures and densities reveal that the fast negative component corresponds to the disappearance of the phase-space filling effect due to hot carriers around the probe energy and the decay component corresponds to the recombination of carriers near the band edge. The ratio of the fast negative component to the slow positive component is larger in the excitations conducted at the higher carrier densities, which suggests that the carrier temperature increases through Auger recombination. A qualitative analysis using rate equations reinforces this assumption, so we conclude that Auger recombination is the main cause of the population relaxation at carrier densities higher than 1018c m-3 and that we determined the Auger coefficient for B i1.5S b0.5T e1.7S e1.3 as C =0.4 ×10-26c m6/s .

  12. Final Characterization Report for Corrective Action Unit 109: Area 2 U-2BU Crater, Nevada Test Site, Nevada, Revision 1

    SciTech Connect

    ITLV

    1998-12-01

    Corrective Action Unit 109, Area 2 U-2bu Crater, is an inactive Resource Conservation and Recovery Act Part A Permit disposal unit located in Area 2 at the Nevada Test Site, Nevada. The Corrective Action Unit has been characterized under the requirements of the Nevada Test Site Resource Conservation and Recovery Act, Part A Permit (NDEP, 1995) and Title 40 Code of Federal Regulations Part 265 (CFR, 1996). The site characterization was performed under the RCRA Part A Permit Characterization Plan for the U-2bu Subsidence Crater (DOE/NV, 1998c), as approved by the Nevada Division of Environmental Protection (Liebendorfer, 1998). The primary objective of the site characterization activities was to evaluate the presence, concentration, and extent of any Resource Conservation and Recovery Act contaminants in the crater. Surface soil samples were collected on April 22, 1998, and subsurface soil samples and geotechnical samples were collected from April 27-29, 1998. Soil samples were collected using a hand auger or a piston-type drive hammer to advance a 5-centimeter (2-inch) diameter steel sampling tool into the ground. The permit for the Nevada Test Site requires that Corrective Action Unit 109 be closed under 40 Code of Federal Regulations 265 Subpart G and 40 Code of Federal Regulations Part 265.310 (CFR, 1996). Analysis of the data collected during the characterization effort indicates that lead was detected in Study Area 1 at 5.7 milligrams per liter, above the regulatory level in 40 Code of Federal Regulations 261.24 of 5.0 milligrams per liter. Except for the lead detection at a single location within the crater, the original Resource Conservation Recovery Act constituents of potential concern determined between the U.S. Department of Energy, Nevada Operations Office and the Nevada Department of Environmental Protection during the Data Quality Objectives process (DOE/NV, 1998b) were not found to be present at Corrective Action Unit 109 above regulatory levels of

  13. Effects of sex steroid hormones on neuromedin S and neuromedin U2 receptor expression following experimental traumatic brain injury

    PubMed Central

    Khaksari, Mohammad; Maghool, Fatemeh; Asadikaram, Gholamreza; Hajializadeh, Zahra

    2016-01-01

    Objective(s): Neuroprotective effects of female gonadal steroids are mediated through several pathways involving multiple peptides and receptors after traumatic brain injury (TBI). Two of these peptides are including the regulatory peptides neuromedin U (NMU) and neuromedin S (NMS), and their common receptor neuromedin U2 receptor (NMUR2). This study investigates the effects of physiological doses of estradiol and progesterone on brain edema, NMS and NMU as well as NMUR2 expression following TBI. Materials and Methods: Ovariectomized female rats were given high-and low-dose of female sex steroid hormones through implantation of capsules for a week before trauma. The brain NMUR2 expression, prepro-NMS expression, NMU content, and water content (brain edema) were evaluated 24 hr after TBI induced by Marmarou’s method. Results: Percentage of brain water content in high- and low-dose estradiol, and in high- and low- dose progesterone was less than vehicle (P<0.01). Results show high expression of prepro-NMS in high dose progesterone (TBI-HP) rats compared to the high dose estrogen (TBI-HE), as well as vehicle (P<0.01). NMU content in low-dose progesterone (TBI-LP) group was more than that of vehicle group (P<0.001). Furthermore a difference in NMU content observed between TBI-HP compared to TBI-HE, and vehicle (P<0.05). The NMUR2 mRNA expression revealed an upregulation in TBI-HP rats compared to the TBI-HE group (P<0.001). Conclusion: Findings indicate that progesterone attenuates brain edema and induces an increase in NMS and its receptor which may mediate the anti-edematous effect of progesterone after TBI. PMID:27872704

  14. Circulating U2 small nuclear RNA fragments as a novel diagnostic biomarker for primary central nervous system lymphoma

    PubMed Central

    Baraniskin, Alexander; Zaslavska, Elena; Nöpel-Dünnebacke, Stefanie; Ahle, Guido; Seidel, Sabine; Schlegel, Uwe; Schmiegel, Wolff; Hahn, Stephan; Schroers, Roland

    2016-01-01

    Background Primary central nervous system lymphomas (PCNSLs) are highly aggressive tumors. Chemotherapy has improved prognosis significantly; however, early diagnosis is crucial for effective treatment. Presently, the diagnosis of PCNSL depends on histopathology of tumor biopsies. We have previously demonstrated differential expression of microRNAs in cerebrospinal fluid (CSF) samples from patients with PCNSL. Based on promising findings about circulating U2 small nuclear RNA fragments (RNU2-1f) as novel blood-based biomarkers for pancreatic, colorectal, and lung cancer, we investigated RNU2-1f in the CSF of PCNSL patients. Methods CSF was collected from patients with PCNSL (n = 72) and control patients with various neurologic disorders (n = 47). Sequential CSF samples were collected from 9 PCNSL patients. RNU2-1f levels were measured by real-time polymerase chain reaction. Results Measurement of RNU2-1f levels in CSF enabled the differentiation of patients with PCNSL from controls with an area under the curve (AUC) of 0.909 with a sensitivity of 68.1% and a specificity of 91.4%. The diagnostic accuracy was further improved by combined determination of RNU2-1f and miR-21, resulting in AUC of 0.987 with a sensitivity of 91.7% and a specificity of 95.7%. In consecutive measurements of RNU2-1f, which were performed in 9 patients at different stages of the disease course, RNU2-1f CSF levels paralleled the course of the disease. Conclusions Our data suggest that the measurement of RNU2-1f detected in CSF can be used as a diagnostic marker and also as a possible marker for treatment monitoring. These promising results need to be evaluated within a larger patient cohort. PMID:26250566

  15. Draft Genome Sequence of Streptomyces sp. AVP053U2 Isolated from Styela clava, a Tunicate Collected in Long Island Sound

    PubMed Central

    deMayo, James A.; Maas, Kendra R.

    2016-01-01

    Streptomyces sp. AVP053U2 is a marine bacterium isolated from Styela clava, a tunicate collected in Long Island Sound. Here, we report a draft genome for this bacterium, which was found to contain a high capacity for secondary metabolite production based on analysis and identification of numerous biosynthetic gene clusters. PMID:27738023

  16. Muscleblind-like 1 activates insulin receptor exon 11 inclusion by enhancing U2AF65 binding and splicing of the upstream intron.

    PubMed

    Echeverria, Gloria V; Cooper, Thomas A

    2014-02-01

    Alternative splicing regulates developmentally and tissue-specific gene expression programs, disruption of which have been implicated in numerous diseases. Muscleblind-like 1 (MBNL1) regulates splicing transitions, which are disrupted on loss of MBNL1 function in myotonic dystrophy type 1 (DM1). One such event is MBNL1-mediated activation of insulin receptor exon 11 inclusion, which requires an intronic enhancer element downstream of exon 11. The mechanism of MBNL1-mediated activation of exon inclusion is unknown. We developed an in vitro splicing assay, which robustly recapitulates MBNL1-mediated splicing activation of insulin receptor exon 11 and found that MBNL1 activates removal of the intron upstream of exon 11 upon binding its functional response element in the downstream intron. MBNL1 enhances early spliceosome assembly as evidenced by enhanced complex A formation and binding of U2 small nuclear ribonucleoprotein auxiliary factor 65 kDa subunit (U2AF65) on the upstream intron. We demonstrated that neither the 5' splice site nor exon 11 sequences are required for MBNL1-activated U2AF65 binding. Interestingly, the 5' splice site is required for MBNL1-mediated activation of upstream intron removal, although MBNL1 has no effect on U1 snRNA recruitment. These results suggest that MBNL1 directly activates binding of U2AF65 to enhance upstream intron removal to ultimately activate alternative exon inclusion.

  17. The Mouse Murr1 Gene Is Imprinted in the Adult Brain, Presumably Due to Transcriptional Interference by the Antisense-Oriented U2af1-rs1 Gene

    PubMed Central

    Wang, Youdong; Joh, Keiichiro; Masuko, Sadahiko; Yatsuki, Hitomi; Soejima, Hidenobu; Nabetani, Akira; Beechey, Colin V.; Okinami, Satoshi; Mukai, Tsunehiro

    2004-01-01

    The mouse Murr1 gene contains an imprinted gene, U2af1-rs1, in its first intron. U2af1-rs1 shows paternal allele-specific expression and is transcribed in the direction opposite to that of the Murr1 gene. In contrast to a previous report of biallelic expression of Murr1 in neonatal mice, we have found that the maternal allele is expressed predominantly in the adult brain and also preferentially in other adult tissues. This maternal-predominant expression is not observed in embryonic and neonatal brains. In situ hybridization experiments that used the adult brain indicated that Murr1 gene was maternally expressed in neuronal cells in all regions of the brain. We analyzed the developmental change in the expression levels of both Murr1 and U2af1-rs1 in the brain and liver, and we propose that the maternal-predominant expression of Murr1 results from transcriptional interference of the gene by U2af1-rs1 through the Murr1 promoter region. PMID:14673161

  18. Inactive allele-specific methylation and chromatin structure of the imprinted gene U2af1-rs1 on mouse chromosome 11

    SciTech Connect

    Shibata, Hideo; Yoshino, Kiyoshi; Kamiya, Mamoru

    1996-07-01

    The imprinted U2Af1-rs1 gene that maps to mouse chromosome 11 is predominately expressed from the paternal allele. We examined the methylation of genomic sequences in and around the U2af1-rs1 locus to establish the extent of sequence modifications that accompanied the silencing of the maternal allele. The analysis of HapII or HhaI sites showed that the silent maternal allele was hypermethylated in a block of CpG sequences that covered more than 10 kb. By comparison, the expressed paternal allele was unmethylated from a CpG island upstream of the transcribed region through 2 kb. An analysis of DNaseI hypersensitivity of a putative promoter of U2af1-rs1 showed an open chromatin conformation only on the unmethylated, expressed paternal allele. These results suggest that allele-specific hypermethylation covering the gene and its upstream CpG island plays a role in maternal allele repression of U2af1-rs1, which is reflected in altered chromatin conformation of DNaseI hypersensitive sites. 9 refs., 2 figs.

  19. Molecular cloning and in silico characterization of knottin peptide, U2-SCRTX-Lit2, from brown spider (Loxosceles intermedia) venom glands.

    PubMed

    Meissner, Gabriel Otto; de Resende Lara, Pedro Túlio; Scott, Luis Paulo Barbour; Braz, Antônio Sérgio Kimus; Chaves-Moreira, Daniele; Matsubara, Fernando Hitomi; Soares, Eduardo Mendonça; Trevisan-Silva, Dilza; Gremski, Luiza Helena; Veiga, Silvio Sanches; Chaim, Olga Meiri

    2016-09-01

    Inhibitor cystine knots (ICKs) are a family of structural peptides with a large number of cysteine residues that form intramolecular disulfide bonds, resulting in a knot. These peptides are involved in a variety of biological functions including predation and defense, and are found in various species, such as spiders, scorpions, sea anemones, and plants. The Loxosceles intermedia venom gland transcriptome identified five groups of ICK peptides that represent more than 50 % of toxin-coding transcripts. Here, we describe the molecular cloning of U2-Sicaritoxin-Lit2 (U2-SCRTX-Lit2), bioinformatic characterization, structure prediction, and molecular dynamic analysis. The sequence of U2-SCRTX-Lit2 obtained from the transcriptome is similar to that of μ-Hexatoxin-Mg2, a peptide that inhibits the insect Nav channel. Bioinformatic analysis of sequences classified as ICK family members also showed a conservation of cysteine residues among ICKs from different spiders, with the three dimensional molecular model of U2-SCRTX-Lit2 similar in structure to the hexatoxin from μ-hexatoxin-Mg2a. Molecular docking experiments showed the interaction of U2-SCRTX-Lit2 to its predictable target-the Spodoptera litura voltage-gated sodium channel (SlNaVSC). After 200 ns of molecular dynamic simulation, the final structure of the complex showed stability in agreement with the experimental data. The above analysis corroborates the existence of a peptide toxin with insecticidal activity from a novel ICK family in L. intermedia venom and demonstrates that this peptide targets Nav channels.

  20. Vaccinia Virus B1 Kinase Is Required for Postreplicative Stages of the Viral Life Cycle in a BAF-Independent Manner in U2OS Cells

    PubMed Central

    Jamin, Augusta; Ibrahim, Nouhou; Wicklund, April; Weskamp, Kaitlin

    2015-01-01

    ABSTRACT The vaccinia virus B1R gene encodes a highly conserved protein kinase that is essential for the poxviral life cycle. As demonstrated in many cell types, B1 plays a critical role during viral DNA replication when it inactivates the cellular host defense effector barrier to autointegration factor (BAF or BANF1). To better understand the role of B1 during infection, we have characterized the growth of a B1-deficient temperature-sensitive mutant virus (Cts2 virus) in U2OS osteosarcoma cells. In contrast to all other cell lines tested to date, we found that in U2OS cells, Cts2 viral DNA replication is unimpaired at the nonpermissive temperature. However, the Cts2 viral yield in these cells was reduced more than 10-fold, thus indicating that B1 is required at another stage of the vaccinia virus life cycle. Our results further suggest that the host defense function of endogenous BAF may be absent in U2OS cells but can be recovered through either overexpression of BAF or fusion of U2OS cells with mouse cells in which the antiviral function of BAF is active. Interestingly, examination of late viral proteins during Cts2 virus infection demonstrated that B1 is required for optimal processing of the L4 protein. Finally, execution point analyses as well as electron microscopy studies uncovered a role for B1 during maturation of poxviral virions. Overall, this work demonstrates that U2OS cells are a novel model system for studying the cell type-specific regulation of BAF and reveals a role for B1 beyond DNA replication during the late stages of the viral life cycle. IMPORTANCE The most well characterized role for the vaccinia virus B1 kinase is to facilitate viral DNA replication by phosphorylating and inactivating BAF, a cellular host defense responsive to foreign DNA. Additional roles for B1 later in the viral life cycle have been postulated for decades but are difficult to examine directly due to the importance of B1 during DNA replication. Here, we demonstrate that

  1. Expanding the Chemistry of Molecular U(2+) Complexes: Synthesis, Characterization, and Reactivity of the {[C5 H3 (SiMe3 )2 ]3 U}(-) Anion.

    PubMed

    Windorff, Cory J; MacDonald, Matthew R; Meihaus, Katie R; Ziller, Joseph W; Long, Jeffrey R; Evans, William J

    2016-01-11

    The synthesis of new molecular complexes of U(2+) has been pursued to make comparisons in structure, physical properties, and reactivity with the first U(2+) complex, [K(2.2.2-cryptand)][Cp'3 U], 1 (Cp'=C5 H4 SiMe3 ). Reduction of Cp''3 U [Cp''=C5 H3 (SiMe3 )2 ] with KC8 in the presence of 2.2.2-cryptand or 18-crown-6 generates [K(2.2.2-cryptand)][Cp''3 U], 2-K(crypt), or [K(18-crown-6)(THF)2 ][Cp''3 U], 2-K(18c6), respectively. The UV/Vis spectra of 2-K and 1 are similar, and they are much more intense than those of U(3+) analogues. Variable temperature magnetic susceptibility data for 1 and 2-K(crypt) reveal lower room temperature χM T values relative to the experimental values for the 5f(3) U(3+) precursors. Stability studies monitored by UV/Vis spectroscopy show that 2-K(crypt) and 2-K(18c6) have t1/2 values of 20 and 15 h at room temperature, respectively, vs. 1.5 h for 1. Complex 2-K(18c6) reacts with H2 or PhSiH3 to form the uranium hydride, [K(18-crown-6)(THF)2 ][Cp''3 UH], 3. Complexes 1 and 2-K(18c6) both reduce cyclooctatetraene to form uranocene, (C8 H8 )2 U, as well as the U(3+) byproducts [K(2.2.2-cryptand)][Cp'4 U], 4, and Cp''3 U, respectively.

  2. Bufalin Induces Apoptosis of Human Osteosarcoma U-2 OS Cells through Endoplasmic Reticulum Stress, Caspase- and Mitochondria-Dependent Signaling Pathways.

    PubMed

    Lee, Ching-Hsiao; Shih, Yung-Luen; Lee, Mei-Hui; Au, Man-Kuan; Chen, Yung-Liang; Lu, Hsu-Feng; Chung, Jing-Gung

    2017-03-10

    Bone cancer is one of the cancer-related diseases, and there are increased numbers of patients with bone cancer worldwide. Therefore the efficacy of treatment of bone cancer is considered extremely vital. Bufalin has been showed to have biological activities including anticancer activities in vitro and in vivo. However, the exact associated mechanisms for bufalin induced apoptosis in human bone cancer cells are still unclear. In the present study, we investigated the effect of bufalin on the cytotoxic effects in U-2 OS human osteosarcoma cells. For examining apoptotic cell deaths, we used flow cytometry assay, Annexin V/PI double staining, and TUNNEL assay. Reactive oxygen species (ROS), Ca(2+), mitochondrial membrane potential (ΔΨm), and caspase-8, -9 and -3 activities were measured by flow cytometry assay. Furthermore, western blotting and a confocal laser microscopy examination were used for measuring the alterations of apoptotic associated protein expression and translocation, respectively. The results indicated that bufalin induced cell morphological changes, decreased the viable cell number, induced apoptotic cell death, and increased the apoptotic cell number, and affected apoptotic associated protein expression in U-2 OS cells. Bufalin increased apoptotic proteins such as Bak, and decreased anti-apoptotic proteins such as Bcl-2 and Bcl-x in U-2 OS cells. Furthermore, bufalin increased the protein levels of cytochrome c (Cyto c), AIF (Apoptosis inducing factor) and Endo G (Endonuclease G) in cytoplasm that were also confirmed by confocal microscopy examination. Based on those findings, bufalin induced apoptotic cell death in U-2 OS cells may be via endoplasmic reticulum (ER) stress, caspase-, and mitochondria-dependent pathways; thus, we may suggest that bufalin could be used as an anti-cancer agent for the treatment of osteosarcoma in the future, and further in vivo studies are needed.

  3. Isolation and sequence of four small nuclear U RNA genes of Trypanosoma brucei subsp. brucei: identification of the U2, U4, and U6 RNA analogs.

    PubMed Central

    Mottram, J; Perry, K L; Lizardi, P M; Lührmann, R; Agabian, N; Nelson, R G

    1989-01-01

    Trypanosomes use trans splicing to place a common 39-nucleotide spliced-leader sequence on the 5' ends of all of their mRNAs. To identify likely participants in this reaction, we used antiserum directed against the characteristic U RNA 2,2,7-trimethylguanosine (TMG) cap to immunoprecipitate six candidate U RNAs from total trypanosome RNA. Genomic Southern analysis using oligonucleotide probes constructed from partial RNA sequence indicated that the four largest RNAs (A through D) are encoded by single-copy genes that are not closely linked to one another. We have cloned and sequenced these genes, mapped the 5' ends of the encoded RNAs, and identified three of the RNAs as the trypanosome U2, U4, and U6 analogs by virtue of their sequences and structural homologies with the corresponding metazoan U RNAs. The fourth RNA, RNA B (144 nucleotides), was not sufficiently similar to known U RNAs to allow us to propose an identify. Surprisingly, none of these U RNAs contained the consensus Sm antigen-binding site, a feature totally conserved among several classes of U RNAs, including U2 and U4. Similarly, the sequence of the U2 RNA region shown to be involved in pre-mRNA branchpoint recognition in yeast, and exactly conserved in metazoan U2 RNAs, was totally divergent in trypanosomes. Like all other U6 RNAs, trypanosome U6 did not contain a TMG cap and was immunoprecipitated from deproteinized RNA by anti-TMG antibody because of its association with the TMG-capped U4 RNA. These two RNAs contained extensive regions of sequence complementarity which phylogenetically support the secondary-structure model proposed by D. A. Brow and C. Guthrie (Nature [London] 334:213-218, 1988) for the organization of the analogous yeast U4-U6 complex. Images PMID:2725495

  4. Isolation and sequence of four small nuclear U RNA genes of Trypanosoma brucei subsp. brucei: Identification of the U2, U4, and U6 RNA analogs

    SciTech Connect

    Mottram, J. ); Perry, K.L.; Agabian, N. . School of Medicine); Lizardi, P.M. ); Luhrmann, R. ); Nelson, R.G. . Dept. of Pharmaceutical Chemistry)

    1989-03-01

    Trypanosomes use trans splicing to place a common 39-nucleotide spliced-leader sequence on the 5' ends of all of their mRNAs. To identify likely participants in this reaction, the authors used antiserum directed against the characteristic U RNA 2,2,7-trimehtylguanosine (TMG) cap to immunoprecipitate six candidate U RNAs from total trypanosome RNA. Genomic Southern analysis using oligonucleotide probes constructed frm partial RNA sequence indicated that the four largest RNAs (A through D) are encoded by single-copy genes that are not closely linked to one another. The authors have cloned and sequenced these genes, mapped the 5' ends of the encoded RNAs,and identified three of the RNAs as the trypanosome U2, U4, and U6 analogs by virtue of their sequences and structural homologies with the corresponding metazoan U RNAs. The fourth RNA, RNA B (144 nucleotides), was not sufficiently similar to known U RNAs to allow them to propose an identity. Surprisingly, none of the U RNAs contained the consensus Sm antigen-binding site, a feature totally conserved among several classes of U RNAs, including U2 and U4. Similarly, the sequence of the U2 RNA region shown to be involved in pre-mRNA branchpoint recognition in yeast, and exactly conserved in metazoan U2 RNAs, was totally divergent in trypanosomes. Like all other U6 RNAs, trypanosome U6 did not contain a TMG cap and was immunoprecipitated from deproteinized RNA by anti-TMG antibody because of its association with the TMG-capped U4 RNA. These two RNAs contained extensive regions of sequence complementarity which phylogenetically support the secondary-structure model proposed by D.A. Brow and C. Guthrie (Nature (London) 334:213-218, 1988) for the organization of the analogous yeast U4-U6 complex.

  5. Carbon dioxide, hydrographic, and chemical data obtained in the Central South Pacific Ocean (WOCE sections P17S and P16S) during the tunes-2-expedition of the R/V Thomas Washington, July--August 1991

    SciTech Connect

    1991-12-31

    This data documentation discusses the procedures and methods used to measure total carbon dioxide (TCO{sub 2}), discrete partial pressure of TCO{sub 2} (pCO{sub 2}), and total alkalinity (TALK), during the Research Vessel (R/V) Thomas Washington TUNES Leg 2 Expedition in the central South Pacific Ocean. Conducted as part of the World Ocean Circulation Experiment (WOCE), the cruise began in Papeete, Tahiti, French Polynesia, on July 16, 1991, and returned to Papeete on August 25, 1991. WOCE Meridional Sections P17S along 135{degrees} W and P16S along 150{degrees} W were completed during the 40-day expedition. A total of 97 hydrographic stations were occupied. Hydrographic and chemical measurements made along WOCE Sections P17S and P16S included pressure, temperature, salinity, and oxygen measured by conductivity, temperature and depth sensor; bottle salinity; oxygen; phosphate; nitrate; nitrite; silicate; CFC-12; CFC- 11; TCO{sub 2}; TALK; and pCO{sub 2} measured at 20{degrees}C. The TCO{sub 2} concentration in 1000 seawater samples was determined with a coulometric analysis system, the pCO{sub 2} in 940 water samples was determined with an equilibrator/gas chromatograph system, while the TALK concentration in 139 samples was determined on shore at the laboratory of C. Goyet of Woods Hole Oceanographic Institution with an alkalinity titration system. In addition, 156 coulometric measurements for the Certified Reference Material (Batch {number_sign}6) were made and yielded a mean value of 2303.2 {plus_minus} 1.5 {mu}mol/kg. This mean value agrees within a standard deviation of the 2304.6 {plus_minus} 1.6 {mu}mol/kg (N=9) value determined with the manometer of C. D. Keeling at Scripps Institution of Oceanography (SIO). Replicate samples from 11 Niskin bottles at 4 stations were also collected for later shore-based reference analyses of TCO{sub 2} and TALK by vacuum extraction and manometry in the laboratory of C. D. Keeling of SIO.

  6. Human regulator of telomere elongation helicase 1 (RTEL1) is required for the nuclear and cytoplasmic trafficking of pre-U2 RNA

    PubMed Central

    Schertzer, Michael; Jouravleva, Karina; Perderiset, Mylene; Dingli, Florent; Loew, Damarys; Le Guen, Tangui; Bardoni, Barbara; de Villartay, Jean-Pierre; Revy, Patrick; Londoño-Vallejo, Arturo

    2015-01-01

    Hoyeraal-Hreidarsson syndrome (HHS) is a severe form of Dyskeratosis congenita characterized by developmental defects, bone marrow failure and immunodeficiency and has been associated with telomere dysfunction. Recently, mutations in Regulator of Telomere ELongation helicase 1 (RTEL1), a helicase first identified in Mus musculus as being responsible for the maintenance of long telomeres, have been identified in several HHS patients. Here we show that RTEL1 is required for the export and the correct cytoplasmic trafficking of the small nuclear (sn) RNA pre-U2, a component of the major spliceosome complex. RTEL1-HHS cells show abnormal subcellular partitioning of pre-U2, defects in the recycling of ribonucleotide proteins (RNP) in the cytoplasm and splicing defects. While most of these phenotypes can be suppressed by re-expressing the wild-type protein in RTEL1-HHS cells, expression of RTEL1 mutated variants in immortalized cells provokes cytoplasmic mislocalizations of pre-U2 and other RNP components, as well as splicing defects, thus phenocopying RTEL1-HHS cellular defects. Strikingly, expression of a cytoplasmic form of RTEL1 is sufficient to correct RNP mislocalizations both in RTEL1–HHS cells and in cells expressing nuclear mutated forms of RTEL1. This work unravels completely unanticipated roles for RTEL1 in RNP trafficking and strongly suggests that defects in RNP biogenesis pathways contribute to the pathology of HHS. PMID:25628358

  7. 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

  8. Up-up-down-down magnetic chain structure of the spin-1/2 tetragonally distorted spinel GeC u2O4

    NASA Astrophysics Data System (ADS)

    Zou, T.; Cai, Y.-Q.; dela Cruz, C. R.; Garlea, V. O.; Mahanti, S. D.; Cheng, J.-G.; Ke, X.

    2016-12-01

    GeC u2O4 spinel exhibits a tetragonal structure due to the strong Jahn-Teller distortion associated with C u2 + ions. We show that its magnetic structure can be described as slabs composed of a pair of layers with orthogonally oriented spin-1/2 Cu chains in the basal a b plane. The spins between the two layers within a slab are collinearly aligned while the spin directions of neighboring slabs are perpendicular to each other. Interestingly, we find that spins along each chain form an unusual up-up-down-down (UUDD) pattern, suggesting a non-negligible nearest-neighbor biquadratic exchange interaction in the effective classical spin Hamiltonian. We hypothesize that spin-orbit coupling and orbital mixing of C u2 + ions in this system are non-negligible, which calls for future calculations using perturbation theory with extended Hilbert (spin and orbital) space and calculations based on density functional theory including spin-orbit coupling and looking at the global stability of the UUDD state.

  9. Concerted evolution of the tandemly repeated genes encoding primate U2 small nuclear RNA (the RNU2 locus) does not prevent rapid diversification of the (CT){sub n} {center_dot} (GA){sub n} microsatellite embedded within the U2 repeat unit

    SciTech Connect

    Liao, D.; Weiner, A.M.

    1995-12-10

    The RNU2 locus encoding human U2 small nuclear RNA (snRNA) is organized as a nearly perfect tandem array containing 5 to 22 copies of a 5.8-kb repeat unit. Just downstream of the U2 snRNA gene in each 5.8-kb repeat unit lies a large (CT){sub n}{center_dot}(GA){sub n} dinucleotide repeat (n {approx} 70). This form of genomic organization, in which one repeat is embedded within another, provides an unusual opportunity to study the balance of forces maintaining the homogeneity of both kinds of repeats. Using a combination of field inversion gel electrophoresis and polymerase chain reaction, we have been able to study the CT microsatellites within individual U2 tandem arrays. We find that the CT microsatellites within an RNU2 allele exhibit significant length polymorphism, despite the remarkable homogeneity of the surrounding U2 repeat units. Length polymorphism is due primarily to loss or gain of CT dinucleotide repeats, but other types of deletions, insertions, and substitutions are also frequent. Polymorphism is greatly reduced in regions where pure (CT){sub n} tracts are interrupted by occasional G residues, suggesting that irregularities stabilize both the length and the sequence of the dinucleotide repeat. We further show that the RNU2 loci of other catarrhine primates (gorilla, chimpanzee, ogangutan, and baboon) contain orthologous CT microsatellites; these also exhibit length polymorphism, but are highly divergent from each other. Thus, although the CT microsatellite is evolving far more rapidly than the rest of the U2 repeat unit, it has persisted through multiple speciation events spanning >35 Myr. The persistence of the CT microsatellite, despite polymorphism and rapid evolution, suggests that it might play a functional role in concerted evolution of the RNU2 loci, perhaps as an initiation site for recombination and/or gene conversion. 70 refs., 5 figs.

  10. Identification of a sequence element directing a protein to nuclear speckles.

    PubMed

    Eilbracht, J; Schmidt-Zachmann, M S

    2001-03-27

    SF3b(155) is an essential spliceosomal protein, highly conserved during evolution. It has been identified as a subunit of splicing factor SF3b, which, together with a second multimeric complex termed SF3a, interacts specifically with the 12S U2 snRNP and converts it into the active 17S form. The protein displays a characteristic intranuclear localization. It is diffusely distributed in the nucleoplasm but highly concentrated in defined intranuclear structures termed "speckles," a subnuclear compartment enriched in small ribonucleoprotein particles and various splicing factors. The primary sequence of SF3b(155) suggests a multidomain structure, different from those of other nuclear speckles components. To identify which part of SF3b(155) determines its specific intranuclear localization, we have constructed expression vectors encoding a series of epitope-tagged SF3b(155) deletion mutants as well as chimeric combinations of SF3b(155) sequences with the soluble cytoplasmic protein pyruvate kinase. Following transfection of cultured mammalian cells, we have identified (i) a functional nuclear localization signal of the monopartite type (KRKRR, amino acids 196--200) and (ii) a molecular segment with multiple threonine-proline repeats (amino acids 208--513), which is essential and sufficient to confer a specific accumulation in nuclear speckles. This latter sequence element, in particular amino acids 208--440, is required for correct subcellular localization of SF3b(155) and is also sufficient to target a reporter protein to nuclear speckles. Moreover, this "speckle-targeting sequence" transfers the capacity for interaction with other U2 snRNP components.

  11. Dihydroptychantol A, a macrocyclic bisbibenzyl derivative, induces autophagy and following apoptosis associated with p53 pathway in human osteosarcoma U2OS cells

    SciTech Connect

    Li Xia; Wu, William K.K.; Sun Bin; Cui Min; Liu Shanshan; Gao Jian; Lou Hongxiang

    2011-03-01

    Dihydroptychantol A (DHA), a novel macrocyclic bisbibenzyl compound extracted from liverwort Asterella angusta, has antifungal and multi-drug resistance reversal properties. Here, the chemically synthesized DHA was employed to test its anti-cancer activities in human osteosarcoma U2OS cells. Our results demonstrated that DHA induced autophagy followed by apoptotic cell death accompanied with G{sub 2}/M-phase cell cycle arrest in U2OS cells. DHA-induced autophagy was morphologically characterized by the formation of double membrane-bound autophagic vacuoles recognizable at the ultrastructural level. DHA also increased the levels of LC3-II, a marker of autophagy. Surprisingly, DHA-mediated apoptotic cell death was potentiated by the autophagy inhibitor 3-methyladenine, suggesting that autophagy may play a protective role that impedes the eventual cell death. Furthermore, p53 was shown to be involved in DHA-meditated autophagy and apoptosis. In this connection, DHA increased nuclear expression of p53, induced p53 phosphorylation, and upregulated p53 target gene p21{sup Waf1/Cip1}. In contrast, cytoplasmic p53 was reduced by DHA, which contributed to the stimulation of autophagy. In relation to the cell cycle, DHA decreased the expression of cyclin B{sub 1}, a cyclin required for progression through the G{sub 2}/M phase. Taken together, DHA induces G{sub 2}/M-phase cell cycle arrest and apoptosis in U2OS cells. DHA-induced apoptosis was preceded by the induction of protective autophagy. DHA-mediated autophagy and apoptosis are associated with the cytoplasmic and nuclear functions of p53.

  12. Salicylate 5-Hydroxylase from Ralstonia sp. Strain U2: a Monooxygenase with Close Relationships to and Shared Electron Transport Proteins with Naphthalene Dioxygenase

    PubMed Central

    Zhou, Ning-Yi; Al-Dulayymi, Jumáa; Baird, Mark S.; Williams, Peter A.

    2002-01-01

    The genes from the oxygenase cluster nagAaGHAbAcAd of naphthalene-degrading Ralstonia sp. strain U2 were cloned and overexpressed. Salicylate 5-hydroxylase (S5H) activity, converting salicylate to gentisate, was present in vitro only in the single extract of cells with overexpressed nagAaGHAb or in a mixture of three cell extracts containing, respectively, NagGH (the oxygenase components), NagAa (ferredoxin reductase), and NagAb (ferredoxin). Each of the three extracts required for S5H activity was rate limiting in the presence of excess of the others but, when in excess, did not affect the rate of catalysis. S5H catalyzed the 5-hydroxylation of the aromatic rings of 3- and 4-substituted salicylates. However, the methyl group of 5-methylsalicylate was hydroxylated to produce the 5-hydroxymethyl derivative and the 6-position on the ring of 5-chlorosalicylate was hydroxylated, producing 5-chloro-2,6-dihydroxybenzoate. In an assay for the nag naphthalene dioxygenase (NDO) based on the indole-linked oxidation of NADH, three extracts were essential for activity (NagAcAd, NagAa, and NagAb). NDO and S5H were assayed in the presence of all possible combinations of the nag proteins and the corresponding nah NDO proteins from the “classical” naphthalene degrader P. putida NCIMB9816. All three oxygenase components functioned with mixed combinations of the electron transport proteins from either strain. The S5H from strain U2 is a unique monooxygenase which shares sequence similarity with dioxygenases such as NDO but is also sufficiently similar in structure to interact with the same electron transport chain and probably does so in vivo during naphthalene catabolism in strain U2. PMID:11872705

  13. Kaempferol suppresses cell metastasis via inhibition of the ERK-p38-JNK and AP-1 signaling pathways in U-2 OS human osteosarcoma cells.

    PubMed

    Chen, Hui-Jye; Lin, Chung-Ming; Lee, Chao-Ying; Shih, Nai-Chen; Peng, Shu-Fen; Tsuzuki, Minoru; Amagaya, Sakae; Huang, Wen-Wen; Yang, Jai-Sing

    2013-08-01

    Kaempferol is a natural flavonoid that possesses anti-proliferative and apoptosis-inducing activities in several cancer cell lines. In the present study, we investigated the anti-metastatic activity of kaempferol and its molecular mechanism(s) of action in human osteosarcoma cells. Kaempferol displayed inhibitory effects on the invasion and adhesion of U-2 osteosarcoma (OS) cells in a concentration-dependent manner by Matrigel Transwell assay and cell adhesion assay. Kaempferol also inhibited the migration of U-2 OS cells in a concentration-dependent manner at different treatment time points by wound-healing assay. Additional experiments showed that kaempferol treatment reduced the enzymatic activities and protein levels of matrix metalloproteinase (MMP)-2, MMP-9 and urokinase plasminogen activator (uPA) by gelatin and casein-plasminogen zymography assays and western blot analyses. Kaempferol also downregulated the mRNA levels of MMP-2 and MMP-9 by quantitative PCR analyses. Furthermore, kaempferol was able to reduce the protein phosphorylation of ERK, p38 and JNK by western blotting. By electrophoretic mobility-shift assay (EMSA), we demonstrated that kaempferol decreased the DNA binding activity of AP-1, an action likely to result in the reduced expression of MMP-2, MMP-9 and uPA. Collectively, our data showed that kaempferol attenuated the MAPK signaling pathways including ERK, JNK and p38 and resulted in the decreased DNA binding ability of AP-1, and hence, the downregulation in the expression and enzymatic activities of MMP-2, MMP-9 and uPA, contributing to the inhibition of metastasis of U-2 OS cells. Our results suggest a potential role of kaempferol in the therapy of tumor metastasis of OS.

  14. Upregulation of NRF2 through autophagy/ERK 1/2 ameliorates ionizing radiation induced cell death of human osteosarcoma U-2 OS.

    PubMed

    Chen, Ni; Zhang, Rui; Konishi, Teruaki; Wang, Jun

    2017-01-01

    The antioxidative response mediated by transcription factor NRF2 is thought to be a pivotal cellular defense system against various extrinsic stresses. It has been reported that activation of the NRF2 pathway confers cells with resistance to ionizing radiation-induced damage. However, the underlying mechanism remains largely unknown. In the current research, it was found that α-particle radiation has the ability to stimulate NRF2 expression in human osteosarcoma U-2 OS cells. Knockdown of cellular NRF2 level by shRNA-mediated gene silencing decreased the survival rate, increased the micronucleus formation rate and apoptosis rate in irradiated cells. Consistently, knockdown of NRF2 resulted in decreased expression of p65 and Bcl-2, and increased expression of p53 and Bax. Besides, it was observed that increased expression of NRF2 was partially dependent on radiation induced phosphorylation of ERK 1/2. Further results showed that radiation promoted autophagy flux which leads to the enhanced phosphorylation of ERK 1/2, as evidenced by the resultls that knockdown of ATG5 (Autophagy protein 5) gene by shRNA suppressed both radiation induced ERK 1/2 phosphorylation and NRF2 upregulation. Based on these results, it is proposed that attenuation of NRF2 antioxidative pathway can sensitize U-2 OS cells to radiation, where NRF2 antioxidative response is regulated by autophagy mediated activation of ERK 1/2 kinases.

  15. Analysis of the structure of Tetrahymena nuclear RNAs in vivo: telomerase RNA, the self-splicing rRNA intron, and U2 snRNA.

    PubMed Central

    Zaug, A J; Cech, T R

    1995-01-01

    Dimethyl sulfate modification of RNA in living Tetrahymena thermophila allowed assessment of RNA secondary structure and protein association. The self-splicing rRNA intron had the same methylation pattern in vivo as in vitro, indicating that the structures are equivalent and suggesting that this RNA is not stably associated with protein in the nucleolus. Methylation was consistent with the current secondary structure model. Much of telomerase RNA was protected from methylation in vivo, but the A's and C's in the template region were very reactive. Thus, most telomerase is not base paired to telomeres in vivo. Protein-free telomerase RNA adopts a structure different from that in vivo, especially in the template and pseudoknot regions. The U2 snRNA showed methylation protection at the Sm protein-binding sequence and the mRNA branch site recognition sequence. For both telomerase RNA and U2 snRNA, the in vivo methylation pattern corresponded much better to the structure determined by comparative sequence analysis than did the in vitro methylation pattern. Thus, as expected, comparative analysis gives the structure of the RNA in vivo. Images FIGURE 1 FIGURE 2 FIGURE 3 FIGURE 5 PMID:7493315

  16. Dosage of the Abcg1-U2af1 region modifies locomotor and cognitive deficits observed in the Tc1 mouse model of Down syndrome.

    PubMed

    Marechal, Damien; Lopes Pereira, Patricia; Duchon, Arnaud; Herault, Yann

    2015-01-01

    Down syndrome (DS) results from one extra copy of human chromosome 21 and leads to several alterations including intellectual disabilities and locomotor defects. The transchromosomic Tc1 mouse model carrying an extra freely-segregating copy of human chromosome 21 was developed to better characterize the relation between genotype and phenotype in DS. The Tc1 mouse exhibits several locomotor and cognitive deficits related to DS. In this report we analyzed the contribution of the genetic dosage of 13 conserved mouse genes located between Abcg1 and U2af1, in the telomeric part of Hsa21. We used the Ms2Yah model carrying a deletion of the corresponding interval in the mouse genome to rescue gene dosage in the Tc1/Ms2Yah compound mice to determine how the different behavioral phenotypes are affected. We detected subtle changes with the Tc1/Ms2Yah mice performing better than the Tc1 individuals in the reversal paradigm of the Morris water maze. We also found that Tc1/Ms2Yah compound mutants performed better in the rotarod than the Tc1 mice. This data support the impact of genes from the Abcg1-U2af1 region as modifiers of Tc1-dependent memory and locomotor phenotypes. Our results emphasize the complex interactions between triplicated genes inducing DS features.

  17. S U (2 ) gauge field theories, gauge-invariant angular momenta, and a Coulomb theorem: A new viewpoint on the resolution of the nucleon spin crisis

    NASA Astrophysics Data System (ADS)

    Huang, Changyu; Huang, Yong-Chang; Zhou, Bao-Hua

    2015-09-01

    We investigate the inner structure of a general S U (2 ) [naturally including S O (3 )] symmetry system—the fermion-gauge field interaction system—and achieve naturally a set of gauge-invariant spin and orbital angular momentum operators of fermion and gauge fields by Noether's theorem in general field theory. Some new relations concerning non-Abelian field strengths are discovered, e.g., the covariant transverse condition, covariant parallel condition (i.e., non-Abelian divergence, non-Abelian curl), and simplified S U (2 ) Coulomb theorem. And we show that the condition that Chen et al. obtained to construct their gauge-invariant angular momentum operators is a result of some fundamental equations in the general field theory. The results obtained in this paper present a new perspective for looking at the overall structure of the gauge field, and provide a new viewpoint to the final resolution of the nucleon spin crisis in the general field theory. Especially, the achieved theory in this paper can calculate the strong interactions with isospin symmetry and solves the serious problem without gauge-invariant angular momenta in strong interaction systems with isospin symmetry, and then the achieved predictions in the calculations can be exactly measured by particle physics experiments due to their gauge invariant properties.

  18. Electronic structures of C u2O ,C u4O3 , and CuO: A joint experimental and theoretical study

    NASA Astrophysics Data System (ADS)

    Wang, Y.; Lany, S.; Ghanbaja, J.; Fagot-Revurat, Y.; Chen, Y. P.; Soldera, F.; Horwat, D.; Mücklich, F.; Pierson, J. F.

    2016-12-01

    A joint experimental and theoretical study is presented for the electronic structures of copper oxides including C u2O , CuO, and the metastable mixed-valence oxide C u4O3 . The optical band gap is determined by experimental optical absorption coefficient, and the electronic structure in valence and conduction bands is probed by photoemission and electron energy loss spectroscopies, respectively. The experimental results are compared with many-body G W calculations utilizing an additional on-site potential for d -orbital energies that facilitates tractable and predictive computations. The side-by-side comparison between the three oxides, including a band insulator (C u2O ) and two Mott/charge-transfer insulators (CuO, C u4O3 ) leads to a consistent picture for the optical and band-structure properties of the Cu oxides, strongly supporting indirect band gaps of about 1.2 and 0.8 eV in CuO and C u4O3 , respectively. This comparison also points towards surface oxidation and reduction effects that can complicate the interpretation of the photoemission spectra.

  19. Préparation et structure cristalline d'un nouvel oxychlorure d'uranium: Le dioxypentachlorodiuranium, U 2O 2Cl 5

    NASA Astrophysics Data System (ADS)

    Levet, J. C.; Potel, M.; Le Marouille, J. Y.

    1980-05-01

    The preparation of a new uranium oxychloride, U 2O 2Cl 5, is described. The compound is orthorhombic, Cmmm, with a=8.431(3) , b=13.663(3) , c=4.106(2) , Z=2, Dm=4.76 g cm-3, Dx=4.81. The structure was solved from three-dimensional diffractometer data with Patterson and Fourier syntheses and full-matrix least-squares refinement. The final R value is 0.072 after absorption correction. The structure consists of (UCl 4/2Cl 1/2O 2/2) ∞2 layers parallel to the (010) plane and linked in the b direction by bridging Cl atoms. The uranium atoms show noninteger formal valence while they are structurally equivalent; their coordination polyhedra are regular pentagonal bipyramids. Structural relationships among PaCl 5, β-U 3O 8, U 2O 2Cl 5, and RbIn 2F 7 are discussed in terms of MX7 entities.

  20. Direct Competition between hnRNP C and U2AF65 Protects the Transcriptome from the Exonization of Alu Elements

    PubMed Central

    Zarnack, Kathi; König, Julian; Tajnik, Mojca; Martincorena, Iñigo; Eustermann, Sebastian; Stévant, Isabelle; Reyes, Alejandro; Anders, Simon; Luscombe, Nicholas M.; Ule, Jernej

    2013-01-01

    Summary There are ∼650,000 Alu elements in transcribed regions of the human genome. These elements contain cryptic splice sites, so they are in constant danger of aberrant incorporation into mature transcripts. Despite posing a major threat to transcriptome integrity, little is known about the molecular mechanisms preventing their inclusion. Here, we present a mechanism for protecting the human transcriptome from the aberrant exonization of transposable elements. Quantitative iCLIP data show that the RNA-binding protein hnRNP C competes with the splicing factor U2AF65 at many genuine and cryptic splice sites. Loss of hnRNP C leads to formation of previously suppressed Alu exons, which severely disrupt transcript function. Minigene experiments explain disease-associated mutations in Alu elements that hamper hnRNP C binding. Thus, by preventing U2AF65 binding to Alu elements, hnRNP C plays a critical role as a genome-wide sentinel protecting the transcriptome. The findings have important implications for human evolution and disease. PMID:23374342

  1. Dosage of the Abcg1-U2af1 Region Modifies Locomotor and Cognitive Deficits Observed in the Tc1 Mouse Model of Down Syndrome

    PubMed Central

    Marechal, Damien; Pereira, Patricia Lopes; Duchon, Arnaud; Herault, Yann

    2015-01-01

    Down syndrome (DS) results from one extra copy of human chromosome 21 and leads to several alterations including intellectual disabilities and locomotor defects. The transchromosomic Tc1 mouse model carrying an extra freely-segregating copy of human chromosome 21 was developed to better characterize the relation between genotype and phenotype in DS. The Tc1 mouse exhibits several locomotor and cognitive deficits related to DS. In this report we analyzed the contribution of the genetic dosage of 13 conserved mouse genes located between Abcg1 and U2af1, in the telomeric part of Hsa21. We used the Ms2Yah model carrying a deletion of the corresponding interval in the mouse genome to rescue gene dosage in the Tc1/Ms2Yah compound mice to determine how the different behavioral phenotypes are affected. We detected subtle changes with the Tc1/Ms2Yah mice performing better than the Tc1 individuals in the reversal paradigm of the Morris water maze. We also found that Tc1/Ms2Yah compound mutants performed better in the rotarod than the Tc1 mice. This data support the impact of genes from the Abcg1-U2af1 region as modifiers of Tc1-dependent memory and locomotor phenotypes. Our results emphasize the complex interactions between triplicated genes inducing DS features. PMID:25706610

  2. Organically templated uranium(IV) fluorooxalates with layer structures: (H4TREN)[U2F6(C2O4)3].4H2O (TREN = tris(2-aminoethyl)amine) and (H4APPIP)[U2F6(C2O4)3].4H2O (APPIP = 1,4-bis(3-amino-propyl)piperazine).

    PubMed

    Wang, Chih-Min; Wu, Yi-Ying; Chen, Pei-Lin; Lii, Kwang-Hwa

    2007-03-14

    Two organically-templated layered uranium(IV) fluorooxalates, (H(4)TREN)[U(2)F(6)(C(2)O(4))(3)].4H(2)O (1) (TREN = tris(2-aminoethyl)amine) and (H(4)APPIP)[U(2)F(6)(C(2)O(4))(3)].4H(2)O (2) (APPIP = 1,4-bis(3-aminopropyl)piperazine), have been synthesized by hydrothermal methods and structurally characterized by single-crystal X-ray diffraction, thermogravimetric analysis, and magnetic susceptibility. Both structures consist of anionic [U(2)F(6)(C(2)O(4))(3)](4-) layers separated by organic ammonium cations and lattice water molecules. The UF(3)O(6) polyhedra are connected by oxalate ligands in different ways within the layers. They are the first examples of organically-templated uranium fluorooxalates. Crystal data for compound 1 follow: monoclinic, P2(1)/c (No. 14), a = 19.1563(5) A, b = 8.9531(2) A, c = 16.6221(4) A, beta = 114.633(1) degrees, and Z = 4. Crystal data for compound are the same as those for 1 except a = 10.3309(8) A, b = 15.564(1) A, c = 17.537(1) A, and beta = 95.430(4) degrees.

  3. SF3A1 — EDRN Public Portal

    Cancer.gov

    From NCBI Gene: This gene encodes a subunit of the splicing factor 3a protein complex. The splicing factor 3a heterotrimer is a component of the mature U2 small nuclear ribonucleoprotein particle (snRNP). U2 small nuclear ribonucleoproteins play a critical role in spliceosome assembly and pre-mRNA splicing. [provided by RefSeq, Aug 2014

  4. 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.

  5. 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

  6. Mutations in the Caenorhabditis elegans U2AF Large Subunit UAF-1 Alter the Choice of a 3′ Splice Site In Vivo

    PubMed Central

    Ma, Long; Horvitz, H. Robert

    2009-01-01

    The removal of introns from eukaryotic RNA transcripts requires the activities of five multi-component ribonucleoprotein complexes and numerous associated proteins. The lack of mutations affecting splicing factors essential for animal survival has limited the study of the in vivo regulation of splicing. From a screen for suppressors of the Caenorhabditis elegans unc-93(e1500) rubberband Unc phenotype, we identified mutations in genes that encode the C. elegans orthologs of two splicing factors, the U2AF large subunit (UAF-1) and SF1/BBP (SFA-1). The uaf-1(n4588) mutation resulted in temperature-sensitive lethality and caused the unc-93 RNA transcript to be spliced using a cryptic 3′ splice site generated by the unc-93(e1500) missense mutation. The sfa-1(n4562) mutation did not cause the utilization of this cryptic 3′ splice site. We isolated four uaf-1(n4588) intragenic suppressors that restored the viability of uaf-1 mutants at 25°C. These suppressors differentially affected the recognition of the cryptic 3′ splice site and implicated a small region of UAF-1 between the U2AF small subunit-interaction domain and the first RNA recognition motif in affecting the choice of 3′ splice site. We constructed a reporter for unc-93 splicing and using site-directed mutagenesis found that the position of the cryptic splice site affects its recognition. We also identified nucleotides of the endogenous 3′ splice site important for recognition by wild-type UAF-1. Our genetic and molecular analyses suggested that the phenotypic suppression of the unc-93(e1500) Unc phenotype by uaf-1(n4588) and sfa-1(n4562) was likely caused by altered splicing of an unknown gene. Our observations provide in vivo evidence that UAF-1 can act in regulating 3′ splice-site choice and establish a system that can be used to investigate the in vivo regulation of RNA splicing in C. elegans. PMID:19893607

  7. Highly Similar Morphologies Between Chromosomes Bearing U2 snRNA Gene Clusters in the Group Astyanax Baird and Girard, 1854 (Characiformes, Characidae): An Evolutionary Approach in Species with 2n = 36, 46, 48, and 50.

    PubMed

    Piscor, Diovani; Centofante, Liano; Parise-Maltempi, Patricia Pasquali

    2016-12-01

    Repetitive sequences and their chromosomal locations have been widely studied in species of the Astyanax genus. However, the chromosomal organization of U2 snDNA remains largely unknown. The aims of this study were to examine the chromosomal contexts of U2 snRNA and 5S rRNA genes in Astyanax species and determine the degree of chromosome morphological similarity between species with different diploid numbers. Clusters of U2 snDNA and 5S rDNA were determined in nine species of Astyanax, including two karyomorphs of Astyanax fasciatus Cuvier, 1819. All species exhibited U2 snDNA clusters on two chromosome pairs, except Astyanax mexicanus De Filippi, 1853 (one pair). The 5S rDNA clusters were located on one chromosome pair in Astyanax altiparanae Garutti and Britski, 2000, and Astyanax marionae Eigenmann, 1911, two pairs in Astyanax abramis Jenyns, 1842, Astyanax asuncionensis Géry, 1972, Astyanax bockmanni Vari and Castro, 2007, Astyanax eigenmanniorum Cope, 1894, A. fasciatus (karyomorphs I and II), and Astyanax schubarti Britski, 1964, and four pairs in A. mexicanus. The relationships between the repetitive sequences in different species suggest that A. schubarti and A. mexicanus exhibit an unusual U2 snDNA chromosomal format as a result of events occurring in the evolutionary history of the Astyanax group.

  8. Gauge-independent "Abelian" and magnetic-monopole dominance, and the dual Meissner effect in lattice S U (2 ) Yang-Mills theory

    NASA Astrophysics Data System (ADS)

    Kato, Seikou; Kondo, Kei-Ichi; Shibata, Akihiro

    2015-02-01

    In the S U (2 ) Yang-Mills theory on the four-dimensional Euclidean lattice, we confirm the gauge-independent "Abelian" dominance (or the restricted field dominance) and gauge-independent magnetic-monopole dominance in the string tension of the linear potential extracted from the Wilson loop in the fundamental representation. The dual Meissner effect is observed by demonstrating the squeezing of the chromoelectric field flux connecting a pair of a quark and an antiquark. In addition, the circular magnetic-monopole current is induced around the chromoelectric flux. The type of the dual superconductivity is also determined by fitting the result with the dual Ginzburg-Landau model. Thus, the dual superconductor picture for quark confinement is supported in a gauge-independent manner. These results are obtained based on a reformulation of the lattice Yang-Mills theory based on the change of variables à la Cho-Duan-Ge-Faddeev-Niemi combined with a non-Abelian Stokes theorem for the Wilson loop operator. We give a new procedure (called the reduction) for obtaining the color direction field that plays the central role in this reformulation.

  9. Processing of U-2.5Zr-7.5Nb and U-3Zr-9Nb alloys by sintering process

    SciTech Connect

    Dos Santos, A. M. M.; Ferraz, W. B.; Lameiras, F. S.; Mazzeu, T. D. O.

    2012-07-01

    To minimize the risk of nuclear proliferation, there is worldwide interest in reducing fuel enrichment of research and test reactors. To achieve this objective while still guaranteeing criticality and cycle length requirements, there is need of developing high density uranium metallic fuels. Alloying elements such as Zr, Nb and Mo are added to uranium to improve fuel performance in reactors. In this context, the Centro de Desenvolvimento da Tecnologia Nuclear (CDTN) is developing the U-2.5Zr-7.5Nb and U-3Zr-9Nb (weight %) alloys by the innovative process of sintering that utilizes raw materials in the form of powders. The powders were pressed at 400 MPa and then sintered under a vacuum of about 1x10{sup -4} Torr at temperatures ranging from 1050 deg. to 1500 deg.C. The densities of the alloys were measured geometrically and by hydrostatic method and the phases identified by X ray diffraction (XRD). The microstructures of the pellets were observed by scanning electron microscopy (SEM) and the alloying elements were analyzed by energy dispersive X-ray spectroscopy (EDS). The results obtained showed the fuel density to slightly increase with the sintering temperature. The highest density achieved was approximately 80% of theoretical density. It was observed in the pellets a superficial oxide layer formed during the sintering process. (authors)

  10. The Naphthalene Catabolic (nag) Genes of Ralstonia sp. Strain U2 Are an Operon That Is Regulated by NagR, a LysR-Type Transcriptional Regulator

    PubMed Central

    Jones, Rheinallt M.; Britt-Compton, Bethan; Williams, Peter A.

    2003-01-01

    In Ralstonia sp. strain U2, the nag catabolic genes, which encode the enzymes for the pathway that catabolizes naphthalene via the alternative ring cleavage gentisate pathway, are transcribed as an operon under the same promoter. nagR, which encodes a LysR-type transcriptional regulator, is divergently transcribed compared to the nag catabolic genes. A 4-bp frameshift deletion in nagR demonstrated that NagR is required for expression of the nag operon. The transcriptional start of the nag operon was mapped, and a putative −10, −35 σ70-type promoter binding site was identified. Further upstream, a site proximal to the promoter was identified as a site that has bases which have been found to be conserved in the activator-binding motif of other naphthalene pathways. Transcriptional fusion studies demonstrated that NagR regulates the expression of the nag operon positively in the presence of salicylate and to a lesser extent in the presence of 2-nitrobenzoate. Mutation of the LysR-type activator-binding motif in the nag promoter-proximal region resulted in a loss of inducibility of a lacZ reporter gene transcriptionally fused to nagAa, the first gene of the operon. However, other mutations in the region increased the effectiveness of salicylate as an inducer. PMID:13129957

  11. Analysis of a cDNA clone expressing a human autoimmune antigen: full-length sequence of the U2 small nuclear RNA-associated B antigen

    SciTech Connect

    Habets, W.J.; Sillekens, P.T.G.; Hoet, M.H.; Schalken, J.A.; Roebroek, A.J.M.; Leunissen, J.A.M.; Van de Ven, W.J.M.; Van Venrooij, W.J.

    1987-04-01

    A U2 small nuclear RNA-associated protein, designated B'', was recently identified as the target antigen for autoimmune sera from certain patients with systemic lupus erythematosus and other rheumatic diseases. Such antibodies enabled them to isolate cDNA clone lambdaHB''-1 from a phage lambdagt11 expression library. This clone appeared to code for the B'' protein as established by in vitro translation of hybrid-selected mRNA. The identity of clone lambdaHB''-1 was further confirmed by partial peptide mapping and analysis of the reactivity of the recombinant antigen with monospecific and monoclonal antibodies. Analysis of the nucleotide sequence of the 1015-base-pair cDNA insert of clone lambdaHB''-1 revealed a large open reading frame of 800 nucleotides containing the coding sequence for a polypeptide of 25,457 daltons. In vitro transcription of the lambdaHB''-1 cDNA insert and subsequent translation resulted in a protein product with the molecular size of the B'' protein. These data demonstrate that clone lambdaHB''-1 contains the complete coding sequence of this antigen. The deduced polypeptide sequence contains three very hydrophilic regions that might constitute RNA binding sites and/or antigenic determinants. These findings might have implications both for the understanding of the pathogenesis of rheumatic diseases as well as for the elucidation of the biological function of autoimmune antigens.

  12. Modulation of TGFbeta 2 levels by lamin A in U2-OS osteoblast-like cells: understanding the osteolytic process triggered by altered lamins

    PubMed Central

    Evangelisti, Camilla; Bernasconi, Pia; Cavalcante, Paola; Cappelletti, Cristina; D'Apice, Maria Rosaria; Sbraccia, Paolo; Novelli, Giuseppe; Prencipe, Sabino; Lemma, Silvia; Baldini, Nicola; Avnet, Sofia; Squarzoni, Stefano; Martelli, Alberto M.; Lattanzi, Giovanna

    2015-01-01

    Transforming growth factor beta (TGFbeta) plays an essential role in bone homeostasis and deregulation of TGFbeta occurs in bone pathologies. Patients affected by Mandibuloacral Dysplasia (MADA), a progeroid disease linked to LMNA mutations, suffer from an osteolytic process. Our previous work showed that MADA osteoblasts secrete excess amount of TGFbeta 2, which in turn elicits differentiation of human blood precursors into osteoclasts. Here, we sought to determine how altered lamin A affects TGFbeta signaling. Our results show that wild-type lamin A negatively modulates TGFbeta 2 levels in osteoblast-like U2-OS cells, while the R527H mutated prelamin A as well as farnesylated prelamin A do not, ultimately leading to increased secretion of TGFbeta 2. TGFbeta 2 in turn, triggers the Akt/mTOR pathway and upregulates osteoprotegerin and cathepsin K. TGFbeta 2 neutralization rescues Akt/mTOR activation and the downstream transcriptional effects, an effect also obtained by statins or RAD001 treatment. Our results unravel an unexpected role of lamin A in TGFbeta 2 regulation and indicate rapamycin analogs and neutralizing antibodies to TGFbeta 2 as new potential therapeutic tools for MADA. PMID:25823658

  13. The Activation-Induced Assembly of an RNA/Protein Interactome Centered on the Splicing Factor U2AF2 Regulates Gene Expression in Human CD4 T Cells.

    PubMed

    Whisenant, Thomas C; Peralta, Eigen R; Aarreberg, Lauren D; Gao, Nina J; Head, Steven R; Ordoukhanian, Phillip; Williamson, Jamie R; Salomon, Daniel R

    2015-01-01

    Activation of CD4 T cells is a reaction to challenges such as microbial pathogens, cancer and toxins that defines adaptive immune responses. The roles of T cell receptor crosslinking, intracellular signaling, and transcription factor activation are well described, but the importance of post-transcriptional regulation by RNA-binding proteins (RBPs) has not been considered in depth. We describe a new model expanding and activating primary human CD4 T cells and applied this to characterizing activation-induced assembly of splicing factors centered on U2AF2. We immunoprecipitated U2AF2 to identify what mRNA transcripts were bound as a function of activation by TCR crosslinking and costimulation. In parallel, mass spectrometry revealed the proteins incorporated into the U2AF2-centered RNA/protein interactome. Molecules that retained interaction with the U2AF2 complex after RNAse treatment were designated as "central" interactome members (CIMs). Mass spectrometry also identified a second class of activation-induced proteins, "peripheral" interactome members (PIMs), that bound to the same transcripts but were not in physical association with U2AF2 or its partners. siRNA knockdown of two CIMs and two PIMs caused changes in activation marker expression, cytokine secretion, and gene expression that were unique to each protein and mapped to pathways associated with key aspects of T cell activation. While knocking down the PIM, SYNCRIP, impacts a limited but immunologically important set of U2AF2-bound transcripts, knockdown of U2AF1 significantly impairs assembly of the majority of protein and mRNA components in the activation-induced interactome. These results demonstrated that CIMs and PIMs, either directly or indirectly through RNA, assembled into activation-induced U2AF2 complexes and play roles in post-transcriptional regulation of genes related to cytokine secretion. These data suggest an additional layer of regulation mediated by the activation-induced assembly of RNA

  14. The Activation-Induced Assembly of an RNA/Protein Interactome Centered on the Splicing Factor U2AF2 Regulates Gene Expression in Human CD4 T Cells

    PubMed Central

    Aarreberg, Lauren D.; Gao, Nina J.; Head, Steven R.; Ordoukhanian, Phillip; Williamson, Jamie R.; Salomon, Daniel R.

    2015-01-01

    Activation of CD4 T cells is a reaction to challenges such as microbial pathogens, cancer and toxins that defines adaptive immune responses. The roles of T cell receptor crosslinking, intracellular signaling, and transcription factor activation are well described, but the importance of post-transcriptional regulation by RNA-binding proteins (RBPs) has not been considered in depth. We describe a new model expanding and activating primary human CD4 T cells and applied this to characterizing activation-induced assembly of splicing factors centered on U2AF2. We immunoprecipitated U2AF2 to identify what mRNA transcripts were bound as a function of activation by TCR crosslinking and costimulation. In parallel, mass spectrometry revealed the proteins incorporated into the U2AF2-centered RNA/protein interactome. Molecules that retained interaction with the U2AF2 complex after RNAse treatment were designated as “central” interactome members (CIMs). Mass spectrometry also identified a second class of activation-induced proteins, “peripheral” interactome members (PIMs), that bound to the same transcripts but were not in physical association with U2AF2 or its partners. siRNA knockdown of two CIMs and two PIMs caused changes in activation marker expression, cytokine secretion, and gene expression that were unique to each protein and mapped to pathways associated with key aspects of T cell activation. While knocking down the PIM, SYNCRIP, impacts a limited but immunologically important set of U2AF2-bound transcripts, knockdown of U2AF1 significantly impairs assembly of the majority of protein and mRNA components in the activation-induced interactome. These results demonstrated that CIMs and PIMs, either directly or indirectly through RNA, assembled into activation-induced U2AF2 complexes and play roles in post-transcriptional regulation of genes related to cytokine secretion. These data suggest an additional layer of regulation mediated by the activation-induced assembly

  15. Metastable phases determination of U-2.5Zr-7.5Nb and U-3.0Zr-9.0Nb alloys by Rietveld method

    SciTech Connect

    Dias Pais, R. W.; Dos Santos, A. M. M.; Lameiras, F. S.; Cantagalli, N. M.; De Paula, R. G.; Ferraz, W. B.

    2012-07-01

    The Rietveld refinement has been employed for study of metastable phase of alloys U-2.5Zr-7.5Nb(wt%) and U-3Zr-9Nb(wt%). The ingots of both alloys were produced in vacuum induction furnace at temperature of about 1500 deg.C followed by cooling to room temperature. The samples with 2.5 cm in diameter and 0.3 cm of thickness was homogenized at 1000 deg.C/16 hours and treated isothermally at (i) 600 deg.C for 0.5, 3 and 24 hours and (ii) 300 deg.C for 4 minutes, 20 minutes and 17.5 hours. At the end of each treatment the samples were water quenched. Data from X-ray diffraction were collected at room temperature with a Rigaku diffractometer D Max-RAPID radiation Cuk{alpha} using steps of 0.02 deg. (2{theta}) with scan angle in the range of 20-80 deg. (2{theta}). The full diffraction pattern was analyzed by the Rietveld method using the GSAS program. The result shows that the non-resolved appearance of the XRD patterns added to the proximity of the Bragg reflections of the transition phase makes the refinement of alloys a challenging task. For the isothermal treatment at 600 deg.C during 0.5 and 3 hours both alloys showed the majority presence of {gamma}{sup S} phase fallow by {gamma}{sup 0} phase in minor amounts. For 24 hours at 600 deg.C occurred the decomposition of phases with the presence of {gamma}{sup S} + {alpha}. Isothermal treatment at 300 deg.C for both alloys is characterized by the presence of phases {gamma}{sup 0} + {alpha}'' where the concentration of the {alpha}'' phase increases with time of heat treatment. (authors)

  16. Similarities in the endocrine-disrupting potencies of indoor dust and flame retardants by using human osteosarcoma (U2OS) cell-based reporter gene assays.

    PubMed

    Suzuki, Go; Tue, Nguyen Minh; Malarvannan, Govindan; Sudaryanto, Agus; Takahashi, Shin; Tanabe, Shinsuke; Sakai, Shin-ichi; Brouwer, Abraham; Uramaru, Naoto; Kitamura, Shigeyuki; Takigami, Hidetaka

    2013-03-19

    Indoor dust is a sink for many kinds of pollutants, including flame retardants (FRs), plasticizers, and their contaminants and degradation products. These pollutants can be migrated to indoor dust from household items such as televisions and computers. To reveal high-priority end points of and contaminant candidates in indoor dust, using CALUX reporter gene assays based on human osteosarcoma (U2OS) cell lines, we evaluated and characterized the endocrine-disrupting potencies of crude extracts of indoor dust collected from Japan (n = 8), the United States (n = 21), Vietnam (n = 10), the Philippines (n = 17), and Indonesia (n = 10) and for 23 selected FRs. The CALUX reporter gene assays used were specific for compounds interacting with the human androgen receptor (AR), estrogen receptor α (ERα), progesterone receptor (PR), glucocorticoid receptor (GR), and peroxisome proliferator-activated receptor γ2 (PPARγ2). Indoor dust extracts were agonistic to ERα, GR, and PPARγ2 and antagonistic against AR, PR, GR, and PPARγ2. In comparison, a majority of FRs was agonistic to ERα and PPARγ2 only, and some FRs demonstrated receptor-specific antagonism against all tested nuclear receptors. Hierarchical clustering clearly indicated that agonism of ERα and antagonism of AR and PR were common, frequently detected end points for indoor dust and tested FRs. Given our previous results regarding the concentrations of FRs in indoor dust and in light of our current results, candidate contributors to these effects include not only internationally controlled brominated FRs but also alternatives such as some phosphorus-containing FRs. In the context of indoor pollution, high-frequency effects of FRs such as agonism of ERα and antagonism of AR and PR are candidate high-priority end points for further investigation.

  17. Abundance of Dioxygenase Genes Similar to Ralstonia sp. Strain U2 nagAc Is Correlated with Naphthalene Concentrations in Coal Tar-Contaminated Freshwater Sediments

    PubMed Central

    Dionisi, Hebe M.; Chewning, Christopher S.; Morgan, Katherine H.; Menn, Fu-Min; Easter, James P.; Sayler, Gary S.

    2004-01-01

    We designed a real-time PCR assay able to recognize dioxygenase large-subunit gene sequences with more than 90% similarity to the Ralstonia sp. strain U2 nagAc gene (nagAc-like gene sequences) in order to study the importance of organisms carrying these genes in the biodegradation of naphthalene. Sequencing of PCR products indicated that this real-time PCR assay was specific and able to detect a variety of nagAc-like gene sequences. One to 100 ng of contaminated-sediment total DNA in 25-μl reaction mixtures produced an amplification efficiency of 0.97 without evident PCR inhibition. The assay was applied to surficial freshwater sediment samples obtained in or in close proximity to a coal tar-contaminated Superfund site. Naphthalene concentrations in the analyzed samples varied between 0.18 and 106 mg/kg of dry weight sediment. The assay for nagAc-like sequences indicated the presence of (4.1 ± 0.7) × 103 to (2.9 ± 0.3) × 105 copies of nagAc-like dioxygenase genes per μg of DNA extracted from sediment samples. These values corresponded to (1.2 ± 0.6) × 105 to (5.4 ± 0.4) × 107 copies of this target per g of dry weight sediment when losses of DNA during extraction were taken into account. There was a positive correlation between naphthalene concentrations and nagAc-like gene copies per microgram of DNA (r = 0.89) and per gram of dry weight sediment (r = 0.77). These results provide evidence of the ecological significance of organisms carrying nagAc-like genes in the biodegradation of naphthalene. PMID:15240274

  18. Binding of hnRNP H and U2AF65 to Respective G-codes and a Poly-Uridine Tract Collaborate in the N50-5'ss Selection of the REST N Exon in H69 Cells

    PubMed Central

    Ortuño-Pineda, Carlos; Galindo-Rosales, José Manuel; Calderón-Salinas, José Victor; Villegas-Sepúlveda, Nicolás; Saucedo-Cárdenas, Odila; De Nova-Ocampo, Mónica; Valdés, Jesús

    2012-01-01

    The splicing of the N exon in the pre-mRNA coding for the RE1-silencing transcription factor (REST) results in a truncated protein that modifies the expression pattern of some of its target genes. A weak 3'ss, three alternative 5'ss (N4-, N50-, and N62-5'ss) and a variety of putative target sites for splicing regulatory proteins are found around the N exon; two GGGG codes (G2-G3) and a poly-Uridine tract (N-PU) are found in front of the N50-5'ss. In this work we analyzed some of the regulatory factors and elements involved in the preferred selection of the N50-5'ss (N50 activation) in the small cell lung cancer cell line H69. Wild type and mutant N exon/β-globin minigenes recapitulated N50 exon splicing in H69 cells, and showed that the N-PU and the G2-G3 elements are required for N50 exon splicing. Biochemical and knockdown experiments identified these elements as U2AF65 and hnRNP H targets, respectively, and that they are also required for N50 exon activation. Compared to normal MRC5 cells, and in keeping with N50 exon activation, U2AF65, hnRNP H and other splicing factors were highly expressed in H69 cells. CLIP experiments revealed that hnRNP H RNA-binding occurs first and is a prerequisite for U2AF65 RNA binding, and EMSA and CLIP experiments suggest that U2AF65-RNA recognition displaces hnRNP H and helps to recruit other splicing factors (at least U1 70K) to the N50-5'ss. Our results evidenced novel hnRNP H and U2AF65 functions: respectively, U2AF65-recruiting to a 5'ss in humans and the hnRNP H-displacing function from two juxtaposed GGGG codes. PMID:22792276

  19. Remodeling of U2-U6 snRNA helix I during pre-mRNA splicing by Prp16 and the NineTeen Complex protein Cwc2

    PubMed Central

    Hogg, Rebecca; de Almeida, Rogerio Alves; Ruckshanthi, Jayalath P.D.; O'Keefe, Raymond T.

    2014-01-01

    Removal of intron regions from pre-messenger RNA (pre-mRNA) requires spliceosome assembly with pre-mRNA, then subsequent spliceosome remodeling to allow activation for the two steps of intron removal. Spliceosome remodeling is carried out through the action of DExD/H-box ATPases that modulate RNA–RNA and protein–RNA interactions. The ATPase Prp16 remodels the spliceosome between the first and second steps of splicing by catalyzing release of first step factors Yju2 and Cwc25 as well as destabilizing U2-U6 snRNA helix I. How Prp16 destabilizes U2-U6 helix I is not clear. We show that the NineTeen Complex (NTC) protein Cwc2 displays genetic interactions with the U6 ACAGAGA, the U6 internal stem loop (ISL) and the U2-U6 helix I, all RNA elements that form the spliceosome active site. We find that one function of Cwc2 is to stabilize U2-U6 snRNA helix I during splicing. Cwc2 also functionally cooperates with the NTC protein Isy1/NTC30. Mutation in Cwc2 can suppress the cold sensitive phenotype of the prp16-302 mutation indicating a functional link between Cwc2 and Prp16. Specifically the prp16-302 mutation in Prp16 stabilizes Cwc2 interactions with U6 snRNA and destabilizes Cwc2 interactions with pre-mRNA, indicating antagonistic functions of Cwc2 and Prp16. We propose that Cwc2 is a target for Prp16-mediated spliceosome remodeling during pre-mRNA splicing. PMID:24848011

  20. TEG-1 CD2BP2 regulates stem cell proliferation and sex determination in the C. elegans germ line and physically interacts with the UAF-1 U2AF65 splicing factor

    PubMed Central

    Wang, Chris; Wilson-Berry, Laura; Schedl, Tim; Hansen, Dave

    2012-01-01

    Background For a stem cell population to exist over an extended period, a balance must be maintained between self-renewing (proliferating) and differentiating daughter cells. Within the Caenorhabditis elegans germ line, this balance is controlled by a genetic regulatory pathway, which includes the canonical Notch signaling pathway. Results Genetic screens identified the gene teg-1 as being involved in regulating the proliferation vs. differentiation decision in the C. elegans germ line. Cloning of TEG-1 revealed that it is a homolog of mammalian CD2BP2, which has been implicated in a number of cellular processes, including in U4/U6.U5 tri-snRNP formation in the pre-mRNA splicing reaction. The position of teg-1 in the genetic pathway regulating the proliferation vs. differentiation decision, its single mutant phenotype, and its enrichment in nuclei, all suggest TEG-1 also functions as a splicing factor. TEG-1, as well as its human homolog, CD2BP2, directly bind to UAF-1 U2AF65, a component of the U2 auxiliary factor. Conclusions TEG-1 functions as a splicing factor and acts to regulate the proliferation vs. meiosis decision. The interaction of TEG-1 CD2BP2 with UAF-1 U2AF65, combined with its previously described function in U4/U6.U5 tri-snRNP, suggests that TEG-1 CD2BP2 functions in two distinct locations in the splicing cascade. PMID:22275078

  1. Syntheses and crystal structures of the quaternary uranium lanthanide oxyselenides UYb2O2Se3 and U2Ln2O4Se3 (Ln=Pr, Sm, Gd)

    NASA Astrophysics Data System (ADS)

    Raw, Adam D.; Ibers, James A.

    2012-02-01

    Single crystals of the new uranium lanthanide oxyselenide compounds UYb2O2Se3 and U2Ln2O4Se3 (Ln=Pr, Sm, Gd) have been synthesized from an Sb2Se3 flux. The structures have been determined from single-crystal X-ray diffraction data. UYb2O2Se3 is isostructural to UYb2O2S3. The structure comprises layers of edge-sharing YbSe6 octahedra and double layers of disordered (U/Ln)O4Se4 square antiprisms. The U2Ln2O4Se3 (Ln=Pr, Sm, Gd) compounds are isostructural to U2Ln2O4S3 (Ln=La-Gd) whose structure had been deduced previously from X-ray powder diffraction data. In the structure a dodecahedron of four O atoms and four Se atoms surrounds a site primarily occupied by U and a distorted bicapped octahedron of five Se atoms and three O atoms surrounds a site primarily occupied by the lanthanide. These compounds represent the first examples of quaternary uranium oxyselenides.

  2. Inactivation of the WNT5A Alternative Promoter B Is Associated with DNA Methylation and Histone Modification in Osteosarcoma Cell Lines U2OS and SaOS-2.

    PubMed

    Vaidya, Himani; Rumph, Candie; Katula, Karen S

    2016-01-01

    WNT5A is a secreted ligand involved in Wnt pathway signaling and has a role in cell movement and differentiation. Altered WNT5A expression is associated with various cancers, although in most studies the focus has been on only one of the known WNT5A isoforms. In this study, we analyzed expression from two of the major WNT5A promoters, termed promoter A and promoter B, in normal human osteoblasts, SaOS-2 and U2OS osteosarcoma cell lines, and osteosarcoma tumor tissue. We found that both promoters A and B are active in normal osteoblasts with nearly 11-fold more promoter B than A transcripts. Promoter B but not promoter A transcripts are decreased or nearly undetectable in the SaOS-2 and U2OS cell lines and osteosarcoma tumor tissues. Transient transfection of promoter A and promoter B reporter constructs confirmed that SaOS-2 cells have the necessary factors to transcribe both promoters. Bisulfite sequencing analysis revealed that three CpG enriched regions upstream of the promoter B exon 1βare highly methylated in both SaOS-2 and U2OS cells. The CpG island sub-region R6 located in promoter B exon 1β was approximately 51% methylated in SaOS-2 and 25% methylated in U2OS. Region 3 was approximately 28% methylated in normal osteoblasts, whereas the others were unmethylated. Promoter B was re-activated by treatment of SaOS-2 cells with 1 μM 5-azacytidine, which was associated with only a small insignificant change in methylation of sub-region R6. ChIP analysis of U2OS and SaOS-2 cells indicated that the promoter B region is less enriched in the active histone mark H3K4me3, in comparison to promoter A and that there is increased enrichment of the repressive mark H3K27me3 in association with the promoter B genomic region in the cell line SaOS-2. These findings show that epigenetic inactivation of the WNT5A promoter B involves both DNA methylation and histone modifications and suggest that differential expression of the WNT5A alternative promoters A and B is a

  3. Gas-phase reactions of the bare Th2+ and U2+ ions with small alkanes, CH4, C2H6, and C3H8: experimental and theoretical study of elementary organoactinide chemistry.

    PubMed

    Di Santo, Emanuela; Santos, Marta; Michelini, Maria C; Marçalo, Joaquim; Russo, Nino; Gibson, John K

    2011-02-16

    The gas-phase reactions of two dipositive actinide ions, Th(2+) and U(2+), with CH(4), C(2)H(6), and C(3)H(8) were studied by both experiment and theory. Fourier transform ion cyclotron resonance mass spectrometry was employed to study the bimolecular ion-molecule reactions; the potential energy profiles (PEPs) for the reactions, both observed and nonobserved, were computed by density functional theory (DFT). The experiments revealed that Th(2+) reacts with all three alkanes, including CH(4) to produce ThCH(2)(2+), whereas U(2+) reacts with C(2)H(6) and C(3)H(8), with different product distributions than for Th(2+). The comparative reactivities of Th(2+) and U(2+) toward CH(4) are well explained by the computed PEPs. The PEPs for the reactions with C(2)H(6) effectively rationalize the observed reaction products, ThC(2)H(2)(2+) and UC(2)H(4)(2+). For C(3)H(8) several reaction products were experimentally observed; these and additional potential reaction pathways were computed. The DFT results for the reactions with C(3)H(8) are consistent with the observed reactions and the different products observed for Th(2+) and U(2+); however, several exothermic products which emerge from energetically favorable PEPs were not experimentally observed. The comparison between experiment and theory reveals that DFT can effectively exclude unfavorable reaction pathways, due to energetic barriers and/or endothermic products, and can predict energetic differences in similar reaction pathways for different ions. However, and not surprisingly, a simple evaluation of the PEP features is insufficient to reliably exclude energetically favorable pathways. The computed PEPs, which all proceed by insertion, were used to evaluate the relationship between the energetics of the bare Th(2+) and U(2+) ions and the energies for C-H and C-C activation. It was found that the computed energetics for insertion are entirely consistent with the empirical model which relates insertion efficiency to the

  4. A 23Na magic angle spinning nuclear magnetic resonance, XANES, and high-temperature X-ray diffraction study of NaUO3, Na4UO5, and Na2U2O7.

    PubMed

    Smith, A L; Raison, P E; Martel, L; Charpentier, T; Farnan, I; Prieur, D; Hennig, C; Scheinost, A C; Konings, R J M; Cheetham, A K

    2014-01-06

    The valence state of uranium has been confirmed for the three sodium uranates NaU(V)O3/[Rn](5f(1)), Na4U(VI)O5/[Rn](5f(0)), and Na2U(VI)2O7/[Rn](5f(0)), using X-ray absorption near-edge structure (XANES) spectroscopy. Solid-state (23)Na magic angle spinning nuclear magnetic resonance (MAS NMR) measurements have been performed for the first time, yielding chemical shifts at -29.1 (NaUO3), 15.1 (Na4UO5), and -14.1 and -19 ppm (Na1 8-fold coordinated and Na2 7-fold coordinated in Na2U2O7), respectively. The [Rn]5f(1) electronic structure of uranium in NaUO3 causes a paramagnetic shift in comparison to Na4UO5 and Na2U2O7, where the electronic structure is [Rn]5f(0). A (23)Na multi quantum magic angle spinning (MQMAS) study on Na2U2O7 has confirmed a monoclinic rather than rhombohedral structure with evidence for two distinct Na sites. DFT calculations of the NMR parameters on the nonmagnetic compounds Na4UO5 and Na2U2O7 have permitted the differentiation between the two Na sites of the Na2U2O7 structure. The linear thermal expansion coefficients of all three compounds have been determined using high-temperature X-ray diffraction: αa = 22.7 × 10(-6) K(-1), αb = 12.9 × 10(-6) K(-1), αc = 16.2 × 10(-6) K(-1), and αvol = 52.8 × 10(-6) K(-1) for NaUO3 in the range 298-1273 K; αa = 37.1 × 10(-6) K(-1), αc = 6.2 × 10(-6) K(-1), and αvol = 81.8 × 10(-6) K(-1) for Na4UO5 in the range 298-1073 K; αa = 6.7 × 10(-6) K(-1), αb = 14.4 × 10(-6) K(-1), αc = 26.8 × 10(-6) K(-1), αβ = -7.8 × 10(-6) K(-1), and αvol = -217.6 × 10(-6) K(-1) for Na2U2O7 in the range 298-573 K. The α to β phase transition reported for the last compound above about 600 K was not observed in the present studies, either by high-temperature X-ray diffraction or by differential scanning calorimetry.

  5. Inhibition of fatty acid synthase suppresses U-2 OS cell invasion and migration via downregulating the activity of HER2/PI3K/AKT signaling pathway in vitro

    SciTech Connect

    Wang, Tao Fang; Wang, Heng; Peng, Ai Fen; Luo, Qing Feng; Liu, Zhi Li; Zhou, Rong Ping; Gao, Song; Zhou, Yang; Chen, Wen Zhao

    2013-10-18

    Highlights: •We investigate the relationship between FASN and HER2 or p-HER2 by IHC in OS tissues. •We construct FASN-specific RNAi plasmid. •Inhibiting FASN down-regulates HER2/PI3K/AKT cell signaling in U-2 OS. •Inhibiting FASN blocks U-2 OS cell invasion and migration. -- Abstract: FASN plays an important role in the malignant phenotype of various tumors. Our previous studies show that inhibition FASN could induce apoptosis and inhibit proliferation in human osteosarcoma (OS) cell in vivo and vitro. The aim in this study was to investigate the effect of inhibition FASN on the activity of HER2/PI3K/AKT axis and invasion and migration of OS cell. The expression of FASN, HER2 and p-HER2(Y1248) proteins was detected by immunohistochemistry in OS tissues from 24 patients with pulmonary metastatic disease, and the relationship between FASN and p-HER2 as well as HER2 was investigated. The results showed that there was a positive correlation between FASN and HER2 as well as p-HER2 protein expression. The U-2 OS cells were transfected with either the FASN specific RNAi plasmid or the negative control RNAi plasmid. FASN mRNA was measured by RT-PCR. Western blot assays was performed to examine the protein expression of FASN, HER2, p-HER2(Y1248), PI3K, Akt and p-Akt (Ser473). Migration and invasion of cells were investigated by wound healing and transwell invasion assays. The results showed that the activity of HER2/PI3K/AKT signaling pathway was suppressed by inhibiting FASN. Meanwhile, the U-2OS cells migration and invasion were also impaired by inhibiting the activity of FASN/HER2/PI3K/AKT. Our results indicated that inhibition of FASN suppresses OS cell invasion and migration via down-regulation of the “HER2/PI3K/AKT” axis in vitro. FASN blocker may be a new therapeutic strategy in OS management.

  6. Use of a novel Förster resonance energy transfer method to identify locations of site-bound metal ions in the U2-U6 snRNA complex.

    PubMed

    Yuan, Faqing; Griffin, Laura; Phelps, LauraJane; Buschmann, Volker; Weston, Kenneth; Greenbaum, Nancy L

    2007-01-01

    U2 and U6 snRNAs pair to form a phylogenetically conserved complex at the catalytic core of the spliceosome. Interactions with divalent metal ions, particularly Mg(II), at specific sites are essential for its folding and catalytic activity. We used a novel Förster resonance energy transfer (FRET) method between site-bound luminescent lanthanide ions and a covalently attached fluorescent dye, combined with supporting stoichiometric and mutational studies, to determine locations of site-bound Tb(III) within the human U2-U6 complex. At pH 7.2, we detected three metal-ion-binding sites in: (1) the consensus ACACAGA sequence, which forms the internal loop between helices I and III; (2) the four-way junction, which contains the conserved AGC triad; and (3) the internal loop of the U6 intra-molecular stem loop (ISL). Binding at each of these sites is supported by previous phosphorothioate substitution studies and, in the case of the ISL site, by NMR. Binding of Tb(III) at the four-way junction and the ISL sites was found to be pH-dependent, with no ion binding observed below pH 6 and 7, respectively. This pH dependence of metal ion binding suggests that the local environment may play a role in the binding of metal ions, which may impact on splicing activity.

  7. Differences in snRNP localization between transformed and nontransformed cells.

    PubMed Central

    Spector, D L; Lark, G; Huang, S

    1992-01-01

    We have examined the localization of snRNPs in a variety of mammalian cells and have observed differences in the organization of these factors in transformed cells, immortal cells, and cells of defined passage number. Cells of defined passage number exhibit a speckled staining pattern after immunolabeling with anti-Sm, anti-B'', or anti-m3G antibodies. Furthermore, 2-3% of the cells, in a given population, exhibit labeling of 1 or 2 round coiled bodies in addition to the speckled-labeling pattern. However, transformed cells exhibited 1-4 intensely stained coiled bodies, in 81-99% of the cells, in addition to the speckled-labeling pattern. Immortal cells exhibited 1-4 intensely stained smaller coiled bodies in 4-40% of the cells, in addition to the speckled-labeling pattern. When immortal cells (REF-52) that had been transformed by adenovirus (REF-52Ad5.4) were examined, these cells exhibited an increase in the percentage of cells containing 1 or 2 intensely stained coiled bodies, in addition to the speckled labeling, from 24 to 99%. On the basis of this study, we conclude that the organization of snRNPs within the mammalian cell nucleus is a reflection of the physiology of the cell that may change upon transformation or immortalization. Images PMID:1535243

  8. 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

  9. The LANDSAT story: Module U-2

    NASA Technical Reports Server (NTRS)

    1980-01-01

    A review of the various LANDSAT program elements which are relevant to user participation is provided. Sources for additional information and assistance where potential users may acquire more details and further guidance in using LANDSAT data are identified. The multispectral imagery capability of the LANDSAT satellites is emphasized.

  10. 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.

  11. Protein engineering of the archetypal nitroarene dioxygenase of Ralstonia sp. strain U2 for activity on aminonitrotoluenes and dinitrotoluenes through alpha-subunit residues leucine 225, phenylalanine 350, and glycine 407.

    PubMed

    Keenan, Brendan G; Leungsakul, Thammajun; Smets, Barth F; Mori, Masa-aki; Henderson, David E; Wood, Thomas K

    2005-05-01

    Naphthalene dioxygenase (NDO) from Ralstonia sp. strain U2 has not been reported to oxidize nitroaromatic compounds. Here, saturation mutagenesis of NDO at position F350 of the alpha-subunit (NagAc) created variant F350T that produced 3-methyl-4-nitrocatechol from 2,6-dinitrotoluene (26DNT), that released nitrite from 23DNT sixfold faster than wild-type NDO, and that produced 3-amino-4-methyl-5-nitrocatechol and 2-amino-4,6-dinitrobenzyl alcohol from 2-amino-4,6-dinitrotoluene (2A46DNT) (wild-type NDO has no detectable activity on 26DNT and 2A46DNT). DNA shuffling identified the beneficial NagAc mutation G407S, which when combined with the F350T substitution, increased the rate of NDO oxidation of 26DNT, 23DNT, and 2A46DNT threefold relative to variant F350T. DNA shuffling of NDO nagAcAd also generated the NagAc variant G50S/L225R/A269T with an increased rate of 4-amino-2-nitrotoluene (4A2NT; reduction product of 2,4-dinitrotoluene) oxidation; from 4A2NT, this variant produced both the previously uncharacterized oxidation product 4-amino-2-nitrocresol (enhanced 11-fold relative to wild-type NDO) as well as 4-amino-2-nitrobenzyl alcohol (4A2NBA; wild-type NDO does not generate this product). G50S/L225R/A269T also had increased nitrite release from 23DNT (14-fold relative to wild-type NDO) and generated 2,3-dinitrobenzyl alcohol (23DNBA) fourfold relative to wild-type NDO. The importance of position L225 for catalysis was confirmed through saturation mutagenesis; relative to wild-type NDO, NDO variant L225R had 12-fold faster generation of 4-amino-2-nitrocresol and production of 4A2NBA from 4A2NT as well as 24-fold faster generation of nitrite and 15-fold faster generation of 23DNBA from 23DNT. Hence, random mutagenesis discovered two new residues, G407 and L225, that influence the regiospecificity of Rieske non-heme-iron dioxygenases.

  12. Protein Engineering of the Archetypal Nitroarene Dioxygenase of Ralstonia sp. Strain U2 for Activity on Aminonitrotoluenes and Dinitrotoluenes through Alpha-Subunit Residues Leucine 225, Phenylalanine 350, and Glycine 407

    PubMed Central

    Keenan, Brendan G.; Leungsakul, Thammajun; Smets, Barth F.; Mori, Masa-aki; Henderson, David E.; Wood, Thomas K.

    2005-01-01

    Naphthalene dioxygenase (NDO) from Ralstonia sp. strain U2 has not been reported to oxidize nitroaromatic compounds. Here, saturation mutagenesis of NDO at position F350 of the α-subunit (NagAc) created variant F350T that produced 3-methyl-4-nitrocatechol from 2,6-dinitrotoluene (26DNT), that released nitrite from 23DNT sixfold faster than wild-type NDO, and that produced 3-amino-4-methyl-5-nitrocatechol and 2-amino-4,6-dinitrobenzyl alcohol from 2-amino-4,6-dinitrotoluene (2A46DNT) (wild-type NDO has no detectable activity on 26DNT and 2A46DNT). DNA shuffling identified the beneficial NagAc mutation G407S, which when combined with the F350T substitution, increased the rate of NDO oxidation of 26DNT, 23DNT, and 2A46DNT threefold relative to variant F350T. DNA shuffling of NDO nagAcAd also generated the NagAc variant G50S/L225R/A269T with an increased rate of 4-amino-2-nitrotoluene (4A2NT; reduction product of 2,4-dinitrotoluene) oxidation; from 4A2NT, this variant produced both the previously uncharacterized oxidation product 4-amino-2-nitrocresol (enhanced 11-fold relative to wild-type NDO) as well as 4-amino-2-nitrobenzyl alcohol (4A2NBA; wild-type NDO does not generate this product). G50S/L225R/A269T also had increased nitrite release from 23DNT (14-fold relative to wild-type NDO) and generated 2,3-dinitrobenzyl alcohol (23DNBA) fourfold relative to wild-type NDO. The importance of position L225 for catalysis was confirmed through saturation mutagenesis; relative to wild-type NDO, NDO variant L225R had 12-fold faster generation of 4-amino-2-nitrocresol and production of 4A2NBA from 4A2NT as well as 24-fold faster generation of nitrite and 15-fold faster generation of 23DNBA from 23DNT. Hence, random mutagenesis discovered two new residues, G407 and L225, that influence the regiospecificity of Rieske non-heme-iron dioxygenases. PMID:15866914

  13. Large-scale remodeling of a repressed exon ribonucleoprotein to an exon definition complex active for splicing

    PubMed Central

    Wongpalee, Somsakul Pop; Vashisht, Ajay; Sharma, Shalini; Chui, Darryl; Wohlschlegel, James A; Black, Douglas L

    2016-01-01

    Polypyrimidine-tract binding protein PTBP1 can repress splicing during the exon definition phase of spliceosome assembly, but the assembly steps leading to an exon definition complex (EDC) and how PTBP1 might modulate them are not clear. We found that PTBP1 binding in the flanking introns allowed normal U2AF and U1 snRNP binding to the target exon splice sites but blocked U2 snRNP assembly in HeLa nuclear extract. Characterizing a purified PTBP1-repressed complex, as well as an active early complex and the final EDC by SILAC-MS, we identified extensive PTBP1-modulated changes in exon RNP composition. The active early complex formed in the absence of PTBP1 proceeded to assemble an EDC with the eviction of hnRNP proteins, the late recruitment of SR proteins, and binding of the U2 snRNP. These results demonstrate that during early stages of splicing, exon RNP complexes are highly dynamic with many proteins failing to bind during PTBP1 arrest. DOI: http://dx.doi.org/10.7554/eLife.19743.001 PMID:27882870

  14. Genetic analysis of the structure and function of 7SK small nuclear ribonucleoprotein (snRNP) in cells.

    PubMed

    Fujinaga, Koh; Luo, Zeping; Peterlin, B Matija

    2014-07-25

    The positive transcription elongation factor b (P-TEFb), comprised of cyclin-dependent kinase 9 (CDK9) and cyclins T1 (CycT1) or T2 (CycT2), activates eukaryotic transcription elongation. In growing cells, P-TEFb exists in active and inactive forms. In the latter, it is incorporated into the 7SK small nuclear ribonucleoprotein, which contains hexamethylene bisacetamide-induced proteins (HEXIM) 1 or 2, La-related protein 7 (LaRP7), methyl phosphate capping enzyme, and 7SK small nuclear RNA (7SK). HEXIM1 inhibits the kinase activity of CDK9 via interactions between 7SK, HEXIM1, and CycT1. LaRP7 and methyl phosphate capping enzyme interact with 7SK independently of HEXIM1 and P-TEFb. To analyze genetic interactions between HEXIM1 and/or LaRP7 and 7SK using a cell-based system, we established artificial heterologous RNA tethering assays in which reporter gene expression depended on interactions between selected regions of 7SK and its cognate binding partners fused to a strong activator. This system enabled us to map the HEXIM1- and LaRP7- binding regions of 7SK. Assays with various mutant 7SK plasmid targets revealed that the 5'U-Ubulge and central loop of stem-loop I or RNA motif 3 of 7SK are required for transactivation, suggesting that HEXIM1 and CycT1 form a combinatorial binding surface for 7SK. Moreover, a region in HEXIM1 C-terminal to its previously mapped RNA-binding motif was also required for interactions between HEXIM1 and 7SK. Finally, a tyrosine-to-alanine mutation in HEXIM1, which is critical for its inhibitory effect on CDK9, changed HEXIM1 into an activator. These cell-based assays elucidate this important aspect of transcription elongation in vivo.

  15. Specific interactions between proteins implicated in splice site selection and regulated alternative splicing.

    PubMed

    Wu, J Y; Maniatis, T

    1993-12-17

    Specific recognition and pairing of the 5' and 3' splice sites are critical steps in pre-mRNA splicing. We report that the splicing factors SC35 and SF2/ASF specifically interact with both the integral U1 small nuclear ribonucleoprotein (snRNP U1-70K) and with the 35 kd subunit of the splicing factor U2AF (U2AF35). Previous studies indicated that the U1 snRNP binds specifically to the 5' splice site, while U2AF35-U2AF65 heterodimer binds to the 3' splice site. Together, these observations suggest that SC35 and other members of the SR family of splicing factors may function in splice site selection by acting as a bridge between components bound to the 5' and 3' splice sites. Interestingly, SC35, SF2/ASF, and U2AF35 also interact with the Drosophila splicing regulators Transformer (Tra) and Transformer-2 (Tra2), suggesting that protein-protein interactions mediated by SR proteins may also play an important role in regulating alternative splicing.

  16. 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

  17. Determination of film processing specifications for the Apollo 17 S-209 lunar sounder experiment

    NASA Technical Reports Server (NTRS)

    Weinstein, M. S.

    1972-01-01

    The lunar sounder is described as a radar system operating at carrier frequencies of 5, 15, and 150 MHz. The radar echoes are recorded onto Kodak type S0-394 film through the use of an optical recorder utilizing a cathode ray tube as the exposing device. A processing configuration is determined with regard to linearity, dynamic range, and noise.

  18. High temperature redox reactions with uranium: Synthesis and characterization of Cs(UO2)Cl(SeO3), Rb2(UO2)3O2(SeO3)2, and RbNa5U2(SO4)7

    NASA Astrophysics Data System (ADS)

    Babo, Jean-Marie; Albrecht-Schmitt, Thomas E.

    2013-10-01

    Cs(UO2)Cl(SeO3) (1), Rb2(UO2)3O2(SeO3)3 (2), and RbNa5U2(SO4)7 (3) single crystals were synthesized using CsCl, RbCl, and a CuCl/NaCl eutectic mixture as fluxes, respectively. Their lattice parameters and space groups are as follows: P21/n (a=6.548(1) Å, b=11.052(2) Å, c=10.666(2) Å and β=93.897(3)°), P1bar (a=7.051(2) Å, b=7.198(2) Å, c=8.314(2) Å, α=107.897(3)°, β=102.687(3)° and γ=100.564(3)°) and C2/c (a=17.862(4) Å, b=6.931(1) Å, c=20.133(4) Å and β=109.737(6)°. The small anionic building units found in these compounds are SeO32- and SO42- tetrahedra, oxide, and chloride. The crystal structure of the first compound is composed of [(UO2)2Cl2(SeO3)2]2- chains separated by Cs+ cations. The structure of (2) is constructed from [(UO2)3O11]16- chains further connected through selenite units into layers stacked perpendicularly to the [0 1 0] direction, with Rb+ cations intercalating between them. The structure of compound (3) is made of uranyl sulfate layers formed by edge and vertex connections between dimeric [U2O16] and [SO4] polyhedra. These layers contain unusual sulfate-metal connectivity as well as large voids.

  19. 322-R2U2 Engineering Assessment - August 2015

    SciTech Connect

    Abri, M.; Griffin, D.

    2015-08-13

    This Engineering Assessment and Certification of Integrity of retention tank system 322-R2 has been prepared for tank systems that store and neutralizes hazardous waste and have secondary containment. The regulations require that this assessment be completed periodically and certified by an independent, qualified, California-registered professional engineer. Abri Environmental Engineering performed an inspection of the 322-R2 Tank system at the Lawrence Livermore National Laboratory (LLNL) in Livermore, CA. Mr. William W. Moore, P.E., conducted this inspection on March 16, 2015. Mr. Moore is a California Registered Civil Engineer, with extensive experience in civil engineering, and hazardous waste management.

  20. 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.

  1. Coilin Can Form a Complex with the U7 Small Nuclear Ribonucleoprotein

    PubMed Central

    Bellini, Michel; Gall, Joseph G.

    1998-01-01

    Coiled bodies (CBs) in the amphibian oocyte nucleus are spherical structures up to 10 μm or more in diameter, much larger than their somatic counterparts, which rarely exceed 1 μm. Oocyte CBs may have smaller granules attached to their surface or embedded within them, which are identical in structure and composition to the many hundreds of B-snurposomes found free in the nucleoplasm. The matrix of the CBs contains the diagnostic protein p80-coilin, which is colocalized with the U7 small nuclear ribonucleoprotein (snRNP), whereas the attached and embedded B-snurposomes contain splicing snRNPs. A few of the 50–100 CBs in the oocyte nucleus are attached to lampbrush chromosomes at the histone gene loci. By coimmunoprecipitation we show that coilin and the U7 snRNP can form a weak but specific complex in the nucleoplasm, which is dependent on the special U7 Sm-binding site. Under the same conditions coilin does not associate with the U1 and U2 snRNPs. Coilin is a nucleic acid-binding protein, as shown by its interaction with single-stranded DNA and with poly r(U) and poly r(G). We suggest that an important function of coilin is to form a transient complex with the U7 snRNP and accompany it to the CBs. In the case of CBs attached to chromosomes at the histone gene loci, the U7 snRNP is thus brought close to the actual site of histone pre-mRNA transcription. PMID:9763457

  2. 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

  3. Sabers, Lances, B-17s and F-105s: An Essay on the Human Element, Napoleonic Warfare, and Air Combat.

    DTIC Science & Technology

    1987-04-01

    the best in a series of examinations of the pyschology of the battlefield. More recently, Richard Holmes’ Acts of War focuses on combat experiences...an "organic" approach to war. This would require a focus on the pyschology of combatants and the role of friction in conflict. It implies a view of war

  4. Monoclonal autoantibody recognizing a unique set of small nuclear ribonucleoprotein complexes.

    PubMed

    Winkler, A; Watson-McKown, R; Wise, K S

    1988-01-01

    A murine IgG2a, kappa-monoclonal autoantibody (mAb) F78 is described that recognizes a novel epitope associated with small nuclear ribonucleoprotein complexes (snRNP). F78 selectively immunoprecipitated a unique pattern of small nuclear RNA (U1, U2, and U4 to U6) characterized by a marked depletion of U1 and an elevated proportion of U2 compared with known patterns immunoprecipitated by previously described anti-RNP (2.73) and anti-Sm (7.13, Y12) mAb. Analysis of immunoprecipitated RNA from extracts previously cleared with mAb F78 and probed with anti-RNP mAb 2.73 further indicated the presence of two distinct subsets of U1. Immunoblots of whole cell extracts separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) without heating showed that F78 selectively bound to a trypsin-sensitive component of apparent m.w. greater than 120,000 which was decreased in size following RNase A treatment. The anti-Sm mAb, but not the anti-RNP mAb, also recognized this component in unheated samples. Heating before SDS-PAGE resulted in abrogation of binding to the F78 epitope. Immunoprecipitation of unlabeled or [35S]methionine-labeled cell extracts with F78 revealed the presence of most snRNP peptides, but the absence of peptide C and the 68,000 m.w. component, known to be selectively associated with U1-specific snRNP. Two-dimensional SDS-PAGE analysis of F78 immunoprecipitates confirmed that the epitope recognized by this mAb resides on a heat-dissociable complex containing snRNP-related peptides B, B', D, E, F, and G, but lacking U1-associated peptides. F78 mAb therefore defines a subset of snRNP which lack anti-RNP associated U1 RNA as well as peptides known to be selectively associated with this RNA species. It apparently recognizes an epitope associated with an assembled form of these particles and may be useful in examining structures involved in RNA processing.

  5. Achieving targeted and quantifiable alteration of mRNA splicing with Morpholino oligos

    SciTech Connect

    Morcos, Paul A. . E-mail: pmorcos@gene-tools.com

    2007-06-29

    This work represents the first guide for using steric-block antisense oligos as tools for effective and targeted modification of RNA splicing. Comparison of several steric-block oligo types shows the properties of Morpholinos provide significant advantages over other potential splice-blocking oligos. The procedures and complications of designing effective splice-blocking Morpholino oligos are described. The design process requires complete pre-mRNA sequence for defining suitable targets, which usually generate specific predictable messengers. To validate the targeting procedure, the level and nature of transcript alteration is characterized by RT-PCR analysis of splice modification in a {beta}-globin splice model system. An oligo-walking study reveals that while U1 and U2 small nuclear RiboNucleoProtein (snRNP) binding sites are the most effective targets for blocking splicing, inclusion of these sites is not required to achieve effective splice modifications. The most effective targeting strategy employs simultaneously blocking snRNP binding sites and splice-junctions. The work presented here continues to be the basis for most of the successful Morpholino oligos designed for the worldwide research community to block RNA splicing.

  6. Structural basis for recognition of intron branchpoint RNA by yeast Msl5 and selective effects of interfacial mutations on splicing of yeast pre-mRNAs.

    PubMed

    Jacewicz, Agata; Chico, Lidia; Smith, Paul; Schwer, Beate; Shuman, Stewart

    2015-03-01

    Saccharomyces cerevisiae Msl5 orchestrates spliceosome assembly by binding the intron branchpoint sequence 5'-UACUAAC and, with its heterodimer partner protein Mud2, establishing cross intron-bridging interactions with the U1 snRNP at the 5' splice site. Here we define the central Msl5 KH-QUA2 domain as sufficient for branchpoint RNA recognition. The 1.8 Å crystal structure of Msl5-(KH-QUA2) bound to the branchpoint highlights an extensive network of direct and water-mediated protein-RNA and intra-RNA atomic contacts at the interface that illuminate how Msl5 recognizes each nucleobase of the UACUAAC element. The Msl5 structure rationalizes a large body of mutational data and inspires new functional studies herein, which reveal how perturbations of the Msl5·RNA interface impede the splicing of specific yeast pre-mRNAs. We also identify interfacial mutations in Msl5 that bypass the essentiality of Sub2, a DExD-box ATPase implicated in displacing Msl5 from the branchpoint in exchange for the U2 snRNP. These studies establish an atomic resolution framework for understanding splice site selection and early spliceosome dynamics.

  7. The ribonucleotidyl transferase USIP-1 acts with SART3 to promote U6 snRNA recycling

    PubMed Central

    Rüegger, Stefan; Miki, Takashi S.; Hess, Daniel; Großhans, Helge

    2015-01-01

    The spliceosome is a large molecular machine that serves to remove the intervening sequences that are present in most eukaryotic pre-mRNAs. At its core are five small nuclear ribonucleoprotein complexes, the U1, U2, U4, U5 and U6 snRNPs, which undergo dynamic rearrangements during splicing. Their reutilization for subsequent rounds of splicing requires reversion to their original configurations, but little is known about this process. Here, we show that ZK863.4/USIP-1 (U Six snRNA-Interacting Protein-1) is a ribonucleotidyl transferase that promotes accumulation of the Caenorhabditis elegans U6 snRNA. Endogenous USIP-1–U6 snRNA complexes lack the Lsm proteins that constitute the protein core of the U6 snRNP, but contain the U6 snRNP recycling factor SART3/B0035.12. Furthermore, co-immunoprecipitation experiments suggest that SART3 but not USIP-1 occurs also in a separate complex containing both the U4 and U6 snRNPs. Based on this evidence, genetic interaction between usip-1 and sart-3, and the apparent dissociation of Lsm proteins from the U6 snRNA during spliceosome activation, we propose that USIP-1 functions upstream of SART3 to promote U6 snRNA recycling. PMID:25753661

  8. The alternative splicing program of differentiated smooth muscle cells involves concerted non-productive splicing of post-transcriptional regulators

    PubMed Central

    Llorian, Miriam; Gooding, Clare; Bellora, Nicolas; Hallegger, Martina; Buckroyd, Adrian; Wang, Xiao; Rajgor, Dipen; Kayikci, Melis; Feltham, Jack; Ule, Jernej; Eyras, Eduardo; Smith, Christopher W.J.

    2016-01-01

    Alternative splicing (AS) is a key component of gene expression programs that drive cellular differentiation. Smooth muscle cells (SMCs) are important in the function of a number of physiological systems; however, investigation of SMC AS has been restricted to a handful of events. We profiled transcriptome changes in mouse de-differentiating SMCs and observed changes in hundreds of AS events. Exons included in differentiated cells were characterized by particularly weak splice sites and by upstream binding sites for Polypyrimidine Tract Binding protein (PTBP1). Consistent with this, knockdown experiments showed that that PTBP1 represses many smooth muscle specific exons. We also observed coordinated splicing changes predicted to downregulate the expression of core components of U1 and U2 snRNPs, splicing regulators and other post-transcriptional factors in differentiated cells. The levels of cognate proteins were lower or similar in differentiated compared to undifferentiated cells. However, levels of snRNAs did not follow the expression of splicing proteins, and in the case of U1 snRNP we saw reciprocal changes in the levels of U1 snRNA and U1 snRNP proteins. Our results suggest that the AS program in differentiated SMCs is orchestrated by the combined influence of auxiliary RNA binding proteins, such as PTBP1, along with altered activity and stoichiometry of the core splicing machinery. PMID:27317697

  9. Functional Genomic Screening Reveals Splicing of the EWS-FLI1 Fusion Transcript as a Vulnerability in Ewing Sarcoma.

    PubMed

    Grohar, Patrick J; Kim, Suntae; Rangel Rivera, Guillermo O; Sen, Nirmalya; Haddock, Sara; Harlow, Matt L; Maloney, Nichole K; Zhu, Jack; O'Neill, Maura; Jones, Tamara L; Huppi, Konrad; Grandin, Magdalena; Gehlhaus, Kristen; Klumpp-Thomas, Carleen A; Buehler, Eugen; Helman, Lee J; Martin, Scott E; Caplen, Natasha J

    2016-01-26

    Ewing sarcoma cells depend on the EWS-FLI1 fusion transcription factor for cell survival. Using an assay of EWS-FLI1 activity and genome-wide RNAi screening, we have identified proteins required for the processing of the EWS-FLI1 pre-mRNA. We show that Ewing sarcoma cells harboring a genomic breakpoint that retains exon 8 of EWSR1 require the RNA-binding protein HNRNPH1 to express in-frame EWS-FLI1. We also demonstrate the sensitivity of EWS-FLI1 fusion transcripts to the loss of function of the U2 snRNP component, SF3B1. Disrupted splicing of the EWS-FLI1 transcript alters EWS-FLI1 protein expression and EWS-FLI1-driven expression. Our results show that the processing of the EWS-FLI1 fusion RNA is a potentially targetable vulnerability in Ewing sarcoma cells.

  10. Materials Data on U2Al19Co6 (SG:12) by Materials Project

    SciTech Connect

    Kristin Persson

    2016-04-22

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  11. 46 CFR 54.01-5 - Scope (modifies U-1 and U-2).

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... pressure; or (2) If one chamber is a vacuum chamber, the maximum allowable working pressure (absolute) in the other chamber minus the least operating pressure (absolute) in the vacuum chamber. Table 54.01-5(a... a pressure vessel has more than one independent chamber and the chambers have...

  12. 46 CFR 54.01-5 - Scope (modifies U-1 and U-2).

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... pressure; or (2) If one chamber is a vacuum chamber, the maximum allowable working pressure (absolute) in the other chamber minus the least operating pressure (absolute) in the vacuum chamber. Table 54.01-5(a... a pressure vessel has more than one independent chamber and the chambers have...

  13. Materials Data on U2CrN3 (SG:71) by Materials Project

    SciTech Connect

    Kristin Persson

    2014-11-02

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  14. Materials Data on U2MnN3 (SG:71) by Materials Project

    SciTech Connect

    Kristin Persson

    2014-07-09

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  15. Materials Data on U2BiN2 (SG:139) by Materials Project

    SciTech Connect

    Kristin Persson

    2014-11-02

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  16. Magnetism and superconductivity in U2PtxRh1-xC2

    DOE PAGES

    Wakeham, N.; Ni, Ni; Bauer, E. D.; ...

    2015-01-09

    We report the phase diagram of the doping series U₂PtxRh(1–x)C₂, studied through measurements of resistivity, specific heat, and magnetic susceptibility. The Néel temperature of U₂Rh₂C₂ of ~ 22 K is suppressed with increasing Pt content, reaching zero temperature close to x = 0.7, where we observed signatures of increased quantum fluctuations. Additionally, evidence is presented that the antiferromagnetic state undergoes a spin-reorientation transition upon application of an applied magnetic field. This transition shows non-monotonic behavior as a function of x, peaking at around x = 0.3. Superconductivity is observed for x ≥ 0.9, with Tc increasing with increasing x. Themore » reduction in Tc and increase in residual resistivity with decreasing Pt content is inconsistent with the extension of the Abrikosov-Gor'kov theory to unconventional superconductivity.« less

  17. Materials Data on U2N3 (SG:206) by Materials Project

    SciTech Connect

    Kristin Persson

    2016-02-10

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  18. Materials Data on U2Ga8Ru (SG:123) by Materials Project

    DOE Data Explorer

    Kristin Persson

    2016-02-10

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  19. 46 CFR 54.01-5 - Scope (modifies U-1 and U-2).

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... III pressure vessels that have a net internal volume of less than 0.14 cubic meters (5 cubic feet) and... or electricity): (a) Steam: More than 103 kPa (15 psig) 52 2 62 or 63 Equal to or less than 103 kPa...) Evaporators and heat exchangers: More than 103 kPa (15 psig) 4 54 NA (d) Unfired hot water supply or...

  20. 46 CFR 54.01-5 - Scope (modifies U-1 and U-2).

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... III pressure vessels that have a net internal volume of less than 0.14 cubic meters (5 cubic feet) and... or electricity): (a) Steam: More than 103 kPa (15 psig) 52 2 62 or 63 Equal to or less than 103 kPa...) Evaporators and heat exchangers: More than 103 kPa (15 psig) 4 54 NA (d) Unfired hot water supply or...

  1. Materials Data on U2Ti (SG:191) by Materials Project

    SciTech Connect

    Kristin Persson

    2016-02-05

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  2. Materials Data on Rb2U2O5 (SG:123) by Materials Project

    SciTech Connect

    Kristin Persson

    2016-08-21

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  3. Materials Data on Rb2U2Mo3O16 (SG:33) by Materials Project

    SciTech Connect

    Kristin Persson

    2016-04-22

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  4. Materials Data on Y3U2O10 (SG:12) by Materials Project

    DOE Data Explorer

    Kristin Persson

    2016-02-10

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  5. Materials Data on U2Bi2O7 (SG:51) by Materials Project

    SciTech Connect

    Kristin Persson

    2016-02-10

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  6. Caffeinated Tube Food Effect on Pilot Performance During a 9-Hour, Simulated Nighttime U-2 Mission

    DTIC Science & Technology

    2006-10-01

    Stomach Cramp 4 1 General Discomfort 3 2 Swelling 1 0 Headache 1 0 Thirst 0 1 Increased Appetite 0 1 Tingling 1 0 Increased Saliva 0 1 Vertigo 0 1...Lieberman HR. The effects of ginseng , ephedrine and caffeine on cognitive performance, mood and energy. Nutr Rev 2001; 59: 91–102. 14. Lieberman HR

  7. NASA Thunderstorm Overflight Program - Research in Atmospheric Electricity from an Instrumentated U-2 Aircraft Platform

    DTIC Science & Technology

    1983-08-01

    x 50 element photo- diode array manufactured by Reticon with a FOV of 1 radian, observes the lightning flash through a narrow-band interference...technical content. Review of any information concerning Department of Defense or nuclear energy activities or programs has been made by the MSFC Security

  8. Materials Data on U2PS (SG:141) by Materials Project

    SciTech Connect

    Kristin Persson

    2016-02-10

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  9. Materials Data on Na2U2O7 (SG:11) by Materials Project

    SciTech Connect

    Kristin Persson

    2016-02-04

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  10. Materials Data on BaU2O7 (SG:141) by Materials Project

    SciTech Connect

    Kristin Persson

    2016-02-04

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  11. Materials Data on U2(Al3Co)3 (SG:63) by Materials Project

    SciTech Connect

    Kristin Persson

    2016-02-10

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  12. Materials Data on Rb2U2O7 (SG:14) by Materials Project

    SciTech Connect

    Kristin Persson

    2016-02-04

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  13. Materials Data on U2AsSe (SG:12) by Materials Project

    SciTech Connect

    Kristin Persson

    2016-02-10

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  14. Materials Data on Rb2U2O7 (SG:2) by Materials Project

    SciTech Connect

    Kristin Persson

    2014-07-09

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  15. Materials Data on MgU2O6 (SG:15) by Materials Project

    SciTech Connect

    Kristin Persson

    2016-02-10

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  16. Materials Data on K2U2O7 (SG:2) by Materials Project

    SciTech Connect

    Kristin Persson

    2014-07-09

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  17. Materials Data on CsU2O6 (SG:148) by Materials Project

    SciTech Connect

    Kristin Persson

    2014-07-09

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  18. Materials Data on CsU2O6 (SG:227) by Materials Project

    SciTech Connect

    Kristin Persson

    2016-02-05

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  19. Materials Data on Sr4U2O9 (SG:2) by Materials Project

    SciTech Connect

    Kristin Persson

    2014-07-09

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  20. 46 CFR 54.01-5 - Scope (modifies U-1 and U-2).

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... accordance with the requirements in Section VIII, division 1, of the ASME Boiler and Pressure Vessel Code... ASME Boiler and Pressure Vessel Code. The certification must appear on all drawings and analyses. The... Main (power) boiler: All 52 62 Pressure vessel: All 54 NA Fired auxiliary boiler 1 (combustion...

  1. White Matter Hyperintensities on MRI in High-Altitude U-2 Pilots

    DTIC Science & Technology

    2013-08-19

    degenerative neurologic disease; substance or drug abuse or dependence; or any systemic disease with the potential for neurologic involvement. All...the limita- tions of a 2-dimensional thick -slice (5- to 10-mm) clinical imaging protocol and to permit increased detection of smaller lesions with...les, halo-like rarefaction of myelinated fibers surround- ing the atrophic neuropil, and a suggestion of focally decreased permeability of the

  2. Materials Data on U2S3 (SG:62) by Materials Project

    SciTech Connect

    Kristin Persson

    2014-11-02

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  3. The Role of U2AF1 Mutations in the Pathogenesis of Myelodysplastic Syndromes

    DTIC Science & Technology

    2014-10-01

    measured by Annexin V (F) and phosphorylated H2AX (G). PB, peripheral blood. BM, bone marrow. ). rtTA, reverse tetracycline -controlled...reverse tetracycline - controlled transactivator . WT, wild- type. MUT, S34F mutant. * pɘ.05, ** p≤0.01, ***p≤0.001 2 (Figure 1). In...and tertiary recipients (C). rtTA, reverse tetracycline -controlled transactivator . WT, wild-type. MUT, S34F mutant. * pɘ.05, ** p≤0.01, ***p

  4. Materials Data on U2Zn17 (SG:194) by Materials Project

    SciTech Connect

    Kristin Persson

    2016-05-02

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  5. Materials Data on Cs3U2Ge2O11 (SG:14) by Materials Project

    SciTech Connect

    Kristin Persson

    2016-02-10

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  6. Materials Data on Rb3U2Ge2O11 (SG:14) by Materials Project

    SciTech Connect

    Kristin Persson

    2016-02-10

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  7. Structure–function analysis and genetic interactions of the SmG, SmE, and SmF subunits of the yeast Sm protein ring

    PubMed Central

    Schwer, Beate; Kruchten, Joshua; Shuman, Stewart

    2016-01-01

    A seven-subunit Sm protein ring forms a core scaffold of the U1, U2, U4, and U5 snRNPs that direct pre-mRNA splicing. Using human snRNP structures to guide mutagenesis in Saccharomyces cerevisiae, we gained new insights into structure–function relationships of the SmG, SmE, and SmF subunits. An alanine scan of 19 conserved amino acids of these three proteins, comprising the Sm RNA binding sites or inter-subunit interfaces, revealed that, with the exception of Arg74 in SmF, none are essential for yeast growth. Yet, for SmG, SmE, and SmF, as for many components of the yeast spliceosome, the effects of perturbing protein–RNA and protein–protein interactions are masked by built-in functional redundancies of the splicing machine. For example, tests for genetic interactions with non-Sm splicing factors showed that many benign mutations of SmG, SmE, and SmF (and of SmB and SmD3) were synthetically lethal with null alleles of U2 snRNP subunits Lea1 and Msl1. Tests of pairwise combinations of SmG, SmE, SmF, SmB, and SmD3 alleles highlighted the inherent redundancies within the Sm ring, whereby simultaneous mutations of the RNA binding sites of any two of the Sm subunits are lethal. Our results suggest that six intact RNA binding sites in the Sm ring suffice for function but five sites may not. PMID:27417296

  8. Structure-function analysis and genetic interactions of the SmG, SmE, and SmF subunits of the yeast Sm protein ring.

    PubMed

    Schwer, Beate; Kruchten, Joshua; Shuman, Stewart

    2016-09-01

    A seven-subunit Sm protein ring forms a core scaffold of the U1, U2, U4, and U5 snRNPs that direct pre-mRNA splicing. Using human snRNP structures to guide mutagenesis in Saccharomyces cerevisiae, we gained new insights into structure-function relationships of the SmG, SmE, and SmF subunits. An alanine scan of 19 conserved amino acids of these three proteins, comprising the Sm RNA binding sites or inter-subunit interfaces, revealed that, with the exception of Arg74 in SmF, none are essential for yeast growth. Yet, for SmG, SmE, and SmF, as for many components of the yeast spliceosome, the effects of perturbing protein-RNA and protein-protein interactions are masked by built-in functional redundancies of the splicing machine. For example, tests for genetic interactions with non-Sm splicing factors showed that many benign mutations of SmG, SmE, and SmF (and of SmB and SmD3) were synthetically lethal with null alleles of U2 snRNP subunits Lea1 and Msl1. Tests of pairwise combinations of SmG, SmE, SmF, SmB, and SmD3 alleles highlighted the inherent redundancies within the Sm ring, whereby simultaneous mutations of the RNA binding sites of any two of the Sm subunits are lethal. Our results suggest that six intact RNA binding sites in the Sm ring suffice for function but five sites may not.

  9. Autoantigenic epitopes of the B and D polypeptides of the U1 snRNP. Analysis of domains recognized by the Y12 monoclonal anti-Sm antibody and by patient sera.

    PubMed

    Hirakata, M; Craft, J; Hardin, J A

    1993-04-15

    Anti-Sm antibodies, a specific marker for SLE, are directed against the B'/B and D polypeptides of Sm small nuclear ribonucleoproteins. The Y12 monoclonal anti-Sm antibody (Y12 mAb), as well as many anti-Sm patient sera, recognize cross-reactive epitopes on the B'/B and D polypeptides. This immunoreactive site is of special interest since polypeptides B and D share little amino acid sequence homology. In the present study, we have sought to establish the autoantigenic domain of polypeptides B and D that accounts for this epitope. We tested the ability of the Y12 mAb and anti-Sm sera to immunoprecipitate truncated forms of polypeptides B and D translated in vitro from mRNA bearing 5' and 3' end deletions. Most anti-Sm sera bound epitopes at the carboxyl-terminus of polypeptide B, however, autoantigenic epitopes were also found at the amino-terminus (amino acids 1 to 83 and 104 to 115). Surprisingly, the Y12 mAb recognized nonoverlapping amino-terminal and carboxyl-terminal halves of polypeptide B. One putative Y12 mAb binding site (amino acids 104 to 115) indicated by carboxyl-terminal deletion studies was confirmed through recognition of a corresponding synthetic peptide. Deletion studies with polypeptide D demonstrated a major autoantigenic domain on the carboxyl-terminus (amino acids 85 to 119) that was necessary for recognition by the Y12 mAb and by 7/14 patient sera. These results indicate that a cross-reactive epitope on B'/B and D, as defined by the Y12 mAb, resides on at least two different domains of polypeptide B and localizes to the carboxyl-terminus of polypeptide D. From the shared homology of truncated forms of B and D polypeptides recognizable with the Y12 mAb, we suspect that some form of GRG motif is involved in developing the Y12 mAb epitope that may involve other residues and be largely conformational in nature.

  10. Characterization of U4 and U6 interactions with the 5' splice site using a S. cerevisiae in vitro trans-splicing system.

    PubMed

    Johnson, T L; Abelson, J

    2001-08-01

    Spliceosome assembly has been characterized as the ordered association of the snRNP particles U1, U2, and U4/U6.U5 onto pre-mRNA. We have used an in vitro trans-splicing/cross-linking system in Saccharomyces cerevisiae nuclear extracts to examine the first step of this process, 5' splice site recognition. This trans-splicing reaction has ATP, Mg(2+), and splice-site sequence requirements similar to those of cis-splicing reactions. Using this system, we identified and characterized a novel U4-5' splice site interaction that is ATP-dependent, but does not require the branch point, the 3' splice site, or the 5' end of the U1 snRNA. Additionally, we identified several ATP-dependent U6 cross-links at the 5' splice site, indicating that different regions of U6 sample it before a U6-5' splice site interaction is stabilized that persists through the first step of splicing. This work provides evidence for ATP-dependent U4/U6 association with the 5' splice site independent of ATP-mediated U2 association with the branch point. Furthermore, it defines specific nucleotides in U4 and U6 that interact with the 5' splice site at this early stage, even in the absence of base-pairing with the U1 snRNA.

  11. Altered mRNA Splicing, Chondrocyte Gene Expression and Abnormal Skeletal Development due to SF3B4 Mutations in Rodriguez Acrofacial Dysostosis

    PubMed Central

    Nevarez, Lisette; Pogue, Robert; Krakow, Deborah; Cohn, Daniel H.

    2016-01-01

    The acrofacial dysostoses (AFD) are a genetically heterogeneous group of inherited disorders with craniofacial and limb abnormalities. Rodriguez syndrome is a severe, usually perinatal lethal AFD, characterized by severe retrognathia, oligodactyly and lower limb abnormalities. Rodriguez syndrome has been proposed to be a severe form of Nager syndrome, a non-lethal AFD that results from mutations in SF3B4, a component of the U2 small nuclear ribonucleoprotein particle (U2 snRNP). Furthermore, a case with a phenotype intermediate between Rodriguez and Nager syndromes has been shown to have an SF3B4 mutation. We identified heterozygosity for SF3B4 mutations in Rodriguez syndrome, confirming that the phenotype is a dominant disorder that is allelic with Nager syndrome. The mutations led to reduced SF3B4 synthesis and defects in mRNA splicing, primarily exon skipping. The mutations also led to reduced expression in growth plate chondrocytes of target genes, including the DLX5, DLX6, SOX9, and SOX6 transcription factor genes, which are known to be important for skeletal development. These data provide mechanistic insight toward understanding how SF3B4 mutations lead to the skeletal abnormalities observed in the acrofacial dysostoses. PMID:27622494

  12. αCP binding to a cytosine-rich subset of polypyrimidine tracts drives a novel pathway of cassette exon splicing in the mammalian transcriptome

    PubMed Central

    Ji, Xinjun; Park, Juw Won; Bahrami-Samani, Emad; Lin, Lan; Duncan-Lewis, Christopher; Pherribo, Gordon; Xing, Yi; Liebhaber, Stephen A.

    2016-01-01

    Alternative splicing (AS) is a robust generator of mammalian transcriptome complexity. Splice site specification is controlled by interactions of cis-acting determinants on a transcript with specific RNA binding proteins. These interactions are frequently localized to the intronic U-rich polypyrimidine tracts (PPT) located 5′ to the majority of splice acceptor junctions. αCPs (also referred to as polyC-binding proteins (PCBPs) and hnRNPEs) comprise a subset of KH-domain proteins with high affinity and specificity for C-rich polypyrimidine motifs. Here, we demonstrate that αCPs promote the splicing of a defined subset of cassette exons via binding to a C-rich subset of polypyrimidine tracts located 5′ to the αCP-enhanced exonic segments. This enhancement of splice acceptor activity is linked to interactions of αCPs with the U2 snRNP complex and may be mediated by cooperative interactions with the canonical polypyrimidine tract binding protein, U2AF65. Analysis of αCP-targeted exons predicts a substantial impact on fundamental cell functions. These findings lead us to conclude that the αCPs play a direct and global role in modulating the splicing activity and inclusion of an array of cassette exons, thus driving a novel pathway of splice site regulation within the mammalian transcriptome. PMID:26896798

  13. Re-evaluation of the Role of Calcium Homeostasis Endoplasmic Reticulum Protein (CHERP) in Cellular Calcium Signaling*

    PubMed Central

    Lin-Moshier, Yaping; Sebastian, Peter J.; Higgins, LeeAnn; Sampson, Natalie D.; Hewitt, Jane E.; Marchant, Jonathan S.

    2013-01-01

    Changes in cytoplasmic Ca2+ concentration, resulting from activation of intracellular Ca2+ channels within the endoplasmic reticulum, regulate several aspects of cellular growth and differentiation. Ca2+ homeostasis endoplasmic reticulum protein (CHERP) is a ubiquitously expressed protein that has been proposed as a regulator of both major families of endoplasmic reticulum Ca2+ channels, inositol 1,4,5-trisphosphate receptors (IP3Rs) and ryanodine receptors (RyRs), with resulting effects on mitotic cycling. However, the manner by which CHERP regulates intracellular Ca2+ channels to impact cellular growth is unknown. Here, we challenge previous findings that CHERP acts as a direct cytoplasmic regulator of IP3Rs and RyRs and propose that CHERP acts in the nucleus to impact cellular proliferation by regulating the function of the U2 snRNA spliceosomal complex. The previously reported effects of CHERP on cellular growth therefore are likely indirect effects of altered spliceosomal function, consistent with prior data showing that loss of function of U2 snRNP components can interfere with cell growth and induce cell cycle arrest. PMID:23148228

  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. Materials Data on K6U2(Cu4S5)3 (SG:230) by Materials Project

    SciTech Connect

    Kristin Persson

    2016-05-02

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  16. Materials Data on Na2U2Si(O4F)2 (SG:141) by Materials Project

    SciTech Connect

    Kristin Persson

    2016-02-04

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  17. Occupational Survey Report, AFSC 2A3X1, A-10/F-15/U-2 Avonics Systems

    DTIC Science & Technology

    2006-05-31

    specific data – Did not evaluate electronics principles section of STS • STS is generally supported by survey data – Seven STS items were unsupported... electronics principles section of STS for possible references 27 2A3X1 Percent Members Performing Unit Learning Objective Prof Code

  18. Relationships between chlorophyll density and ocean radiance as measured by U2/OCS: Algorithms, examples and comparison

    NASA Technical Reports Server (NTRS)

    Kim, H. H.; Hart, W. D.

    1983-01-01

    An ocean atmosphere radiative transfer process computation method which is suitable for determining lower boundary ocean albedo and other radiation components from spectral measurements of upwelling radiance taken from a high altitude platform is described. The method was applied to a set of color scanner data taken from slope water of the South Atlantic Bight to determine the influence of cholorophyll-a pigments in the sea on the ratio of upwelling radiance to down welling irradiance as a function of wavelength. The resulting chlorophyll concentrations are compared with measurements made by ships stationed along the flight path.

  19. Decompression Sickness and U-2 Operations: Summary of Research, Findings, and Recommendations Regarding Use of Exercise During Prebreathe

    DTIC Science & Technology

    2010-03-01

    Fischer MD, Wiegman JF, Webb JT. Exercise-induced altitude decompression sickness. Aviat Space Environ Med 1999; 70:22-9. 14. Pilmanis AA...22. Webb JT, Dixon GA, Wiegman JF. Potential for reduction of decompression sickness by prebreathing with 100% oxygen while exercising. SAE Technical

  20. Small nuclear ribonucleoproteins and heterogeneous nuclear ribonucleoproteins in the amphibian germinal vesicle: loops, spheres, and snurposomes

    PubMed Central

    1991-01-01

    We have examined the distribution of snRNPs in the germinal vesicle (GV) of frogs and salamanders by immunofluorescent staining and in situ nucleic acid hybridization. The major snRNAs involved in pre-mRNA splicing (U1, U2, U4, U5, and U6) occur together in nearly all loops of the lampbrush chromosomes, and in hundreds to thousands of small granules (1-4 microns diameter) suspended in the nucleoplasm. The loops and granules also contain several antigens that are regularly associated with snRNAs or spliceosomes (the Sm antigen, U1- and U2- specific antigens, and the splicing factor SC35). A second type of granule, often distinguishable by morphology, contains only U1 snRNA and associated antigens. We propose the term "snurposome" to describe the granules that contain snRNPs ("snurps"). Those that contain only U1 snRNA are A snurposomes, whereas those that contain all the splicing snRNAs are B snurposomes. GVs contain a third type of snRNP granule, which we call the C snurposome. C snurposomes range in size from less than 1 micron to giant structures greater than 20 microns in diameter. Usually, although not invariably, they have B snurposomes on their surface. They may also contain from one to hundreds of inclusions. Because of their remarkably spherical shape, C snurposomes with their associated B snurposomes have long been referred to as spheres or sphere organelles. Most spheres are free in the nucleoplasm, but a few are attached to chromosomes at specific chromosome loci, the sphere organizers (SOs). The relationship of sphere organelles to other snRNP- containing structures in the GV is obscure. We show by immunofluorescent staining that the lampbrush loops and B snurposomes also react with antibodies against heterogeneous nuclear ribonucleoproteins (hnRNPs). Transcription units on the loops are uniformly stained by anti-hnRNP and anti-snRNP antibodies, suggesting that nascent transcripts are associated with hnRNPs and snRNPs along their entire length, perhaps

  1. 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.

  2. 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

  3. A Broad Set of Chromatin Factors Influences Splicing

    PubMed Central

    Allemand, Eric; Myers, Michael P.; Garcia-Bernardo, Jose; Harel-Bellan, Annick; Krainer, Adrian R.; Muchardt, Christian

    2016-01-01

    Several studies propose an influence of chromatin on pre-mRNA splicing, but it is still unclear how widespread and how direct this phenomenon is. We find here that when assembled in vivo, the U2 snRNP co-purifies with a subset of chromatin-proteins, including histones and remodeling complexes like SWI/SNF. Yet, an unbiased RNAi screen revealed that the outcome of splicing is influenced by a much larger variety of chromatin factors not all associating with the spliceosome. The availability of this broad range of chromatin factors impacting splicing further unveiled their very context specific effect, resulting in either inclusion or skipping, depending on the exon under scrutiny. Finally, a direct assessment of the impact of chromatin on splicing using an in vitro co-transcriptional splicing assay with pre-mRNAs transcribed from a nucleosomal template, demonstrated that chromatin impacts nascent pre-mRNP in their competence for splicing. Altogether, our data show that numerous chromatin factors associated or not with the spliceosome can affect the outcome of splicing, possibly as a function of the local chromatin environment that by default interferes with the efficiency of splicing. PMID:27662573

  4. 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

  5. Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia.

    PubMed

    Quesada, Víctor; Conde, Laura; Villamor, Neus; Ordóñez, Gonzalo R; Jares, Pedro; Bassaganyas, Laia; Ramsay, Andrew J; Beà, Sílvia; Pinyol, Magda; Martínez-Trillos, Alejandra; López-Guerra, Mónica; Colomer, Dolors; Navarro, Alba; Baumann, Tycho; Aymerich, Marta; Rozman, María; Delgado, Julio; Giné, Eva; Hernández, Jesús M; González-Díaz, Marcos; Puente, Diana A; Velasco, Gloria; Freije, José M P; Tubío, José M C; Royo, Romina; Gelpí, Josep L; Orozco, Modesto; Pisano, David G; Zamora, Jorge; Vázquez, Miguel; Valencia, Alfonso; Himmelbauer, Heinz; Bayés, Mónica; Heath, Simon; Gut, Marta; Gut, Ivo; Estivill, Xavier; López-Guillermo, Armando; Puente, Xose S; Campo, Elías; López-Otín, Carlos

    2011-12-11

    Here we perform whole-exome sequencing of samples from 105 individuals with chronic lymphocytic leukemia (CLL), the most frequent leukemia in adults in Western countries. We found 1,246 somatic mutations potentially affecting gene function and identified 78 genes with predicted functional alterations in more than one tumor sample. Among these genes, SF3B1, encoding a subunit of the spliceosomal U2 small nuclear ribonucleoprotein (snRNP), is somatically mutated in 9.7% of affected individuals. Further analysis in 279 individuals with CLL showed that SF3B1 mutations were associated with faster disease progression and poor overall survival. This work provides the first comprehensive catalog of somatic mutations in CLL with relevant clinical correlates and defines a large set of new genes that may drive the development of this common form of leukemia. The results reinforce the idea that targeting several well-known genetic pathways, including mRNA splicing, could be useful in the treatment of CLL and other malignancies.

  6. 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.

  7. All 17 S-locus F-box proteins of the S2 - and S3 -haplotypes of Petunia inflata are assembled into similar SCF complexes with a specific function in self-incompatibility.

    PubMed

    Li, Shu; Williams, Justin S; Sun, Penglin; Kao, Teh-Hui

    2016-09-01

    The collaborative non-self-recognition model for S-RNase-based self-incompatibility predicts that multiple S-locus F-box proteins (SLFs) produced by pollen of a given S-haplotype collectively mediate ubiquitination and degradation of all non-self S-RNases, but not self S-RNases, in the pollen tube, thereby resulting in cross-compatible pollination but self-incompatible pollination. We had previously used pollen extracts containing GFP-fused S2 -SLF1 (SLF1 with an S2 -haplotype) of Petunia inflata for co-immunoprecipitation (Co-IP) and mass spectrometry (MS), and identified PiCUL1-P (a pollen-specific Cullin1), PiSSK1 (a pollen-specific Skp1-like protein) and PiRBX1 (a conventional Rbx1) as components of the SCF(S) (2-) (SLF) (1) complex. Using pollen extracts containing PiSSK1:FLAG:GFP for Co-IP/MS, we identified two additional SLFs (SLF4 and SLF13) that were assembled into SCF(SLF) complexes. As 17 SLF genes (SLF1 to SLF17) have been identified in S2 and S3 pollen, here we examined whether all 17 SLFs are assembled into similar complexes and, if so, whether these complexes are unique to SLFs. We modified the previous Co-IP/MS procedure, including the addition of style extracts from four different S-genotypes to pollen extracts containing PiSSK1:FLAG:GFP, to perform four separate experiments. The results taken together show that all 17 SLFs and an SLF-like protein, SLFLike1 (encoded by an S-locus-linked gene), co-immunoprecipitated with PiSSK1:FLAG:GFP. Moreover, of the 179 other F-box proteins predicted by S2 and S3 pollen transcriptomes, only a pair with 94.9% identity and another pair with 99.7% identity co-immunoprecipitated with PiSSK1:FLAG:GFP. These results suggest that SCF(SLF) complexes have evolved specifically to function in self-incompatibility.

  8. Purification of the major UsnRNPs from broad bean nuclear extracts and characterization of their protein constituents.

    PubMed Central

    Pálfi, Z; Bach, M; Solymosy, F; Lührmann, R

    1989-01-01

    Small nuclear ribonucleoprotein particles containing the five major nucleoplasmic snRNAs U1, U2, U4, U5 and U6 as well as two smaller sized snRNAs were purified from broad bean nuclear extracts by anti-m3G, monoclonal antibody, immunoaffinity chromatography. We have so far defined 13 polypeptides of approximate mol. wts. of 11 kd, 11.5 kd, 12.5 kd, 16 kd, 17 kd, 17.5 kd, 18.5 kd, 25 kd (double band), 30 kd, 31 kd, 35 kd, 36 kd and 54 kd. Upon fractionation of the UsnRNPs by anion exchange chromatography, essentially pure U5 snRNPs were obtained, containing the 11 kd, 11.5 kd, 12.5 kd, 16 kd, 17 kd, 17.5 kd, 35 kd and 36 kd polypeptides. These may therefore represent the common snRNP polypeptides and which may also be present in the other snRNPs. By immunoblotting studies, using anti-Sm sera and mouse monoclonal antibodies we show that the 35 kd and 36 kd proteins are immunologically related to the mammalian common B/B' proteins. The broad bean 16 kd and 17 kd proteins appear to share structural elements with the mammalian D protein. The three proteins of mol. wts. 11 kd, 11.5 kd and 12.5 kd probably represent the broad bean polypeptides E, F, and G. Cross-reactivity of proteins of mol. wts of 30 kd and 31 kd with Anti-(U1/U2)RNP antibodies suggests that they may represent the broad bean A and B" polypeptides. The 54 kd protein and the 18.5 kd protein could be candidates for the U1 specific 70 k and C polypeptides. Our results demonstrate a strong similarity between the overall structure of broad bean and mammalian snRNPs. Images PMID:2522185

  9. Structural and Functional Characterization of the N Terminus of Schizosaccharomyces pombe Cwf10

    PubMed Central

    Livesay, S. Brent; Collier, Scott E.; Bitton, Danny A.; Bähler, Jürg

    2013-01-01

    The spliceosome is a dynamic macromolecular machine that catalyzes the removal of introns from pre-mRNA, yielding mature message. Schizosaccharomyces pombe Cwf10 (homolog of Saccharomyces cerevisiae Snu114 and human U5-116K), an integral member of the U5 snRNP, is a GTPase that has multiple roles within the splicing cycle. Cwf10/Snu114 family members are highly homologous to eukaryotic translation elongation factor EF2, and they contain a conserved N-terminal extension (NTE) to the EF2-like portion, predicted to be an intrinsically unfolded domain. Using S. pombe as a model system, we show that the NTE is not essential, but cells lacking this domain are defective in pre-mRNA splicing. Genetic interactions between cwf10-ΔNTE and other pre-mRNA splicing mutants are consistent with a role for the NTE in spliceosome activation and second-step catalysis. Characterization of Cwf10-NTE by various biophysical techniques shows that in solution the NTE contains regions of both structure and disorder. The first 23 highly conserved amino acids of the NTE are essential for its role in splicing but when overexpressed are not sufficient to restore pre-mRNA splicing to wild-type levels in cwf10-ΔNTE cells. When the entire NTE is overexpressed in the cwf10-ΔNTE background, it can complement the truncated Cwf10 protein in trans, and it immunoprecipitates a complex similar in composition to the late-stage U5.U2/U6 spliceosome. These data show that the structurally flexible NTE is capable of independently incorporating into the spliceosome and improving splicing function, possibly indicating a role for the NTE in stabilizing conformational rearrangements during a splice cycle. PMID:24014766

  10. 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

  11. 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

  12. Genetic data on nine STRs (CSF1PO, TPOX, THO1, F13AO1, FESFPS, vWA, D16S539, D7S820 and D13S317) and two VNTRs (D1S80 and D17S5) in Rosario population, Santa Fe Argentine.

    PubMed

    Tenaglia, Mariano; Scollo, Adriana; Tripaldi, Regina; Grappiolo, Irene; Perichón, Armando M

    2004-05-10

    Allele frequencies for nine short tandem repeats (STRs) loci (CSF1PO, TPOX, THO1, F13AO1, FES/FPS, vWA, D16S539, D7S820 and D13S317) and two variable number tandem repeats (VNTRs) were obtained from a sample of 270 unrelated individuals born in the Rosario city, Santa Fe province of Argentina.

  13. Functional analysis of the sea urchin U7 small nuclear RNA

    SciTech Connect

    Gilmartin, G.M.; Schaufele, F.; Schaffner, G.; Birnstiel, M.L.

    1988-03-01

    U7 small nuclear RNA (snRNA) is an essential component of the RNA-processing machinery which generates the 3' end of mature histone mRNA in the sea urchin. The U7 small nuclear ribonucleoprotein particle (snRNP) is classified as a member of the Sm-type U snRNP family by virtue of its recognition by both anti-trimethylguanosine and anti-Sm antibodies. The authors analyzed the function-structure relationship of the U7 snRNP by mutagenesis experiments. These suggested that the U7 snRNP of the sea urchin is composed of three important domains. The fist domain encompasses the 5'-terminal sequence, up to about nucleotides 7, which are accessible to micrococcal nuclease, while the remainder of the RNA is highly protected and hence presumably bound by proteins. This region contains the sequence complementarities between the U7 snRNA and the histone pre-mRNA which have previously been shown to be required for 3' processing. Nucleotides 9 to 20 constitute a second domain which includes sequences for Sm protein binding. The complementarities between the U7 snRNA sequences in this region and the terminal palindrome fo the historne mRNA appear to be fortuitous and play only a secondary, if any, role in 3' processing. The third domain is composed of the terminal palindrome of U7 snRNA, the secondary structure of which must be maintained for the U7 snRNP to function, but its sequence can be drastically altered without any observable effect on snRNP assembly or 3' processing.

  14. 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.

  15. Cajal bodies and snRNPs - friends with benefits.

    PubMed

    Staněk, David

    2016-09-14

    Spliceosomal snRNPs are complex particles that proceed through a fascinating maturation pathway. Several steps of this pathway are closely linked to nuclear non-membrane structures called Cajal bodies. In this review, I summarize the last 20 y of research in this field. I primarily focus on snRNP biogenesis, specifically on the steps that involve Cajal bodies. I also evaluate the contribution of the Cajal body in snRNP quality control and discuss the role of snRNPs in Cajal body formation.

  16. 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

  17. The immunolocalization of small nuclear ribonucleoprotein particles in testicular cells during the cycle of the seminiferous epithelium of the adult rat.

    PubMed

    Moussa, F; Oko, R; Hermo, L

    1994-11-01

    The objective of this study was to determine the cellular and subcellular distribution of small nuclear ribonucleoprotein particles (snRNPs) in the adult rat testis in relation to the different cell types at the various stages of the cycle of the seminiferous epithelium. The distribution of snRNPs in the nucleus and cytoplasm of germ cells was quantitated in an attempt to correlate RNA processing with morphological and functional changes occurring during the development of these cells. Light-microscopic immunoperoxidase staining of rat testes with polyclonal anti-Sm and monoclonal anti-Y12 antibodies localized spliceosome snRNPs in the nuclei and cytoplasm of germ cells up to step 10 spermatids. Nuclear staining was intense in Sertoli cells, spermatogonia, spermatocytes, and in the early steps of round spermatid development. Although comparatively weaker, cytoplasmic staining for snRNPs was strongest in mid and late pachytene spermatocytes and early round spermatids. Quantitative electron-microscopic immunogold labeling of Lowicryl embedded testicular sections confirmed the light-microscopic observations but additionally showed that the snRNP content peaked in the cytoplasm of midpachytene spermatocytes and in the nuclei of late pachytene spermatocytes. The immunogold label tended to aggregate into distinct loci over the nuclear chromatin. The chromatoid body of spermatids and spermatocytes and the finely granular material in the interstices of mitochondrial aggregates of spermatocytes were found to be additional sites of snRNP localization and were intensely labeled. This colocalization suggests that these dense cytoplasmic structures may be functionally related. Anti-U1 snRNP antibodies applied to frozen sections showed the same LM localization pattern as spliceosome snRNPs. Anti-U3 snRNP antibodies applied to frozen sections stained nucleoli of germ cells where pre-rRNA is spliced.

  18. 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.

  19. FUS/TLS contributes to replication-dependent histone gene expression by interaction with U7 snRNPs and histone-specific transcription factors

    PubMed Central

    Raczynska, Katarzyna Dorota; Ruepp, Marc-David; Brzek, Aleksandra; Reber, Stefan; Romeo, Valentina; Rindlisbacher, Barbara; Heller, Manfred; Szweykowska-Kulinska, Zofia; Jarmolowski, Artur; Schümperli, Daniel

    2015-01-01

    Replication-dependent histone genes are up-regulated during the G1/S phase transition to meet the requirement for histones to package the newly synthesized DNA. In mammalian cells, this increment is achieved by enhanced transcription and 3′ end processing. The non-polyadenylated histone mRNA 3′ ends are generated by a unique mechanism involving the U7 small ribonucleoprotein (U7 snRNP). By using affinity purification methods to enrich U7 snRNA, we identified FUS/TLS as a novel U7 snRNP interacting protein. Both U7 snRNA and histone transcripts can be precipitated by FUS antibodies predominantly in the S phase of the cell cycle. Moreover, FUS depletion leads to decreased levels of correctly processed histone mRNAs and increased levels of extended transcripts. Interestingly, FUS antibodies also co-immunoprecipitate histone transcriptional activator NPAT and transcriptional repressor hnRNP UL1 in different phases of the cell cycle. We further show that FUS binds to histone genes in S phase, promotes the recruitment of RNA polymerase II and is important for the activity of histone gene promoters. Thus, FUS may serve as a linking factor that positively regulates histone gene transcription and 3′ end processing by interacting with the U7 snRNP and other factors involved in replication-dependent histone gene expression. PMID:26250115

  20. A new type of mutation causes a splicing defect in ATM.

    PubMed

    Pagani, Franco; Buratti, Emanuele; Stuani, Cristiana; Bendix, Regina; Dörk, Thilo; Baralle, Francisco E

    2002-04-01

    Disease-causing splicing mutations described in the literature primarily produce changes in splice sites and, to a lesser extent, variations in exon-regulatory sequences such as the enhancer elements. The gene ATM is mutated in individuals with ataxia-telangiectasia; we have identified the aberrant inclusion of a cryptic exon of 65 bp in one affected individual with a deletion of four nucleotides (GTAA) in intron 20. The deletion is located 12 bp downstream and 53 bp upstream from the 5' and 3' ends of the cryptic exon, respectively. Through analysis of the splicing defect using a hybrid minigene system, we identified a new intron-splicing processing element (ISPE) complementary to U1 snRNA, the RNA component of the U1 small nuclear ribonucleoprotein (snRNP). This element mediates accurate intron processing and interacts specifically with U1 snRNP particles. The 4-nt deletion completely abolished this interaction, causing activation of the cryptic exon. On the basis of this analysis, we describe a new type of U1 snRNP binding site in an intron that is essential for accurate intron removal. Deletion of this sequence is directly involved in the splicing processing defect.

  1. Crystal structure of (acetato-κO)(ethanol-κO)[(9S,17S,21S,29S)-9,17,21,29-tetra-hydroxy-18,30-dioxa-octa-cyclo-[18.10.0.0(2,7).0(8,19).0(9,17).0(11,16).0(21,29).0(23,28)]triaconta-1,3,5,7,11(16),12,14,19,23(28),24,26-undeca-ene-10,22-dione-κ(3) O (18),O (21),O (22)]caesium ethanol monosolvate.

    PubMed

    Bengiat, Ravell; Gil, Maayan; Klein, Asne; Bogoslavsky, Benny; Cohen, Shmuel; Yardeni, Guy; Zilbermann, Israel; Almog, Joseph

    2016-07-01

    The title compound, [Cs(CH3COO)(C28H16O8)(C2H5OH)]·C2H5OH, is the product of the complexation between one vasarene analogue [1], bis ninhydrin naphthalene-1,3-diol and CsF, where the F(-) ion has reacted with residual acetic acid (AcOH), to form a [1]·CsOAc complex. The inter-molecular inter-actions with the multiple oxygen-containing functional groups of the ligand, as well as O-H⋯O hydrogen bonds involving the ethanol solvent mol-ecules, stabilize the complex, forming a chain along [100]. Additional parallel-displaced π-π stacking, with an inter-planar distance of 3.669 (1) Å, connect several unit cells in a three-dimensional supra-molecular structure, though, the larger size of AcO(-) (1.60 Å) compared to F(-) (1.33 Å) prevents the tight packing that was once achieved with other vasarene complexes of CsF.

  2. Crystal structures of the Lsm complex bound to the 3' end sequence of U6 small nuclear RNA.

    PubMed

    Zhou, Lijun; Hang, Jing; Zhou, Yulin; Wan, Ruixue; Lu, Guifeng; Yin, Ping; Yan, Chuangye; Shi, Yigong

    2014-02-06

    Splicing of precursor messenger RNA (pre-mRNA) in eukaryotic cells is carried out by the spliceosome, which consists of five small nuclear ribonucleoproteins (snRNPs) and a number of accessory factors and enzymes. Each snRNP contains a ring-shaped subcomplex of seven proteins and a specific RNA molecule. The U6 snRNP contains a unique heptameric Lsm protein complex, which specifically recognizes the U6 small nuclear RNA at its 3' end. Here we report the crystal structures of the heptameric Lsm complex, both by itself and in complex with a 3' fragment of U6 snRNA, at 2.8 Å resolution. Each of the seven Lsm proteins interacts with two neighbouring Lsm components to form a doughnut-shaped assembly, with the order Lsm3-2-8-4-7-5-6. The four uridine nucleotides at the 3' end of U6 snRNA are modularly recognized by Lsm3, Lsm2, Lsm8 and Lsm4, with the uracil base specificity conferred by a highly conserved asparagine residue. The uracil base at the extreme 3' end is sandwiched by His 36 and Arg 69 from Lsm3, through π-π and cation-π interactions, respectively. The distinctive end-recognition of U6 snRNA by the Lsm complex contrasts with RNA binding by the Sm complex in the other snRNPs. The structural features and associated biochemical analyses deepen mechanistic understanding of the U6 snRNP function in pre-mRNA splicing.

  3. 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.

  4. The Central Region of the Drosophila Co-repressor Groucho as a Regulatory Hub*

    PubMed Central

    Kwong, Pak N.; Chambers, Michael; Vashisht, Ajay A.; Turki-Judeh, Wiam; Yau, Tak Yu; Wohlschlegel, James A.; Courey, Albert J.

    2015-01-01

    Groucho (Gro) is a Drosophila co-repressor that regulates the expression of a large number of genes, many of which are involved in developmental control. Previous studies have shown that its central region is essential for function even though its three domains are poorly conserved and intrinsically disordered. Using these disordered domains as affinity reagents, we have now identified multiple embryonic Gro-interacting proteins. The interactors include protein complexes involved in chromosome organization, mRNA processing, and signaling. Further investigation of the interacting proteins using a reporter assay showed that many of them modulate Gro-mediated repression either positively or negatively. The positive regulators include components of the spliceosomal subcomplex U1 small nuclear ribonucleoprotein (U1 snRNP). A co-immunoprecipitation experiment confirms this finding and suggests that a sizable fraction of nuclear U1 snRNP is associated with Gro. The use of RNA-seq to analyze the gene expression profile of cells subjected to knockdown of Gro or snRNP-U1-C (a component of U1 snRNP) showed a significant overlap between genes regulated by these two factors. Furthermore, comparison of our RNA-seq data with Gro and RNA polymerase II ChIP data led to a number of insights, including the finding that Gro-repressed genes are enriched for promoter-proximal RNA polymerase II. We conclude that the Gro central domains mediate multiple interactions required for repression, thus functioning as a regulatory hub. Furthermore, interactions with the spliceosome may contribute to repression by Gro. PMID:26483546

  5. Complete MALDI-ToF MS analysis of cross-linked peptide–RNA oligonucleotides derived from nonlabeled UV-irradiated ribonucleoprotein particles

    PubMed Central

    KÜHN-HÖLSKEN, EVA; LENZ, CHRISTOF; SANDER, BJÖRN; LÜHRMANN, REINHARD; URLAUB, HENNING

    2005-01-01

    Protein–RNA cross-linking combined with mass spectrometry is a powerful tool to elucidate hitherto noncharacterized protein–RNA contacts in ribonucleoprotein particles, as, for example, within spliceosomes. Here, we describe an improved methodology for the sequence analysis of purified peptide–RNA oligonucleotide cross-links that is based solely on MALDI-ToF mass spectrometry. The utility of this methodology is demonstrated on cross-links isolated from UV-irradiated spliceosomal particles; these were (1) [15.5K–61K–U4atac] small nuclear ribonucleoprotein (snRNP) particles prepared by reconstitution in vitro, and (2) U1 snRNP particles purified from HeLa cells. We show that the use of 2′,4′,6′-trihydroxyacetophenone (THAP) as MALDI matrix allows analysis of cross-linked peptide–RNA oligonucleotides in the reflectron mode at high resolution, enabling sufficient accuracy to assign unambiguously cross-linked RNA sequences. Most important, post-source decay (PSD) analysis under these conditions was successfully applied to obtain sequence information about the cross-linked peptide and RNA moieties within a single spectrum, including the identification of the actual cross-linking site. Thus, in U4atac snRNA we identified His270 in the spliceosomal U4/U6 snRNP-specific protein 61K (hPrp31p) cross-linked to U44; in the U1 snRNP we show that Leu175 of the U1 snRNP-specific 70K protein is cross-linked to U30 of U1 snRNA. This type of analysis is applicable to any type of RNP complex and may be expected to pave the way for the further analysis of protein–RNA complexes in much lower abundance and/or of cross-links that are obtained in low yield. PMID:16314460

  6. Next-generation SELEX identifies sequence and structural determinants of splicing factor binding in human pre-mRNA sequence

    PubMed Central

    Reid, Daniel C.; Chang, Brian L.; Gunderson, Samuel I.; Alpert, Lauren; Thompson, William A.; Fairbrother, William G.

    2009-01-01

    Many splicing factors interact with both mRNA and pre-mRNA. The identification of these interactions has been greatly improved by the development of in vivo cross-linking immunoprecipitation. However, the output carries a strong sampling bias in favor of RNPs that form on more abundant RNA species like mRNA. We have developed a novel in vitro approach for surveying binding on pre-mRNA, without cross-linking or sampling bias. Briefly, this approach entails specifically designed oligonucleotide pools that tile through a pre-mRNA sequence. The pool is then partitioned into bound and unbound fractions, which are quantified by a two-color microarray. We applied this approach to locating splicing factor binding sites in and around ∼4000 exons. We also quantified the effect of secondary structure on binding. The method is validated by the finding that U1snRNP binds at the 5′ splice site (5′ss) with a specificity that is nearly identical to the splice donor motif. In agreement with prior reports, we also show that U1snRNP appears to have some affinity for intronic G triplets that are proximal to the 5′ss. Both U1snRNP and the polypyrimidine tract binding protein (PTB) avoid exonic binding, and the PTB binding map shows increased enrichment at the polypyrimidine tract. For PTB, we confirm polypyrimidine specificity and are also able to identify structural determinants of PTB binding. We detect multiple binding motifs enriched in the PTB bound fraction of oligonucleotides. These motif combinations augment binding in vitro and are also enriched in the vicinity of exons that have been determined to be in vivo targets of PTB. PMID:19861426

  7. Cancer-Associated Perturbations in Alternative Pre-messenger RNA Splicing.

    PubMed

    Shkreta, Lulzim; Bell, Brendan; Revil, Timothée; Venables, Julian P; Prinos, Panagiotis; Elela, Sherif Abou; Chabot, Benoit

    2013-01-01

    For most of our 25,000 genes, the removal of introns by pre-messenger RNA (pre-mRNA) splicing represents an essential step toward the production of functional messenger RNAs (mRNAs). Alternative splicing of a single pre-mRNA results in the production of different mRNAs. Although complex organisms use alternative splicing to expand protein function and phenotypic diversity, patterns of alternative splicing are often altered in cancer cells. Alternative splicing contributes to tumorigenesis by producing splice isoforms that can stimulate cell proliferation and cell migration or induce resistance to apoptosis and anticancer agents. Cancer-specific changes in splicing profiles can occur through mutations that are affecting splice sites and splicing control elements, and also by alterations in the expression of proteins that control splicing decisions. Recent progress in global approaches that interrogate splicing diversity should help to obtain specific splicing signatures for cancer types. The development of innovative approaches for annotating and reprogramming splicing events will more fully establish the essential contribution of alternative splicing to the biology of cancer and will hopefully provide novel targets and anticancer strategies. Metazoan genes are usually made up of several exons interrupted by introns. The introns are removed from the pre-mRNA by RNA splicing. In conjunction with other maturation steps, such as capping and polyadenylation, the spliced mRNA is then transported to the cytoplasm to be translated into a functional protein. The basic mechanism of splicing requires accurate recognition of each extremity of each intron by the spliceosome. Introns are identified by the binding of U1 snRNP to the 5' splice site and the U2AF65/U2AF35 complex to the 3' splice site. Following these interactions, other proteins and snRNPs are recruited to generate the complete spliceosomal complex needed to excise the intron. While many introns are constitutively

  8. Two patients with duplication of 17p11.2: The reciprocal of the Smith-Magenis syndrome deletion?

    SciTech Connect

    Brown, A. |; Phelan, M.C.; Rogers, R.C.

    1996-05-17

    J.M. and H.G. are two unrelated male patients with developmental delay. Cytogenetic analysis detected a duplication of 17p11.2 in both patients. The extent of the duplicated region was determined using single copy DNA probes: cen-D17S58-D17S29-D17S258-D17S71-D17S445-D17S122-tel. Four of the six markers, D17S29, D17S258, D17S71, and D17S445, were duplicated by dosage analysis. Fluorescent in situ hybridization (FISH) analysis of H.G., using cosmids for locus D17S29, confirmed the duplication in 17p11.2. Because the deletion that causes the Smith-Magenis syndrome involves the same region of 17p11.2 as the duplication in these patients, the mechanism may be similar to that proposed for the reciprocal deletion/ duplication event observed in Hereditary Neuropathy with Liability to Pressure Palsies (HNPP) and Charcot-Marie-Tooth Type 1A disease (CMT1A). 30 refs., 3 figs., 1 tab.

  9. Immobile survival of motoneuron (SMN) protein stored in Cajal bodies can be mobilized by protein interactions.

    PubMed

    Förthmann, Benjamin; Brinkmann, Hella; Ratzka, Andreas; Stachowiak, Michal K; Grothe, Claudia; Claus, Peter

    2013-07-01

    Reduced levels of survival of motoneuron (SMN) protein lead to spinal muscular atrophy, but it is still unknown how SMN protects motoneurons in the spinal cord against degeneration. In the nucleus, SMN is associated with two types of nuclear bodies denoted as gems and Cajal bodies (CBs). The 23 kDa isoform of fibroblast growth factor-2 (FGF-2(23)) is a nuclear protein that binds to SMN and destabilizes the SMN-Gemin2 complex. In the present study, we show that FGF-2(23) depletes SMN from CBs without affecting their general structure. FRAP analysis of SMN-EGFP in CBs demonstrated that the majority of SMN in CBs remained mobile and allowed quantification of fast, slow and immobile nuclear SMN populations. The potential for SMN release was confirmed by in vivo photoconversion of SMN-Dendra2, indicating that CBs concentrate immobile SMN that could have a specialized function in CBs. FGF-2(23) accelerated SMN release from CBs, accompanied by a conversion of immobile SMN into a mobile population. Furthermore, FGF-2(23) caused snRNP accumulation in CBs. We propose a model in which Cajal bodies store immobile SMN that can be mobilized by its nuclear interaction partner FGF-2(23), leading to U4 snRNP accumulation in CBs, indicating a role for immobile SMN in tri-snRNP assembly.

  10. Periodic expression of Sm proteins parallels formation of nuclear Cajal bodies and cytoplasmic snRNP-rich bodies.

    PubMed

    Smoliński, Dariusz J; Wróbel, Bogdan; Noble, Anna; Zienkiewicz, Agnieszka; Górska-Brylass, Alicja

    2011-11-01

    Small nuclear ribonucleoproteins (snRNPs) play a fundamental role in pre-mRNA processing in the nucleus. The biogenesis of snRNPs involves a sequence of events that occurs in both the nucleus and cytoplasm. Despite the wealth of biochemical information about the cytoplasmic assembly of snRNPs, little is known about the spatial organization of snRNPs in the cytoplasm. In the cytoplasm of larch microsporocytes, a cyclic appearance of bodies containing small nuclear RNA (snRNA) and Sm proteins was observed during anther meiosis. We observed a correlation between the occurrence of cytoplasmic snRNP bodies, the levels of Sm proteins, and the dynamic formation of Cajal bodies. Larch microsporocytes were used for these studies. This model is characterized by natural fluctuations in the level of RNA metabolism, in which periods of high transcriptional activity are separated from periods of low transcriptional activity. In designing experiments, the authors considered the differences between the nuclear and cytoplasmic phases of snRNP maturation and generated a hypothesis about the direct participation of Sm proteins in a molecular switch triggering the formation of Cajal bodies.

  11. Cajal bodies are linked to genome conformation.

    PubMed

    Wang, Qiuyan; Sawyer, Iain A; Sung, Myong-Hee; Sturgill, David; Shevtsov, Sergey P; Pegoraro, Gianluca; Hakim, Ofir; Baek, Songjoon; Hager, Gordon L; Dundr, Miroslav

    2016-03-21

    The mechanisms underlying nuclear body (NB) formation and their contribution to genome function are unknown. Here we examined the non-random positioning of Cajal bodies (CBs), major NBs involved in spliceosomal snRNP assembly and their role in genome organization. CBs are predominantly located at the periphery of chromosome territories at a multi-chromosome interface. Genome-wide chromosome conformation capture analysis (4C-seq) using CB-interacting loci revealed that CB-associated regions are enriched with highly expressed histone genes and U small nuclear or nucleolar RNA (sn/snoRNA) loci that form intra- and inter-chromosomal clusters. In particular, we observed a number of CB-dependent gene-positioning events on chromosome 1. RNAi-mediated disassembly of CBs disrupts the CB-targeting gene clusters and suppresses the expression of U sn/snoRNA and histone genes. This loss of spliceosomal snRNP production results in increased splicing noise, even in CB-distal regions. Therefore, we conclude that CBs contribute to genome organization with global effects on gene expression and RNA splicing fidelity.

  12. Depletion of SMN by RNA interference in HeLa cells induces defects in Cajal body formation.

    PubMed

    Girard, Cyrille; Neel, Henry; Bertrand, Edouard; Bordonné, Rémy

    2006-01-01

    Neuronal degeneration in spinal muscular atrophy (SMA) is caused by reduced expression of the survival of motor neuron (SMN) protein. The SMN protein is ubiquitously expressed and is present both in the cytoplasm and in the nucleus where it localizes in Cajal bodies. The SMN complex plays an essential role for the biogenesis of spliceosomal U-snRNPs. In this article, we have used an RNA interference approach in order to analyse the effects of SMN depletion on snRNP assembly in HeLa cells. Although snRNP profiles are not perturbed in SMN-depleted cells, we found that SMN depletion gives rise to cytoplasmic accumulation of a GFP-SmB reporter protein. We also demonstrate that the SMN protein depletion induces defects in Cajal body formation with coilin being localized in multiple nuclear foci and in nucleolus instead of canonical Cajal bodies. Interestingly, the coilin containing foci do not contain snRNPs but appear to co-localize with U85 scaRNA. Because Cajal bodies represent the location in which snRNPs undergo 2'-O-methylation and pseudouridylation, our results raise the possibility that SMN depletion might give rise to a defect in the snRNA modification process.

  13. 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.

  14. Splicing enhancement in the yeast rp51b intron.

    PubMed Central

    Libri, D; Lescure, A; Rosbash, M

    2000-01-01

    Splicing enhancement in higher eukaryotes has been linked to SR proteins, to U1 snRNP, and to communication between splice sites across introns or exons mediated by protein-protein interactions. It has been previously shown that, in yeast, communication mediated by RNA-RNA interactions between the two ends of introns is a basis for splicing enhancement. We designed experiments of randomization-selection to isolate splicing enhancers that would work independently from RNA secondary structures. Surprisingly, one of the two families of sequences selected was essentially composed of 5' splice site variants. We show that this sequence enhances splicing independently of secondary structure, is exportable to heterologous contexts, and works in multiple copies with additive effects. The data argue in favor of an early role for splicing enhancement, possibly coincident with commitment complex formation. Genetic compensation experiments with U1 snRNA mutants suggest that U1 snRNP binding to noncanonical locations is required for splicing enhancement. PMID:10744020

  15. Modulation of a P-TEFb Functional Equilibrium for the Global Control of Cell Growth and Differentiation

    PubMed Central

    He, Nanhai; Pezda, Andrea C.; Zhou, Qiang

    2006-01-01

    P-TEFb phosphorylates RNA polymerase II and negative elongation factors to stimulate general transcriptional elongation. It is kept in a functional equilibrium through alternately interacting with its positive (the Brd4 protein) and negative (the HEXIM1 protein and 7SK snRNA) regulators. To investigate the physiological significance of this phenomenon, we analyzed the responses of HeLa cells and murine erythroleukemia cells (MELC) to hexamethylene bisacetamide (HMBA), which inhibits growth and induces differentiation of many cell types. For both cell types, an efficient, albeit temporary disruption of the 7SK-HEXIM1-P-TEFb snRNP and enhanced formation of the Brd4-P-TEFb complex occurred soon after the treatment started. When the P-TEFb-dependent HEXIM1 expression markedly increased as the treatment continued, the abundant HEXIM1 pushed the P-TEFb equilibrium back toward the 7SK/HEXIM1-bound state. For HeLa cells, as HMBA produced only a minor, temporary effect on their growth, the equilibrium gradually returned to its pretreatment level. In contrast, long-term treatment of MELC induced terminal division and differentiation. Concurrently, the P-TEFb equilibrium was shifted overwhelmingly toward the 7SK snRNP side. Together, these data link the P-TEFb equilibrium to the intracellular transcriptional demand and proliferative/differentiated states of cells. PMID:16980611

  16. 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

  17. Promoter-proximal polyadenylation sites reduce transcription activity

    PubMed Central

    Andersen, Pia K.; Lykke-Andersen, Søren; Jensen, Torben Heick

    2012-01-01

    Gene expression relies on the functional communication between mRNA processing and transcription. We previously described the negative impact of a point-mutated splice donor (SD) site on transcription. Here we demonstrate that this mutation activates an upstream cryptic polyadenylation (CpA) site, which in turn causes reduced transcription. Functional depletion of U1 snRNP in the context of the wild-type SD triggers the same CpA event accompanied by decreased RNA levels. Thus, in accordance with recent findings, U1 snRNP can shield premature pA sites. The negative impact of unshielded pA sites on transcription requires promoter proximity, as demonstrated using artificial constructs and supported by a genome-wide data set. Importantly, transcription down-regulation can be recapitulated in a gene context devoid of splice sites by placing a functional bona fide pA site/transcription terminator within ∼500 base pairs of the promoter. In contrast, promoter-proximal positioning of a pA site-independent histone gene terminator supports high transcription levels. We propose that optimal communication between a pA site-dependent gene terminator and its promoter critically depends on gene length and that short RNA polymerase II-transcribed genes use specialized termination mechanisms to maintain high transcription levels. PMID:23028143

  18. Interaction between RNA helicase ROOT INITIATION DEFECTIVE 1 and GAMETOPHYTIC FACTOR 1 is involved in female gametophyte development in Arabidopsis

    PubMed Central

    Zhu, Dong Zi; Zhao, Xue Fang; Liu, Chang Zhen; Ma, Fang Fang; Wang, Fang; Gao, Xin-Qi; Zhang, Xian Sheng

    2016-01-01

    ROOT INITIATION DEFECTIVE 1 (RID1) is an Arabidopsis DEAH/RHA RNA helicase. It functions in hypocotyl de-differentiation, de novo meristem formation, and cell specification of the mature female gametophyte (FG). However, it is unclear how RID1 regulates FG development. In this study, we observed that mutations to RID1 disrupted the developmental synchrony and retarded the progression of FG development. RID1 exhibited RNA helicase activity, with a preference for unwinding double-stranded RNA in the 3′ to 5′ direction. Furthermore, we found that RID1 interacts with GAMETOPHYTIC FACTOR 1 (GFA1), which is an integral protein of the spliceosome component U5 small nuclear ribonucleoprotein (snRNP) particle. Substitution of specific RID1 amino acids (Y266F and T267I) inhibited the interaction with GFA1. In addition, the mutated RID1 could not complement the seed-abortion phenotype of the rid1 mutant. The rid1 and gfa1 mutants exhibited similar abnormalities in pre-mRNA splicing and down-regulated expression of some genes involved in FG development. Our results suggest that an interaction between RID1 and the U5 snRNP complex regulates essential pre-mRNA splicing of the genes required for FG development. This study provides new information regarding the mechanism underlying the FG developmental process. PMID:27683728

  19. Cajal bodies are linked to genome conformation

    PubMed Central

    Wang, Qiuyan; Sawyer, Iain A.; Sung, Myong-Hee; Sturgill, David; Shevtsov, Sergey P.; Pegoraro, Gianluca; Hakim, Ofir; Baek, Songjoon; Hager, Gordon L.; Dundr, Miroslav

    2016-01-01

    The mechanisms underlying nuclear body (NB) formation and their contribution to genome function are unknown. Here we examined the non-random positioning of Cajal bodies (CBs), major NBs involved in spliceosomal snRNP assembly and their role in genome organization. CBs are predominantly located at the periphery of chromosome territories at a multi-chromosome interface. Genome-wide chromosome conformation capture analysis (4C-seq) using CB-interacting loci revealed that CB-associated regions are enriched with highly expressed histone genes and U small nuclear or nucleolar RNA (sn/snoRNA) loci that form intra- and inter-chromosomal clusters. In particular, we observed a number of CB-dependent gene-positioning events on chromosome 1. RNAi-mediated disassembly of CBs disrupts the CB-targeting gene clusters and suppresses the expression of U sn/snoRNA and histone genes. This loss of spliceosomal snRNP production results in increased splicing noise, even in CB-distal regions. Therefore, we conclude that CBs contribute to genome organization with global effects on gene expression and RNA splicing fidelity. PMID:26997247

  20. An Alu-derived intronic splicing enhancer facilitates intronic processing and modulates aberrant splicing in ATM.

    PubMed

    Pastor, Tibor; Talotti, Gabriele; Lewandowska, Marzena Anna; Pagani, Franco

    2009-11-01

    We have previously reported a natural GTAA deletion within an intronic splicing processing element (ISPE) of the ataxia telangiectasia mutated (ATM) gene that disrupts a non-canonical U1 snRNP interaction and activates the excision of the upstream portion of the intron. The resulting pre-mRNA splicing intermediate is then processed to a cryptic exon, whose aberrant inclusion in the final mRNA is responsible for ataxia telangiectasia. We show here that the last 40 bases of a downstream intronic antisense Alu repeat are required for the activation of the cryptic exon by the ISPE deletion. Evaluation of the pre-mRNA splicing intermediate by a hybrid minigene assay indicates that the identified intronic splicing enhancer represents a novel class of enhancers that facilitates processing of splicing intermediates possibly by recruiting U1 snRNP to defective donor sites. In the absence of this element, the splicing intermediate accumulates and is not further processed to generate the cryptic exon. Our results indicate that Alu-derived sequences can provide intronic splicing regulatory elements that facilitate pre-mRNA processing and potentially affect the severity of disease-causing splicing mutations.

  1. Functional studies on the ATM intronic splicing processing element.

    PubMed

    Lewandowska, Marzena A; Stuani, Cristiana; Parvizpur, Alireza; Baralle, Francisco E; Pagani, Franco

    2005-01-01

    In disease-associated genes, the understanding of the functional significance of deep intronic nucleotide variants may represent a difficult challenge. We have previously reported a new disease-causing mechanism that involves an intronic splicing processing element (ISPE) in ATM, composed of adjacent consensus 5' and 3' splice sites. A GTAA deletion within ISPE maintains potential adjacent splice sites, disrupts a non-canonical U1 snRNP interaction and activates an aberrant exon. In this paper, we demonstrate that binding of U1 snRNA through complementarity within a approximately 40 nt window downstream of the ISPE prevents aberrant splicing. By selective mutagenesis at the adjacent consensus ISPE splice sites, we show that this effect is not due to a resplicing process occurring at the ISPE. Functional comparison of the ATM mouse counterpart and evaluation of the pre-mRNA splicing intermediates derived from affected cell lines and hybrid minigene assays indicate that U1 snRNP binding at the ISPE interferes with the cryptic acceptor site. Activation of this site results in a stringent 5'-3' order of intron sequence removal around the cryptic exon. Artificial U1 snRNA loading by complementarity to heterologous exonic sequences represents a potential therapeutic method to prevent the usage of an aberrant CFTR cryptic exon. Our results suggest that ISPE-like intronic elements binding U1 snRNPs may regulate correct intron processing.

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

    SciTech Connect

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

    1988-07-01

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

  4. Structural requirements for protein-catalyzed annealing of U4 and U6 RNAs during di-snRNP assembly

    PubMed Central

    Didychuk, Allison L.; Montemayor, Eric J.; Brow, David A.; Butcher, Samuel E.

    2016-01-01

    Base-pairing of U4 and U6 snRNAs during di-snRNP assembly requires large-scale remodeling of RNA structure that is chaperoned by the U6 snRNP protein Prp24. We investigated the mechanism of U4/U6 annealing in vitro using an assay that enables visualization of ribonucleoprotein complexes and faithfully recapitulates known in vivo determinants for the process. We find that annealing, but not U6 RNA binding, is highly dependent on the electropositive character of a 20 Å-wide groove on the surface of Prp24. During annealing, we observe the formation of a stable ternary complex between U4 and U6 RNAs and Prp24, indicating that displacement of Prp24 in vivo requires additional factors. Mutations that stabilize the U6 ‘telestem’ helix increase annealing rates by up to 15-fold, suggesting that telestem formation is rate-limiting for U4/U6 pairing. The Lsm2–8 complex, which binds adjacent to the telestem at the 3′ end of U6, provides a comparable rate enhancement. Collectively, these data identify domains of the U6 snRNP that are critical for one of the first steps in assembly of the megaDalton U4/U6.U5 tri-snRNP complex, and lead to a dynamic model for U4/U6 pairing that involves a striking degree of evolved cooperativity between protein and RNA. PMID:26673715

  5. Structural requirements for protein-catalyzed annealing of U4 and U6 RNAs during di-snRNP assembly.

    PubMed

    Didychuk, Allison L; Montemayor, Eric J; Brow, David A; Butcher, Samuel E

    2016-02-18

    Base-pairing of U4 and U6 snRNAs during di-snRNP assembly requires large-scale remodeling of RNA structure that is chaperoned by the U6 snRNP protein Prp24. We investigated the mechanism of U4/U6 annealing in vitro using an assay that enables visualization of ribonucleoprotein complexes and faithfully recapitulates known in vivo determinants for the process. We find that annealing, but not U6 RNA binding, is highly dependent on the electropositive character of a 20 Å-wide groove on the surface of Prp24. During annealing, we observe the formation of a stable ternary complex between U4 and U6 RNAs and Prp24, indicating that displacement of Prp24 in vivo requires additional factors. Mutations that stabilize the U6 'telestem' helix increase annealing rates by up to 15-fold, suggesting that telestem formation is rate-limiting for U4/U6 pairing. The Lsm2-8 complex, which binds adjacent to the telestem at the 3' end of U6, provides a comparable rate enhancement. Collectively, these data identify domains of the U6 snRNP that are critical for one of the first steps in assembly of the megaDalton U4/U6.U5 tri-snRNP complex, and lead to a dynamic model for U4/U6 pairing that involves a striking degree of evolved cooperativity between protein and RNA.

  6. RNA-sequencing of a mouse-model of spinal muscular atrophy reveals tissue-wide changes in splicing of U12-dependent introns

    PubMed Central

    Doktor, Thomas Koed; Hua, Yimin; Andersen, Henriette Skovgaard; Brøner, Sabrina; Liu, Ying Hsiu; Wieckowska, Anna; Dembic, Maja; Bruun, Gitte Hoffmann; Krainer, Adrian R.; Andresen, Brage Storstein

    2017-01-01

    Spinal Muscular Atrophy (SMA) is a neuromuscular disorder caused by insufficient levels of the Survival of Motor Neuron (SMN) protein. SMN is expressed ubiquitously and functions in RNA processing pathways that include trafficking of mRNA and assembly of snRNP complexes. Importantly, SMA severity is correlated with decreased snRNP assembly activity. In particular, the minor spliceosomal snRNPs are affected, and some U12-dependent introns have been reported to be aberrantly spliced in patient cells and animal models. SMA is characterized by loss of motor neurons, but the underlying mechanism is largely unknown. It is likely that aberrant splicing of genes expressed in motor neurons is involved in SMA pathogenesis, but increasing evidence indicates that pathologies also exist in other tissues. We present here a comprehensive RNA-seq study that covers multiple tissues in an SMA mouse model. We show elevated U12-intron retention in all examined tissues from SMA mice, and that U12-dependent intron retention is induced upon siRNA knock-down of SMN in HeLa cells. Furthermore, we show that retention of U12-dependent introns is mitigated by ASO treatment of SMA mice and that many transcriptional changes are reversed. Finally, we report on missplicing of several Ca2+ channel genes that may explain disrupted Ca2+ homeostasis in SMA and activation of Cdk5. PMID:27557711

  7. Functional studies on the ATM intronic splicing processing element

    PubMed Central

    Lewandowska, Marzena A.; Stuani, Cristiana; Parvizpur, Alireza; Baralle, Francisco E.; Pagani, Franco

    2005-01-01

    In disease-associated genes, the understanding of the functional significance of deep intronic nucleotide variants may represent a difficult challenge. We have previously reported a new disease-causing mechanism that involves an intronic splicing processing element (ISPE) in ATM, composed of adjacent consensus 5′ and 3′ splice sites. A GTAA deletion within ISPE maintains potential adjacent splice sites, disrupts a non-canonical U1 snRNP interaction and activates an aberrant exon. In this paper, we demonstrate that binding of U1 snRNA through complementarity within a ∼40 nt window downstream of the ISPE prevents aberrant splicing. By selective mutagenesis at the adjacent consensus ISPE splice sites, we show that this effect is not due to a resplicing process occurring at the ISPE. Functional comparison of the ATM mouse counterpart and evaluation of the pre-mRNA splicing intermediates derived from affected cell lines and hybrid minigene assays indicate that U1 snRNP binding at the ISPE interferes with the cryptic acceptor site. Activation of this site results in a stringent 5′–3′ order of intron sequence removal around the cryptic exon. Artificial U1 snRNA loading by complementarity to heterologous exonic sequences represents a potential therapeutic method to prevent the usage of an aberrant CFTR cryptic exon. Our results suggest that ISPE-like intronic elements binding U1 snRNPs may regulate correct intron processing. PMID:16030351

  8. Specific genomic cues regulate Cajal body assembly.

    PubMed

    Sawyer, Iain A; Hager, Gordon L; Dundr, Miroslav

    2016-10-07

    The assembly of specialized sub-nuclear microenvironments known as nuclear bodies (NBs) is important for promoting efficient nuclear function. In particular, the Cajal body (CB), a prominent NB that facilitates spliceosomal snRNP biogenesis, assembles in response to genomic cues. Here, we detail the factors that regulate CB assembly and structural maintenance. These include the importance of transcription at nucleating gene loci, the grouping of these genes on human chromosomes 1, 6 and 17, as well as cell cycle and biochemical regulation of CB protein function. We also speculate on the correlation between CB formation and RNA splicing levels in neurons and cancer. The timing and location of these specific molecular events is critical to CB assembly and its contribution to genome function. However, further work is required to explore the emerging biophysical characteristics of CB assembly and the impact upon subsequent genome reorganization.

  9. 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.

  10. p54nrb/NonO and PSF promote U snRNA nuclear export by accelerating its export complex assembly.

    PubMed

    Izumi, Hiroto; McCloskey, Asako; Shinmyozu, Kaori; Ohno, Mutsuhito

    2014-04-01

    The assembly of spliceosomal U snRNPs in metazoans requires nuclear export of U snRNA precursors. Four factors, nuclear cap-binding complex (CBC), phosphorylated adaptor for RNA export (PHAX), the export receptor CRM1 and RanGTP, gather at the m(7)G-cap-proximal region and form the U snRNA export complex. Here we show that the multifunctional RNA-binding proteins p54nrb/NonO and PSF are U snRNA export stimulatory factors. These proteins, likely as a heterodimer, accelerate the recruitment of PHAX, and subsequently CRM1 and Ran onto the RNA substrates in vitro, which mediates efficient U snRNA export in vivo. Our results reveal a new layer of regulation for U snRNA export and, hence, spliceosomal U snRNP biogenesis.

  11. Identification and characterisation of a nuclear localisation signal in the SMN associated protein, Gemin4

    SciTech Connect

    Lorson, Monique A.; Dickson, Alexa M.; Shaw, Debra J.; Todd, Adrian G.; Young, Elizabeth C.; Morse, Robert; Wolstencroft, Catherine; Lorson, Christian L.; Young, Philip J.

    2008-10-10

    Gemin4 is a ubiquitously expressed multifunctional protein that is involved in U snRNP assembly, apoptosis, nuclear/cytoplasmic transportation, transcription, and RNAi pathways. Gemin4 is one of the core components of the Gemin-complex, which also contains survival motor neuron (SMN), the seven Gemin proteins (Gemin2-8), and Unrip. Mutations in the SMN1 gene cause the autosomal recessive disorder spinal muscular atrophy (SMA). Although the functions assigned to Gemin4 predominantly occur in the nucleus, the mechanisms that mediate the nuclear import of Gemin4 remain unclear. Here, using a novel panel of Gemin4 constructs we identify a canonical nuclear import sequence (NLS) in the N-terminus of Gemin4. The Gemin4 NLS is necessary and independently sufficient to mediate nuclear import of Gemin4. This is the first functional NLS identified within the SMN-Gemin complex.

  12. 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

  13. 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.

  14. Mixed connective tissue disease-enigma variations?

    PubMed

    Ciang, Natalia C O; Pereira, Nídia; Isenberg, David A

    2017-03-01

    In 1972, Sharp et al. described a new autoimmune rheumatic disease that they called MCTD, characterized by overlapping features of SSc, SLE, PM/DM, high levels of anti-U1snRNP and low steroid requirements with good prognosis. MCTD was proposed as a distinct disease. However, soon after the original description, questions about the existence of such a syndrome as well as disputes over the features initially described began to surface. The conundrum of whether MCTD is a distinct disease entity remains controversial. We undertook a literature review, focusing on the articles reporting new data about MCTD published in the last decade, to determine whether any new observations help to answer the conundrum of MCTD. After reviewing recent data, we question whether the term MCTD is appropriately retained, preferring to use the term undifferentiated autoimmune rheumatic disease.

  15. Monoubiquitination of survival motor neuron regulates its cellular localization and Cajal body integrity.

    PubMed

    Han, Ke-Jun; Foster, Daniel; Harhaj, Edward W; Dzieciatkowska, Monika; Hansen, Kirk; Liu, Chang-Wei

    2016-04-01

    Low levels of the survival motor neuron (SMN) protein cause spinal muscular atrophy, the leading genetic disorder for infant mortality. SMN is ubiquitously expressed in various cell types and localizes in both the cytoplasm and the nucleus, where it concentrates in two subnuclear structures termed Cajal body (CB) and gems. In addition, SMN can also be detected in the nucleolus of neurons. Mechanisms that control SMN sorting in the cell remain largely unknown. Here, we report that the ubiquitin (Ub) ligase Itch directly interacts with and monoubiquitinates SMN. Monoubiquitination of SMN has a mild effect on promoting proteasomal degradation of SMN. We generated two SMN mutants, SMN(K0), in which all lysines are mutated to arginines and thereby abolishing SMN ubiquitination, and Ub-SMN(K0), in which a single Ub moiety is fused at the N-terminus of SMN(K0) and thereby mimicking SMN monoubiquitination. Immunostaining assays showed that SMN(K0) mainly localizes in the nucleus, whereas Ub-SMN(K0) localizes in both the cytoplasm and the nucleolus in neuronal SH-SY5Y cells. Interestingly, canonical CB foci and coilin/small nuclear ribonucleoprotein (snRNP) co-localization are significantly impaired in SH-SY5Y cells stably expressing SMN(K0) or Ub-SMN(K0). Thus, our studies discover that Itch monoubiquitinates SMN and monoubiquitination of SMN plays an important role in regulating its cellular localization. Moreover, mislocalization of SMN disrupts CB integrity and likely impairs snRNP maturation.

  16. Strategies for H-score Normalization of Preanalytical Technical Variables with Potential Utility to Immunohistochemical-Based Biomarker Quantitation in Therapeutic Reponse Diagnostics

    PubMed Central

    Pierceall, William E.; Wolfe, Michele; Suschak, Jessica; Chang, Hua; Chen, Yan; Sprott, Kam M.; Kutok, Jeffery L.; Quan, Stella; Weaver, David T.; Ward, Brian E.

    2011-01-01

    Digital quantitative immunohistochemical analysis of protein biomarker expression offers a broad dynamic range against which clinical outcomes may be measured. Semi-quantitative expression data represented as an H-score is produced by computer generated average intensity of positive staining given weight by the percentage of cells showing positive staining. While patient H-scores vary for biological reasons, variation may also arise from preanalytic technical issues, such as differences in fixation protocols. In this study, we present data on two candidate calibrator nuclear-localized proteins, SNRPA and SnRNP70, with robust and consistent expression levels across breast cancers. Quantitative expression measurement of these two candidate biomarkers may potentially be used to eliminate the effect of differences in preanalytic processing of specimens by normalizing H-scores derived from test biomarkers of interest. To examine the effects of preanalytical fixation variation on biomarker quantitation and potential utility of candidate calibrators to address such issues, 6 surgically-resected human breast cancer patient specimens were divided into 6 portions and fixed under distinct conditions (fixation following resection in formalin for 2 hr, 8 hr or 48 hr, or held overnight at 4°C in buffered saline prior to formalin fixation for 2 hr, 8 hr, or 48 hr). We find H-score variation between fixation conditions within individual patient's tumors that were stained for XPF, ATM, BRCA1, pMK2 and PARP1. Most interestingly, detectable expression of SNRPA and SnRNP70 is covariant to test biomarkers under distinct fixation conditions and so these hold the potential for serving as calibration standards for general antigen preservation and reactivity. PMID:21677381

  17. Mapping the interaction network of key proteins involved in histone mRNA generation - a hydrogen/deuterium exchange study

    PubMed Central

    Skrajna, Aleksandra; Yang, Xiao-cui; Tarnowski, Krzysztof; Fituch, Kinga; Marzluff, William F.; Dominski, Zbigniew; Dadlez, Michał

    2016-01-01

    Histone pre-mRNAs are cleaved at the 3′ end by a complex that contains U7 snRNP, the FLICE-Associated Huge protein (FLASH) and Histone pre-mRNA Cleavage Complex (HCC) consisting of several polyadenylation factors. Within the complex, the N-terminus of FLASH interacts with the N-terminus of the U7 snRNP protein Lsm11 and together they recruit the HCC. FLASH through its distant C-terminus independently interacts with the C-terminal SANT/Myb-like domain of Nuclear Protein, Ataxia-Telangiectasia locus (NPAT), a transcriptional co-activator required for expression of histone genes in S-phase. To gain structural information on these interactions, we used mass spectrometry to monitor hydrogen/deuterium (H/D) exchange in various regions of FLASH, Lsm11 and NPAT alone or in the presence of their respective binding partners. Our results indicate that the FLASH-interacting domain in Lsm11 is highly dynamic, while the more downstream region required for recruiting the HCC exchanges deuterium slowly and likely folds into a stable structure. In FLASH, a stable structure is adopted by the domain that interacts with Lsm11 and this domain is further stabilized by binding Lsm11. Notably, both H/D exchange experiments and in vitro binding assays demonstrate that Lsm11, in addition to interacting with the N-terminal region of FLASH, also contacts the C-terminal SANT/Myb-like domain of FLASH, the same region that binds NPAT. However, while NPAT stabilizes this domain, Lsm11 causes its partial relaxation. These competing reactions may play a role in regulating histone gene expression in vivo. PMID:26860583

  18. 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.

  19. 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

  20. Drosophila SMN complex proteins Gemin2, Gemin3, and Gemin5 are components of U bodies

    SciTech Connect

    Cauchi, Ruben J.; Sanchez-Pulido, Luis; Liu, Ji-Long

    2010-08-15

    Uridine-rich small nuclear ribonucleoproteins (U snRNPs) play key roles in pre-mRNA processing in the nucleus. The assembly of most U snRNPs takes place in the cytoplasm and is facilitated by the survival motor neuron (SMN) complex. Discrete cytoplasmic RNA granules called U bodies have been proposed to be specific sites for snRNP assembly because they contain U snRNPs and SMN. U bodies invariably associate with P bodies, which are involved in mRNA decay and translational control. However, it remains unknown whether other SMN complex proteins also localise to U bodies. In Drosophila there are four SMN complex proteins, namely SMN, Gemin2/CG10419, Gemin3 and Gemin5/Rigor mortis. Drosophila Gemin3 was originally identified as the Drosophila orthologue of human and yeast Dhh1, a component of P bodies. Through an in silico analysis of the DEAD-box RNA helicases we confirmed that Gemin3 is the bona fide Drosophila orthologue of vertebrate Gemin3 whereas the Drosophila orthologue of Dhh1 is Me31B. We then made use of the Drosophila egg chamber as a model system to study the subcellular distribution of the Gemin proteins as well as Me31B. Our cytological investigations show that Gemin2, Gemin3 and Gemin5 colocalise with SMN in U bodies. Although they are excluded from P bodies, as components of U bodies, Gemin2, Gemin3 and Gemin5 are consistently found associated with P bodies, wherein Me31B resides. In addition to a role in snRNP biogenesis, SMN complexes residing in U bodies may also be involved in mRNP assembly and/or transport.

  1. A murine cytomegalovirus-neutralizing monoclonal antibody exhibits autoreactivity and induces tissue damage in vivo.

    PubMed Central

    Chapman, A J; Farrell, H E; Thomas, J A; Papadimitriou, J M; Garlepp, M J; Scalzo, A A; Shellam, G R

    1994-01-01

    The autoreactivity of murine cytomegalovirus (MCMV)-neutralizing monoclonal antibody (mAb) AC1 was examined in vitro and in vivo. Both mAb AC1 and a human antiserum reactive with U1-small nuclear ribonucleoprotein (U1-snRNP) stained uninfected mouse embryo fibroblasts (MEF) in a speckled nuclear pattern and reacted with 70,000 molecular weight (MW) MEF nuclear antigens by immunoblotting, suggesting that mAb AC1 cross-reacted with the 70,000 MW component of U1-snRNP. However, only mAb AC1 cross-reacted with an additional epithelial cytoplasmic autoantigen present in cultured HEp2 cells. On tissue sections from uninfected mice, mAb AC1 predominantly reacted with a component of central and peripheral nervous systems, although cross-reactivity with the stratum spinosum of the skin and the outer sheath of hair follicles was also observed. Immunoblotting revealed that mAb AC1 reacted with phosphorylated epitopes present on a 98,000 MW MCMV structural protein and the 200,000 MW mouse neurofilament protein (NFP). Treatment of uninfected mice with mAb AC1 resulted in a severe interstitial pneumonia with greatly thickened and congested alveolar septa. Severe oedema of the hypodermis and a mild mesangial proliferative glomerulonephritis were also observed. These results demonstrate that a mAb reacting with a MCMV structural phosphoprotein which can protect mice against the dissemination of MCMV, can also promote the development of autoimmune disease. Therefore, the production of such cross-reactive antibodies may be an important mechanism in the development of autoimmunity following viral infection. Images Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 PMID:7515848

  2. Structure and conformational plasticity of the U6 small nuclear ribonucleoprotein core.

    PubMed

    Montemayor, Eric J; Didychuk, Allison L; Liao, Honghong; Hu, Panzhou; Brow, David A; Butcher, Samuel E

    2017-01-01

    U6 small nuclear RNA (snRNA) is a key component of the active site of the spliceosome, a large ribonucleoprotein complex that catalyzes the splicing of precursor messenger RNA. Prior to its incorporation into the spliceosome, U6 is bound by the protein Prp24, which facilitates unwinding of the U6 internal stem-loop (ISL) so that it can pair with U4 snRNA. A previously reported crystal structure of the `core' of the U6 small nuclear ribonucleoprotein (snRNP) contained an ISL-stabilized A62G mutant of U6 bound to all four RNA-recognition motif (RRM) domains of Prp24 [Montemayor et al. (2014), Nature Struct. Mol. Biol. 21, 544-551]. The structure revealed a novel topology containing interlocked rings of protein and RNA that was not predicted by prior biochemical and genetic data. Here, the crystal structure of the U6 snRNP core with a wild-type ISL is reported. This complex crystallized in a new space group, apparently owing in part to the presence of an intramolecular cross-link in RRM1 that was not observed in the previously reported U6-A62G structure. The structure exhibits the same protein-RNA interface and maintains the unique interlocked topology. However, the orientation of the wild-type ISL is altered relative to the A62G mutant structure, suggesting inherent structural dynamics that may facilitate its pairing with U4. Consistent with their similar architectures in the crystalline state, the wild-type and A62G variants of U6 exhibit similar Prp24-binding affinities and electrophoretic mobilities when analyzed by gel-shift assay.

  3. An intron element modulating 5' splice site selection in the hnRNP A1 pre-mRNA interacts with hnRNP A1.

    PubMed Central

    Chabot, B; Blanchette, M; Lapierre, I; La Branche, H

    1997-01-01

    The hnRNP A1 pre-mRNA is alternatively spliced to yield the A1 and A1b mRNAs, which encode proteins differing in their ability to modulate 5' splice site selection. Sequencing a genomic portion of the murine A1 gene revealed that the intron separating exon 7 and the alternative exon 7B is highly conserved between mouse and human. In vitro splicing assays indicate that a conserved element (CE1) from the central portion of the intron shifts selection toward the distal donor site when positioned in between the 5' splice sites of exon 7 and 7B. In vivo, the CE1 element promotes exon 7B skipping. A 17-nucleotide sequence within CE1 (CE1a) is sufficient to activate the distal 5' splice site. RNase T1 protection/immunoprecipitation assays indicate that hnRNP A1 binds to CE1a, which contains the sequence UAGAGU, a close match to the reported optimal A1 binding site, UAGGGU. Replacing CE1a by different oligonucleotides carrying the sequence UAGAGU or UAGGGU maintains the preference for the distal 5' splice site. In contrast, mutations in the AUGAGU sequence activate the proximal 5' splice site. In support of a direct role of the A1-CE1 interaction in 5'-splice-site selection, we observed that the amplitude of the shift correlates with the efficiency of A1 binding. Whereas addition of SR proteins abrogates the effect of CE1, the presence of CE1 does not modify U1 snRNP binding to competing 5' splice sites, as judged by oligonucleotide-targeted RNase H protection assays. Our results suggest that hnRNP A1 modulates splice site selection on its own pre-mRNA without changing the binding of U1 snRNP to competing 5' splice sites. PMID:9121425

  4. Structure of yeast U6 snRNPs: arrangement of Prp24p and the LSm complex as revealed by electron microscopy.

    PubMed

    Karaduman, Ramazan; Dube, Prakash; Stark, Holger; Fabrizio, Patrizia; Kastner, Berthold; Lührmann, Reinhard

    2008-12-01

    Protein components of the U6 snRNP (Prp24p and LSm2-8) are thought to act cooperatively in facilitating the annealing of U6 and U4 snRNAs during U4/U6 di-snRNP formation. To learn more about the spatial arrangement of these proteins in S. cerevisiae U6 snRNPs, we investigated the structure of this particle by electron microscopy. U6 snRNPs, purified by affinity chromatography and gradient centrifugation, and then immediately adsorbed to the carbon film support, revealed an open form in which the Prp24 protein and the ring formed by the LSm proteins were visible as two separate morphological domains, while particles stabilized by chemical cross-linking in solution under mild conditions before binding to the carbon film exhibited a compact form, with the two domains in close proximity to one another. In the open form, individual LSm proteins were located by a novel approach employing C-terminal genetic tagging of the LSm proteins with yECitrine. These studies show the Prp24 protein at defined distances from each subunit of the LSm ring, which in turn suggests that the LSm ring is positioned in a consistent manner on the U6 RNA. Furthermore, in agreement with the EM observations, UV cross-linking revealed U6 RNA in contact with the LSm2 protein at the interface between Prp24p and the LSm ring. Further, LSmp-Prp24p interactions may be restricted to the closed form, which appears to represent the solution structure of the U6 snRNP particle.

  5. Ground states of the spin-1 Bose-Hubbard model.

    PubMed

    Katsura, Hosho; Tasaki, Hal

    2013-03-29

    We prove basic theorems about the ground states of the S=1 Bose-Hubbard model. The results are quite universal and depend only on the coefficient U2 of the spin-dependent interaction. We show that the ground state exhibits saturated ferromagnetism if U2<0, is spin-singlet if U2>0, and exhibits "SU(3)-ferromagnetism" if U2=0, and completely determine the degeneracy in each region.

  6. The Future of Airborne Reconnaissance

    DTIC Science & Technology

    1996-01-01

    biplanes to the worldwide Cold War missions of the U - 2 and SR-71, airborne reconnaissance has become an indispensable tool to the intelligence community...Reconnaissance Operations (SRO) procedures, such as the U - 2 , RC- 135, and the EP-3, and traditional theater/fleet tactical reconnaissance systems like...upgraded sensor package on the U -2.14 The Army Staffs argument centers around command and control of the asset. The Army agreed that the U - 2 ’s

  7. Nonlinear Theory for Partially Cavitating Cascade Flows.

    DTIC Science & Technology

    1978-09-01

    velocity normalized by U2 = £n(q/U2)~ potential function stream function w hodograph variable = e+iT) vi Subscripts: 1 and 2 denotes quantities...a hodograph variable ~ = q e~~ 8 = U2e~~~ (6) or (7) ~ L n(g/U 2 ) (8) where denotes the ve locity at downstream inf ini ty , we can express the

  8. Neurological Effects of Exposure to Non-Hypoxic Hypobaria

    DTIC Science & Technology

    2014-04-16

    were compared to 83 USAF pilot controls ( AFP ). White matter hyperintensities (WMH) are more prevalent in PHY (volume p=0.020/count p=0.040) and U2P...demonstrated in U2P compared to AFP . Lower neurocognitive test performance within the U2P shows lower performance in the domains of reasoning...demonstrates measurable lower neurocognitive test performance in otherwise highly functioning U2P compared to AFP and furthermore demonstrates higher WMH

  9. Rhizobacteria-induced priming in Arabidopsis is dependent on ethylene, jasmonic acid, and NPR1.

    PubMed

    Ahn, Il-Pyung; Lee, Sang-Woo; Suh, Seok-Cheol

    2007-07-01

    A nonpathogenic rhizobacterium, Pseudomonas putida LSW17S, elicited systemic protection against Fusarium wilt and pith necrosis caused by Fusarium oxysporum f. sp. lycopersici and P. corrugata in tomato (Lycopersicon esculentum L.). LSW17S also confers disease resistance against P. syringae pv. tomato DC3000 (DC3000) on Arabidopsis ecotype Col-0. To investigate mechanisms underlying disease protection, expression patterns of defense-related genes PR1, PR2, PR5, and PDF1.2 and cellular defense responses such as hydrogen peroxide accumulation and callose deposition were investigated. LSW17S treatment exhibited the typical phenomena of priming. Strong and faster transcription of defense-related genes was induced and hydrogen peroxide or callose were accumulated in Arabidopsis treated with LSW17S and infected with DC3000. In contrast, individual actions of LSW17S and DC3000 did not elicit rapid molecular and cellular defense responses. Priming by LSW17S was translocated systemically and retained for more than 10 days. Treatment with LSW17S reduced pathogen proliferation in Arabidopsis ecotype Col-0 expressing bacterial NahG; however, npr1, etr1, and jar1 mutations impaired inhibition of pathogen growth. Cellular and molecular priming responses support these results. In sum, LSW17S primes Arabidopsis for NPR1-, ethylene-, and jasmonic acid-dependent disease resistance, and efficient molecular and cellular defense responses.

  10. Effect of aging on mechanical properties of aluminum-alloy rivets

    NASA Technical Reports Server (NTRS)

    Roop, Frederick C

    1941-01-01

    Curves and tabular data present the results of strength tests made during and after 2 1/2 years of aging on rivets and rivet wire of 3/16-inch nominal diameter. The specimens were of aluminum alloy: 24s, 17s, and a17s of the duralumin type and 53s of the magnesium-silicide type.

  11. Effect of aging on mechanical properties of aluminum-alloy rivets

    NASA Technical Reports Server (NTRS)

    Roop, Frederick C

    1941-01-01

    Curves and tabular data present the results of strength tests made during and after 2 1/2 years of aging on rivets and rivet wire of 3/16-inch nominal diameter. The specimens were of aluminum alloy: 24S, 17S, and A17S of the duralumin type and 53S of the magnesium-silicide type.

  12. Microsatellite mapping of the deletion in patients with hereditary neuropathy with liability to pressure palsies (HNPP): new molecular tools for the study of the region 17p12 --> p11 and for diagnosis.

    PubMed

    LeGuern, E; Ravise, N; Gouider, R; Gugenheim, M; Lopes, J; Bouche, P; Agid, Y; Brice, A

    1996-01-01

    Hereditary neuropathy with liability to pressure palsies (HNPP) is an autosomal dominant peripheral neuropathy characterized by recurrent episodes of nerve palsies. We have analyzed 11 microsatellite markers from chromosome 17p12 --> p11 in nine French families with HNPP. The three microsatellites D17S839 (afm200yb12), D17S955 (afm317ygl), and D17S921 (afm191xh12) were localized in the deleted region. In allele segregation analyses, the microsatellite D17S793 (afm165zd4) detected two chromosome 17-linked loci, one of which was deleted in HNPP patients. Using these STR markers, we found that the deletion coincided with the CMT1A/HNPP monomer unit in eight of the nine families. In the remaining pedigree, the deletion lay between the centromeric microsatellite D17S805 (afm234tal) and the telomeric marker D17S922 (afm197xh6), which flank the CMT1A monomer unit. Comparison of these data with the available genetic and physical maps of 17p12 --> p11 shows that this region, which is frequently subject to rearrangement-inducing diseases, such as Smith-Magenis syndrome, Charcot-Marie-Tooth type 1A, and HNPP, presents recombination hot spots. Finally, this study demonstrates the usefulness of the D17S122 (RM11GT) and D17S921 (afm191xh12) microsatellites as tools for the molecular diagnosis of HNPP.

  13. A breast-ovarian cancer susceptibility gene maps to chromosome 17q21

    SciTech Connect

    Feunteun, J. ); Narod, S.A.; Parboosingh, J. ); Lynch, H.T.; Watson, P.; Conway, T.; Lynch, J. ); O'Connell, P.; White, R. ); Lenoir, G.M. )

    1993-04-01

    Nineteen North American Caucasian families that contain a minimum of four confirmed cases of breast or ovarian cancer have been studied. Four polymorphisms (cLB17.1, D17S579, D17S588, and D17S74), which span a region of approximately 15 cM on chromosome 17q12, were typed. The data confirm the location of a dominant gene conferring susceptibility to breast and ovarian cancer (maximum lod = 9.78) and suggest that the breast-ovarian cancer syndrome is genetically heterogeneous. Two recombinants in one large family suggest that the breast-ovarian cancer locus lies between D17S588 and D17S579. 14 refs., 3 figs., 3 tabs.

  14. Priming by rhizobacterium protects tomato plants from biotrophic and necrotrophic pathogen infections through multiple defense mechanisms.

    PubMed

    Ahn, Il-Pyung; Lee, Sang-Woo; Kim, Min Gab; Park, Sang-Ryeol; Hwang, Duk-Ju; Bae, Shin-Chul

    2011-07-01

    A selected strain of rhizobacterium, Pseudomonas putida strain LSW17S (LSW17S), protects tomato plants (Lycopersicon esculentum L. cv. Seokwang) from bacterial speck by biotrophic Pseudomonas syringae pv. tomato strain DC3000 (DC3000) and bacterial wilt by necrotrophic Ralstonia solanacearum KACC 10703 (Rs10703). To investigate defense mechanisms induced by LSW17S in tomato plants, transcription patterns of pathogenesis-related (PR) genes and H(2)O(2) production were analyzed in plants treated with LSW17S and subsequent pathogen inoculation. LSW17S alone did not induce transcriptions of employed PR genes in leaves and roots. DC3000 challenge following LSW17S triggered rapid transcriptions of PR genes and H(2)O(2) production in leaves and roots. Catalase infiltration with DC3000 attenuated defense-related responses and resistance against DC3000 infection. Despite depriving H(2)O(2) production and PR1b transcription by the same treatment, resistance against Rs10703 infection was not deterred significantly. H(2)O(2) is indispensable for defense signaling and/or mechanisms primed by LSW17S and inhibition of bacterial speck, however, it is not involved in resistance against bacterial wilt.

  15. Bifurcating Jets at High Reynolds Numbers

    DTIC Science & Technology

    1988-12-07

    its natural state to some desired state. Due to the Kelvin- Helmholtz instability, the shear layer of a jet naturally rolls up into distinct vortex... Hermann 1982, Ho & Huerre 1984, Gaster et al. 1985, Samet & Petersen 1987, and Monkewitz 1988). These features include amplification of disturbances...downstream from the jet exit (Michalke & Hermann 1982). The velocity ratio of a mixing layer is typically defined as (U1 - U2 )/(U 1 + U2), where U1 and U2

  16. Location, Suppression, and Destruction of Enemy Air Defenses: Linking Missions to Realize Advanced Capabilities

    DTIC Science & Technology

    2008-01-01

    1960 when the Soviets downed a U - 2 high- altitude reconnaissance plane flown by Francis Gary Powers.9 Five years later, Soviet SA- 2 2 batteries were...This article offered a personal recollection of the SA- 2 shootdown of a U - 2 spyplane . Price, Dr. Alfred. Instruments ofDarkness: The History...LDIHD) assets. The EC-130H was used to tackle voice communications ofthe lADS and opposing fighters. 9 RC-135 and U - 2 flights attempted geolocation

  17. Mutations in Splicing Factor Genes Are a Major Cause of Autosomal Dominant Retinitis Pigmentosa in Belgian Families

    PubMed Central

    Coppieters, Frauke; Roels, Dimitri; De Jaegere, Sarah; Flipts, Helena; De Zaeytijd, Julie; Walraedt, Sophie; Claes, Charlotte; Fransen, Erik; Van Camp, Guy; Depasse, Fanny; Casteels, Ingele; de Ravel, Thomy

    2017-01-01

    Purpose Autosomal dominant retinitis pigmentosa (adRP) is characterized by an extensive genetic heterogeneity, implicating 27 genes, which account for 50 to 70% of cases. Here 86 Belgian probands with possible adRP underwent genetic testing to unravel the molecular basis and to assess the contribution of the genes underlying their condition. Methods Mutation detection methods evolved over the past ten years, including mutation specific methods (APEX chip analysis), linkage analysis, gene panel analysis (Sanger sequencing, targeted next-generation sequencing or whole exome sequencing), high-resolution copy number screening (customized microarray-based comparative genomic hybridization). Identified variants were classified following American College of Medical Genetics and Genomics (ACMG) recommendations. Results Molecular genetic screening revealed mutations in 48/86 cases (56%). In total, 17 novel pathogenic mutations were identified: four missense mutations in RHO, five frameshift mutations in RP1, six mutations in genes encoding spliceosome components (SNRNP200, PRPF8, and PRPF31), one frameshift mutation in PRPH2, and one frameshift mutation in TOPORS. The proportion of RHO mutations in our cohort (14%) is higher than reported in a French adRP population (10.3%), but lower than reported elsewhere (16.5–30%). The prevalence of RP1 mutations (10.5%) is comparable to other populations (3.5%-10%). The mutation frequency in genes encoding splicing factors is unexpectedly high (altogether 19.8%), with PRPF31 the second most prevalent mutated gene (10.5%). PRPH2 mutations were found in 4.7% of the Belgian cohort. Two families (2.3%) have the recurrent NR2E3 mutation p.(Gly56Arg). The prevalence of the recurrent PROM1 mutation p.(Arg373Cys) was higher than anticipated (3.5%). Conclusions Overall, we identified mutations in 48 of 86 Belgian adRP cases (56%), with the highest prevalence in RHO (14%), RP1 (10.5%) and PRPF31 (10.5%). Finally, we expanded the molecular

  18. Rapid diagnosis of CMT1A duplications and HNPP deletions by multiplex microsatellite PCR.

    PubMed

    Choi, Byung-Ok; Kim, Joonki; Lee, Kyung Lyong; Yu, Jin Seok; Hwang, Jung Hee; Chung, Ki Wha

    2007-02-28

    Charcot-Marie-Tooth (CMT) disease and hereditary neuropathy with liability to pressure palsies (HNPP) are frequent forms of genetically heterogeneous peripheral neuropathies. Reciprocal unequal crossover between flanking CMT1A-REPs on chromosome 17p11.2-p12 is a major cause of CMT type 1A (CMT1A) and HNPP. The importance of a sensitive and rapid method for identifying the CMT1A duplication and HNPP deletion is being emphasized. In the present study, we established a molecular diagnostic method for the CMT1A duplication and HNPP deletion based on hexaplex PCR of 6 microsatellite markers (D17S921, D17S9B, D17S9A, D17S918, D17S4A and D17S2230). The method is highly time-, cost- and sample-saving because the six markers are amplified by a single PCR reaction and resolved with a single capillary in 3 h. Several statistical and forensic estimates indicated that most of these markers are likely to be useful for diagnosing the peripheral neuropathies. Reproducibility, as determined by concordance between independent tests, was estimated to be 100%. The likelihood that genotypes of all six markers are homozygous in randomly selected individuals was calculated to be 1.6 x 10(-4) which indicates that the statistical error rate for this diagnosis of HNPP deletion is only 0.016%.

  19. Modeling Sorption and Degradation of 17β-Estradiol-17-Sulfate in Agricultural Soils

    NASA Astrophysics Data System (ADS)

    Bai, X.; Casey, F. X.; Hakk, H.; Shrestha, S. L.; DeSutter, T.; Khan, E.; Oduor, P. G.

    2011-12-01

    The natural steroid hormone, 17β-estradiol (E2), can be an endocrine disruptor at part-per trillion levels. Laboratory studies indicate a low potential for E2 persistence and mobility in the environment; however, field studies consistently indicate the presence of E2 and its primary metabolite, estrone, at levels sufficiently high to impact water quality. To facilitate urine excretion, animals may release E2 as a sulfated conjugate, which would have a higher aqueous solubility than the parent compound. We hypothesize that E2 conjugates contribute to the detection of free estrogens in the environment. The objective of this study was to determine the sorption, degradation, and mobility of a model conjugate, 17β-estradiol-17-sulfate (E2-17S), in agricultural soils. Radiolabeled E2-17S ([14C]E2-17S) was chemically synthesized in a three-step process, and then batch experiments were conducted in natural and sterile soils. Additionally, soil organic carbon (OC) was varied (1.29 and 0.26%) to investigate its effect on the fate of [14C]E2-17S. Liquid scintillation counting (LSC) was used in concert with high performance liquid chromatography (HPLC) to detect and quantitate parent compound and metabolites of E2-17S in the aqueous and bound phases. Residual soil was combusted to determine non-extractable levels of 14C. The E2-17S was relatively stable in the aqueous phase for natural and sterile soils. Mono- and di- hydroxyl E2-17S were detected as metabolites of E2-17S in the aqueous phase above both sterile and natural soil. Deconjugation to form E2 was not observed in aqueous phase; however, E2 and estrone were extracted from both natural and sterile soils. A conceptual model was developed to simulate and identify the fate and transport processes of E2-17S. Organic carbon was found to be an important factor affecting the sorption and degradation of E2-17S in soils.

  20. A role for the Cajal-body-associated SUMO isopeptidase USPL1 in snRNA transcription mediated by RNA polymerase II.

    PubMed

    Hutten, Saskia; Chachami, Georgia; Winter, Ulrike; Melchior, Frauke; Lamond, Angus I

    2014-03-01

    Cajal bodies are nuclear structures that are involved in biogenesis of snRNPs and snoRNPs, maintenance of telomeres and processing of histone mRNA. Recently, the SUMO isopeptidase USPL1 was identified as a component of Cajal bodies that is essential for cellular growth and Cajal body integrity. However, a cellular function for USPL1 is so far unknown. Here, we use RNAi-mediated knockdown in human cells in combination with biochemical and fluorescence microscopy approaches to investigate the function of USPL1 and its link to Cajal bodies. We demonstrate that levels of snRNAs transcribed by RNA polymerase (RNAP) II are reduced upon knockdown of USPL1 and that downstream processes such as snRNP assembly and pre-mRNA splicing are compromised. Importantly, we find that USPL1 associates directly with U snRNA loci and that it interacts and colocalises with components of the Little Elongation Complex, which is involved in RNAPII-mediated snRNA transcription. Thus, our data indicate that USPL1 plays a key role in RNAPII-mediated snRNA transcription.

  1. In vivo kinetics of U4/U6·U5 tri-snRNP formation in Cajal bodies.

    PubMed

    Novotný, Ivan; Blažíková, Michaela; Staněk, David; Herman, Petr; Malinsky, Jan

    2011-02-15

    The U4/U6·U5 tri-small nuclear ribonucleoprotein particle (tri-snRNP) is an essential pre-mRNA splicing factor, which is assembled in a stepwise manner before each round of splicing. It was previously shown that the tri-snRNP is formed in Cajal bodies (CBs), but little is known about the dynamics of this process. Here we created a mathematical model of tri-snRNP assembly in CBs and used it to fit kinetics of individual snRNPs monitored by fluorescence recovery after photobleaching. A global fitting of all kinetic data determined key reaction constants of tri-snRNP assembly. Our model predicts that the rates of di-snRNP and tri-snRNP assemblies are similar and that ∼230 tri-snRNPs are assembled in one CB per minute. Our analysis further indicates that tri-snRNP assembly is approximately 10-fold faster in CBs than in the surrounding nucleoplasm, which is fully consistent with the importance of CBs for snRNP formation in rapidly developing biological systems. Finally, the model predicted binding between SART3 and a CB component. We tested this prediction by Förster resonance energy transfer and revealed an interaction between SART3 and coilin in CBs.

  2. Reorganization of Cajal bodies and nucleolar targeting of coilin in motor neurons of type I spinal muscular atrophy.

    PubMed

    Tapia, Olga; Bengoechea, Rocío; Palanca, Ana; Arteaga, Rosa; Val-Bernal, J Fernando; Tizzano, Eduardo F; Berciano, María T; Lafarga, Miguel

    2012-05-01

    Type I spinal muscular atrophy (SMA) is an autosomal recessive disorder caused by loss or mutations of the survival motor neuron 1 (SMN1) gene. The reduction in SMN protein levels in SMA leads to degeneration and death of motor neurons. In this study, we have analyzed the nuclear reorganization of Cajal bodies, PML bodies and nucleoli in type I SMA motor neurons with homozygous deletion of exons 7 and 8 of the SMN1 gene. Western blot analysis is is revealed a marked reduction of SMN levels compared to the control sample. Using a neuronal dissociation procedure to perform a careful immunocytochemical and quantitative analysis of nuclear bodies, we demonstrated a severe decrease in the mean number of Cajal bodies per neuron and in the proportion of motor neurons containing these structures in type I SMA. Moreover, most Cajal bodies fail to recruit SMN and spliceosomal snRNPs, but contain the proteasome activator PA28, a molecular marker associated with the cellular stress response. Neuronal stress in SMA motor neurons also increases PML body number. The existence of chromatolysis and eccentric nuclei in SMA motor neurons correlates with Cajal body disruption and nucleolar relocalization of coil in, a Cajal body marker. Our results indicate that the Cajal body is a pathophysiological target in type I SMA motor neurons. They also suggest the Cajal body-dependent dysfunction of snRNP biogenesis and, therefore, pre-mRNA splicing in these neurons seems to be an essential component for SMA pathogenesis.

  3. The coilin interactome identifies hundreds of small noncoding RNAs that traffic through Cajal bodies.

    PubMed

    Machyna, Martin; Kehr, Stephanie; Straube, Korinna; Kappei, Dennis; Buchholz, Frank; Butter, Falk; Ule, Jernej; Hertel, Jana; Stadler, Peter F; Neugebauer, Karla M

    2014-11-06

    Coilin protein scaffolds Cajal bodies (CBs)-subnuclear compartments enriched in small nuclear RNAs (snRNAs)-and promotes efficient spliceosomal snRNP assembly. The molecular function of coilin, which is intrinsically disordered with no defined motifs, is poorly understood. We use UV crosslinking and immunoprecipitation (iCLIP) to determine whether mammalian coilin binds RNA in vivo and to identify targets. Robust detection of snRNA transcripts correlated with coilin ChIP-seq peaks on snRNA genes, indicating that coilin binding to nascent snRNAs is a site-specific CB nucleator. Surprisingly, several hundred small nucleolar RNAs (snoRNAs) were identified as coilin interactors, including numerous unannotated mouse and human snoRNAs. We show that all classes of snoRNAs concentrate in CBs. Moreover, snoRNAs lacking specific CB retention signals traffic through CBs en route to nucleoli, consistent with the role of CBs in small RNP assembly. Thus, coilin couples snRNA and snoRNA biogenesis, making CBs the cellular hub of small ncRNA metabolism.

  4. 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

  5. An experimental study of Saccharomyces cerevisiae U3 snRNA conformation in solution.

    PubMed Central

    Ségault, V; Mougin, A; Grégoire, A; Banroques, J; Branlant, C

    1992-01-01

    The conformation of Saccharomyces cerevisiae U3 snRNA (snR17A RNA) in solution was studied using enzymatic and chemical probes. In vitro synthesized and authentic snR17A RNAs have a similar conformation in solution. The S. cerevisiae U3 snRNA is folded in two distinct domains. The 5'-domain has a low degree of compactness; it is constituted of two stem-loop structures separated by a single-stranded segment, which has recently been proposed to basepair with the 5'-ETS of pre-ribosomal RNA. We demonstrate that, as previously proposed, the 5'-terminal region of U3 snRNA has a different structure in higher and lower eukaryotes and that this may be related to pre-rRNA 5'-ETS evolution. The S. cerevisiae U3 snRNA 3'-domain has a cruciform secondary structure and a compact conformation resulting from an higher order structure involving the single-stranded segments at the center of the cross and the bottom parts of helices. Compared to tRNA, where long range interactions take place between terminal loops, this represents another kind of tertiary folding of RNA molecules that will deserve further investigation, especially since the implicated single-strands have highly evolutionarily conserved primary structures that are involved in snRNP protein binding. Images PMID:1630915

  6. Investigation of osteosarcoma genomics and its impact on targeted therapy: an international collaboration to conquer human osteosarcoma

    PubMed Central

    Yang, Ji-Long

    2014-01-01

    Osteosarcoma is a genetically unstable malignancy that most frequently occurs in children and young adults. The lack of progress in managing this devastating disease in the clinic has prompted international researchers to collaborate to profile key genomic alterations that define osteosarcoma. A team of researchers and clinicians from China, Finland, and the United States investigated human osteosarcoma by integrating transcriptome sequencing (RNA-seq), high-density genome-wide array comparative genomic hybridization (aCGH), fluorescence in situ hybridization (FISH), reverse transcription-polymerase chain reaction (RT-PCR), Sanger sequencing, cell culture, and molecular biological approaches. Systematic analysis of genetic/genomic alterations and further functional studies have led to several important findings, including novel rearrangement hotspots, osteosarcoma-specific LRP1-SNRNP25 and KCNMB4-CCND3 fusion genes, VEGF and Wnt signaling pathway alterations, deletion of the WWOX gene, and amplification of the APEX1 and RUNX2 genes. Importantly, these genetic events associate significantly with pathogenesis, prognosis, progression, and therapeutic activity in osteosarcoma, suggesting their potential impact on improved managements of human osteosarcoma. This international initiative provides opportunities for developing new treatment modalities to conquer osteosarcoma. PMID:25418192

  7. The dynamics of coiled bodies in the nucleus of adenovirus-infected cells.

    PubMed Central

    Rebelo, L; Almeida, F; Ramos, C; Bohmann, K; Lamond, A I; Carmo-Fonseca, M

    1996-01-01

    The coiled body is a specific intranuclear structure of unknown function that is enriched in splicing small nuclear ribonucleoproteins (snRNPs). Because adenoviruses make use of the host cell-splicing machinery and subvert the normal subnuclear organization, we initially decided to investigate the effect of adenovirus infection on the coiled body. The results indicate that adenovirus infection induces the disassembly of coiled bodies and that this effect is probably secondary to the block of host protein synthesis induced by the virus. Furthermore, coiled bodies are shown to be very labile structures, with a half-life of approximately 2 h after treatment of HeLa cells with protein synthesis inhibitors. After blocking of protein synthesis, p80 coilin was detected in numerous microfoci that do not concentrate snRNP. These structures may represent precursor forms of the coiled body, which goes through a rapid cycle of assembly/disassembly in the nucleus and requires ongoing protein synthesis to reassemble. Images PMID:8862526

  8. Microinjection of Anti-coilin Antibodies Affects the Structure of Coiled Bodies

    PubMed Central

    Almeida, Fátima; Saffrich, Rainer; Ansorge, Wilhelm; Carmo-Fonseca, Maria

    1998-01-01

    The coiled body is a distinct subnuclear domain enriched in small nuclear ribonucleoprotein particles (snRNPs) involved in processing of pre-mRNA. Although the function of the coiled body is still unknown, current models propose that it may have a role in snRNP biogenesis, transport, or recycling. Here we describe that anti-coilin antibodies promote a specific disappearance of the coiled body in living human cells, thus providing a novel tool for the functional analysis of this structure. Monoclonal antibodies (mAbs) were raised against recombinant human coilin, the major structural protein of the coiled body. Four mAbs are shown to induce a progressive disappearance of coiled bodies within ∼6 h after microinjection into the nucleus of HeLa cells. After their disappearance, coiled bodies are not seen to re-form, although injected cells remain viable for at least 3 d. Epitope mapping reveals that the mAbs recognize distinct amino acid motifs scattered along the complete coilin sequence. By 24 and 48 h after injection of antibodies that promote coiled body disappearance, splicing snRNPs are normally distributed in the nucleoplasm, the nucleolus remains unaffected, and the cell cycle progresses normally. Furthermore, cells devoid of coiled bodies for ∼24 h maintain the ability to splice both adenoviral pre-mRNAs and transiently overexpressed human β-globin transcripts. In conclusion, within the time range of this study, no major nuclear abnormalities are detected after coiled body disappearance. PMID:9722604

  9. Compensatory induction of MYC expression by sustained CDK9 inhibition via a BRD4-dependent mechanism

    PubMed Central

    Lu, Huasong; Xue, Yuhua; Yu, Guoying K; Arias, Carolina; Lin, Julie; Fong, Susan; Faure, Michel; Weisburd, Ben; Ji, Xiaodan; Mercier, Alexandre; Sutton, James; Luo, Kunxin; Gao, Zhenhai; Zhou, Qiang

    2015-01-01

    CDK9 is the kinase subunit of positive transcription elongation factor b (P-TEFb) that enables RNA polymerase (Pol) II's transition from promoter-proximal pausing to productive elongation. Although considerable interest exists in CDK9 as a therapeutic target, little progress has been made due to lack of highly selective inhibitors. Here, we describe the development of i-CDK9 as such an inhibitor that potently suppresses CDK9 phosphorylation of substrates and causes genome-wide Pol II pausing. While most genes experience reduced expression, MYC and other primary response genes increase expression upon sustained i-CDK9 treatment. Essential for this increase, the bromodomain protein BRD4 captures P-TEFb from 7SK snRNP to deliver to target genes and also enhances CDK9's activity and resistance to inhibition. Because the i-CDK9-induced MYC expression and binding to P-TEFb compensate for P-TEFb's loss of activity, only simultaneously inhibiting CDK9 and MYC/BRD4 can efficiently induce growth arrest and apoptosis of cancer cells, suggesting the potential of a combinatorial treatment strategy. DOI: http://dx.doi.org/10.7554/eLife.06535.001 PMID:26083714

  10. Endogenous spar tin, mutated in hereditary spastic paraplegia, has a complex subcellular localization suggesting diverse roles in neurons

    SciTech Connect

    Robay, Dimitri; Patel, Heema; Simpson, Michael A.; Brown, Nigel A.; Crosby, Andrew H. . E-mail: acrosby@sgul.ac.uk

    2006-09-10

    Mutation of spartin (SPG20) underlies a complicated form of hereditary spastic paraplegia, a disorder principally defined by the degeneration of upper motor neurons. Using a polyclonal antibody against spartin to gain insight into the function of the endogenous molecule, we show that the endogenous molecule is present in two main isoforms of 85 kDa and 100 kDa, and 75 kDa and 85 kDa in human and murine, respectively, with restricted subcellular localization. Immunohistochemical studies on human and mouse embryo sections and in vitro cell studies indicate that spartin is likely to possess both nuclear and cytoplasmic functions. The nuclear expression of spartin closely mirrors that of the snRNP (small nuclear ribonucleoprotein) marker {alpha}-Sm, a component of the spliceosome. Spartin is also enriched at the centrosome within mitotic structures. Notably we show that spartin protein undergoes dynamic positional changes in differentiating human SH-SY5Y cells. In undifferentiated non-neuronal cells, spartin displays a nuclear and diffuse cytosolic profile, whereas spartin transiently accumulates in the trans-Golgi network and subsequently decorates discrete puncta along neurites in terminally differentiated neuroblastic cells. Investigation of these spartin-positive vesicles reveals that a large proportion colocalizes with the synaptic vesicle marker synaptotagmin. Spartin is also enriched in synaptic-like structures and in synaptic vesicle-enriched fraction.

  11. 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

  12. A role for the Cajal-body-associated SUMO isopeptidase USPL1 in snRNA transcription mediated by RNA polymerase II

    PubMed Central

    Hutten, Saskia; Chachami, Georgia; Winter, Ulrike; Melchior, Frauke; Lamond, Angus I.

    2014-01-01

    ABSTRACT Cajal bodies are nuclear structures that are involved in biogenesis of snRNPs and snoRNPs, maintenance of telomeres and processing of histone mRNA. Recently, the SUMO isopeptidase USPL1 was identified as a component of Cajal bodies that is essential for cellular growth and Cajal body integrity. However, a cellular function for USPL1 is so far unknown. Here, we use RNAi-mediated knockdown in human cells in combination with biochemical and fluorescence microscopy approaches to investigate the function of USPL1 and its link to Cajal bodies. We demonstrate that levels of snRNAs transcribed by RNA polymerase (RNAP) II are reduced upon knockdown of USPL1 and that downstream processes such as snRNP assembly and pre-mRNA splicing are compromised. Importantly, we find that USPL1 associates directly with U snRNA loci and that it interacts and colocalises with components of the Little Elongation Complex, which is involved in RNAPII-mediated snRNA transcription. Thus, our data indicate that USPL1 plays a key role in RNAPII-mediated snRNA transcription. PMID:24413172

  13. Plant small nuclear RNAs. V. U4 RNA is present in broad bean plants in the form of sequence variants and is base-paired with U6 RNA.

    PubMed Central

    Kiss, T; Jakab, G; Antal, M; Pálfi, Z; Hegyi, H; Kis, M; Solymosy, F

    1988-01-01

    U4 RNA, which is known to play an indispensable role in pre-mRNA splicing, is present in plant nuclei, has a canonical m3 2,2,7 G cap at its 5' end and is associated with U6 RNA in snRNP particles. It occurs in broad bean in the form of a number of sequence variants. Two of these were sequenced: U4A RNA is 154 and U4B RNA is 152 nucleotides long. Sequence similarity of broad bean U4B RNA is 94 per cent to broad bean U4A RNA, 65 per cent to rat U4A RNA, 61 per cent to Drosophila U4A RNA and 50 per cent to snR14, the U4 RNA equivalent of the yeast Saccharomyces cerevisiae. Sequence conservation is much more pronounced in the 5' half of the molecule than in its 3' half. The secondary structure of both variants of broad bean U4 RNA perfectly fits with that of all other U4 RNAs sequenced so far. Nucleotide changes between broad bean U4A and U4B RNAs are restricted to molecular regions that affect the thermodynamic stability of these molecules. A model is proposed for the base pairing interaction of broad bean U4 RNA with broad bean U6 RNA. This is the first report on the structure of a plant U4 RNA. Images PMID:3387237

  14. 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.

  15. Spatial distribution of the Sm antigen in Drosophila early embryos.

    PubMed

    Ségalat, L; Lepesant, J A

    1992-01-01

    Anti-Sm antibodies recognize the major small nuclear RNA-protein particles (snRNPs) involved in pre-mRNA processing. The spatial distribution of the snRNPs has been investigated in Drosophila embryos up to the cellularization stage (cycle 14), using the Y12 anti-Sm antibody. Our results show that: 1) all or most of the Sm antigen is localized in the cytoplasm of the syncytial blastoderm until the 12th cycle of division, in both the nuclear and cytoplasmic compartments at cycle 13, and then in the nuclei at cycle 14 and later. This relocalization takes place when zygotic transcriptional activation occurs; 2) at the subcellular level, the Sm antigen localizes in a speckled pattern and in foci-like structures within the nucleus of Drosophila blastoderm embryos; 3) strikingly, some nuclei of embryos at the 14th cycle appear to contain more snRNPs than others. The position of these nuclei differs from one embryo to another, and their distribution does not resemble any known developmental pattern of Drosophila embryogenesis. We propose that random differences in snRNP concentration may serve as an epigenetic signal for stochastic events occurring during development.

  16. Association of HLA-DRB1 alleles with susceptibility to mixed connective tissue disease in Polish patients.

    PubMed

    Paradowska-Gorycka, A; Stypińska, B; Olesińska, M; Felis-Giemza, A; Mańczak, M; Czuszynska, Z; Zdrojewski, Z; Wojciechowicz, J; Jurkowska, M

    2015-11-09

    Mixed connective tissue disease (MCTD) is a systemic autoimmune disease, originally defined as a connective tissue inflammatory syndrome with overlapping features of systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), polymyositis/dermatomyositis (PM/DM) and systemic sclerosis (SSc), characterized by the presence of antibodies against components of the U1 small nuclear ribonucleoprotein (U1snRNP). The aim of the study was to assess the frequency of (high-resolution-typed) DRB1 alleles in a cohort of Polish patients with MCTD (n = 103). Identification of the variants potentially associated with risk and protection was carried out by comparison with the DKMS Polish Bone Marrow Donor Registry (41306 alleles). DRB1*15:01 (odds ratio (OR): 6.06; 95% confidence interval (CI) 4.55-8.06), DRB1*04 (OR: 3.69; 95% CI 2.69-5.01) and *09:01 (OR: 8.12; 95% CI 2.15-21.75) were identified as risk alleles for MCTD, while HLA-DRB1*07:01 allele was found to be protective (OR: 0.50; 95% CI 0.28-0.83). The carrier frequency of the DRB1*01 was higher in MCTD patients compared with controls, although the differences were not statistically significant. Our results confirm the modulating influence of HLA-DRB1 genotypes on development of connective tissue diseases such as MCTD.

  17. The diagnosis and classification of mixed connective tissue disease.

    PubMed

    Tani, Chiara; Carli, Linda; Vagnani, Sabrina; Talarico, Rosaria; Baldini, Chiara; Mosca, Marta; Bombardieri, Stefano

    2014-01-01

    The term "mixed connective tissue disease" (MCTD) concerns a systemic autoimmune disease typified by overlapping features between two or more systemic autoimmune diseases and the presence of antibodies against the U1 small nuclear ribonucleoprotein autoantigen (U1snRNP). Since the first description of this condition in 1972, the understanding of clinical manifestations and long-term outcome of MCTD have significantly advanced. Polyarthritis, Raynaud's phenomenon, puffy fingers, lung involvement and esophageal dysmotility are the most frequently reported symptoms among the different cohorts during the course of the disease. Moreover, in recent years a growing interest has been focused on severe organ involvement such as pulmonary arterial hypertension and interstitial lung disease which can accrue during the long-term follow-up and can still significantly influence disease prognosis. Over the last years, significant advances have been made also in disease pathogenesis understanding and a central pathogenetic role of anti-U1RNP autoantibodies has clearly emerged. Although controversies on disease definition and classification still persist, MCTD identifies a group of patients in whom increased surveillance for specific manifestations and prognostic stratification became mandatory to improve patient's outcomes.

  18. 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

  19. Residual Cajal bodies in coilin knockout mice fail to recruit Sm snRNPs and SMN, the spinal muscular atrophy gene product

    PubMed Central

    Tucker, Karen E.; Berciano, Maria Teresa; Jacobs, Erica Y.; LePage, David F.; Shpargel, Karl B.; Rossire, Jennifer J.; Chan, Edward K.L.; Lafarga, Miguel; Conlon, Ronald A.; Matera, A. Gregory

    2001-01-01

    Cajal bodies (CBs) are nuclear suborganelles involved in the biogenesis of small nuclear ribonucleoproteins (snRNPs). In addition to snRNPs, they are highly enriched in basal transcription and cell cycle factors, the nucleolar proteins fibrillarin (Fb) and Nopp140 (Nopp), the survival motor neuron (SMN) protein complex, and the CB marker protein, p80 coilin. We report the generation of knockout mice lacking the COOH-terminal 487 amino acids of coilin. Northern and Western blot analyses demonstrate that we have successfully removed the full-length coilin protein from the knockout animals. Some homozygous mutant animals are viable, but their numbers are reduced significantly when crossed to inbred backgrounds. Analysis of tissues and cell lines from mutant animals reveals the presence of extranucleolar foci that contain Fb and Nopp but not other typical nucleolar markers. These so-called “residual” CBs neither condense Sm proteins nor recruit members of the SMN protein complex. Transient expression of wild-type mouse coilin in knockout cells results in formation of CBs and restores these missing epitopes. Our data demonstrate that full-length coilin is essential for proper formation and/or maintenance of CBs and that recruitment of snRNP and SMN complex proteins to these nuclear subdomains requires sequences within the coilin COOH terminus. PMID:11470819

  20. 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.

  1. Association of HLA-DRB1 alleles with susceptibility to mixed connective tissue disease in Polish patients.

    PubMed

    Paradowska-Gorycka, A; Stypińska, B; Olesińska, M; Felis-Giemza, A; Mańczak, M; Czuszynska, Z; Zdrojewski, Z; Wojciechowicz, J; Jurkowska, M

    2016-01-01

    Mixed connective tissue disease (MCTD) is a systemic autoimmune disease, originally defined as a connective tissue inflammatory syndrome with overlapping features of systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), polymyositis/dermatomyositis (PM/DM) and systemic sclerosis (SSc), characterized by the presence of antibodies against components of the U1 small nuclear ribonucleoprotein (U1snRNP). The aim of the study was to assess the frequency of (high-resolution-typed) DRB1 alleles in a cohort of Polish patients with MCTD (n = 103). Identification of the variants potentially associated with risk and protection was carried out by comparison with the DKMS Polish Bone Marrow Donor Registry (41306 alleles). DRB1*15:01 (odds ratio (OR): 6.06; 95% confidence interval (CI) 4.55-8.06), DRB1*04 (OR: 3.69; 95% CI 2.69-5.01) and *09:01 (OR: 8.12; 95% CI 2.15-21.75) were identified as risk alleles for MCTD, while HLA-DRB1*07:01 allele was found to be protective (OR: 0.50; 95% CI 0.28-0.83). The carrier frequency of the DRB1*01 was higher in MCTD patients compared with controls, although the differences were not statistically significant. Our results confirm the modulating influence of HLA-DRB1 genotypes on development of connective tissue diseases such as MCTD.

  2. Real-time imaging of cotranscriptional splicing reveals a kinetic model that reduces noise: implications for alternative splicing regulation

    PubMed Central

    Schmidt, Ute; Robert, Marie-Cécile; Yoshida, Minoru; Villemin, Jean-Philippe; Auboeuf, Didier; Aitken, Stuart

    2011-01-01

    Splicing is a key process that expands the coding capacity of genomes. Its kinetics remain poorly characterized, and the distribution of splicing time caused by the stochasticity of single splicing events is expected to affect regulation efficiency. We conducted a small-scale survey on 40 introns in human cells and observed that most were spliced cotranscriptionally. Consequently, we constructed a reporter system that splices cotranscriptionally and can be monitored in live cells and in real time through the use of MS2–GFP. All small nuclear ribonucleoproteins (snRNPs) are loaded on nascent pre-mRNAs, and spliceostatin A inhibits splicing but not snRNP recruitment. Intron removal occurs in minutes and is best described by a model where several successive steps are rate limiting. Each pre-mRNA molecule is predicted to require a similar time to splice, reducing kinetic noise and improving the regulation of alternative splicing. This model is relevant to other kinetically controlled processes acting on few molecules. PMID:21624952

  3. Screening of genes related to sulfide metabolism in Urechis unicinctus (Echiura, Urechidae) using suppression subtractive hybridization and cDNA microarray analysis.

    PubMed

    Shi, Xiaoli; Shao, Mingyu; Zhang, Litao; Ma, Yubin; Zhang, Zhifeng

    2012-09-01

    Exogenous sulfide can generally induce metabolic injuries in most organisms and even cause death. However, organisms inhabiting intertidal zones, hydrothermal vents, and cold seeps, can tolerate, metabolize, and utilize sulfide. In this study, both suppression subtractive hybridization and cDNA microarray analysis were employed to screen sulfide metabolism-related genes from the body wall in echiuran worm Urechis unicinctus, a marine sediment species. A total of 3456 monoclones were isolated and 82 were identified as differentially expressed genes in worms exposed to 50 μM sulfide for 24 h, compared to controls. The identified genes encoded proteins with multiple processes, including metabolism, cellular process, biological regulation, response to stimulus, multicellular organismal process, localization, development, and cellular component organization. Eight genes, serase, vacuolar protein, src tyrosine kinase, sulfide oxidase-like oxidoreductase, aprataxin, SN-RNP, aminopeptidase, and predicted protein, were selected to verify expression in the worm using qRT-PCR. The agreement of gene expression evaluation was 62.5% between the results of microarray analysis and qRT-PCR. These new data will provide clues for further probing of the molecular mechanism of sulfide metabolism.

  4. Splicing-Mediated Autoregulation Modulates Rpl22p Expression in Saccharomyces cerevisiae

    PubMed Central

    Gabunilas, Jason

    2016-01-01

    In Saccharomyces cerevisiae, splicing is critical for expression of ribosomal protein genes (RPGs), which are among the most highly expressed genes and are tightly regulated according to growth and environmental conditions. However, knowledge of the precise mechanisms by which RPG pre-mRNA splicing is regulated on a gene-by-gene basis is lacking. Here we show that Rpl22p has an extraribosomal role in the inhibition of splicing of the RPL22B pre-mRNA transcript. A stem loop secondary structure within the intron is necessary for pre-mRNA binding by Rpl22p in vivo and splicing inhibition in vivo and in vitro and can rescue splicing inhibition in vitro when added in trans to splicing reactions. Splicing inhibition by Rpl22p may be partly attributed to the reduction of co-transcriptional U1 snRNP recruitment to the pre-mRNA at the RPL22B locus. We further demonstrate that the inhibition of RPL22B pre-mRNA splicing contributes to the down-regulation of mature transcript during specific stress conditions, and provide evidence hinting at a regulatory role for this mechanism in conditions of suppressed ribosome biogenesis. These results demonstrate an autoregulatory mechanism that fine-tunes the expression of the Rpl22 protein and by extension Rpl22p paralog composition according to the cellular demands for ribosome biogenesis. PMID:27097027

  5. High prevalence of mutations affecting the splicing process in a Spanish cohort with autosomal dominant retinitis pigmentosa

    PubMed Central

    Ezquerra-Inchausti, Maitane; Barandika, Olatz; Anasagasti, Ander; Irigoyen, Cristina; López de Munain, Adolfo; Ruiz-Ederra, Javier

    2017-01-01

    Retinitis pigmentosa is the most frequent group of inherited retinal dystrophies. It is highly heterogeneous, with more than 80 disease-causing genes 27 of which are known to cause autosomal dominant RP (adRP), having been identified. In this study a total of 29 index cases were ascertained based on a family tree compatible with adRP. A custom panel of 31 adRP genes was analysed by targeted next-generation sequencing using the Ion PGM platform in combination with Sanger sequencing. This allowed us to detect putative disease-causing mutations in 14 out of the 29 (48.28%) families analysed. Remarkably, around 38% of all adRP cases analysed showed mutations affecting the splicing process, mainly due to mutations in genes coding for spliceosome factors (SNRNP200 and PRPF8) but also due to splice-site mutations in RHO. Twelve of the 14 mutations found had been reported previously and two were novel mutations found in PRPF8 in two unrelated patients. In conclusion, our results will lead to more accurate genetic counselling and will contribute to a better characterisation of the disease. In addition, they may have a therapeutic impact in the future given the large number of studies currently underway based on targeted RNA splicing for therapeutic purposes. PMID:28045043

  6. 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

  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. U bodies respond to nutrient stress in Drosophila

    SciTech Connect

    Buckingham, Mickey; Liu, Ji-Long

    2011-12-10

    The neurodegenerative disease spinal muscular atrophy (SMA) is caused by mutation of the survival motor neuron 1 (SMN1) gene. Cytoplasmic SMN protein-containing granules, known as U snRNP bodies (U bodies), are thought to be responsible for the assembly and storage of small nuclear ribonucleoproteins (snRNPs) which are essential for pre-mRNA splicing. U bodies exhibit close association with cytoplasmic processing bodies (P bodies), which are involved in mRNA decay and translational repression. The close association of the U body and P body in Drosophila resemble that of the stress granule and P body in yeast and mammalian cells. However, it is unknown whether the U body is responsive to any stress. Using Drosophila oogenesis as a model, here we show that U bodies increase in size following nutritional deprivation. Despite nutritional stress, U bodies maintain their close association with P bodies. Our results show that U bodies are responsive to nutrition changes, presumably through the U body-P body pathway.

  9. Extensive interactions of PRP8 protein with the 5' and 3' splice sites during splicing suggest a role in stabilization of exon alignment by U5 snRNA.

    PubMed Central

    Teigelkamp, S; Newman, A J; Beggs, J D

    1995-01-01

    Precursor RNAs containing 4-thiouridine at specific sites were used with UV-crosslinking to map the binding sites of the yeast protein splicing factor PRP8. PRP8 protein interacts with a region of at least eight exon nucleotides at the 5' splice site and a minimum of 13 exon nucleotides and part of the polypyrimidine tract in the 3' splice site region. Crosslinking of PRP8 to mutant and duplicated 3' splice sites indicated that the interaction is not sequence specific, nor does it depend on the splice site being functional. Binding of PRP8 to the 5' exon was established before step 1 and to the 3' splice site region after step 1 of splicing. These interactions place PRP8 close to the proposed catalytic core of the spliceosome during both transesterification reactions. To date, this represents the most extensive mapping of the binding site(s) of a splicing factor on the substrate RNA. We propose that the large binding sites of PRP8 stabilize the intrinsically weaker interactions of U5 snRNA with both exons at the splice sites for exon alignment by the U5 snRNP. Images PMID:7781612

  10. Coilin association with Box C/D scaRNA suggests a direct role for the Cajal body marker protein in scaRNP biogenesis

    PubMed Central

    Enwerem, Isioma I.; Velma, Venkatramreddy; Broome, Hanna J.; Kuna, Marija; Begum, Rowshan A.; Hebert, Michael D.

    2014-01-01

    ABSTRACT Spliceosomal small nuclear ribonucleoproteins (snRNPs) are enriched in the Cajal body (CB). Guide RNAs, known as small Cajal body-specific RNAs (scaRNAs), direct modification of the small nuclear RNA (snRNA) component of the snRNP. The protein WRAP53 binds a sequence motif (the CAB box) found in many scaRNAs and the RNA component of telomerase (hTR) and targets these RNAs to the CB. We have previously reported that coilin, the CB marker protein, associates with certain non-coding RNAs. For a more comprehensive examination of the RNAs associated with coilin, we have sequenced the RNA isolated from coilin immunocomplexes. A striking preferential association of coilin with the box C/D scaRNAs 2 and 9, which lack a CAB box, was observed. This association varied by treatment condition and WRAP53 knockdown. In contrast, reduction of WRAP53 did not alter the level of coilin association with hTR. Additional studies showed that coilin degrades/processes scaRNA 2 and 9, associates with active telomerase and can influence telomerase activity. These findings suggest that coilin plays a novel role in the biogenesis of box C/D scaRNPs and telomerase. PMID:24659245

  11. Core structure of the U6 small nuclear ribonucleoprotein at 1.7-Å resolution.

    PubMed

    Montemayor, Eric J; Curran, Elizabeth C; Liao, Hong Hong; Andrews, Kristie L; Treba, Christine N; Butcher, Samuel E; Brow, David A

    2014-06-01

    The spliceosome is a dynamic assembly of five small nuclear ribonucleoproteins (snRNPs) that removes introns from eukaryotic pre-mRNA. U6, the most conserved of the spliceosomal small nuclear RNAs (snRNAs), participates directly in catalysis. Here, we report the crystal structure of the Saccharomyces cerevisiae U6 snRNP core containing most of the U6 snRNA and all four RRM domains of the Prp24 protein. It reveals a unique interlocked RNP architecture that sequesters the 5' splice site-binding bases of U6 snRNA. RRMs 1, 2 and 4 of Prp24 form an electropositive groove that binds double-stranded RNA and may nucleate annealing of U4 and U6 snRNAs. Substitutions in Prp24 that suppress a mutation in U6 localize to direct RNA-protein contacts. Our results provide the most comprehensive view to date of a multi-RRM protein bound to RNA and reveal striking coevolution of protein and RNA structure.

  12. High prevalence of mutations affecting the splicing process in a Spanish cohort with autosomal dominant retinitis pigmentosa.

    PubMed

    Ezquerra-Inchausti, Maitane; Barandika, Olatz; Anasagasti, Ander; Irigoyen, Cristina; López de Munain, Adolfo; Ruiz-Ederra, Javier

    2017-01-03

    Retinitis pigmentosa is the most frequent group of inherited retinal dystrophies. It is highly heterogeneous, with more than 80 disease-causing genes 27 of which are known to cause autosomal dominant RP (adRP), having been identified. In this study a total of 29 index cases were ascertained based on a family tree compatible with adRP. A custom panel of 31 adRP genes was analysed by targeted next-generation sequencing using the Ion PGM platform in combination with Sanger sequencing. This allowed us to detect putative disease-causing mutations in 14 out of the 29 (48.28%) families analysed. Remarkably, around 38% of all adRP cases analysed showed mutations affecting the splicing process, mainly due to mutations in genes coding for spliceosome factors (SNRNP200 and PRPF8) but also due to splice-site mutations in RHO. Twelve of the 14 mutations found had been reported previously and two were novel mutations found in PRPF8 in two unrelated patients. In conclusion, our results will lead to more accurate genetic counselling and will contribute to a better characterisation of the disease. In addition, they may have a therapeutic impact in the future given the large number of studies currently underway based on targeted RNA splicing for therapeutic purposes.

  13. Recombinant hnRNP protein A1 and its N-terminal domain show preferential affinity for oligodeoxynucleotides homologous to intron/exon acceptor sites.

    PubMed Central

    Buvoli, M; Cobianchi, F; Biamonti, G; Riva, S

    1990-01-01

    The reported binding preference of human hnRNP protein A1 for the 3'-splice site of some introns (Swanson and Dreyfuss (1988) EMBO J. 7, 3519-3529; Mayrand and Pederson (1990) Nucleic Acids Res. 18, 3307-3318) was tested by assaying in vitro the binding of purified recombinant A1 protein (expressed in bacteria) to synthetic oligodeoxynucleotides (21-mers) of suitable sequence. In such a minimal system we find preferential binding of protein A1 to oligodeoxynucleotide sequences corresponding to the 3'-splice site of IVS1 of human beta-globin pre-mRNA and of IVS1 of Adenovirus type 2 major late transcript. Mutation studies demonstrate that the binding specificity is dependent on the known critical domains of this intron region, the AG splice site dinucleotide and polypyrimidine tract, and resides entirely in the short oligonucleotide sequence. Moreover specific binding does not require the presence of other hnRNP proteins or of snRNP particles. Studies with a truncated recombinant protein demonstrated that the minimal protein sequence determinants for A1 recognition of 3'-splice acceptor site reside entirely in the N-terminal 195 aa of the unmodified protein. Images PMID:2251120

  14. Bottom-up design of small molecules that stimulate exon 10 skipping in mutant MAPT pre-mRNA.

    PubMed

    Luo, Yiling; Disney, Matthew D

    2014-09-22

    One challenge in chemical biology is to develop small molecules that control cellular protein content. The amount and identity of proteins are influenced by the RNAs that encode them; thus, protein content in a cell could be affected by targeting mRNA. However, RNA has been traditionally difficult to target with small molecules. In this report, we describe controlling the protein products of the mutated microtubule-associated protein tau (MAPT) mature mRNA with a small molecule. MAPT mutations in exon 10 are associated with inherited frontotemporal dementia and Parkinsonism linked to chromosome 17 (FTDP-17), an incurable disease that is directly caused by increased inclusion of exon 10 in MAPT mRNA. Recent studies have shown that mutations within a hairpin at the MAPT exon 10-intron junction decrease the thermodynamic stability of the RNA, increasing binding to U1 snRNP and thus exon 10 inclusion. Therefore, we designed small molecules that bind and stabilize a mutant MAPT by using Inforna, a computational approach based on information about RNA-small-molecule interactions. The optimal compound selectively bound the mutant MAPT hairpin and thermodynamically stabilized its folding, facilitating exon 10 exclusion.

  15. Splicing-Mediated Autoregulation Modulates Rpl22p Expression in Saccharomyces cerevisiae.

    PubMed

    Gabunilas, Jason; Chanfreau, Guillaume

    2016-04-01

    In Saccharomyces cerevisiae, splicing is critical for expression of ribosomal protein genes (RPGs), which are among the most highly expressed genes and are tightly regulated according to growth and environmental conditions. However, knowledge of the precise mechanisms by which RPG pre-mRNA splicing is regulated on a gene-by-gene basis is lacking. Here we show that Rpl22p has an extraribosomal role in the inhibition of splicing of the RPL22B pre-mRNA transcript. A stem loop secondary structure within the intron is necessary for pre-mRNA binding by Rpl22p in vivo and splicing inhibition in vivo and in vitro and can rescue splicing inhibition in vitro when added in trans to splicing reactions. Splicing inhibition by Rpl22p may be partly attributed to the reduction of co-transcriptional U1 snRNP recruitment to the pre-mRNA at the RPL22B locus. We further demonstrate that the inhibition of RPL22B pre-mRNA splicing contributes to the down-regulation of mature transcript during specific stress conditions, and provide evidence hinting at a regulatory role for this mechanism in conditions of suppressed ribosome biogenesis. These results demonstrate an autoregulatory mechanism that fine-tunes the expression of the Rpl22 protein and by extension Rpl22p paralog composition according to the cellular demands for ribosome biogenesis.

  16. [The role of RNA splicing in the pathogenesis of spinal muscular atrophy and development of its therapeutics].

    PubMed

    Sahashi, Kentaro; Sobue, Gen

    2014-12-01

    Loss-of-function mutations in SMN1 cause spinal muscular atrophy (SMA), a leading genetic cause of infant mortality. Degeneration of alpha-motor neurons that results in progressive paralysis is a pathological hallmark of SMA. Recently, peripheral-tissue involvement has also been reported in SMA. Patients have low levels of functional SMN which is attributed to alternative splicing in SMN2, a gene closely-related to SMN1. This decrease in the expression of SMN, a ubiquitously expressed protein involved in promoting snRNP assembly required for splicing, is responsible for SMA. However, the mechanism through which decrease in SMN levels causes SMA remains unclear. Currently, no curative treatment is available for SMA, but SMN restoration is thought to be necessary and sufficient for cure. Antisense oligonucleotides (ASOs) can be designed to specifically alter splicing patterns of target pre-mRNAs. We identified an ASO that redirects SMN2 splicing and is currently in clinical trials for use as RNA-targeting therapeutics. Further, we have also reported a novel application of splicing-modulating ASOs--creation of animal phenocopy models of diseases by inducing mis-splicing. Exploring the relationship between the spatial and temporal effects of therapeutic and pathogenic ASOs yields relevant insights into the roles of SMN in SMA pathogenesis and into its normal physiological functions. This knowledge, in turn, contributes to the ongoing development of targeted therapeutics.

  17. The Roles and Identification of Innovators and Linkers in the Technology Transfer Process.

    DTIC Science & Technology

    1977-09-01

    I u - 2 7 u - 0 u u + O ’ u + 2 0 WOOLLEY HCCI -IBERGER (1977) Figure 7 . The hy pothes i zed distribution of innovators based on...icers of the Civil Engine ering Corps. Monterey. California. Naval Postgraduate School. NPS ( 1973) . 12. Creighton . J. W .. J. A. Jolly. and S. A

  18. 49 CFR 572.183 - Neck assembly.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... subpart E pendulum test fixture as shown in Figure U2-A in appendix A to this subpart, so that the... pendulum longitudinal centerline shown in Figure U2-A. Torque the half-spherical screws (175-2004) located... equivalent; (3) Release the pendulum from a height sufficient to allow it to fall freely to achieve an...

  19. 49 CFR 572.183 - Neck assembly.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... subpart E pendulum test fixture as shown in Figure U2-A in appendix A to this subpart, so that the... pendulum longitudinal centerline shown in Figure U2-A. Torque the half-spherical screws (175-2004) located... equivalent; (3) Release the pendulum from a height sufficient to allow it to fall freely to achieve an...

  20. 49 CFR 572.183 - Neck assembly.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... subpart E pendulum test fixture as shown in Figure U2-A in appendix A to this subpart, so that the... pendulum longitudinal centerline shown in Figure U2-A. Torque the half-spherical screws (175-2004) located... equivalent; (3) Release the pendulum from a height sufficient to allow it to fall freely to achieve an...

  1. 49 CFR 572.183 - Neck assembly.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... subpart E pendulum test fixture as shown in Figure U2-A in appendix A to this subpart, so that the... pendulum longitudinal centerline shown in Figure U2-A. Torque the half-spherical screws (175-2004) located... equivalent; (3) Release the pendulum from a height sufficient to allow it to fall freely to achieve an...

  2. 49 CFR 572.183 - Neck assembly.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... subpart E pendulum test fixture as shown in Figure U2-A in appendix A to this subpart, so that the... pendulum longitudinal centerline shown in Figure U2-A. Torque the half-spherical screws (175-2004) located... equivalent; (3) Release the pendulum from a height sufficient to allow it to fall freely to achieve an...

  3. 51. Photographic copy of the original construction drawing, 192627, by ...

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

    51. Photographic copy of the original construction drawing, 1926-27, by Harrington, Howard, and Ash, Consulting Engineers, from microfilm copy at Bridge Division, Missouri Highway and Transportation Department, Jefferson City, Missouri. 671 FT. SPAN, JOINTS L0, U2 TO U4, PORTAL AT U2 - Cape Girardeau Bridge, Spanning Mississippi River at State Highway 146, Cape Girardeau, Cape Girardeau County, MO

  4. 40 CFR 98.214 - Monitoring and QA/QC requirements.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... requirements. (a) The annual mass of carbonate consumed (for Equation U-1 of this subpart) or carbonate inputs (for Equation U-2 of this subpart) must be determined annually from monthly measurements using the same... weigh hoppers or weigh belt feeders. (b) The annual mass of carbonate outputs (for Equation U-2 of...

  5. 40 CFR 98.214 - Monitoring and QA/QC requirements.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... requirements. (a) The annual mass of carbonate consumed (for Equation U-1 of this subpart) or carbonate inputs (for Equation U-2 of this subpart) must be determined annually from monthly measurements using the same... weigh hoppers or weigh belt feeders. (b) The annual mass of carbonate outputs (for Equation U-2 of...

  6. 40 CFR 98.214 - Monitoring and QA/QC requirements.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... requirements. (a) The annual mass of carbonate consumed (for Equation U-1 of this subpart) or carbonate inputs (for Equation U-2 of this subpart) must be determined annually from monthly measurements using the same... weigh hoppers or weigh belt feeders. (b) The annual mass of carbonate outputs (for Equation U-2 of...

  7. 40 CFR 98.214 - Monitoring and QA/QC requirements.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... requirements. (a) The annual mass of carbonate consumed (for Equation U-1 of this subpart) or carbonate inputs (for Equation U-2 of this subpart) must be determined annually from monthly measurements using the same... weigh hoppers or weigh belt feeders. (b) The annual mass of carbonate outputs (for Equation U-2 of...

  8. Coordinates of the quantum plane as q-tensor operators in U{sub q} (su(2) * su(2))

    SciTech Connect

    Biedenharn, L.C.; Lohe, M.A.

    1995-01-13

    The relation between the set of transformations M{sub q}(2) of the quantum plane and the quantum universal enveloping algebra U{sub q}(u(2)) is investigated by constructing representations of the factor algebra U{sub q} (u(2) * u(2)). The non-commuting coordinates of M{sub q}(2), on which U{sub q}(2) * U{sub q}(2) acts, are realized as q-spinors with respect to each U{sub q}(u(2)) algebra. The representation matrices of U{sub q}(2) are constructed as polynomials in these spinor components. This construction allows a derivation of the commutation relations of the noncommuting coordinates of M{sub q}(2) directly from properties of U{sub q}(u(2)). The generalization of these results to U{sub q}(u(n)) and M{sub q}(n) is also discussed.

  9. A gene for Leber's congenital amaurosis maps to chromosome 17p.

    PubMed

    Camuzat, A; Dollfus, H; Rozet, J M; Gerber, S; Bonneau, D; Bonnemaison, M; Briard, M L; Dufier, J L; Ghazi, I; Leowski, C

    1995-08-01

    Leber's congenital amaurosis (LCA) is an autosomal recessive disease responsible for congenital blindness. It is the most early and severe form of inherited retinopathy and accounts for 5% of all inherited retinal dystrophies. Here we report the first mapping of a gene for LCA to the distal short arm of chromosome 17 by linkage analysis in 15 multiplex families (Zmax = 5.14 at theta = 0.15 for probe AFM070xg5 at the D17S1353 locus). When our sample was split into two groups according to the ethnic origin of the patients we were able to confirm the presence of a gene for LCA on chromosome 17p by both homozygosity mapping and linkage analysis in five families of Maghrebian origin (LCA1, Zmax = 7.21 at theta = 0.01 at the D17S1353 locus), while negative results were found in 10 families of French ancestry. Haplotype analyses supported the placement of LCA1 between loci D17S796 and D17S786 (maximum likelihood estimate for location of the disease gene over the D17S1353 locus). The genetic heterogeneity of LCA will complicate the prenatal detection of this frequent cause of congenital blindness.

  10. A gene for autosomal dominant progressive cone dystrophy (CORD5) maps to chromosome 17p12-p13

    SciTech Connect

    Balciuniene, J.; Holmgren, G.; Forsman, K.

    1995-11-20

    Inherited retinal dystrophy is a common cause of visual impairment. Cone dystrophy affects the cone function and is manifested as progressive loss of the central vision, defective color vision, and photophobia. Linkage was demonstrated between progressive cone dystrophy (CORD5) and genetic markers on chromosome 17p12-p13 in a five-generation family. Multipoint analysis gave a maximum lod score of 7.72 at the marker D17S938. Recombinant haplotypes in the family suggest that the cone dystrophy locus is located in a 25-cM interval between the markers D17S926/D17S849 and D17S804/D17S945. Furthermore, one recombination was detected between the disease locus and a microsatellite marker in the candidate gene RCV1, encoding the retinal protein recoverin. Two additional candidate genes encoding retinal guanylate cyclase (GUC2D) and pigment epithelium-derived factor (PEDF) are located at 17p13.1. Moreover, loci for retinitis pigmentosa and Leber congenital amaurosis have been mapped to the same region. Identification of the cone dystrophy locus may be of importance not only for identifying functional genes in the cone system, but also for identifying genes for other retinal disorders. 34 refs., 3 figs., 2 tabs.

  11. Genetic homogeneity in Sjoegren-Larsson syndrome: Linkage to chromosome 17p in families of different non-Swedish ethnic origins

    SciTech Connect

    Rogers, G.R.; Lee, M.; Compton, J.G.

    1995-11-01

    Sjoegren-Larsson syndrome (SLS) is a rare, autosomal recessive disorder that is characterized by congenital ichthyosis, mental retardation, and spastic diplegia or tetraplegia. Three United States families, three Egyptian families, and one Israeli Arab family were investigated for linkage of the SLS gene to a region of chromosome 17. Pairwise and multipoint linkage analysis with nine markers mapped the SLS gene to the same region of the genome as that reported in Swedish SLS pedigrees. Examination of recombinants by haplotype analysis showed that the gene lies in the region containing the markers D17S953, D17S805, D17S689, and D17S842. D17S805 is pericentromeric on 17p. Patients in two consanguineous Egyptian families were homozygous at the nine marker loci tested, and another patient from a third family was homozygous for eight of the nine, suggesting that within each of these families the region of chromosome 17 carrying the SLS gene is identical by descent. Linkage of the SLS gene to chromosome 17p in families of Arabic, mixed European, Native American, and Swedish descent provides evidence for a single SLS locus and should prove useful for diagnosis and carrier detection in worldwide cases. 25 refs., 4 figs., 1 tab.

  12. Autosomal dominant zonular cataract with sutural opacities localized to chromosome 17q11-12

    SciTech Connect

    Padma, T.; Ayyagari, R.; Murty, J.S.

    1995-10-01

    Congenital cataracts constitute a morphologically and genetically heterogeneous group of diseases that are a major cause of childhood blindness. Different loci for hereditary congenital cataracts have been mapped to chromosomes 1, 2, 16, and 17q24. We report linkage of a gene causing a unique form of autosomal dominant zonular cataracts with Y-sutural opacities to chromosome 17q11-12 in a three-generation family exhibiting a maximum lod score of 3.9 at D17S805. Multipoint analysis gave a Mod confidence interval of 17 cM. This interval is bounded by the markers D17S799 and D17S798, a region that would encompass a number of candidate genes including that coding for {Beta}A3/A1-crystallin. 30 refs., 2 figs., 1 tab.

  13. Molecular analysis of two patients with a duplicated 17p11.2 indicates that this entity may be the reciprocal of the deletion seen in Smith-Magenis syndrome

    SciTech Connect

    Brown, A.; Schwartz, C.; Rogers, R.C.

    1994-09-01

    J.M. and H.G. are two unrelated patients that presented at an early age with developmental delay and failure to thrive. Clinical features specific to J.M. include unusual facies, global developmental delay, and clinodactyly of the fifth toe. A cytogenetic analysis of H.G. was performed on amniocytes obtained due to a low MSAFP conducted as part of a routine screening. In both J.M. and H.G., a duplication of chromosome 17p11.2 was discovered. The extent of the duplicated region was determined using single copy DNA probes: cen-D17S58-D17S29-D17S258-D17S71-D17S445-tel. All of the markers were found to be duplicated by dosage analysis except for D17S58. FISH analysis of H.G., using the Smith-Magenis diagnostic probe obtained from ONCOR, also detected a duplication in 17p11.2. The chromosome containing the duplication could be the result of unequal crossing over due to a misalignment of the two chromosomes during meiosis I. It has been shown that the markers deleted in Smith-Magenis syndrome (SMS) patients are the same as those markers duplicated in J.M. and H.G. Therefore, the chromosomal duplication in 17p11.2 observed in these two patients could be the reciprocal of the chromosomal deletion seen in Smith-Magenis syndrome patients. Interestingly, a similar reciprocal duplication/deletion event is observed for CMT1A and HNPP (hereditary neuropathy with liability to pressure palsies) just distal to the SMS region.

  14. Allelic loss on distal chromosome 17p is associated with poor prognosis in a group of Brazilian breast cancer patients.

    PubMed Central

    Nagai, M. A.; Pacheco, M. M.; Brentani, M. M.; Marques, L. A.; Brentani, R. R.; Ponder, B. A.; Mulligan, L. M.

    1994-01-01

    We examined loss of heterozygosity (LOH) for two loci on chromosome 17p (D17S5 and TP53), and erbB-2 gene amplification, in primary breast cancers from 67 Brazilian patients. We identified two distinct regions of LOH on chromosome 17p, one spanning TP53 and the other a more telomeric region (D17S5). Based on a short-term follow-up, Kaplan-Meier analyses of patients' disease-free survival showed that patients with LOH for D17S5, but retaining heterozygosity for TP53, were at higher risk of recurrence (P = 0.007) than those who retained heterozygosity for D17S5. Bivariate analyses indicated that patients with LOH for D17S5 alone had an increased risk of recurrence (hazard ratio = 7.2) over patients with erbB-2 amplification (hazard ratio = 3.7), when compared with patients with neither alteration (hazard ratio = 1.0). Further, lymph node-positive patients whose tumours had both LOH for D17S5 and erbB-2 gene amplification had a higher risk of recurrence than patients whose tumours had neither of these genetic alterations. Our data confirm previous reports of a putative tumour-suppressor gene, distinct from TP53, on distal chromosome 17p which is associated with breast cancer. They further suggest that LOH for loci in this region may provide an independent indicator to identify patients with poor prognosis. Images Figure 1 Figure 3 PMID:7908218

  15. Hereditary neuropathy with liability to pressure palsies (HNPP) patients of Korean ancestry with chromosome 17p11.2-p12 deletion.

    PubMed

    Kim, Seung Min; Chung, Ki Wha; Choi, Byung Ok; Yoon, Eui Soo; Choi, Jung Young; Park, Kee Duk; Sunwoo, Il Nam

    2004-02-29

    Hereditary neuropathy with liability to pressure palsies (HNPP) is an autosomal dominant inherited disorder characterized by recurrent pressure palsies. Most HNPP patients have a 1.5 mb deletion in chromosome 17p11.2-p12. The present study aimed at evaluating the deletion of the 17p11.2-p12 region in Korean subjects with families exhibiting HNPP phenotype, and to determine the clinical, electrophysiological and morphological aspects specifically associated with this deletion in HNPP patients. By genotyping six microsatellite markers (D17S921, D17S955, D17S1358, D17S839, D17S122 and D17S261), HNPP with the deletion was observed in 79% (19 of 24) of HNPP families. Nerve conduction studies were performed in 35 HNPP patients from these 19 families. The observed HNPP deletion frequency in Koreans is consistent with findings in other populations. Disease onset occurred at a significantly earlier age in patients with recurrent pressure palsies than in those with a single attack (P < 0.01). Nerve conduction studies demonstrated diffuse mild to moderate slowing of nerve conduction velocities that were worse over the common entrapment sites, regardless of the clinical manifestations. A long duration of compound muscle action potentials without a conduction block or a temporal dispersion is a characteristic of this disease. A sural nerve biopsy with teasing was performed in four patients, and tomacula of the myelin sheath was found in 56.4%. Our findings appear to support the existence of a phenotype/genotype correlation in HNPP patients of Korean ancestry with the deletion, and suggest that HNPP patients with earlier symptom onset face an increased chance of having recurrent attacks.

  16. Solitary solutions for a class of Schrödinger equations in R^3

    NASA Astrophysics Data System (ADS)

    Wang, Youjun

    2016-08-01

    In this paper, we consider a model problem arising from a classical planar Heisenberg ferromagnetic spin chain -Δ u + (λ + ɛ') u ∓ Δ √{1-u2}u/√{1- u2} - ɛ'u/√{1 - u2} = 0, x in R3, where {λ} and {ɛ'}are real constants. By variational methods and perturbation arguments, we study the existence of positive classical solutions. Our results generalize the previous results in one-dimensional space given by Brüll et al. [4].

  17. All Prime Contract Awards by State or Country, Place, and Contractor, FY83, Part 5 (LaGrange, Indiana-Escanaba, Michigan).

    DTIC Science & Technology

    1983-01-01

    N00024-80- 02146 B C A 1 2 2 1900 000 A3 FRIGATES AND CORVETTES 8 A 7 5 A 1001 5 B U 2 K 26 2 L BS786 1199 N00024-80-G2146 B C A 1 2 2 1900 000 A3 FRIGATES...CORVETTES 8 A 7 5 A 1001 5 B U 2 A 27 2 5 BS786 3537 N00024-80- 02146 B C A 1 2 2 1900 000 A3 FRIGATES AND CORVETTES 8 A 4 5 A 1001 5 B U 2 A 210 2 B BS786

  18. Aero-Hydroacoustics for Ships. Volume 2

    DTIC Science & Technology

    1984-06-01

    OVER CURVED SURFACES ................ . 785 . 7.5.1 Transition to Turbulence . . . . .............. 785 ś.5.2 Adverse and Favorable Static Pressure...quantifiable class of 624 , • .- • % %𔃿. boundary layers that includes those subjected to a particular type of streanwise static pressure gradient... static pressure in the direction normal to the surface(U2’<U U2 112) 1 , 3 2) 3 (u 1 u24UJ 1U2) - 2 -i - This relationship shows that if the boundary

  19. Simulation of High-Speed Cavity Flows in a Scramjet Engine by the Space-Time CESE Method

    DTIC Science & Technology

    2005-09-01

    considered here share a common flow velocity u. Let the total specific energy def U 2 E = e+- (2.33) 2 11 Letd),, i = 1,2,..., N, be the net mass of...x and the y directions, respectively; p is the static pressure; e = E + ½ (u2 + v2) is the specific total energy with E as the specific internal...p.u. 2, and the total energy by p.uCOc2 . The subscript 0o denotes the free stream condition. The cavity depth d is used as the length scale, and the

  20. Thermal properties of nonstoichiometry uranium dioxide

    NASA Astrophysics Data System (ADS)

    Kavazauri, R.; Pokrovskiy, S. A.; Baranov, V. G.; Tenishev, A. V.

    2016-04-01

    In this paper, was developed a method of oxidation pure uranium dioxide to a predetermined deviation from the stoichiometry. Oxidation was carried out using the thermogravimetric method on NETZSCH STA 409 CD with a solid electrolyte galvanic cell for controlling the oxygen potential of the environment. 4 samples uranium oxide were obtained with a different ratio of oxygen-to-metal: O / U = 2.002, O / U = 2.005, O / U = 2.015, O / U = 2.033. For the obtained samples were determined basic thermal characteristics of the heat capacity, thermal diffusivity, thermal conductivity. The error of heat capacity determination is equal to 5%. Thermal diffusivity and thermal conductivity of the samples decreased with increasing deviation from stoichiometry. For the sample with O / M = 2.033, difference of both values with those of stoichiometric uranium dioxide is close to 50%.

  1. Task 1: Correlation of satellite and ground data in air pollution studies. Task 2: Investigation to relate the chlorophyll and suspended sediment content in the waters of the lower Chesapeake Bay to ERTS-1 imagery. Task 3: The use of ERTS-1 to more fully utilize and apply marine station data to the study of productivity along the Eastern Shelf expanded waters of the United States

    NASA Technical Reports Server (NTRS)

    Copeland, G. E. (Principal Investigator); Bandy, A. R.; Fleischer, P.; Ludwick, J. C. (Principal Investigator); Hanna, W. J.; Gosink, T. A.; Bowker, D. W.; Marshall, H. G. (Principal Investigator)

    1972-01-01

    The author has identified the following significant results. Analysis of U-2 imagery of CARETS site indicates smoke plumes can be easily detected. First look at selected ERTS-1 color composites demonstrates plumes from forest fires can be detected.

  2. Indentifying environmental features for land management decisions. [Uinta Basin, Davis County foothills, and Farmington Bay in Utah

    NASA Technical Reports Server (NTRS)

    1980-01-01

    The wetlands and water-related land use in the Uinta Basin were classified and mapped using photointerpretation of U-2 infrared photography and digital LANDSAT data. The digital maps were used to augment photointerpretations. A highly effective diagnostic tool emerged when the LANDSAT digital print was photoreduced to a film positive at the same scale as the U-2 film and overlain on the U-2 color film. As a result of this merging technique, cover types can be identified more accurately and probablistic statements can be made about the relative amounts of water being consumed in one pasture vs. another. The hazards to urban development on sensitive and unstable land in the foothills of Davis County were studied using NASA U-2 photography. Shoreline fluctuations were mapped in the Farmington Bay using LANDSAT digital data.

  3. Initial oxidation behaviors of nitride surfaces of uranium by XPS analysis

    NASA Astrophysics Data System (ADS)

    Liu, Kezhao; Luo, Lizu; Luo, Lili; Long, Zhong; Hong, Zhanglian; Yang, Hui; Wu, Sheng

    2013-09-01

    The nitride surfaces of uranium were prepared by the surface glow plasma nitriding (SGPN) and plasma immersion ion implantation (PIII) methods. The initial oxidation behaviors of modified surfaces were studied by X-ray photoelectron spectroscopy (XPS). The SGPN on the uranium surface led to a single layer of uranium sesquinitride (U2N3), while the PIII on the surface resulted in a compound layer composed of U2N3 and uranium dioxide (UO2). The oxygen covered on these modified layers led to the formation of UO2 from U2N3 and U2N3 from UN. The oxidized nitrogen species were also observed on the two types of nitriding layers, with the discussion of the N-O coaction behaviors.

  4. A Weeks-Long Hiatus During the Quilotoa 800 BP VEI 6 Eruption

    NASA Astrophysics Data System (ADS)

    Ort, M. H.; Cashman, K. V.; Best, J. A.; Mothes, P. A.; Bustillos, J.; di Muro, A.; Rosi, M.; Ruscitto, D. M.; Hall, M. L.

    2009-12-01

    How eruptions start and stop is a fundamental question in volcanology. We address this by examining an unusual eruptive sequence produced by Quilotoa Volcano, Ecuador, about 800 BP. The eruption covered central Ecuador with dacitic fallout and, more proximally, pyroclastic density current deposits that can be divided into four distinct depositional units (U1-4), each consisting of distinct sub-units. U1 (~5.3 km3 DRE) and U3 (~1 km3 DRE) are similar, consisting of fallout and surge beds that grade upward into pyroclastic flow deposits. U2 (~0.05 km3 DRE), the focus of this study, consists of two sub-units, each made up of many individual beds. The lower sub-unit, U2A, is a series of pumiceous surge deposits found only within 3-4 km of the crater rim. U2B is a vitric-poor, crystal- and lithic-rich fallout distributed to about 15 km from the crater. U4 is a phreatomagmatic ash emplaced during the waning stages of the eruption. An ash volume roughly equivalent to the U1-4 deposits was deposited as distal fallout. The small crater volume (<2 km3) is about an order of magnitude less than the erupted volume and implies that caldera collapse did not occur. The entire 800 BP sequence sits atop a black soil that overlies a series of seven similar pyroclastic deposits. A U2-like deposit occurs in the 14.8 ka tephra sequence that immediately underlies the 800 BP deposits and may indicate that the cause is systemic. A time break between U1 and U2 indicates a hiatus in the paroxysmal eruption. A fine ash, interpreted to represent atmosphere clearing after U1, lies at the top of U1, and very minor sheet-flood deposits overlie U1 beneath U2. The top of U1, as well as secondary pyroclastic flow deposits above U1, are oxidized but the overlying U2 is not. Deposits from local phreatic explosions in the U1 ignimbrite are interbedded with U2. These field observations constrain the hiatus length to days to weeks. U2 appears to represent a vent-clearing sequence at the end of this

  5. Conduit Magma Storage during the 800 BP Quilotoa Eruption, Ecuador

    NASA Astrophysics Data System (ADS)

    Ort, M. H.; Cashman, K. V.; Di Muro, A.; Best, J. A.; Rosi, M.; Mothes, P. A.; Bustillos, J.

    2013-12-01

    The 800 BP eruption of Quilotoa produced two large ignimbrites, U1 (~5.8 km3 DRE) and U3 (~1.8 km3 DRE). These eruptions were separated by a series of much smaller eruptions over one to several weeks, as inferred from 1) the intercalation of secondary pyroclastic and debris flow deposits between U1 and U3, 2) deposits from phreatic explosions from the U1 ignimbrite surface, 3) oxidation of the upper 2 m of U1, and 4) a lack of erosion of the U1 surface. Why did the main phase of the eruption (U1) stall when eruptable magma was available? How did explosive activity stop and restart? We address these questions by examining deposits (U2) emplaced during the 'hiatus' that provide information on the conditions in the conduit and vent area between explosive episodes. The lowest sub-unit, U2a, forms a series of pumiceous surge deposits found only within 5 km of the crater rim. U2b is a vitric-poor, crystal- and lithic-rich fall deposit distributed to about 15 km from the crater. U2c is a thin gray fine ash containing 2-5-mm-diameter rhyolite lapilli that is present within 6 km of the vent. Similar lapilli also occur in the lowermost few centimeters of U3 and appear to be from a dome that exploded as the new magma arrived at the surface; their presence as small ballistic fragments ties U2c to lowermost U3 in time. U2a appears to have been emplaced by episodic surges and weak fallout plumes, whereas U2b and U2c were deposited from a series of sustained eruption columns. Moreover, the lack of U2b grain-size variation with distance suggests that the grain size was determined at the vent, not by transport. FTIR analysis of CO2 and H2O in melt inclusions (MIs) indicates that a deep magma chamber (>400 MPa; ~12 km) fed U1. U2a and U2b MIs plot along vapor isopleths, suggesting equilibration at pressures to about 300 MPa as CO2 outgassed. U2b MIs have lower CO2 than U2a, perhaps indicating continued degassing during the 'hiatus'. MIs from the lower few centimeters of U3 lie along

  6. Games with Non-Probabilistic Uncertainty

    DTIC Science & Technology

    2010-05-13

    continue similar analysis for π = (O,P ) and π = (P,O). For any θi, one can easily show that the following inequalities hold: U1, OP > U1,PP > U1,PO...U1,OO for all θ2 ∈ Θ2, and U2,PO > U2,PP > U2, OP > U2,OO for all θ1 ∈ Θ1. Thus, in this positive externality game, the ex-post utilities when both...OO) ≥ u1(PO) and (ii) u1( OP ) ≥ u1(PP ) for every θ2 ∈ [α2, β2]. By algebra, u1(OO)− u1(PO) ≥ ∆2[θ1 − θ1]/12, which is non-negative for all θ1 ≤ θ1

  7. Non-canonical Cajal bodies form in the nucleus of late stage avian oocytes lacking functional nucleolus.

    PubMed

    Khodyuchenko, Tatiana; Gaginskaya, Elena; Krasikova, Alla

    2012-07-01

    In the somatic cell nucleus, there are several universal domains such as nucleolus, SC35-domains, Cajal bodies (CBs) and histone locus bodies (HLBs). Among them, CBs were described more than 100 years ago; however, we still do not have a final understanding of their nature and biological significance. The giant nucleus of avian and amphibian growing oocytes represents an advantageous model for analysis of functions and biogenesis of various nuclear domains. Nevertheless, in large-sized avian oocytes that contain transcriptionally active lampbrush chromosomes, CB-like organelles have not been identified yet. Here we demonstrate that in the pigeon (Columba livia) oocyte nucleus, characterized by absence of any functional nucleoli, extrachromosomal spherical bodies contain TMG-capped spliceosomal snRNAs, core proteins of Sm snRNPs and the protein coilin typical for CBs, but not splicing factor SC35 nor the histone pre-mRNA 3'-end processing factor symplekin. The results establish that coilin-rich nuclear organelles in pigeon late-stage oocyte are not the equivalents of HLBs but belong to a group of CBs. At the same time, they do not contain the snoRNP/scaRNP protein fibrillarin involved in 2'-O-methylation of snoRNAs and snRNAs. Thus, the nucleus of late-stage pigeon oocytes houses CB-like organelles that have an unusual molecular composition and are implicated in the snRNP biogenesis pathway. These data demonstrate that snRNP-rich non-canonical CBs can form in the absence of nucleolus. We argue that pigeon oocytes represent a new promising model to investigate CB modular organization, functions and formation mechanism.

  8. Eubacterial components similar to small nuclear ribonucleoproteins: identification of immunoprecipitable proteins and capped RNAs in a cyanobacterium and a gram-positive eubacterium.

    PubMed Central

    Kovacs, S A; O'Neil, J; Watcharapijarn, J; Moe-Kirvan, C; Vijay, S; Silva, V

    1993-01-01

    Small nuclear ribonucleoprotein (snRNP) particles play an important role in the processing of pre-mRNA. snRNPs have been identified immunologically in a variety of cells, but none have ever been observed in prokaryotic systems. This report provides the first evidence for the presence of snRNP-like components in two types of prokaryotic cells: those of the cyanobacterium Synechococcus leopoliensis and those of the gram-positive eubacterium Bacillus subtilis. These components consist of snRNP-immunoreactive proteins and RNAs, including some with the snRNP-unique 5' m2,2,7G (m3G) cap. Immunoreactivity was determined by immunoprecipitation procedures, with either antinuclear-antibody-positive (RNP- and Sm-monospecific) patient sera or a m3G monoclonal antibody, with radiolabelled cell extracts that were preadsorbed with antinuclear-antibody-negative sera. S. leopoliensis immunoprecipitates showed the presence of high-molecular-mass proteins (14 to 70 kDa) and RNAs (138 to 243 nucleotides) that are analogous in size to proteins and RNAs found in human (HEp-2) cell immunoprecipitates but absent in Escherichia coli immunoprecipitates. Thin-layer chromatography of S. leopoliensis immunoprecipitates confirmed the presence of a capped nucleotide similar to a capped nucleotide in HEp-2 immunoprecipitates; no such nucleotide was observed in E. coli immunoprecipitates. Immunoreactive RNAs (117-170 nucleotides) were identified in a second eubacterium, B. subtilis, as well. This work suggests that snRNPs or their evolutionary predecessors predate the emergence of eukaryotic cells. Images PMID:8458830

  9. Human p80-coilin is targeted to sphere organelles in the amphibian germinal vesicle.

    PubMed Central

    Wu, Z; Murphy, C; Gall, J G

    1994-01-01

    Cultured vertebrate cells often display one or more coiled bodies in their nuclei. These are spherical structures approximately 0.5-1.0 micron in diameter that contain high concentrations of small nuclear ribonucleoproteins (snRNPs); they are distinct from nuclear speckles and nucleoli, the other major sites of snRNP concentration. Coiled bodies in human cells contain a unique protein, p80-coilin, that has an M(r) = 80 kDa. Cloned p80-coilin cDNA encodes 576 amino acids with a calculated molecular weight of 62.6 kDa. To determine which of several snRNP-containing structures in the amphibian germinal vesicle (GV) might be the homologue of coiled bodies, we injected myc-tagged transcripts of full-length human p80-coilin into the cytoplasm of Xenopus oocytes and followed the fate of the translated proteins with an antibody specific for the tag. Western blots of GV proteins showed rapid appearance of both full-length and truncated p80-coilin in the nucleus. Immunofluorescent staining of spread GV contents demonstrated specific uptake of p80-coilin by the sphere organelle within 1 h after injection. Similar experiments were performed with a series of deletion constructs that lacked progressively longer segments from the carboxy terminus. A construct that contained only the first 102 amino acids (18% of the molecule) was specifically targeted to the sphere organelle. Conversely, a construct lacking the first 92 amino acids failed to localize, although it was imported into the GV. Thus, a relatively short region at the amino terminus of human p80-coilin is both necessary and sufficient for localization in the sphere organelle. Sphere organelles in the GV and coiled bodies in somatic nuclei are clearly related in composition. We suggest that they are homologous organelles with similar functions in preassembly and sorting of RNA processing components. Differences in their composition suggest functional specialization in the two cell types. Images PMID:7532471

  10. Dynamics of Galectin-3 in the Nucleus and Cytoplasm

    PubMed Central

    Haudek, Kevin C.; Spronk, Kimberly J.; Voss, Patricia G.; Patterson, Ronald J.; Wang, John L.; Arnoys, Eric J.

    2009-01-01

    This review summarizes selected studies on galectin-3 (Gal3) as an example of the dynamic behavior of a carbohydrate-binding protein in the cytoplasm and nucleus of cells. Within the 15-member galectin family of proteins, Gal3 (Mr ~30,000) is the sole representative of the chimera subclass in which a proline- and glycine-rich NH2-terminal domain is fused onto a COOH-terminal carbohydrate recognition domain responsible for binding galactose-containing glycoconjugates. The protein shuttles between the cytoplasm and nucleus on the basis of targeting signals that are recognized by importin(s) for nuclear localization and exportin-1 (CRM1) for nuclear export. Depending on the cell type, specific experimental conditions in vitro, or tissue location, Gal3 has been reported to be exclusively cytoplasmic, predominantly nuclear, or distributed between the two compartments. The nuclear versus cytoplasmic distribution of the protein must reflect, then, some balance between nuclear import and export, as well as mechanisms of cytoplasmic anchorage or binding to a nuclear component. Indeed, a number of ligands have been reported for Gal3 in the cytoplasm and in the nucleus. Most of the ligands appear to bind Gal3, however, through protein-protein interactions rather than through protein-carbohydrate recognition. In the cytoplasm, for example, Gal3 interacts with the apoptosis repressor Bcl-2 and this interaction may be involved in Gal3’s anti-apoptotic activity. In the nucleus, Gal3 is a required pre-mRNA splicing factor; the protein is incorporated into spliceosomes via its association with the U1 small nuclear ribonucleoprotein (snRNP) complex. Although the majority of these interactions occur via the carbohydrate recognition domain of Gal3 and saccharide ligands such as lactose can perturb some of these interactions, the significance of the protein’s carbohydrate-binding activity, per se, remains a challenge for future investigations. PMID:19616076

  11. 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

  12. 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.

  13. PRP4K is a HER2-regulated modifier of taxane sensitivity

    PubMed Central

    Corkery, Dale P; Le Page, Cécile; Meunier, Liliane; Provencher, Diane; Mes-Masson, Anne-Marie; Dellaire, Graham

    2015-01-01

    The taxanes are used alone or in combination with anthracyclines or platinum drugs to treat breast and ovarian cancer, respectively. Taxanes target microtubules in cancer cells and modifiers of taxane sensitivity have been identified in vitro, including drug efflux and mitotic checkpoint proteins. Human epidermal growth factor receptor 2 (HER2/ERBB2) gene amplification is associated with benefit from taxane therapy in breast cancer yet high HER2 expression also correlates with poor survival in both breast and ovarian cancer. The pre-mRNA splicing factor 4 kinase PRP4K (PRPF4B), which we identified as a component of the U5 snRNP also plays a role in regulating the spindle assembly checkpoint (SAC) in response to microtubule-targeting drugs. In this study, we found a positive correlation between PRP4K expression and HER2 status in breast and ovarian cancer patient tumors, which we determined was a direct result of PRP4K regulation by HER2 signaling. Knock-down of PRP4K expression reduced the sensitivity of breast and ovarian cancer cell lines to taxanes, and low PRP4K levels correlated with in vitro-derived and patient acquired taxane resistance in breast and ovarian cancer. Patients with high-grade serous ovarian cancer and high HER2 levels had poor overall survival; however, better survival in the low HER2 patient subgroup treated with platinum/taxane-based therapy correlated positively with PRP4K expression (HR = 0.37 [95% CI 0.15-0.88]; p = 0.03). Thus, PRP4K functions as a HER2-regulated modifier of taxane sensitivity that may have prognostic value as a marker of better overall survival in taxane-treated ovarian cancer patients. PMID:25602630

  14. 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.

  15. Fas-activated serine/threonine kinase (FAST K) synergizes with TIA-1/TIAR proteins to regulate Fas alternative splicing.

    PubMed

    Izquierdo, José M; Valcárcel, Juan

    2007-01-19

    The factors and mechanisms that mediate the effects of intracellular signaling cascades on alternative pre-mRNA splicing are poorly understood. TIA-1 (T-cell intracellular antigen 1) and TIAR (TIA-1-related) proteins regulate alternative pre-mRNA splicing by promoting the use of suboptimal 5' splice sites followed by uridine-rich intronic enhancer sequences. These proteins promote, for example, inclusion of Fas receptor exon 6, which leads to an mRNA encoding a pro-apoptotic form of the receptor at the expense of the form that skips exon 6, which encodes an anti-apoptotic form. Fas-activated serine/threonine kinase (FAST K) is known to interact with and phosphorylate TIA-1. Here we have tested the possibility that FAST K influences alternative pre-mRNA splicing by affecting the activity of TIA-1/TIAR. Depletion of FAST K form Jurkat cells leads to skipping of exon 6 from endogenous Fas transcripts. Conversely, FAST K overexpression enhances exon 6 inclusion of Fas reporters transfected in HeLa cells. Consistent with the possibility that the effects of FAST K are mediated by changes in the function of TIA-1/TIAR, the effects of FAST K overexpression (i) are largely suppressed by depletion of TIA-1 and TIAR and (ii) are significantly compromised by mutation of a TIA-1/TIAR-responsive enhancer present downstream of exon 6 5' splice site. Furthermore, in vitro phosphorylation of TIA-1 by FAST K results in enhanced U1 snRNP recruitment. Interestingly, this enhancement is not due to increased binding of TIA-1 to the pre-mRNA. Taken together, the results connect Fas signaling with the activity of splicing factors that modulate Fas alternative splicing, suggesting the existence of an autoregulatory loop that could serve to amplify Fas responses.

  16. 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.

  17. 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.

  18. Modulation of deregulated chaperone-mediated autophagy by a phosphopeptide

    PubMed Central

    Macri, Christophe; Wang, Fengjuan; Tasset, Inmaculada; Schall, Nicolas; Page, Nicolas; Briand, Jean-Paul; Cuervo, Ana Maria; Muller, Sylviane

    2015-01-01

    The P140 peptide, a 21-mer linear peptide (sequence 131–151) generated from the spliceosomal SNRNP70/U1–70K protein, contains a phosphoserine residue at position 140. It significantly ameliorates clinical manifestations in autoimmune patients with systemic lupus erythematosus and enhances survival in MRL/lpr lupus-prone mice. Previous studies showed that after P140 treatment, there is an accumulation of autophagy markers sequestosome 1/p62 and MAP1LC3-II in MRL/lpr B cells, consistent with a downregulation of autophagic flux. We now identify chaperone-mediated autophagy (CMA) as a target of P140 and demonstrate that its inhibitory effect on CMA is likely tied to its ability to alter the composition of HSPA8/HSC70 heterocomplexes. As in the case of HSPA8, expression of the limiting CMA component LAMP2A, which is increased in MRL/lpr B cells, is downregulated after P140 treatment. We also show that P140, but not the unphosphorylated peptide, uses the clathrin-dependent endo-lysosomal pathway to enter into MRL/lpr B lymphocytes and accumulates in the lysosomal lumen where it may directly hamper lysosomal HSPA8 chaperoning functions, and also destabilize LAMP2A in lysosomes as a result of its effect on HSP90AA1. This dual effect may interfere with the endogenous autoantigen processing and loading to major histocompatibility complex class II molecules and as a consequence, lead to lower activation of autoreactive T cells. These results shed light on mechanisms by which P140 can modulate lupus disease and exert its tolerogenic activity in patients. The unique selective inhibitory effect of the P140 peptide on CMA may be harnessed in other pathological conditions in which reduction of CMA activity would be desired. PMID:25719862

  19. Effect of p40tax trans-activator of human T cell lymphotropic virus type I on expression of autoantigens.

    PubMed

    Banki, K; Ablonczy, E; Nakamura, M; Perl, A

    1994-03-01

    The possibility of a retroviral etiology has long been raised in a number of autoimmune disorders. More recently, Sjögren's syndrome and rheumatoid arthritis were noted in transgenic mice carrying the tax gene of human T cell leukemia virus type I (HTLV-I). To evaluate the involvement of HTLV-I Tax in autoimmunity, its effect on expression of autoantigens was investigated. A metallothionein promoter-driven p40tax expression plasmid, pMAXRHneo-1, was stably transfected into Molt4 and Jurkat cells and the p40tax protein was induced with CdCl2. trans-Activation or trans-repression of autoantigens by HTLV-I Tax was studied by Western blot analysis utilizing autoantigen-specific murine monoclonal and rabbit polyvalent antibodies as well as sera from 161 autoimmune patients. Induction of p40tax of HTLV-I had no significant effect on levels of expression of common autoantigens U1 snRNP, Sm, Ro, La, HSP-70, topoisomerase I/Scl70, PCNA, and HRES-1. Expression of two potentially novel autoantigens, 44 and 46 kDa, was induced by p40tax as detected by sera of progressive systemic sclerosis patients, BAK and VAR. By contrast, expression of 24- and 34-kDa proteins was suppressed in response to induction of p40tax as detected by sera of systemic lupus erythematosus patients PUS and HOR. Because none of these patients were infected by HTLV-I, a protein functionally similar to p40tax may be involved in eliciting autoantigen expression and a subsequent autoantibody response in a minority of patients with PSS and SLE. Sera of autoimmune patients may also be utilized to detect novel proteins trans-activated or trans-repressed by p40tax of HTLV-I.

  20. Mixed connective tissue disease.

    PubMed

    Gunnarsson, Ragnar; Hetlevik, Siri Opsahl; Lilleby, Vibke; Molberg, Øyvind

    2016-02-01

    The concept of mixed connective tissue disease (MCTD) as a separate connective tissue disease (CTD) has persisted for more than four decades. High titers of antibodies targeting the U1 small nuclear ribonucleoprotein particle (U1 snRNP) in peripheral blood are a sine qua non for the diagnosis of MCTD, in addition to distinct clinical features including Raynaud's phenomenon (RP), "puffy hands," arthritis, myositis, pleuritis, pericarditis, interstitial lung disease (ILD), and pulmonary hypertension (PH). Recently, population-based epidemiology data from Norway estimated the point prevalence of adult-onset MCTD to be 3.8 per 100,000 and the mean annual incidence to be 2.1 per million per year, supporting the notion that MCTD is the least common CTD. Little is known about the etiology of MCTD, but recent genetic studies have confirmed that MCTD is a strongly HLA (​human leukocyte antigen)-linked disease, as the HLA profiles of MCTD differ distinctly from the corresponding profiles of ethnically matched healthy controls and other CTDs. In the first section of this review, we provide an update on the clinical, immunological, and genetic features of MCTD and discuss the relationship between MCTD and the other CTDs. Then we proceed to discuss the recent advances in therapy and our current understanding of prognosis and prognostic factors, especially those that are associated with the more serious pulmonary and cardiovascular complications of the disease. In the final section, we discuss some of the key, unresolved questions related to anti-RNP-associated diseases and indicate how these questions may be approached in future studies.

  1. The prevalent deep intronic c. 639+919 G>A GLA mutation causes pseudoexon activation and Fabry disease by abolishing the binding of hnRNPA1 and hnRNP A2/B1 to a splicing silencer.

    PubMed

    Palhais, Bruno; Dembic, Maja; Sabaratnam, Rugivan; Nielsen, Kira S; Doktor, Thomas Koed; Bruun, Gitte Hoffmann; Andresen, Brage Storstein

    2016-11-01

    Fabry disease is an X-linked recessive inborn disorder of the glycosphingolipid metabolism, caused by total or partial deficiency of the lysosomal α-galactosidase A enzyme due to mutations in the GLA gene. The prevalent c.639+919 G>A mutation in GLA leads to pathogenic insertion of a 57bp pseudoexon sequence from intron 4, which is responsible for the cardiac variant phenotype. In this study we investigate the splicing regulatory mechanism leading to GLA pseudoexon activation. Splicing analysis of GLA minigenes revealed that pseudoexon activation is influenced by cell-type. We demonstrate that the wild-type sequence harbors an hnRNP A1 and hnRNP A2/B1-binding exonic splicing silencer (ESS) overlapping the 5'splice site (5'ss) that prevents pseudoexon inclusion. The c.639+919 G>A mutation disrupts this ESS allowing U1 snRNP recognition of the 5'ss. We show that the wild-type GLA 5'ss motif with the ESS is also able to inhibit inclusion of an unrelated pseudoexon in the FGB gene, and that also in the FGB context inactivation of the ESS by the c.639+919 G>A mutation causes pseudoexon activation, underscoring the universal nature of the ESS. Finally, we demonstrate that splice switching oligonucleotide (SSO) mediated blocking of the pseudoexon 3'ss and 5'ss effectively restores normal GLA splicing. This indicates that SSO based splicing correction may be a therapeutic alternative in the treatment of Fabry disease.

  2. Crystal structure, mutational analysis and RNA-dependent ATPase activity of the yeast DEAD-box pre-mRNA splicing factor Prp28

    SciTech Connect

    Jacewicz, Agata; Schwer, Beate; Smith, Paul; Shuman, Stewart

    2014-10-10

    Yeast Prp28 is a DEAD-box pre-mRNA splicing factor implicated in displacing U1 snRNP from the 5' splice site. Here we report that the 588-aa Prp28 protein consists of a trypsin-sensitive 126-aa N-terminal segment (of which aa 1–89 are dispensable for Prp28 function in vivo) fused to a trypsin-resistant C-terminal catalytic domain. Purified recombinant Prp28 and Prp28-(127–588) have an intrinsic RNA-dependent ATPase activity, albeit with a low turnover number. The crystal structure of Prp28-(127–588) comprises two RecA-like domains splayed widely apart. AMPPNP•Mg2+ is engaged by the proximal domain, with proper and specific contacts from Phe194 and Gln201 (Q motif) to the adenine nucleobase. The triphosphate moiety of AMPPNP•Mg2+ is not poised for catalysis in the open domain conformation. Guided by the Prp28•AMPPNP structure, and that of the Drosophila Vasa•AMPPNP•Mg2+•RNA complex, we targeted 20 positions in Prp28 for alanine scanning. ATP-site components Asp341 and Glu342 (motif II) and Arg527 and Arg530 (motif VI) and RNA-site constituent Arg476 (motif Va) are essential for Prp28 activity in vivo. Synthetic lethality of double-alanine mutations highlighted functionally redundant contacts in the ATP-binding (Phe194-Gln201, Gln201-Asp502) and RNA-binding (Arg264-Arg320) sites. As a result, overexpression of defective ATP-site mutants, but not defective RNA-site mutants, elicited severe dominant-negative growth defects.

  3. DDX6 transfers P-TEFb kinase to the AF4/AF4N (AFF1) super elongation complex

    PubMed Central

    Mück, Fabian; Bracharz, Silvia; Marschalek, Rolf

    2016-01-01

    AF4/AFF1 and AF5/AFF4 are both backbones for the assembly of “super elongation complexes” (SECs) that exert 2 distinct functions after the recruitment of P-TEFb from the 7SK snRNP: (1) initiation and elongation of RNA polymerase II gene transcription, and (2) modification of transcribed gene regions by distinct histone methylation patterns. In this study we aimed to investigate one of the initial steps, namely how P-TEFb is transferred from 7SK snRNPs to the SECs. In particular, we were interested in the role of DDX6 that we have recently identified as part of the AF4 complex. DDX6 is an evolutionarily conserved member of the DEAD-box RNA helicase family that is known to control miRNA and mRNA biology (translation, storage and degradation). Overexpressed DDX6 is associated with different cancer types and with c-Myc protein overexpression. We could demonstrate that DDX6 binds to 7SK snRNA and causes the release and transfer of P-TEFb to the AF4/AF4N SEC. DDX6 also binds stably to AF4 and AF4N as demonstrated by GST pull-down and co-immunoprecipitation experiments. As a consequence, overexpression of either AF4/AF4N or DDX6 resulted in a strong increase of mRNA production (5-6 fold), while their simultaneous expression increased the cellular mRNA production by 11-fold. Conversely, the corresponding knockdown of DDX6 decreased mRNA production by 70%. In conclusion, AF4/AF4N and DDX6 represent key molecules for the elongation process of gene transcription and a model will be proposed for the hand-over process of P-TEFb to SECs. PMID:27679741

  4. PPS, a large multidomain protein, functions with sex-lethal to regulate alternative splicing in Drosophila.

    PubMed

    Johnson, Matthew L; Nagengast, Alexis A; Salz, Helen K

    2010-03-05

    Alternative splicing controls the expression of many genes, including the Drosophila sex determination gene Sex-lethal (Sxl). Sxl expression is controlled via a negative regulatory mechanism where inclusion of the translation-terminating male exon is blocked in females. Previous studies have shown that the mechanism leading to exon skipping is autoregulatory and requires the SXL protein to antagonize exon inclusion by interacting with core spliceosomal proteins, including the U1 snRNP protein Sans-fille (SNF). In studies begun by screening for proteins that interact with SNF, we identified PPS, a previously uncharacterized protein, as a novel component of the machinery required for Sxl male exon skipping. PPS encodes a large protein with four signature motifs, PHD, BRK, TFS2M, and SPOC, typically found in proteins involved in transcription. We demonstrate that PPS has a direct role in Sxl male exon skipping by showing first that loss of function mutations have phenotypes indicative of Sxl misregulation and second that the PPS protein forms a complex with SXL and the unspliced Sxl RNA. In addition, we mapped the recruitment of PPS, SXL, and SNF along the Sxl gene using chromatin immunoprecipitation (ChIP), which revealed that, like many other splicing factors, these proteins bind their RNA targets while in close proximity to the DNA. Interestingly, while SNF and SXL are specifically recruited to their predicted binding sites, PPS has a distinct pattern of accumulation along the Sxl gene, associating with a region that includes, but is not limited to, the SxlPm promoter. Together, these data indicate that PPS is different from other splicing factors involved in male-exon skipping and suggest, for the first time, a functional link between transcription and SXL-mediated alternative splicing. Loss of zygotic PPS function, however, is lethal to both sexes, indicating that its role may be of broad significance.

  5. 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.

  6. 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.

  7. Crystal structure, mutational analysis and RNA-dependent ATPase activity of the yeast DEAD-box pre-mRNA splicing factor Prp28

    DOE PAGES

    Jacewicz, Agata; Schwer, Beate; Smith, Paul; ...

    2014-10-10

    Yeast Prp28 is a DEAD-box pre-mRNA splicing factor implicated in displacing U1 snRNP from the 5' splice site. Here we report that the 588-aa Prp28 protein consists of a trypsin-sensitive 126-aa N-terminal segment (of which aa 1–89 are dispensable for Prp28 function in vivo) fused to a trypsin-resistant C-terminal catalytic domain. Purified recombinant Prp28 and Prp28-(127–588) have an intrinsic RNA-dependent ATPase activity, albeit with a low turnover number. The crystal structure of Prp28-(127–588) comprises two RecA-like domains splayed widely apart. AMPPNP•Mg2+ is engaged by the proximal domain, with proper and specific contacts from Phe194 and Gln201 (Q motif) to themore » adenine nucleobase. The triphosphate moiety of AMPPNP•Mg2+ is not poised for catalysis in the open domain conformation. Guided by the Prp28•AMPPNP structure, and that of the Drosophila Vasa•AMPPNP•Mg2+•RNA complex, we targeted 20 positions in Prp28 for alanine scanning. ATP-site components Asp341 and Glu342 (motif II) and Arg527 and Arg530 (motif VI) and RNA-site constituent Arg476 (motif Va) are essential for Prp28 activity in vivo. Synthetic lethality of double-alanine mutations highlighted functionally redundant contacts in the ATP-binding (Phe194-Gln201, Gln201-Asp502) and RNA-binding (Arg264-Arg320) sites. As a result, overexpression of defective ATP-site mutants, but not defective RNA-site mutants, elicited severe dominant-negative growth defects.« less

  8. The Gemin Associates of Survival Motor Neuron Are Required for Motor Function in Drosophila

    PubMed Central

    Borg, Rebecca; Cauchi, Ruben J.

    2013-01-01

    Membership of the survival motor neuron (SMN) complex extends to nine factors, including the SMN protein, the product of the spinal muscular atrophy (SMA) disease gene, Gemins 2–8 and Unrip. The best-characterised function of this macromolecular machine is the assembly of the Sm-class of uridine-rich small nuclear ribonucleoprotein (snRNP) particles and each SMN complex member has a key role during this process. So far, however, only little is known about the function of the individual Gemin components in vivo. Here, we make use of the Drosophila model organism to uncover loss-of-function phenotypes of Gemin2, Gemin3 and Gemin5, which together with SMN form the minimalistic fly SMN complex. We show that ectopic overexpression of the dead helicase Gem3ΔN mutant or knockdown of Gemin3 result in similar motor phenotypes, when restricted to muscle, and in combination cause lethality, hence suggesting that Gem3ΔN overexpression mimics a loss-of-function. Based on the localisation pattern of Gem3ΔN, we predict that the nucleus is the primary site of the antimorphic or dominant-negative mechanism of Gem3ΔN-mediated interference. Interestingly, phenotypes induced by human SMN overexpression in Drosophila exhibit similarities to those induced by overexpression of Gem3ΔN. Through enhanced knockdown we also uncover a requirement of Gemin2, Gemin3 and Gemin5 for viability and motor behaviour, including locomotion as well as flight, in muscle. Notably, in the case of Gemin3 and Gemin5, such function also depends on adequate levels of the respective protein in neurons. Overall, these findings lead us to speculate that absence of any one member is sufficient to arrest the SMN-Gemins complex function in a nucleocentric pathway, which is critical for motor function in vivo. PMID:24391840

  9. 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.

  10. A comprehensive survey of non-canonical splice sites in the human transcriptome

    PubMed Central

    Parada, Guillermo E.; Munita, Roberto; Cerda, Cledi A.; Gysling, Katia

    2014-01-01

    We uncovered the diversity of non-canonical splice sites at the human transcriptome using deep transcriptome profiling. We mapped a total of 3.7 billion human RNA-seq reads and developed a set of stringent filters to avoid false non-canonical splice site detections. We identified 184 splice sites with non-canonical dinucleotides and U2/U12-like consensus sequences. We selected 10 of the herein identified U2/U12-like non-canonical splice site events and successfully validated 9 of them via reverse transcriptase-polymerase chain reaction and Sanger sequencing. Analyses of the 184 U2/U12-like non-canonical splice sites indicate that 51% of them are not annotated in GENCODE. In addition, 28% of them are conserved in mouse and 76% are involved in alternative splicing events, some of them with tissue-specific alternative splicing patterns. Interestingly, our analysis identified some U2/U12-like non-canonical splice sites that are converted into canonical splice sites by RNA A-to-I editing. Moreover, the U2/U12-like non-canonical splice sites have a differential distribution of splicing regulatory sequences, which may contribute to their recognition and regulation. Our analysis provides a high-confidence group of U2/U12-like non-canonical splice sites, which exhibit distinctive features among the total human splice sites. PMID:25123659

  11. Solvation of Na2+ in Arn clusters. I. Structures and spectroscopic properties

    NASA Astrophysics Data System (ADS)

    Douady, J.; Jacquet, E.; Giglio, E.; Zanuttini, D.; Gervais, B.

    2008-11-01

    We present a theoretical study of Na2+ solvation in an argon matrix Arn for n =1 to a few tens. We use a model based on an explicit description of valence electron interaction with Na+ and Ar cores by means of core polarization pseudopotential. The electronic structure determination is thus reduced to a one-electron problem, which can be handled efficiently. We investigate the ground state geometry and related optical absorption of Na2+Arn clusters. For n ⩽5, the lowest energy isomers are obtained by aggregation of Ar atoms at one single extremity of Na2+, leading to moderate perturbation of the optical transition. For 6⩽n⩽15, the Ar atoms aggregate at both extremities. This structural change is associated with a strong blueshift of the first optical transition (XΣg+2→AΣu+2), which reveals the confinement of the excited AΣu +2 state. The Na2+ energy spectrum is so strongly perturbed that the AΣu +2 state becomes higher than the BΠu +2 states. The closure of the first solvation shell is observed at n =17. Above this size, the second solvation shell develops. Its structure is dominated by a pentagonal organization around the Na2+ molecular axis. The optical transitions vary smoothly with n and the AΣu +2 and BΠu2 states are no longer inverted, though the first optical transition remains strongly blueshifted.

  12. Consistency and consensus models for group decision-making with uncertain 2-tuple linguistic preference relations

    NASA Astrophysics Data System (ADS)

    Zhang, Zhen; Guo, Chonghui

    2016-08-01

    Due to the uncertainty of the decision environment and the lack of knowledge, decision-makers may use uncertain linguistic preference relations to express their preferences over alternatives and criteria. For group decision-making problems with preference relations, it is important to consider the individual consistency and the group consensus before aggregating the preference information. In this paper, consistency and consensus models for group decision-making with uncertain 2-tuple linguistic preference relations (U2TLPRs) are investigated. First of all, a formula which can construct a consistent U2TLPR from the original preference relation is presented. Based on the consistent preference relation, the individual consistency index for a U2TLPR is defined. An iterative algorithm is then developed to improve the individual consistency of a U2TLPR. To help decision-makers reach consensus in group decision-making under uncertain linguistic environment, the individual consensus and group consensus indices for group decision-making with U2TLPRs are defined. Based on the two indices, an algorithm for consensus reaching in group decision-making with U2TLPRs is also developed. Finally, two examples are provided to illustrate the effectiveness of the proposed algorithms.

  13. Determination of locally perfect discrimination for two-qubit unitary operations

    NASA Astrophysics Data System (ADS)

    Cao, Tian-Qing; Gao, Fei; Yang, Ying-Hui; Zhang, Zhi-Chao; Wen, Qiao-Yan

    2016-01-01

    In the study of local discrimination for multipartite unitary operations, Duan et al. (Phys Rev Lett 100(2):020503, 2008) exhibited an ingenious expression: Any two different unitary operations U_1 and U_2 are perfectly distinguishable by local operations and classical communication in the single-run scenario if and only if 0 is in the local numerical range of U_1^dag U_2. However, how to determine when 0 is in the local numerical range remains unclear. So it is generally hard to decide the local discrimination of nonlocal unitary operations with a single run. In this paper, for two-qubit diagonal unitary matrices V and their local unitary equivalent matrices, we present a necessary and sufficient condition for determining whether the local numerical range is a convex set or not. The result can be used to easily judge the locally perfect distinguishability of any two unitary operations U_1 and U_2 satisfying U_1^dag U_2=V. Moreover, we design the corresponding protocol of local discrimination. Meanwhile, an interesting phenomenon is discovered: Under certain conditions with a single run, U_1 and U_2 such that U_1^dag U_2=V are locally distinguishable with certainty if and only if they are perfectly distinguishable by global operations.

  14. Proceedings of the Quantum Computation for Physical Modeling Workshop Held in North Falmouth, Massachusetts on October 18-19, 2000

    DTIC Science & Technology

    2002-01-01

    particu- tum parallelism due to the superposition and entangle- lar case) at the large-scale called the continuum limit. Beginning in the mid 1990’s...L. Onsager , Phys. Rev. 65 (1944) 117. E-- 0 AIUE (0, - 00))100) A0 Ift) [17] S. Bravyi, A. Kitaev, quant-ph/0003137, unpublished. if the state whose

  15. Brain and Surface Warping via Minimizing Lipschitz Extensions (PREPRINT)

    DTIC Science & Technology

    2006-01-01

    Angenent, S. Haker , A. Tannenbaum, and R. Kikinis, “Conformal geometry and brain flattening,” Proc. MICCAI, pp. 271-278, 1999. 1 [2] G. Aronsson, M...surface mapping,” IEEE Transactions on Medical Imaging, 23:7, 2004. 1 [17] S. Haker , L. Zhu, A. Tannenbaum, and S. An- genent, “Optimal mass transport for

  16. Birt-Hogg-Dubé Syndrome, a Genodermatosis Associated with Spontaneous Pneumothorax and Kidney Neoplasia, Maps to Chromosome 17p11.2

    PubMed Central

    Schmidt, Laura S.; Warren, Michelle B.; Nickerson, Michael L.; Weirich, Gregor; Matrosova, Vera; Toro, Jorge R.; Turner, Maria L.; Duray, Paul; Merino, Maria; Hewitt, Stephen; Pavlovich, Christian P.; Glenn, Gladys; Greenberg, Cheryl R.; Linehan, W. Marston; Zbar, Berton

    2001-01-01

    Birt-Hogg-Dubé syndrome (BHD), an inherited autosomal genodermatosis characterized by benign tumors of the hair follicle, has been associated with renal neoplasia, lung cysts, and spontaneous pneumothorax. To identify the BHD locus, we recruited families with cutaneous lesions and associated phenotypic features of the BHD syndrome. We performed a genomewide scan in one large kindred with BHD and, by linkage analysis, localized the gene locus to the pericentromeric region of chromosome 17p, with a LOD score of 4.98 at D17S740 (recombination fraction 0). Two-point linkage analysis of eight additional families with BHD produced a maximum LOD score of 16.06 at D17S2196. Haplotype analysis identified critical recombinants and defined the minimal region of nonrecombination as being within a <4-cM distance between D17S1857 and D17S805. One additional family, which had histologically proved fibrofolliculomas, did not show evidence of linkage to chromosome 17p, suggesting genetic heterogeneity for BHD. The BHD locus lies within chromosomal band 17p11.2, a genomic region that, because of the presence of low-copy-number repeat elements, is unstable and that is associated with a number of diseases. Identification of the gene for BHD may reveal a new genetic locus responsible for renal neoplasia and for lung and hair-follicle developmental defects. PMID:11533913

  17. MASTER-OAFA, MASTER-SAAO discovery: bright OTs

    NASA Astrophysics Data System (ADS)

    Pogrosheva, T.; Shumkov, V.; Popova, E.; Lipunov, V.; Podesta, R.; Levato, H.; Buckley, D.; Lopez, C.; Podesta, F.; Saffe, C.; Potter, S.; Gorbovskoy, E.; Balanutsa, P.; Tiurina, N.; Kuznetsov, A.; Kornilov, V.; Vladimirov, V.; Gress, O.; Chazov, V.; Ivanov, K.

    2016-11-01

    MASTER-OAFA (located in Argentina) auto-detection system ( Lipunov et al., "MASTER Global Robotic Net", Advances in Astronomy, 2010, 30L ) discovered OT source at (RA, Dec) = 20h 26m 36.17s -44d 07m 22.7s on 2016-11-29.04023 UT. The OT unfiltered magnitude is (mlim=18.6m).

  18. Vision-Based Autonomous Sensor-Tasking in Uncertain Adversarial Environments

    DTIC Science & Technology

    2015-01-02

    registration technique with an applica- tion to stereo vision. Proceedings of Imaging Understanding Workshop, pages 121–130, 1981. [17] S. P. Meyn, A...forecast activities, and analyze complex scenes with multiple interacting entities. Specific applications include autonomous aerial surveillance...Specific applications include autonomous aerial surveillance systems that cover broad areas of military operations, camera security sys- tems that cover

  19. Viral infection correlated with superoxide anion radicals production and natural and synthetic copper complexes.

    PubMed

    Tomas, E; Popescu, A; Titire, A; Cajal, N; Cristescu, C; Tomas, S

    1989-01-01

    Studies conducted on asymmetric triazine derivatives synthetized at the Chemical and Pharmaceutical Research Institute showed that products S1, S16, S17, S19, S20 and S22 have a remarkable O2- radical scavenger activity. Among these derivatives, the product S1 is the most efficient as an antiviral agent.

  20. 27 CFR 9.24 - Chalone.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... appropriate maps for determining the boundaries of the Chalone viticultural area are four U.S.G.S. 7.5 minute..., in their entirety, the western half of Section 5, and the eastern half of Section 18 of T.17 S.,...

  1. Fellowship Behavior in Division 17 and the MOMM Cartel.

    ERIC Educational Resources Information Center

    Horan, John J.; Erickson, Chris D.

    1991-01-01

    Notes that, although the Council of Counseling Psychology Training Programs lists 64 members, graduates and employees of 4 institutions (Minnesota, Ohio State, Maryland, and Missouri) heavily dominate every science and practice organ of the American Psychological Association Division 17's governing body. Cites examples of barriers to professional…

  2. VPE Growth of InP for Electronic Devices.

    DTIC Science & Technology

    1982-05-01

    Varma, "Chemical effects in Schottky barrier formation," Journal of Physics C : Solid State Physics I (1978), L735-L738. ( 12. D.V. Morgan and J...electrodes", Journal of Physics C : Solid State Physics 10, (1977), 4545-4557. 17. S. Von Rump, G. Homsey, M. Reese, and J. Bornholdt, "System for the

  3. Role of Fibronectin in Wound Healing.

    DTIC Science & Technology

    1986-09-12

    Detrick, Frederiek, Nmryland 21701-5012 Contract f. DAl-17-S3-C-3235 Mdloal Colle" of Georgia Augusta, GA 30912 Approved for public distribution...about 30 sec, and replaced In the abdominal cavity. The mucle layer was sutured with 4.0 silk, and the skin was closed with wound clips. Blood samples

  4. Dissipation and transformation of 17B-estradiol-17-sulfate in soil-water systems

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Estrogen conjugates are known to be precursors of endocrine-disrupting free estrogens, e.g. 17B-estradiol (E2) and estrone (E1), in the environment. This study investigated the fate of a sulfate conjugated estrogen, 17B-estradiol-17-sulfate (E2-17S), in agricultural soils using laboratory batch stu...

  5. A Review of Selected Elements of the FY73 Programs on Test and Evaluation of Aircraft Survivability (TEAS). Volume 2. Appendix A: bibliography for Vulnerability and Survivability of Military Aircraft,

    DTIC Science & Technology

    1973-07-31

    17 S 1967 NASC-CREW SYSTEMS ’IV. Battle Damage und Casualty Information for Navy Air Operations In Southeast Aula 386,374L S 196...Fxpirlmental Aircraft Passive Ot f eiise Artnur System 891957L U 1970 AFATI. IK-70-112, BOOK I, II 891958L Bui 11. tic Impact Mechanics

  6. 78 FR 51206 - Filing of Plats of Survey: Oregon/Washington

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-20

    ... date of this publication. Willamette Meridian Oregon T. 10 S., R. 11 E., accepted July 22, 2013 T. 19 S., R. 2 W., accepted July 22, 2013 T. 17 S., R. 7 W., accepted July 26, 2013 T. 41 S., R. 44 E.../Washington. BILLING CODE 4310-33-P...

  7. Strong correlation of major earthquakes with solid-earth tides in part of the eastern United States

    USGS Publications Warehouse

    Weems, R.E.; Perry, W.H.

    1989-01-01

    East of the eastern American continental divide and south of lat. 42.5??N, moderate to large historic earthquakes correlate strongly with times of high and low solid-earth tides. This effect is most pronounced when solar declination lies between 17??N and 17??S. Significant correlation also exist between major earthquakes, time of day, lunar declinations, and lunar phase. -Authors

  8. Localization of genes for autosomal dominant congenital cataracts to chromosomes 2 and 17

    SciTech Connect

    Ayyagari, R.; Scott, M.; Wozencraft, L.

    1994-09-01

    Linkage analysis was performed in a seven generation family in which 28 of 52 individuals examined had autosomal dominant congenital pulverulent cataracts and a five generation family in which 10 of 17 individuals examined had autosomal dominant congenital zonular cataracts with sutural opacities. Initial analysis with 21 microsatellite markers in 7 candidate gene regions localized the pulverulent cataract locus to the long arm of chromosome 2 near the {beta}B2-crystallin gene. A lod score of 3.6 was obtained with D2S72 ({theta}=0.12), 3.5 with CRYG ({theta}=0.06), 3.4 with ({theta}=0.05), 2.0 with D2S117 ({theta}=0.22) and 6.6 with D2S128 ({theta}=0.05). Multipoint linkage analysis gave Zmax=4.2 at D2S157 with a one lod confidence interval covering 19 cM. The closest flanking markers showing obligate recombinants are D2S157 and D2S173. The zonular cataract locus was mapped to chromosome 2 near the {gamma}-crystallin gene cluster. A maximum lod score of 3.8 was obtained with D17S805 ({theta}=0.0), 2.1 with D17S798 ({theta}=0.60), and 3.7 with NF1 ({theta}=0.0). Multipoint analysis showed Zmax=3.81 at D17S805 with a one lod confidence interval covering 17 cM based on the Genethon map, localizing cataracts between markers D17S799 and D17S800. Further efforts are being directed at refining the localization of these cataract loci and examining the nearby crystallin genes for possible mutations.

  9. Molecular analysis of the Smith-Magenis syndrome: a possible contiguous-gene syndrome associated with del(17)(p11.2).

    PubMed Central

    Greenberg, F; Guzzetta, V; Montes de Oca-Luna, R; Magenis, R E; Smith, A C; Richter, S F; Kondo, I; Dobyns, W B; Patel, P I; Lupski, J R

    1991-01-01

    We undertook clinical evaluation (32 cases) and molecular evaluation (31 cases) of unrelated patients affected with Smith-Magenis syndrome (SMS) associated with an interstitial deletion of band p11.2 of chromosome 17. Patients were evaluated both clinically and electrophysiologically for peripheral neuropathy, since markers showing close linkage to one form of Charcot-Marie-Tooth disease (CMT1A) map to this chromosomal region. The common clinical findings were broad flat midface with brachycephaly, broad nasal bridge, brachydactyly, speech delay, and hoarse, deep voice. Fifty-five percent of the patients showed clinical signs (e.g., decreased or absent deep tendon reflexes, pes planus or pes cavus, decreased sensitivity to pain, and decreased leg muscle mass) suggestive of peripheral neuropathy. However, unlike patients with CMT1A, these patients demonstrated normal nerve conduction velocities. Self-destructive behaviors, primarily onychotillomania and polyembolokoilamania, were observed in 67% of the patients, and significant symptoms of sleep disturbance were observed in 62%. The absence of REM sleep was demonstrated by polysomnography in two patients. Southern analysis indicated that most patients were deleted for five 17p11.2 markers--FG1 (D17S446), 1516 (D17S258), pYNM67-R5 (D17S29), pA10-41 (D17S71), and pS6.1-HB2 (D17S445)--thus defining a region which appears to be critical to SMS. The deletion was determined to be of paternal origin in nine patients and of maternal origin in six patients. The apparent random parental origin of deletion documented in 15 patients suggests that genomic imprinting does not play a role in the expression of the SMS clinical phenotype. Our findings suggest that SMS is likely a contiguous-gene deletion syndrome which comprises characteristic clinical features, developmental delay, clinical signs of peripheral neuropathy, abnormal sleep function, and specific behavioral anomalies. Images Figure 2 Figure 3 PMID:1746552

  10. Comparative Phosphoproteomics Reveals the Role of AmpC β-lactamase Phosphorylation in the Clinical Imipenem-resistant Strain Acinetobacter baumannii SK17*

    PubMed Central

    Lai, Juo-Hsin; Yang, Jhih-Tian; Chern, Jeffy; Chen, Te-Li; Wu, Wan-Ling; Liao, Jiahn-Haur; Tsai, Shih-Feng; Liang, Suh-Yuen; Chou, Chi-Chi

    2016-01-01

    Nosocomial infectious outbreaks caused by multidrug-resistant Acinetobacter baumannii have emerged as a serious threat to human health. Phosphoproteomics of pathogenic bacteria has been used to identify the mechanisms of bacterial virulence and antimicrobial resistance. In this study, we used a shotgun strategy combined with high-accuracy mass spectrometry to analyze the phosphoproteomics of the imipenem-susceptible strain SK17-S and -resistant strain SK17-R. We identified 410 phosphosites on 248 unique phosphoproteins in SK17-S and 285 phosphosites on 211 unique phosphoproteins in SK17-R. The distributions of the Ser/Thr/Tyr/Asp/His phosphosites in SK17-S and SK17-R were 47.0%/27.6%/12.4%/8.0%/4.9% versus 41.4%/29.5%/17.5%/6.7%/4.9%, respectively. The Ser-90 phosphosite, located on the catalytic motif S88VS90K of the AmpC β-lactamase, was first identified in SK17-S. Based on site-directed mutagenesis, the nonphosphorylatable mutant S90A was found to be more resistant to imipenem, whereas the phosphorylation-simulated mutant S90D was sensitive to imipenem. Additionally, the S90A mutant protein exhibited higher β-lactamase activity and conferred greater bacterial protection against imipenem in SK17-S compared with the wild-type. In sum, our results revealed that in A. baumannii, Ser-90 phosphorylation of AmpC negatively regulates both β-lactamase activity and the ability to counteract the antibiotic effects of imipenem. These findings highlight the impact of phosphorylation-mediated regulation in antibiotic-resistant bacteria on future drug design and new therapies. PMID:26499836

  11. DIFFERENT REQUIREMENTS OF THE KINASE AND UHM DOMAINS OF KIS FOR ITS NUCLEAR LOCALIZATION AND BINDING TO SPLICING FACTORS

    PubMed Central

    Manceau, Valérie; Kielkopf, Clara L.; Sobel, André; Maucuer, Alexandre

    2008-01-01

    Summary The protein kinase KIS is made by the juxtaposition of a unique kinase domain and a C-terminal domain with a U2AF Homology Motif (UHM), a sequence motif for protein interaction initially identified in the heterodimeric pre-mRNA splicing factor U2AF. This domain of KIS is closely related to the C-terminal UHM domain of the U2AF large subunit, U2AF65. KIS phosphorylates the splicing factor SF1, which in turn enhances SF1 binding to U2AF65 and the 3′ splice site, an event known to take place at an early step of spliceosome assembly. Here, the analysis of the subcellular localization of mutated forms of KIS indicates that the kinase domain of KIS is the necessary domain for its nuclear localization. As in the case of U2AF65, the UHM containing C-terminal domain of KIS is required for binding to the splicing factors SF1 and SF3b155. The efficiency of KIS binding to SF1 and SF3b155 is similar to that of U2AF65 in pull-down assays. These results further support the functional link of KIS with splicing factors. Interestingly, when compared to other UHM containing proteins, KIS presents a different specificity for the UHM docking sites that are present in the N-terminal region of SF3b155, thus providing a new insight into the variety of interactions mediated by UHM domains. PMID:18588901

  12. Evidence of coexistence of change of caged dynamics at T(g) and the dynamic transition at T(d) in solvated proteins.

    PubMed

    Capaccioli, S; Ngai, K L; Ancherbak, S; Paciaroni, A

    2012-02-16

    Mössbauer spectroscopy and neutron scattering measurements on proteins embedded in solvents including water and aqueous mixtures have emphasized the observation of the distinctive temperature dependence of the atomic mean square displacements, <u(2)>, commonly referred to as the dynamic transition at some temperature T(d). At low temperatures, <u(2)> increases slowly, but it assumes stronger temperature dependence after crossing T(d), which depends on the time/frequency resolution of the spectrometer. Various authors have made connection of the dynamics of solvated proteins, including the dynamic transition to that of glass-forming substances. Notwithstanding, no connection is made to the similar change of temperature dependence of <u(2)> obtained by quasielastic neutron scattering when crossing the glass transition temperature T(g), generally observed in inorganic, organic, and polymeric glass-formers. Evidences are presented here to show that such a change of the temperature dependence of <u(2)> from neutron scattering at T(g) is present in hydrated or solvated proteins, as well as in the solvent used, unsurprisingly since the latter is just another organic glass-former. If unaware of the existence of such a crossover of <u(2)> at T(g), and if present, it can be mistaken as the dynamic transition at T(d) with the ill consequences of underestimating T(d) by the lower value T(g) and confusing the identification of the origin of the dynamic transition. The <u(2)> obtained by neutron scattering at not so low temperatures has contributions from the dissipation of molecules while caged by the anharmonic intermolecular potential at times before dissolution of cages by the onset of the Johari-Goldstein β-relaxation or of the merged α-β relaxation. The universal change of <u(2)> at T(g) of glass-formers, independent of the spectrometer resolution, had been rationalized by sensitivity to change in volume and entropy of the dissipation of the caged molecules and its

  13. Ethnic differentiation at VNTR loci, with special reference to forensic applications

    SciTech Connect

    Devlin, B.; Risch, N. )

    1992-09-01

    Allele-rich VNTR loci provide valuable information for forensic inference. Interpretation of this information is complicated by measurement error, which renders discrete alleles difficult to distinguish. Two methods have been used to circumvent this difficulty-i.e, binning methods and direct evaluation of allele frequencies, the latter achieved by modeling the data as a mixture distribution. The authors use this modeling approach to estimate the allele frequency distributions for two loci-D17S79 and D2S44-for black, Caucasian, and Hispanic samples from the Lifecodes and FBI data bases. The databases are differentiated by the restriction enzyme used: PstI (Lifecodes) and HaeIII (FBI). The results show that alleles common in one ethnic group are almost always common in all ethnic groups, and likewise for rare alleles; this pattern holds for both loci. Gene diversity, or heterozygosity, measured as one minus the sum of the squared allele frequencies, is greater for D2S44 than for D17S79, in both data bases. The average gene diversity across ethnic groups when PstI (HaeIII) is used is .918 (.918) for D17S79 and is .985 (.983) for D2S44. The variance in gene diversity among ethnic groups is greater for D17S79 than for D2S44. The number of alleles, like the gene diversity, is greater for D2S44 than for D17S79. The mean numbers of alleles across ethnic groups, estimated from the PstI (HaeIII) data, are 40.25 (41.5) for D 17S79 and 104 (103) for D2S44. The number of alleles is correlated with sample size. The authors use the estimated allele frequency distributions for each ethnic group to explore the effects of unwittingly mixing populations and thereby violating independence assumptions. They show that, even in extreme cases of mixture, the estimated genotype probabilities are good estimates of the true probabilities, contradicting recent claims. 35 refs., 9 figs., 3 tabs.

  14. Using the fluorescence red edge effect to assess the long-term stability of lyophilized protein formulations.

    PubMed

    Qian, Ken K; Grobelny, Pawel J; Tyagi, Madhusudan; Cicerone, Marcus T

    2015-04-06

    Nanosecond relaxation processes in sugar matrices are causally linked through diffusional processes to protein stability in lyophilized formulations. Long-term protein degradation rates track mean-squared displacement (⟨u(2)⟩) of hydrogen atoms in sugar glasses, a parameter describing dynamics on a time scale of picoseconds to nanoseconds. However, measurements of ⟨u(2)⟩ are usually performed by neutron scattering, which is not conducive to rapid formulation screening in early development. Here, we present a benchtop technique to derive a ⟨u(2)⟩ surrogate based on the fluorescence red edge effect. Glycerol, lyophilized trehalose, and lyophilized sucrose were used as model systems. Samples containing 10(-6) mole fraction of rhodamine 6G, a fluorophore, were excited at either 532 nm (main peak) or 566 nm (red edge), and the ⟨u(2)⟩ surrogate was determined based the corresponding Stokes shifts. Results showed reasonable agreement between ⟨u(2)⟩ from neutron scattering and the surrogate from fluorescence, although deviations were observed at very low temperatures. We discuss the sources of the deviations and suggest technique improvements to ameliorate these. We expect that this method will be a valuable tool to evaluate lyophilized sugar matrices with respect to their ability to protect proteins from diffusion-limited degradation processes during long-term storage. Additionally, the method may have broader applications in amorphous pharmaceutical solids.

  15. Adaptive method for quantifying uncertainty in discharge measurements using velocity-area method.

    NASA Astrophysics Data System (ADS)

    Despax, Aurélien; Favre, Anne-Catherine; Belleville, Arnaud

    2015-04-01

    Streamflow information provided by hydrometric services such as EDF-DTG allow real time monitoring of rivers, streamflow forecasting, paramount hydrological studies and engineering design. In open channels, the traditional approach to measure flow uses a rating curve, which is an indirect method to estimate the discharge in rivers based on water level and punctual discharge measurements. A large proportion of these discharge measurements are performed using the velocity-area method; it consists in integrating flow velocities and depths through the cross-section [1]. The velocity field is estimated by choosing a number m of verticals, distributed across the river, where vertical velocity profile is sampled by a current-meter at ni different depths. Uncertainties coming from several sources are related to the measurement process. To date, the framework for assessing uncertainty in velocity-area discharge measurements is the method presented in the ISO 748 standard [2] which follows the GUM [3] approach. The equation for the combined uncertainty in measured discharge u(Q), at 68% level of confidence, proposed by the ISO 748 standard is expressed as: Σ 2 2 2 -q2i[u2(Bi)+-u2(Di)+-u2p(Vi)+-(1ni) ×-[u2c(Vi)+-u2exp(Vi)

  16. Mott lobes evolution of the spin-1 Bose-Hubbard model

    NASA Astrophysics Data System (ADS)

    Hincapie-F, A. F.; Franco, R.; Silva-Valencia, J.

    2016-02-01

    We study spin-1 bosons confined in a one-dimensional optical lattice, taking into consideration both ferromagnetic and antiferromagnetic interaction. Using the density matrix renormalization group, we determine the phase diagram for the two firsts lobes and report the evolution of the first and second Mott lobes with respect to the spin-exchange interaction parameter (U 2). We determine that for the antiferromagnetic case, the first lobe is suppressed while the second grows as |U 2| increases. For the ferromagnetic case, the first and second Mott lobes are suppressed by the spin-exchange interaction parameter. We propose an expresion to describe the evolution of the critical point with the increase in |U 2| for both cases.

  17. The Domain Geometry and the Bubbling Phenomenon of Rank Two Gauge Theory

    NASA Astrophysics Data System (ADS)

    Huang, Hsin-Yuan; Zhang, Lei

    2017-01-01

    Let {Ω} be a flat torus and {G} be the Green's function of {-Δ} on {Ω}. One intriguing mystery of {G} is how the number of its critical points is related to blowup solutions of certain PDEs. In this article we prove that for the following equation that describes a Chern-Simons model in Gauge theory: Δ u_1+1/ɛ^2e^{u_2}(1-e^{u_1})=8πδ_{p1} Δ u_2+1/ɛ^2e^{u_1}(1-e^{u_2})=8πδ_{p2} in quad Ω., quad p_1-p_2 {{ is a half period}}, if fully bubbling solutions of Liouville type exist, {G} has exactly three critical points. In addition we establish necessary conditions for the existence of fully bubbling solutions with multiple bubbles.

  18. Condensation nuclei measurement in the stratosphere for the NASA ACE program

    NASA Technical Reports Server (NTRS)

    Wilson, James Charles

    1994-01-01

    A condensation nucleus counter which operated at stratospheric pressures was developed, designed, and constructed. It was calibrated in the laboratory. Its response as a function of particle size and concentration was reported. This was the first time that the response of such an instrument was verified in the laboratory. An inlet was constructed which provided near isokinetic sampling. The resulting instrument, the U-2 CNC, was deployed on NASA U-2 aircraft in the study of the climatic effects of aerosol. These studies occurred in March, April, May, July, November, and December of 1992 and in April, May, June, and December of 1983. The U-2 CNC was used in the study of the aerosol cloud resulting from the eruption of El Chichon. It permitted the observation of new particle formation in the stratosphere.

  19. Dynamical generation of a nontrivial index on the fuzzy 2-sphere

    NASA Astrophysics Data System (ADS)

    Aoki, Hajime; Iso, Satoshi; Maeda, Toshiharu; Nagao, Keiichi

    2005-02-01

    In the previous paper [H. Aoki, S. Iso, and K. Nagao, Nucl. Phys. B 684, 162 (2004)] we studied the ’t Hooft-Polyakov (TP) monopole configuration in the U(2) gauge theory on the fuzzy 2-sphere and showed that it has a nonzero topological charge in the formalism based on the Ginsparg-Wilson relation. In this paper, by showing that the TP monopole configuration is stabler than the U(2) gauge theory without any condensation in the Yang-Mills-Chern-Simons matrix model, we will present a mechanism for dynamical generation of a nontrivial index. We further analyze the instability and decay processes of the U(2) gauge theory and the TP monopole configuration.

  20. New mixing angles in the left-right symmetric model

    NASA Astrophysics Data System (ADS)

    Kokado, Akira; Saito, Takesi

    2015-12-01

    In the left-right symmetric model neutral gauge fields are characterized by three mixing angles θ12,θ23,θ13 between three gauge fields Bμ,WLμ 3,WRμ 3, which produce mass eigenstates Aμ,Zμ,Zμ', when G =S U (2 )L×S U (2 )R×U (1 )B-L×D is spontaneously broken down until U (1 )em . We find a new mixing angle θ', which corresponds to the Weinberg angle θW in the standard model with the S U (2 )L×U (1 )Y gauge symmetry, from these mixing angles. It is then shown that any mixing angle θi j can be expressed by ɛ and θ', where ɛ =gL/gR is a ratio of running left-right gauge coupling strengths. We observe that light gauge bosons are described by θ' only, whereas heavy gauge bosons are described by two parameters ɛ and θ'.

  1. Evidence of genetic heterogeneity of Leber's congenital amaurosis (LCA) and mapping of LCA1 to chromosome 17p13.

    PubMed

    Camuzat, A; Rozet, J M; Dollfus, H; Gerber, S; Perrault, I; Weissenbach, J; Munnich, A; Kaplan, J

    1996-06-01

    Leber's congenital amaurosis (LCA) is an autosomal recessive disease responsible for congenital blindness. It is the earliest and most severe inherited retinal dystrophy in human and its genetic heterogeneity has long been recognised. We have recently reported on the first localisation of a disease gene (LCA1) to the short arm of chromosome 17 by homozygosity mapping in five families of North African origin. Here, we refine the genetic mapping of LCA1 to chromosome 17p13 between loci D17S938 and D17S1353 and provide strong support for the genetic heterogeneity of this condition (maximum likelihood for heterogeneity, 17.20 in InL; heterogeneity versus homogeneity, P = 0.0002, heterogeneity versus no linkage, P < 0.0001)

  2. On the chemistry of the young massive protostellar core NGC 2264 CMM3

    NASA Astrophysics Data System (ADS)

    Awad, Zainab; Shalabeia, Osama M.

    2017-04-01

    We present the first gas-grain astrochemical model of the NGC 2264 CMM3 protostellar core. The chemical evolution of the core is affected by changing its physical parameters such as the total density and the amount of gas-depletion onto grain surfaces as well as the cosmic ray ionisation rate, ζ. We estimated ζ_{{CMM3}} = 1.6 × 10^{-17} s^{-1}. This value is 1.3 times higher than the standard CR ionisation rate, ζ _{{ISM}} = 1.3 × 10^{-17} s^{-1}. Species response differently to changes into the core physical conditions, but they are more sensitive to changes in the depletion percentage and CR ionisation rate than to variations in the core density. Gas-phase models highlighted the importance of surface reactions as factories of large molecules and showed that for sulphur bearing species depletion is important to reproduce observations.

  3. Localization of disinhibition-dementia-parkinsonism-amyotrophy complex to 17q21-22.

    PubMed Central

    Wilhelmsen, K. C.; Lynch, T.; Pavlou, E.; Higgins, M.; Nygaard, T. G.

    1994-01-01

    Disinhibition-dementia-parkinsonism-amyotrophy complex (DDPAC) is defined by familial adult-onset behavioral disturbance, followed by frontal lobe dementia, parkinsonism, and amyotrophy in variable proportions. A genetic etiology of DDPAC was suspected because of the familial clustering in family Mo, despite their wide geographic distribution. We have mapped the DDPAC locus to a 12-cM (sex averaged) region between D17S800 and D17S787 on chromosome 17q21-22. The basis for the variability of the clinical findings and pathology in DDPAC is unknown but suggests that the DDPAC locus should be screened as a candidate locus in family studies of conditions with behavioral abnormalities and neurological degeneration. PMID:7977375

  4. Electric dipole moments of actinide atoms and RaO molecule

    SciTech Connect

    Flambaum, V. V.

    2008-02-15

    We have calculated the atomic electric dipole moments (EDMs) induced in {sup 229}Pa and {sup 225}Ac by their respective nuclear Schiff moments S. The results are d({sup 229}Pa)=-9.5x10{sup -17} [S/(e fm)]e cm=-1.1x10{sup -20}{eta} e cm and d({sup 225}Ac)=-8.6x10{sup -17} [S/(e fm)]e cm=-0.8x10{sup -21}{eta} e cm. EDM of {sup 229}Pa is 3x10{sup 4} times larger than {sup 199}Hg EDM and 40 times larger than {sup 225}Ra EDM. Possible use of actinides in solid state experiments is also discussed. The (T,P)-odd spin-axis interaction in RaO molecule is 500 times larger than in TlF.

  5. Localization of disinhibition-dementia-parkinsonism-amyotrophy complex to 17q21-22

    SciTech Connect

    Wilhelmsen, K.C.; Lynch, T.; Pavlou, E.; Higgins, M.; Nygaard, T.G.

    1994-12-01

    Disinhibition-dementia-parkinsonism-amyotrophy complex (DDPAC) is defined by familial adult-onset behavioral disturbance, followed by frontal lobe dementia, parkinsonism, and amyotrophy in variable proportions. A genetic etiology of DDPAC was suspected because of the familial clustering in family Mo, despite their wide geographic distribution. We have mapped the DDPAC locus to a 12-cM (sex averaged) region between D17S800 and D17S787 on chromosome 17q21-22. The basis for the variability of the clinical findings and pathology in DDPAC is unknown but suggests that the DDPAC locus should be screened as a candidate locus in family studies of conditions with behavioral abnormalities and neurological degeneration.

  6. BK channels modulate pre- and postsynaptic signaling at reciprocal synapses in retina

    PubMed Central

    Grimes, William N.; Li, Wei; Chávez, Andrés E.; Diamond, Jeffrey S.

    2009-01-01

    In the mammalian retina, A17 amacrine cells provide reciprocal inhibitory feedback to rod bipolar cells, thereby shaping the time course of visual signaling in vivo. Previous results indicate that A17 feedback can be triggered by Ca2+ influx through Ca2+ permeable AMPARs and can occur independently of voltage-gated Ca2+ (Cav) channels, whose presence and functional role in A17 dendrites have not been explored. Here, we combine electrophysiology, calcium imaging and immunohistochemistry to show that L-type Cav channels in rat A17 amacrine cells are located at the sites of reciprocal synaptic feedback, but their contribution to GABA release is diminished by large-conductance Ca2+-activated potassium (BK) channels, which suppress postsynaptic depolarization in A17s and limit Cav channel activation. We also show that BK channels, by limiting GABA release from A17s, regulate the flow of excitatory synaptic transmission through the rod pathway. PMID:19363492

  7. Effects of changing climate on reference crop evapotranspiration over 1961-2013 in Xinjiang, China

    NASA Astrophysics Data System (ADS)

    Yao, Ning; Li, Yi; Sun, Changfeng

    2016-10-01

    To know the importance of different climate variables on reference crop evapotranspiration (ET o), a step-by-step sensitivity analysis of ET o to single, two, and multi-climate variables (C) was conducted. ET o in north, south, and entire Xinjiang Province, China, over 1961-2013 was estimated using the Penman-Monteith equation. Trends in the involved six Cs (i.e., minimum temperature—T min, average temperature—T ave, maximum temperature—T max, wind speed at 2 m—U 2, sunshine hour—n, and relative humidity—RH) were detected by the modified Mann-Kendall test. Nineteen scenarios of changed Cs were preset to obtain recalculated ET o values considering the actual trend in each C and the Pearson's correlation relationship between ET o and Cs. The results showed that ET o was mostly sensitive to T max, U 2, and n. Sensitivity of ET o to the two overlapped changes of T min and T max caused larger increases in ET o than T max and T ave, T ave and T max, T max and (-n), T max and RH, T max and (-U 2), and T min and T ave, but the overlapped changes (-U 2) and (-n) caused larger decreases in ET o than the other two C scenarios. The simultaneously increased T max, T min, T ave, and RH plus decreased U 2 and n had caused the actual decreases in ET o in Xinjiang. In general, the effects of decreased U 2 and n on decreasing ET o compensated the effects of increased T max on decreasing ET o in Xinjiang.

  8. Cwf16p Associating with the Nineteen Complex Ensures Ordered Exon Joining in Constitutive Pre-mRNA Splicing in Fission Yeast.

    PubMed

    Sasaki-Haraguchi, Noriko; Ikuyama, Takeshi; Yoshii, Shogo; Takeuchi-Andoh, Tomoko; Frendewey, David; Tani, Tokio

    2015-01-01

    Exons are ligated in an ordered manner without the skipping of exons in the constitutive splicing of pre-mRNAs with multiple introns. To identify factors ensuring ordered exon joining in constitutive pre-mRNA splicing, we previously screened for exon skipping mutants in Schizosaccharomyces pombe using a reporter plasmid, and characterized three exon skipping mutants named ods1 (ordered splicing 1), ods2, and ods3, the responsible genes of which encode Prp2/U2AF59, U2AF23, and SF1, respectively. They form an SF1-U2AF59-U2AF23 complex involved in recognition of the branch and 3' splice sites in pre-mRNA. In the present study, we identified a fourth ods mutant, ods4, which was isolated in an exon-skipping screen. The ods4+ gene encodes Cwf16p, which interacts with the NineTeen Complex (NTC), a complex thought to be involved in the first catalytic step of the splicing reaction. We isolated two multi-copy suppressors for the ods4-1 mutation, Srp2p, an SR protein essential for pre-mRNA splicing, and Tif213p, a translation initiation factor, in S. pombe. The overexpression of Srp2p suppressed the exon-skipping phenotype of all ods mutants, whereas Tif213p suppressed only ods4-1, which has a mutation in the translational start codon of the cwf16 gene. We also showed that the decrease in the transcriptional elongation rate induced by drug treatment suppressed exon skipping in ods4-1. We propose that Cwf16p/NTC participates in the early recognition of the branch and 3' splice sites and cooperates with the SF1-U2AF59-U2AF23 complex to maintain ordered exon joining.

  9. Initial Incidence of White Matter Hyperintensities on MRI in Astronauts

    NASA Technical Reports Server (NTRS)

    Norcross, Jason; Sherman, Paul; McGuire, Steve; Kochunov, Peter

    2016-01-01

    Introduction: Previous literature has described the increase in white matter hyperintensity (WMH) burden associated with hypobaric exposure in the U-2 and altitude chamber operating personnel. Although astronauts have similar hypobaric exposure pressures to the U2 pilot population, astronauts have far fewer exposures and each exposure would be associated with a much lower level of decompression stress due to rigorous countermeasures to prevent decompression sickness. Therefore, we postulated that the WMH burden in the astronaut population would be less than in U2 pilots. Methods: Twenty-one post-flight de-identified astronaut MRIs (5 mm slice thickness FLAIR sequences) were evaluated for WMH count and volume. The only additional data provided was an age range of the astronauts (43-57) and if they had ever performed an EVA (13 yes, 8 no). Results: WMH count in these 21 astronaut MRI was 21.0 +/- 24.8 (mean+/- SD) and volume was 0.382 +/- 0.602 ml, which was significantly higher than previously published results for the U2 pilots. No significant differences between EVA and no EVA groups existed. Age range of astronaut population is not directly comparable to the U2 population. Discussion: With significantly less frequent (sometimes none) and less stressful hypobaric exposures, yet a much higher incidence of increased WMH, this indicates the possibility of additional mechanisms beyond hypobaric exposure. This increase unlikely to be attributable just to the differences in age between astronauts and U2 pilots. Forward work includes continuing review of post-flight MRI and evaluation of pre to post flight MRI changes if available. Data mining for potential WMH risk factors includes collection of age, sex, spaceflight experience, EVA hours, other hypobaric exposures, hyperoxic exposures, radiation, high performance aircraft experience and past medical history. Finally, neurocognitive and vision/eye results will be evaluated for any evidence of impairment linked to

  10. Radiative Yukawa couplings in the simplest left-right symmetric model

    NASA Astrophysics Data System (ADS)

    Gabrielli, Emidio; Marzola, Luca; Raidal, Martti

    2017-02-01

    We revisit a recent solution to the flavor hierarchy problem based on the paradigm that Yukawa couplings are, rather than fundamental constants, effective low energy couplings radiatively generated by interactions in a hidden sector of the theory. In the present paper we show that the setup required by this scenario can be set by gauge invariance alone, provided that the standard model gauge group be extended to the left-right symmetric group of S U (2 )L×S U (2 )R×U (1 )Y. The simplest scheme in which Yukawa couplings are forbidden at the tree-level organises the right-handed fermions into doublets and presents an additional Higgs S U (2 )R doublet, responsible for the spontaneous breaking of the S U (2 )R gauge sector. The flavor and chiral symmetry breaking induced by the S U (2 )R breaking is transferred at the one-loop level to the standard model via the dynamics of the hidden sector, which effectively regulates the spread of the effective Yukawa couplings. The emerging left-right symmetric framework recovers additional appealing features typical of these models, allowing for instance to identify the hypercharges of the involved fermions with their B -L charges and offering a straightforward solution to the strong C P problem. The scheme gives rise to a distinguishing phenomenology that potentially can be tested at the LHC and future colliders through the same interactions that result in the radiative generation of Yukawa couplings, as well as by exploiting the properties of the additional S U (2 )R Higgs doublet.

  11. Cwf16p Associating with the Nineteen Complex Ensures Ordered Exon Joining in Constitutive Pre-mRNA Splicing in Fission Yeast

    PubMed Central

    Sasaki-Haraguchi, Noriko; Ikuyama, Takeshi; Yoshii, Shogo; Takeuchi-Andoh, Tomoko; Frendewey, David; Tani, Tokio

    2015-01-01

    Exons are ligated in an ordered manner without the skipping of exons in the constitutive splicing of pre-mRNAs with multiple introns. To identify factors ensuring ordered exon joining in constitutive pre-mRNA splicing, we previously screened for exon skipping mutants in Schizosaccharomyces pombe using a reporter plasmid, and characterized three exon skipping mutants named ods1 (ordered splicing 1), ods2, and ods3, the responsible genes of which encode Prp2/U2AF59, U2AF23, and SF1, respectively. They form an SF1-U2AF59-U2AF23 complex involved in recognition of the branch and 3′ splice sites in pre-mRNA. In the present study, we identified a fourth ods mutant, ods4, which was isolated in an exon-skipping screen. The ods4+ gene encodes Cwf16p, which interacts with the NineTeen Complex (NTC), a complex thought to be involved in the first catalytic step of the splicing reaction. We isolated two multi-copy suppressors for the ods4-1 mutation, Srp2p, an SR protein essential for pre-mRNA splicing, and Tif213p, a translation initiation factor, in S. pombe. The overexpression of Srp2p suppressed the exon-skipping phenotype of all ods mutants, whereas Tif213p suppressed only ods4-1, which has a mutation in the translational start codon of the cwf16 gene. We also showed that the decrease in the transcriptional elongation rate induced by drug treatment suppressed exon skipping in ods4-1. We propose that Cwf16p/NTC participates in the early recognition of the branch and 3′ splice sites and cooperates with the SF1-U2AF59-U2AF23 complex to maintain ordered exon joining. PMID:26302002

  12. The gene of an early onset progressive cataract (cerulean cataract) maps to 17q24

    SciTech Connect

    Armitage, M.M.; Ferrell, R.E.; Kivlin, J.D.

    1994-09-01

    Cerulean cataract is an autosomal dominant, fully penetrant, early onset, progressive cataract characterized by blue or white opacifications in the nucleus and cortex of the lens. A five generation family with 44 available affected members in three generations allowed exclusion of linkage of the cerulean cataract phenotype to lens structural protein genes and to all of the chromosomal regions to which autosomal dominant cataract phenotypes have previously been mapped. Exclusion of the plausible candidate instigated a genome-wide search utilizing short tandem repeat polymorphims. The genome search localized the cerulean cataract disease gene to chromosomal region 17q24. The three markers closest to the disease gene are D17S802 [Z({theta})=9.20 at ({theta})=0.086], D17S836 [Z({theta})=4.22 at ({theta})=0.061], and AFMa238yb5 [Z({theta})=7.11 at ({theta})=0.032]. Multipoint analysis yielded a maximum lod score of Z({theta})=11.4 between D17S802 and D17S836 at recombination rates of 0.048 and 0.013 respectively. Three genes that map near the 17q24 chromosomal region and are known to contain highly polymorphic microsatellites were tested for linkage. The genes, DHP-sensitive calcium channel gamma subunit (CACNLG), human somatastatin receptor (SSTR2), and the skeletal muscle sodium channel alpha subunit (SCN4A), were all excluded [Z({theta})=-{infinity} at ({theta})=0] as the gene causing cerulean cataract. The galactokinase (GK1) gene has not been cloned, but its map location is 17q23-q25. Galactokinase deficiency is characterized by a recessive, progressive, early onset cataract. Because of the map location of galactokinase, the age-at-onset, and progressive nature of cataracts associated with galactokinase deficiency, galactokinase is being investigated as a candidate gene for the cerulean cataract phenotype.

  13. Recent developments in laser-driven polarized sources

    NASA Astrophysics Data System (ADS)

    Young, L.; Coulter, K. P.; Holt, R. J.; Kinney, E. R.; Kowalczyk, R. S.; Potterveld, D. H.; Zghiche, A.

    1990-12-01

    Recent progress in the performance of laser-driven sources of polarized hydrogen and deuterium is described. The current status of the prototype source, I = 2.5 times 10(exp 17)s(exp -1), polarization = 0.29 (including atomic fraction), is comparable to classical Stern-Gerlach sources. A scheme to improve source performance by approximately an order of magnitude, using a combination of optical-pumping spin-exchange and RF transitions, is outlined.

  14. Archaeological Sites Inventory of the Training Area 10 and 12 Portions of the Pinon Canyon Maneuver Site, Las Animas County, Colorado. Volume 1

    DTIC Science & Technology

    2004-01-01

    Las Cruces, New Mexico Fort Carson Cultural Resources Management Series 17S Contribution Number 10 This project was prepared for and funded by the...National Park Service, Lincoln, Nebraska Cooperative Agreement No. 1443-CA-6000-98-016 Prepared by The Department of Sociology and Anthropology New Mexico ...State University Las Cruces, New Mexico NATIONALS IL WE Fort Carson Cultural Resources Management Series Contribution Number 10 This project was

  15. Trans World Tidal Gravity Profile.

    DTIC Science & Technology

    1984-12-31

    America Curitiba (BraziZ) This station, situated at the Universidade Federal do Parana, in the Instituto de Ciencias Geod6sicas under Professor C...SUL COMPOSANTE VEPTICALE ERESIL 29 40 17S 53 49 22W H 700M P 2M 0 330KM DEPOTS SEDIMENTAIRES SUk BASALTE DEPT* DE INGENIERIA RURAL-UNIV. FED. DE SANTA...PRECAMBRIENIGNEISS * UNIVERSIDADE FEDERAL DO RIO GRANDE DO NORTE - DEPARTAMENTO DE FISICA TRANS WORLD TIDAL GRAVITY PROFILES P. MELCHIOR CENTRO POLITECNICO

  16. UV Photo-Enhanced MOCVD of Cadmium and Cadmium Telluride

    DTIC Science & Technology

    1988-04-01

    et a1(7,S) in the light of evidence from mass spectroscopy studies performed by Czerniak and Easton(9). These authors identified the presence of... Czerniak and Easton was that the separate decomposition of DETe was autocatalytic, resulting in a reduction of decomposition temperature from 410’C down to... Czerniak and Easton(9) in which they detected the mixed alkyl species. Also they found no change in the decomposition of DETe in the presence of Cd

  17. Molecular analyses of 17p11.2 deletions in 62 Smith-Magenis syndrome patients

    SciTech Connect

    Juyal, R.C.; Figuera, L.E.; Hauge, X.

    1996-05-01

    Smith-Magenis syndrome (SMS) is a clinically recognizable, multiple congenital anomalies/mental retardation syndrome caused by an interstitial deletion involving band p11.2 of chromosome 17. Toward the molecular definition of the interval defining this microdeletion syndrome, 62 unrelated SMS patients in conjunction with 70 available unaffected parents were molecularly analyzed with respect to the presence or absence of 14 loci in the proximal region of the short arm of chromosome 17. A multifaceted approach was used to determine deletion status at the various loci that combined (1) FISH analysis, (2) PCR and Southern analysis of somatic cell hybrids retaining the deleted chromosome 17 from selected patients, and (3) genotype determination of patients for whom a parent(s) was available at four microsatellite marker loci and at four loci with associated RFLPs. The relative order of two novel anonymous markers and a new microsatellite marker was determined in 17p11.2. The results confirmed that the proximal deletion breakpoint in the majority of SMS patients is located between markers D17S58 (EW301) and D17S446 (FG1) within the 17p11.1-17p11.2 region. The common distal breakpoint was mapped between markers cCI17-638, which lies distal to D17S71, and cCI17-498, which lies proximal to the Charcot Marie-Tooth disease type 1A locus. The locus D17S258 was found to be deleted in all 62 patients, and probes from this region can be used for diagnosis of the SMS deletion by FISH. Ten patients demonstrated molecularly distinct deletions; of these, two patients had smaller deletions and will enable the definition of the critical interval for SMS. 49 refs.

  18. Dependence of Crack Propagation/Deflection Mechanism on Characteristics of Fiber Coating or Interphase in Ceramics Matrix Continuous Fiber Reinforced Composites (Postprint)

    DTIC Science & Technology

    2014-07-01

    Information Center (DTIC) (http://www.dtic.mil). AFRL-RX-WP-JA-2014-0172 HAS BEEN REVIEWED AND IS APPROVED FOR PUBLICATION IN ACCORDANCE WITH...another approach, Pompidou and Lamon [17] employed the Cook and Gordon model [13] to estimate Distribution A. Approved for public release; distribution...of Solids and Structures, vol. 41, pp. 6937-6948, 2004. [17] S. Pompidou and J. Lamon, "Analysis of crack deviation in ceramic matrix xomposites

  19. Toxin Production and Immunoassay Development. 1. Palytoxin

    DTIC Science & Technology

    1988-03-31

    1988 March 31 43 16 . SUPPLEMENTARY NOTATION 17. COSATI CODES 18. SUBJECT TERMS (Continue on reverse if necessary and identify by block number) FIELD...Anti-palytoxin CIEIA ... 16 5. Titration of Palytoxin in Rabbit Anti-palytoxin CIEIA Using BSA-PTX-SPDP coating antigen prepared llarch 2, 1987 17 S...the Hana, Maui tidepool originally described by Moore, Helfrich and Patterson (refs 1, 16 ). Since the tidepool is quite small and contains a very

  20. A gene responsible for profound congenital nonsyndromal recessive deafness maps to the pericentromeric region of chromosome 17

    SciTech Connect

    Friedman, T.B.; Liang, Y.; Asher, J.H. Jr.

    1994-09-01

    Autosomal recessive deafness is the most common form of human hereditary hearing loss. Two percent of the 2,185 residents of Bengkala, Bali, Indonesia have profound congenital neurosensory nonsyndromal hereditary deafness due to a fully penetrant autosomal recessive mutation (NARD1). Families, identified through children with profound congenital deafness having hearing parents, give the expected 25% deaf progeny when corrected for ascertainment bias. Congenitally deaf individuals from Bengkala show no response to pure tone audiological examination. Obligate heterozygotes for autosomal recessive deafness in Bengkala have normal or borderline normal hearing. A chromosomal location for NARD1 was assigned directly using a linkage strategy that combines allele-frequency dependent homozygosity mapping (AHM) followed by an analysis of historical recombinants to position NARD1 relative to flanking markers. Thirteen deaf Bengkala villagers of hearing parents were typed initially for 148 STRPs distributed across the human genome and a cluster of tightly linked 17p markers with a significantly higher number of homozygotes than expected under Hardy-Weinberg and linkage equilibrium were identified. NARD1 maps closest to STRPs for D17S261 (Mfd41) and D17S805 (AFM234ta1) that are 3.2 cM apart. Recombinant genotypes for the flanking markers, D17S122 (VAW409) and D17S783 (AFM026vh7), in individuals homozygous for NARD1 place NARD1 in a 5.3 cM interval of the pericentromeric region of chromosome 17 on a refined 17p-17q12 genetic map.